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Sample records for repeated 14co2 pulse-labelling

  1. Recent Trends in Atmospheric 14CO2

    NASA Astrophysics Data System (ADS)

    Turnbull, J. C.; Rayner, P.; Bousquet, P.; Cozic, A.; Miller, J. B.; Lehman, S. J.; Peters, W.; Tans, P. P.; Ciais, P.

    2007-12-01

    The radiocarbon content of atmospheric CO2 (14CO2) varies due to a number of factors. After the near-doubling of the 14CO2 loading in the early 1960s (due to atmospheric nuclear weapons testing), many studies examined the fate of this 'bomb 14C' to understand exchange processes of CO2 with the surface reservoirs. Today, however, the atmosphere and surface reservoirs are close to equilibrium with respect to bomb 14C, and instead, changes in 14CO2 more strongly reflect the response to the addition of 14C-free fossil fuel CO2 to the atmosphere. We use an atmospheric transport model to simulate recent atmospheric 14CO2, and compare this to observations at several sites over the Northern Hemisphere continents. We show that, in the Northern Hemisphere, 14CO2 variability is dominated by the effect of fossil fuel CO2 emissions. The model simulates the time trends quite well, including both the overall secular trend and the seasonal cycle. A seasonal cycle in 14CO2 is observed at the high altitude sites of Niwot Ridge, Colorado, and Jungfraujoch, Switzerland, but the magnitude varies from year to year. Our modeling studies demonstrate that this inter-annual variability can be explained by differences in atmospheric transport. This is in contrast to CO2 concentration seasonal cycles, which are dominated by seasonal changes in CO2 source strengths.

  2. [Uptake 14CO2 from air and accumulation of 14C in hornwort].

    PubMed

    Shi, Jian-Jun

    2011-02-01

    Uptake 14CO2 from air and accumulation of 14C in the hornwort were studied by using the isotope-tracer techniques in order to get a better understanding of the environmental behavior of 14CO2. And the possibility of hornwort used as the indicator plant in the supervisor of 14CO2 air pollution was discussed. The results show that the hornwort could uptake 14CO2 from the air by some way and formed an accumulating trend. The main way was that the hornwort absorbed free 14CO2 and H 14CO3- from the water through photosynthesis. During the introducing 14CO2, the increasing rate of 14C specific activity in dry hornwort and fresh hornwort were between 91.9-95.6 Bq/(g x d) and 6.1-6.3 Bq/(g x d), respectively, which was roughly equal to the increasing rate in the wheat. The results indicate that the hornwort had strong ability of absorbing 14CO2 indirectly through water. The hornwort has an certain concentration of 14CO2. And the concentration factor (CF) values rise with the introduction of 14CO2 and decline slowly after it reached the maximum value. Owing to its accumulation of 14CO2, hornwort can be used as the indicator plant in the supervisor of 14CO2 air pollution. PMID:21528570

  3. Monitoring of atmospheric 14CO2 in central European countries

    NASA Astrophysics Data System (ADS)

    Světlík, I.; Tomášková, L.; Molnár, M.; Svingor, E.; Futó, I.; Pintér, T.; Rulík, P.; Michálek, V.

    2006-01-01

    Carbon-14 is a radionuclide with global occurrence and partly natural origin. The main anthropogenic sources of the 14C were the nuclear weapon tests, namely at the beginning of the 1960s, nowadays the nuclear energy facilities are the main sources. Maximum in the atmospheric 14C activity was observed in 1963. In the following years the considerable 14C activity decrease was due to intensive carbon deposition into oceanic water and sediments particularly. At present the 14C activity approximates the level before nuclear age, corresponding to ˜0 ‰ Δ 14C. Another actual type of anthropogenic influence is the Suess effect, i.e., the dilution of 14C by fossil carbon (fuel combustion). This effect causes a decrease of the 14C activity on a global, regional and local scale. Thus, monitoring of actual reference level of 14C activity gives a possibility to indicate local or global anthropogenic influences. This paper reporting data from the atmospheric 14CO2 monitoring in the Czech Republic and Hungary compares the actual results with other European countries. The observed effects connected with local and regional CO2 releases from fossil fuel combustion are discussed.

  4. Measurement of 14CO2 Assimilation in Soils: an Experiment for the Biological Exploration of Mars

    PubMed Central

    Hubbard, Jerry S.; Hobby, George L.; Horowitz, Norman H.; Geiger, Paul J.; Morelli, Frank A.

    1970-01-01

    A method is described for the measurement of 14CO2 assimilation by microorganisms in soils. A determination involves exposing soil to 14CO2, pyrolyzing the exposed soil, trapping the organic pyrolysis products on a column of firebrick coated with CuO, combusting the trapped organics by heating, and measuring the radioactivity in the CO2 produced in the combustion. The detection of significant levels of 14C in the trapped organic fraction appears to be an unambiguous indication of biological activity. The 14CO2 which is adsorbed or exchanged into soils by nonbiological processes does not interfere. The method easily detects the 14CO2 fixed by 102 to 103 algae after light exposure for 3 to 24 hr. Assimilation of 14C is also demonstrable in dark-exposed soils containing 105 to 106 heterotrophic bacteria. Possible applications of the method in the biological exploration of Mars are discussed. Images PMID:16349879

  5. 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. PMID:11743160

  6. Technique for measuring 14 CO 2 uptake by soil microorganisms in situ.

    PubMed

    Smith, D W; Fliermans, C B; Brock, T D

    1972-03-01

    Uptake of (14)CO(2) in soils due to algae or sulfur-oxidizing bacteria was examined by incubation of soil samples with gaseous (14)CO(2) and subsequent chemical oxidation of biologically fixed radioactive isotope to (14)CO(2) for detection with a liquid scintillation counting system. The (14)CO(2) was added to the soil in the gas phase so that no alteration of the moisture or ionic strength of the soil occurred. Wet oxidation of radioactive organic matter was carried out in sealed ampoules, and the (14)CO(2) produced was transferred to a phenethylamine-liquid scintillation counting system with a simply constructed apparatus. The technique is inexpensive and efficient and does not require elaborate traps since several possible interfering factors were found to have no harmful effects. Experiments in coal mine regions and in geothermal habitats have demonstrated the ecological applicability of this technique for measurement of CO(2) fixation by sulfur-oxidizing bacteria and soil algae. PMID:4553805

  7. High-resolution simulations of the Δ14CO2 gradients from fossil fuels and nuclear power plants over Europe

    NASA Astrophysics Data System (ADS)

    Bozhinova, D.; van der Molen, M. K.; Palstra, S. W.; Meijer, H. A.; Krol, M. C.; Peters, W.

    2012-12-01

    Radiocarbon (14CO2) can be used to quantify fossil fuel CO2 addition to the atmosphere, since fossil CO2 is void of 14C. However, the current observational network is not dense enough to constrain regional emissions in most parts of the world. Furthermore, most sampling sites are not as informative for the regional anthropogenic emissions because they are located outside polluted regions. High resolution modeling of regional fossil fuel CO2 dispersion can help to define sampling locations at which Δ14CO2 gradients will be strong enough to estimate regional fossil fuel emissions. However, an important consideration should be the 14CO2 enrichment due to nuclear power plant 14CO2 production. These point sources contribute little to the global radiocarbon budget, but on a regional scale their importance for the atmospheric Δ14CO2 signature can be considerable. We therefore simulate the fossil fuel CO2 and nuclear 14CO2 transport for Western Europe using the Weather Research and Forecast model (WRF-Chem) and evaluate the gradients and resulting Δ14CO2. We verify our modeling framework with integrated 14CO2, CO2, and meteorological observations. We find that the gradients in daytime fossil fuel CO2 addition can be as high as 10 ppm. Additionally, the effects of the nuclear 14CO2 emitted from the strongest source in the region can be traced to sites more than 500 km away, and their impact on the atmospheric Δ14CO2 signature can sometimes be of the same magnitude as the regional fossil fuel CO2 addition. We will present our findings and possible implications for sampling campaigns and observational sites.lt;img border=0 src="images/A33P-06_B.jpg">

  8. 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.

  9. Multiwell 14CO2-capture assay for evaluation of substrate oxidation rates of cells in culture.

    PubMed

    Collins, C L; Bode, B P; Souba, W W; Abcouwer, S F

    1998-05-01

    14CO2 capture is commonly used to evaluate the cellular oxidation rate of respiratory substrates. A modification of the established 14CO2-capture method was developed that enables the use of cells in adherent culture and easy analysis of multiple samples under different culture conditions. The use of commercially available culture and filter plates designed for use in a multiplate scintillation spectrophotometer enabled substrate oxidation rates to be evaluated for cells in a 24-well plate format without the need to dislodge the cells from the culture substrate as is required in traditional methods. Evaluation of radioactivity captured in potassium hydroxide-saturated filters was accomplished by adding scintillation fluid to the filter plate wells and counting. Alternatively, filters could be removed and placed in vials for evaluation in a conventional scintillation counter. This method was applied to the oxidation of 14C-glutamine by human breast cell lines and demonstrated concentration-dependent linear accumulation of captured counts. PMID:9591130

  10. Carbon Dioxide Exchanges in Leaves. I. Discrimination Between 14CO2 and 12CO2 in Photosynthesis 1

    PubMed Central

    Yemm, E. W.; Bidwell, R. G. S.

    1969-01-01

    In order to measure CO2 exchange reactions by leaves using isotopes of CO2, it is necessary to know precisely the discrimination against 14CO2 by leaves. Earlier determinations of discrimination are at variance, and may be inaccurate because of assumptions made about the rate of photorespiration. Maize leaves evolve little or no CO2 in light, and so provide suitable material for this measurement. Discrimination against 14CO2 in photosynthesis by maize leaves is almost precisely the same as in CO2 absorption by NaOH solution, amounting to 2.1 and 2.0% respectively. The agreement between these values and their close approximation to the relative rates of diffusion of 12CO2 and 14CO2, calculated from Graham's law, shows that diffusion into the leaf is primarily responsible for discrimination against 14CO2 in photosynthesis. PMID:16657206

  11. Design and package of a 14CO2 field analyzer: the Global Monitor Platform (GMP)

    NASA Astrophysics Data System (ADS)

    Marino, Bruno D. V.; Bright, Michelle; Gronniger, Glen

    2011-09-01

    Carbon Capture and Sequestration (CCS) is widely accepted as a means to reduce and eliminate the fossil fuel CO2 (ff- CO2) emissions from coal fired power plants. Success of CCS depends on near zero leakage rates over decadal time scales. Currently no commercial methods to determine leakage of ff-CO2 are available. The Global Monitor Platform (GMP) field analyzer provides high precision analysis of CO2 isotopes [12C (99%), 13C (<1%), 14C (1.2x10-10 %)] that can differentiate between fossil and biogenic CO2 emissions. Fossil fuels contain no 14C; their combustion should lower atmospheric amounts on local to global scales. There is a clear mandate for monitoring, verification and accounting (MVA) of CCS systems nationally and globally to verify CCS integrity, treaty verification (Kyoto Protocol) and to characterize the nuclear fuel cycle. Planetary Emissions Management (PEM), working with the National Secure Manufacturing Center (NSMC), has the goal of designing, ruggedizing and packaging the GMP for field deployment. The system will conduct atmosphere monitoring then adapt to water and soil evaluations. Measuring 14CO2 in real time will provide quantitative concentration data for ff-CO2 in the atmosphere and CCS leakage detection. Initial results will be discussed along with design changes for improved detection sensitivity and manufacturability.

  12. 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

  13. 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

  14. Translocation of Radioactive Carbon after the Application of 14C-Alanine and 14CO2 to Sunflower Leaves 1

    PubMed Central

    Chopowick, R. E.; Forward, D. F.

    1974-01-01

    14C-(UL)-l-Alanine was applied to the surface of mature leaves at the second node of sunflower (Helianthus annuus L. cv Commander) plants, under illumination. The alanine was absorbed during a 4-hour period, and some of it was metabolized by the absorbing tissue. After a lag period of about 15 minutes from first application, distribution of 14C through the plant proceeded in much the same pattern as when 14CO2 is assimilated by similar leaves. Most, if not all, of the 14C exported from the absorbing regions was in sucrose. Only minute amounts appeared in alanine or other amino acids in surrounding parts of the leaf blade or in the petiole, although these were strongly labeled in the tissue absorbing 14C-alanine. When 14CO2 was supplied for 15 minutes to leaves of different ages, amino acids were lightly labeled in the leaf blade. Mature green leaves exported only sucrose. Yellowing leaves on 60-day-old plants exported a variety of substances including amino acids. PMID:16658645

  15. Increased Tolerance to Photoinhibitory Light in Paraquat-Resistant Conyza bonariensis Measured by Photoacoustic Spectroscopy and 14CO2-Fixation

    PubMed Central

    Jansen, Marcel A. K.; Shaaltiel, Yoseph; Kazzes, Dror; Canaani, Ora; Malkin, Shmuel; Gressel, Jonathan

    1989-01-01

    Tolerance to photoinhibition was compared between a paraquat-resistant and a sensitive biotype of Conyza bonariensis (L.). Cronq. Photoinhibitory damage was measured as a decrease in oxygen evolution or energy storage using photoacoustic spectroscopy, or as a decrease of 14CO2-fixation. Prior to exposure to high fluence rates, both biotypes had similar quantum yields of oxygen evolution and energy storage. After exposure to high intensity light, the resistant biotype continued to evolve oxygen and to store energy with a high quantum yield while both energy storage and oxygen evolution were severely reduced in the sensitive biotype. CO2-fixation was less rapidly inhibited in the resistant biotype compared to the sensitive one. The data show that the paraquat resistant biotype with its high constitutive levels of the chloroplast localized enzymes of the oxygen detoxification pathway, is also partially protected from photoinhibition. This supports the theory that an enhanced radical scavenging system can give temporary protection against photooxidative damage from a variety of sources. PMID:16667129

  16. 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. PMID:23546854

  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. 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.

  19. 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

  20. Carbon-14 transfer into potato plants following a short exposure to an atmospheric 14CO2 emission: observations and model predictions.

    PubMed

    Melintescu, A; Galeriu, D; Tucker, S; Kennedy, P; Siclet, F; Yamamoto, K; Uchida, S

    2013-01-01

    To improve the understanding of the environmental (14)C behaviour, the International Atomic Energy Agency (IAEA) coordinated a Tritium and C-14 Working Group (T&C WG) in its EMRAS (Environmental Modelling for Radiation Safety) programme. One of the scenarios developed in the frame of T&C WG involved the prediction of time dependent (14)C concentrations in potato plants. The experimental data used in the scenario were obtained from a study in which potatoes (Solanum tuberosum cv. Romano) were exposed to atmospheric (14)CO(2) in a wind tunnel. The observations were used to test models that predict temporal changes in (14)C concentrations in leaves at each sampling time for each experiment and (14)C concentrations in tubers at the final harvest of each experiment. The experimental data on (14)C dynamics in leaves are poorly reproduced by most of the models, but the predicted concentrations in tubers are in good agreement with the observations. PMID:22995861

  1. 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.

  2. Continuous Turnover of Carotenes and Chlorophyll a in Mature Leaves of Arabidopsis Revealed by 14CO2 Pulse-Chase Labeling[OA

    PubMed Central

    Beisel, Kim Gabriele; Jahnke, Siegfried; Hofmann, Diana; Köppchen, Stephan; Schurr, Ulrich; Matsubara, Shizue

    2010-01-01

    Carotenoid turnover was investigated in mature leaves of Arabidopsis (Arabidopsis thaliana) by 14CO2 pulse-chase labeling under control-light (CL; 130 μmol photons m−2 s−1) and high-light (HL; 1,000 μmol photons m−2 s−1) conditions. Following a 30-min 14CO2 administration, photosynthetically fixed 14C was quickly incorporated in β-carotene (β-C) and chlorophyll a (Chl a) in all samples during a chase of up to 10 h. In contrast, 14C was not detected in Chl b and xanthophylls, even when steady-state amounts of the xanthophyll-cycle pigments and lutein increased markedly, presumably by de novo synthesis, in CL-grown plants under HL. Different light conditions during the chase did not affect the 14C fractions incorporated in β-C and Chl a, whereas long-term HL acclimation significantly enhanced 14C labeling of Chl a but not β-C. Consequently, the maximal 14C signal ratio between β-C and Chl a was much lower in HL-grown plants (1:10) than in CL-grown plants (1:4). In lut5 mutants, containing α-carotene (α-C) together with reduced amounts of β-C, remarkably high 14C labeling was found for α-C while the labeling efficiency of Chl a was similar to that of wild-type plants. The maximum 14C ratios between carotenes and Chl a were 1:2 for α-C:Chl a and 1:5 for β-C:Chl a in CL-grown lut5 plants, suggesting high turnover of α-C. The data demonstrate continuous synthesis and degradation of carotenes and Chl a in photosynthesizing leaves and indicate distinct acclimatory responses of their turnover to changing irradiance. In addition, the results are discussed in the context of photosystem II repair cycle and D1 protein turnover. PMID:20118270

  3. 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

  4. 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.

  5. 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.; Miller, B. R.; Montzka, S. A.; Hall, B.; Neff, W.; Sweeney, C.; Turnbull, J. C.; Wolfe, D. E.; Tans, P. P.; Gurney, K. R.; Guilderson, T. P.

    2013-01-01

    Atmospheric radiocarbon (14CO) represents an important observational constraint on emissions of fossil-fuel derived carbon into the atmosphere due to the absence of 14CO in fossil fuel reservoirs. The high sensitivity and precision that accelerator mass spectrometry (AMS) affords in atmospheric 14CO 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 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 to CO2ff. From these emission ratios, we estimate emissions of these species by using the Vulcan CO2ff high resolution data product as a reference. The species considered in this analysis are carbon monoxide (CO), methane (CH4), acetylene (C2H2), benzene (C6H6), and C3-C5 alkanes. Comparisons of top-down emissions estimates are made to existing inventories of these species for Denver and adjacent counties, as well as to previous efforts to estimate emissions from atmospheric observations over the same area. We find that CO is overestimated in the 2008 National Emissions Inventory (NEI, 2008) 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. The results also suggest that while the oil and gas sector is the largest contributor to the CH4 signal in air arriving from the north and east, it is very likely that other sources, including agricultural sources, contribute to this signal and must be accounted for when attributing these signals to oil and gas industry activity from a top-down perspective. Our results are consistent

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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. PMID:23533365

  12. 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

  13. Carbon transfer from photosynthesis to below ground fine root/hyphae respiration in Quercus serrata using stable carbon isotope pulse labeling

    NASA Astrophysics Data System (ADS)

    Dannoura, M.; Kominami, Y.; Takanashi, S.; Takahashi, K.

    2013-12-01

    Studying carbon allocation in trees is a key to better understand belowground carbon cycle and its response to climate change. Tracing 13C in tree and soil compartments after pulse labeling is one of powerful tool to study the fate of carbon in forest ecosystems. This experiment was conducted in Yamashiro experimental forest, Kyoto, Japan. Annual mean temperature and precipitation from 1994 to 2009 are 15.5 ° C and 1,388 mm respectively. The branch pulse labeling were done 7 times in 2011 using same branch of Quercus serrata (H:11.7 m, DBH; 33.7 cm) to see seasonal variations of carbon velocity. Whole crown labeling of Quercus serrata (H:9 m, DBH; 13.7 cm) was done in 2012 to study carbon allocation and to especially focus on belowground carbon flux until to the hyphae respiration. Pure 13CO2 (99.9%) was injected to the labeling chamber which was set to branch or crown. Then, after one hour of branch labeling and 3.5 hour for crown labeling, the chamber was opened. Trunk respiration chambers, fine root chambers and hyphae chambers were set to the target tree to trace labeled carbon in the CO2 efflux. 41 μm mesh was used to exclude ingrowth of roots into hyphae chambers. The results show that the velocity of carbon through the tree varied seasonally, with higher velocity in summer than autumn, averaging 0.47 m h-1. Half-lives of labeled carbon in autotrophic respiration were similar above and below ground during the growing season, but they were twice longer in trunk than in root in autumn. From the whole crown labeling done end of growing season, the 13CO2 signal was observed 25 hours after labeling in trunk chamber and 34-37.7 hours after labeling in fine root and hyphae respiration almost simultaneously. Half-lives of 13 was longer in trunk than below ground. Trunk respiration was still using labelled carbon during winter suggesting that winter trunk respiration is partly fueled by carbon stored in the trunk at the end of the growing season.

  14. 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

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

    PubMed Central

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

    2015-01-01

    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 13CO2 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 13C fixed by photosynthesis was lost via shoot respiration. Shoots recovered about 19% of total 13C fixed by photosynthesis at both sites. Only about 26% of total fixed 13C was translocated into the belowground pools. Soil organic C pool accounted for 19% and roots recovered about 5–7% of total fixed 13C at both sites. Waterlogging significantly reduced soil respiration and very little 13C 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 13CO2 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. PMID:25797457

  16. 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. PMID:25461119

  17. 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.

  18. More than a century of Grain for Green Program is expected to restore soil carbon stock on alpine grassland revealed by field (13)C pulse labeling.

    PubMed

    Li, Qi; Chen, Dongdong; Zhao, Liang; Yang, Xue; Xu, Shixiao; Zhao, Xinquan

    2016-04-15

    Anthropogenic changes in land use/cover have altered the vegetation, soil, and carbon (C) cycling on the Qinghai-Tibetan Plateau (QTP) over the last ~50years. As a result, the Grain for Green Program (GfGP) has been widely implemented over the last 10years to mitigate the impacts of cultivation. To quantify the effects of the GfGP on C partitioning and turnover rates at the ecosystem scale, an in situ (13)C pulse labeling experiment was conducted on natural and GfGP grasslands in an agro-pastoral ecotone in the Lake Qinghai region on the QTP. We found that there were significant differences in the C stocks of all the considered pools in both the natural and GfGP grasslands, with higher CO2 uptake rates in the GfGP grassland than that in the natural grassland. Partitioning of photoassimilate (% of recovered (13)C) in C pools of both grasslands was similar 25days after labeling, except in the roots of the 0-15 and 5-15cm soil layer. Soil organic C (SOC) sequestration rate in the GfGP grassland was 11.59±1.89gCm(-2)yr(-1) significantly greater than that in the natural grassland. The results confirmed that the GfGP is an efficient approach for grassland restoration and C sequestration. However, it will take more than a century (119.19±20.26yr) to restore the SOC stock from the current cropland baseline level to the approximate level of natural grassland. We suggest that additional measures are needed in the selection of suitable plant species for vegetation restoration, and in reasonable grazing management. PMID:26803680

  19. Repeating thermocouple

    SciTech Connect

    Falk, R. A.

    1985-06-04

    Disclosed herein is a repeating use thermocouple assembly and method of making the same in which a cavity adjacent the tip of the thermocouple is filled with a thermosetting foundry sand and baked in place to provide support for the thermocouple tube without causing stresses during use which could cause breakage of the thermocouple tube.

  20. 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

  1. 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.

  2. 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

  3. Quantifying anthropogenic greenhouse gas emissions using atmospheric 14CO2

    NASA Astrophysics Data System (ADS)

    Miller, J. B.; Lehman, S.; Montzka, S.; Sweeney, C.; Tans, P.; Turnbull, J.

    2008-12-01

    Δ14C, the ratio of radiocarbon to total carbon, is a theoretically ideal tracer for recently added fossil fuel CO2, because fossil fuel is 14C-free. In contrast, all other carbon reservoirs that exchange CO2 with the atmosphere, like the terrestrial biosphere and the oceans, are relatively rich in 14C. Since 2004, NOAA/ESRL and the University of Colorado Institute for Arctic and Alpine Research (INSTAAR) Radiocarbon Laboratory have worked together to make high precision (< 2 ‰) Δ14C measurements. Our two sites in the eastern USA, Portsmouth, NH (NHA) and Cape May, NJ (CMA) exhibit large CO2 signals from anthropogenic and biogenic fluxes. Using Δ14C, however, we are able to quantitatively partition the boundary layer CO2 signal into biogenic and fossil fuel components (Cbio and Cff). Cff exhibits correlations with many anthropogenic species, including many HFCs and HCFCs, which are measured from the same air samples. Furthermore, our preliminary data show many emission ratios changing seasonally. Atmospheric correlations of a given gas to Cff can simply be multiplied by the well-known emissions of fossil fuel-CO2 to give direct emission estimates of the correlated gas. In this presentation we will show calculated emissions of a variety of HFCs and HCFCs for the northeastern U.S.A. in which "footprints" from the FLEXPART Lagrangian particle dispersion model are used to link atmospheric correlations to specific areas.

  4. 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).

  5. Monsoonal influence on Southern Hemisphere 14CO2

    NASA Astrophysics Data System (ADS)

    Hua, Quan; Barbetti, Mike; Levchenko, Vladimir A.; D'Arrigo, Rosanne D.; Buckley, Brendan M.; Smith, Andrew M.

    2012-10-01

    Annual rings of a cross-dated teak tree core from Muna Island, Sulawesi, Indonesia in the southern equatorial tropics were analysed for radiocarbon from 1951-1979. 14C levels at Muna started rising in 1956 and reached a maximum value of 667‰ in early 1965. The Muna Δ14C levels are significantly higher than those derived from the other Southern Hemisphere (SH) 14C records (including tree rings and atmospheric CO2 sampling) for 1959 and 1963-1965. During the growing season of teak tree rings at this location (Nov-Apr) the Inter-tropical Convergence Zone (ITCZ) moves southward of Muna. Our results indicate that the island is strongly influenced by Northern Hemisphere (NH) air masses carried by the winter Asian monsoon, while the other more southerly SH sites remain covered by SH air masses. This monsoonal effect on atmospheric 14C at Muna is evident during the periods of rapidly rising atmospheric 14C (1959 and 1963-1965), when there is an enhanced 14C contrast between northern and southern air masses.

  6. 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

  7. Repeated Course Enrollments.

    ERIC Educational Resources Information Center

    Windham, Patricia

    This report resents tables of repeated course enrollment data in Florida community colleges for the fall 1993 cohort. Overall, the percent of repeats in college preparatory courses was greater than that of college credit courses. Within ICS codes, the highest percentage of credit repeat enrollments was in mathematics; the second highest was in…

  8. Reconfigurable multiport EPON repeater

    NASA Astrophysics Data System (ADS)

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio

    2009-11-01

    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  9. Revisiting the TALE repeat.

    PubMed

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity. PMID:24622844

  10. Quantum repeated games revisited

    NASA Astrophysics Data System (ADS)

    Frąckiewicz, Piotr

    2012-03-01

    We present a scheme for playing quantum repeated 2 × 2 games based on Marinatto and Weber’s approach to quantum games. As a potential application, we study the twice repeated Prisoner’s Dilemma game. We show that results not available in the classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games proposed by Iqbal and Toor. We point out the drawbacks that make their results unacceptable.

  11. The Pentapeptide Repeat Proteins

    SciTech Connect

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  12. Honesty through repeated interactions.

    PubMed

    Rich, Patricia; Zollman, Kevin J S

    2016-04-21

    In the study of signaling, it is well known that the cost of deception is an essential element for stable honest signaling in nature. In this paper, we show how costs for deception can arise endogenously from repeated interactions between individuals. Utilizing the Sir Philip Sidney game as an illustrative case, we show that repeated interactions can sustain honesty with no observable signal costs, even when deception cannot be directly observed. We provide a number of potential experimental tests for this theory which distinguish it from the available alternatives. PMID:26869213

  13. Triggering of repeated earthquakes

    NASA Astrophysics Data System (ADS)

    Sobolev, G. A.; Zakrzhevskaya, N. A.; Sobolev, D. G.

    2016-03-01

    Based on the analysis of the world's earthquakes with magnitudes M ≥ 6.5 for 1960-2013, it is shown that they cause global-scale coherent seismic oscillations which most distinctly manifest themselves in the period interval of 4-6 min during 1-3 days after the event. After these earthquakes, a repeated shock has an increased probability to occur in different seismically active regions located as far away as a few thousand km from the previous event, i.e., a remote interaction of seismic events takes place. The number of the repeated shocks N( t) decreases with time, which characterizes the memory of the lithosphere about the impact that has occurred. The time decay N( t) can be approximated by the linear, exponential, and powerlaw dependences. No distinct correlation between the spatial locations of the initial and repeated earthquakes is revealed. The probable triggering mechanisms of the remote interaction between the earthquakes are discussed. Surface seismic waves traveling several times around the Earth's, coherent oscillations, and global source are the most preferable candidates. This may lead to the accumulation and coalescence of ruptures in the highly stressed or weakened domains of a seismically active region, which increases the probability of a repeated earthquake.

  14. 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…

  15. Bidirectional Manchester repeater

    NASA Technical Reports Server (NTRS)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  16. 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.

  17. 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.

  18. 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.

  19. Repeated measures with zeros.

    PubMed

    Berk, K N; Lachenbruch, P A

    2002-08-01

    Consider repeated measures data with many zeros. For the case with one grouping factor and one repeated measure, we examine several models, assuming that the nonzero data are roughly lognormal. One of the simplest approaches is to model the zeros as left-censored observations from the lognormal distribution. A random effect is assumed for subjects. The censored model makes a strong assumption about the relationship between the zeros and the nonzero values. To check on this, you can instead assume that some of the zeros are 'true' zeros and model them as Bernoulli. Then the other values are modeled with a censored lognormal. A logistic model is used for the Bernoulli p, the probability of a true nonzero. The fit of the pure left-censored lognormal can be assessed by testing the hypothesis that p is 1, as described by Moulton and Halsey. The model can also be simplified by omitting the censoring, leaving a logistic model for the zeros and a lognormal model for the nonzero values. This is approximately equivalent to modeling the zero and nonzero values separately, a two-part model. In contrast to the censored model, this model assumes only a slight relationship (a covariance component) between the occurrence of zeros and the size of the nonzero values. The models are compared in terms of an example with data from children's private speech. PMID:12197298

  20. 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…

  1. 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

  2. 14CO2 dispersion around two PWR nuclear power plants in Brazil.

    PubMed

    Dias, Cíntia Melazo; Stenström, Kristina; Bacelar Leão, Igor Luiz; Santos, Roberto Ventura; Nícoli, Iêda Gomes; Skog, Göran; Ekström, Peter; da Silveira Corrêa, Rosangela

    2009-07-01

    Atmospheric air samples were taken within 3 km from power plants encompassing five different distances and wind directions. Samples were taken between 2002 and 2005 aiming to evaluate the environmental (14)C enrichment due to the operation of Brazilian nuclear power plants. The sampling system consisted of a pump connected to a trapping column filled with a 3M NaOH solution. The trapped CO(2) was analyzed for (14)C by using a single stage accelerator mass spectrometry (SSAMS). All sampling sites revealed measurable (14)C excess values. The maximum excesses were of 15 and 14 mBq/m(3) for sampling sites placed at NE of the power plants, which is the main wind direction in the area. The mean excesses values were 12 mBq/m(3) to the NE direction, 8 mBq/m(3) to the E, 10 mBq/m(3) to the N, 8 mBq/m(3) to the WNW and 7 mBq/m(3) to the W direction (increasing distances from NE to W). Compared to other Light Water Reactors (LWR) data, these means' values are significantly higher than the average worldwide reported value of 3 mBq/m(3). Available data indicate that the observed values are not related to (14)C emission by the power plants vent stack. Other factors, such as topography, seem to have an important role because it affects wind dispersion thus favoring (14)C accumulation in the sampled area. Moreover, the high elevations around the power plants enhance the chances to measure high values of (14)C since the plume can be intercepted before it is drawn to the ground. Modeling of the plume has shown that its dispersion does not follow a Gaussian model and that agreement between atmospheric CO(2) and vegetation (14)C activities occurs only for sampling sites placed at NE of the power plants. PMID:19427084

  3. 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.

  4. Saturation of repeated quantum measurements

    NASA Astrophysics Data System (ADS)

    Haapasalo, Erkka; Heinosaari, Teiko; Kuramochi, Yui

    2016-08-01

    We study sequential measurement scenarios where the system is repeatedly subjected to the same measurement process. We first provide examples of such repeated measurements where further repetitions of the measurement do not increase our knowledge on the system after some finite number of measurement steps. We also prove, however, that repeating the Lüders measurement of an unsharp two-outcome observable never saturates in this sense, and we characterize the observable measured in the limit of infinitely many repetitions. Our result implies that a repeated measurement can be used to correct the inherent noise of an unsharp observable.

  5. 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

  6. Sequence repeats and protein structure

    NASA Astrophysics Data System (ADS)

    Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

    2012-11-01

    Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

  7. 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.

  8. All-photonic quantum repeaters.

    PubMed

    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

  9. Estimating repeatability of egg size

    USGS Publications Warehouse

    Flint, P.L.; Rockwell, R.F.; Sedinger, J.S.

    2001-01-01

    Measures of repeatability have long been used to assess patterns of variation in egg size within and among females. We compared different analytical approaches for estimating repeatability of egg size of Black Brant. Separate estimates of repeatability for eggs of each clutch size and laying sequence number varied from 0.49 to 0.64. We suggest that using the averaging egg size within clutches results in underestimation of variation within females and thereby overestimates repeatability. We recommend a nested design that partitions egg-size variation within clutches, among clutches within females, and among females. We demonstrate little variation in estimates of repeatability resulting from a nested model controlling for egg laying sequence and a nested model in which we assumed laying sequence was unknown.

  10. Protein Repeats from First Principles.

    PubMed

    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

  11. 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

  12. Protein Repeats from First Principles

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  13. Limitations on quantum key repeaters.

    PubMed

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

    2015-01-01

    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. PMID:25903096

  14. 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.

  15. Repeating seismic events in China.

    PubMed

    Schaff, David P; Richards, Paul G

    2004-02-20

    About 10% of seismic events in and near China from 1985 to 2000 were repeating events not more than about 1 kilometer from each other. We cross-correlated seismograms from approximately 14,000 earthquakes and explosions and measured relative arrival times to approximately 0.01 second, enabling lateral location precision of about 100 to 300 meters. Such precision is important for seismic hazard studies, earthquake physics, and nuclear test ban verification. Recognition and measurement of repeating signals in archived data and the resulting improvement in location specificity quantifies the inaccuracy of current procedures for picking onset times and locating events. PMID:14976310

  16. Pure laparoscopic hepatectomy as repeat surgery and repeat hepatectomy

    PubMed Central

    Isetani, Masashi; Morise, Zenichi; Kawabe, Norihiko; Tomishige, Hirokazu; Nagata, Hidetoshi; Kawase, Jin; Arakawa, Satoshi

    2015-01-01

    AIM: To assess clinical outcomes of laparoscopic hepatectomy (LH) in patients with a history of upper abdominal surgery and repeat hepatectomy. METHODS: This study compared the perioperative courses of patients receiving LH at our institution that had or had not previously undergone upper abdominal surgery. Of the 80 patients who underwent LH, 22 had prior abdominal surgeries, including hepatectomy (n = 12), pancreatectomy (n = 3), cholecystectomy and common bile duct excision (n = 1), splenectomy (n = 1), total gastrectomy (n = 1), colectomy with the involvement of transverse colon (n = 3), and extended hysterectomy with extensive lymph-node dissection up to the upper abdomen (n = 1). Clinical indicators including operating time, blood loss, hospital stay, and morbidity were compared among the groups. RESULTS: Eighteen of the 22 patients who had undergone previous surgery had severe adhesions in the area around the liver. However, there were no conversions to laparotomy in this group. In the 58 patients without a history of upper abdominal surgery, the median operative time was 301 min and blood loss was 150 mL. In patients with upper abdominal surgical history or repeat hepatectomy, the operative times were 351 and 301 min, and blood loss was 100 and 50 mL, respectively. The median postoperative stay was 17, 13 and 12 d for patients with no history of upper abdominal surgery, patients with a history, and patients with repeat hepatectomy, respectively. There were five cases with complications in the group with no surgical history, compared to only one case in the group with a prior history. There were no statistically significant differences in the perioperative results between the groups with and without upper abdominal surgical history, or with repeat hepatectomy. CONCLUSION: LH is feasible and safe in patients with a history of upper abdominal surgery or repeat hepatectomy. PMID:25624731

  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. 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

  19. 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.

  20. 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.

  1. 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. PMID:26934226

  2. Telomerase Repeated Amplification Protocol (TRAP)

    PubMed Central

    Mender, Ilgen; Shay, Jerry W.

    2016-01-01

    Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al., 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC- counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al., 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

  3. 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.

  4. 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

  5. 47 CFR 22.1015 - Repeater operation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Repeater operation. 22.1015 Section 22.1015 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES PUBLIC MOBILE SERVICES Offshore Radiotelephone Service § 22.1015 Repeater operation. Offshore central stations may be used as repeater stations provided that...

  6. 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…

  7. 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.

  8. 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

  9. Observations of Soft Gamma Repeaters

    NASA Technical Reports Server (NTRS)

    Kouveliotou, Chryssa

    2005-01-01

    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 emitting hundreds of predominantly soft (kl'=30 kev), short (0.1 - 100 ms long) events. Their quiescent source X-ray light curves exhibit pulsations in the narrow range of 5-1 1 s; estimates of these rotational period rate changes (spin-down) indicate that their magnetic fields are extremely high, of the order of 10A14-10A15 G. Such high B-field objects, dubbed "magnetars", had been predicted to exist in 1992, but the first concrete observational evidence was obtained in 1998 for two of these sources. Very recently, SGR1806-20 emitted a giant flare, which was detected in the radio with a multitude of telescopes under an extensive international campaign. These observations have revealed exciting new results, never seen before in any of the other magnetar sources. I will discuss here these results and their relevance to our understanding of the nature of magnetars.

  10. 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. PMID:27015469

  11. Repeated Sprints: An Independent Not Dependent Variable.

    PubMed

    Taylor, Jonathan M; Macpherson, Tom W; Spears, Iain R; Weston, Matthew

    2016-07-01

    The ability to repeatedly perform sprints has traditionally been viewed as a key performance measure in team sports, and the relationship between repeated-sprint ability (RSA) and performance has been explored extensively. However, when reviewing the repeated-sprint profile of team-sports match play it appears that the occurrence of repeated-sprint bouts is sparse, indicating that RSA is not as important to performance as commonly believed. Repeated sprints are, however, a potent and time-efficient training strategy, effective in developing acceleration, speed, explosive leg power, aerobic power, and high-intensity-running performance--all of which are crucial to team-sport performance. As such, we propose that repeated-sprint exercise in team sports should be viewed as an independent variable (eg, a means of developing fitness) as opposed to a dependent variable (eg, a means of assessing fitness/performance). PMID:27197118

  12. Strengthening concept learning by repeated testing

    PubMed Central

    Wiklund-Hörnqvist, Carola; Jonsson, Bert; Nyberg, Lars

    2014-01-01

    The aim of this study was to examine whether repeated testing with feedback benefits learning compared to rereading of introductory psychology key-concepts in an educational context. The testing effect was examined immediately after practice, after 18 days, and at a five-week delay in a sample of undergraduate students (n = 83). The results revealed that repeated testing with feedback significantly enhanced learning compared to rereading at all delays, demonstrating that repeated retrieval enhances retention compared to repeated encoding in the short- and the long-term. In addition, the effect of repeated testing was beneficial for students irrespectively of working memory capacity. It is argued that teaching methods involving repeated retrieval are important to consider by the educational system. PMID:24313425

  13. 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.

  14. Environmental distribution and long-term dispersion of reactor 14CO2 around two German nuclear power plants.

    PubMed

    Levin, I; Kromer, B; Barabas, M; Münnich, K O

    1988-02-01

    Carbon-14 data on atmospheric CO2 as well as on plant material (tree leaves and wheat) from the vicinity of two German boiling water reactors (Philippsburg and Isar/Ohu) are reported. Atmospheric CO2 samples taken routinely with an integration time of one or two weeks 1.75 km downwind of the Philippsburg reactor (900 MW electrical power) show a maximum 14C excess concentration of delta 14C (excess) = 300 +/- 7%, corresponding to 12.7 mBq m-3 (STP air). The long-term average excess amounts to delta 14C (excess) = 47 +/- 3%, corresponding to 2.0 mBq m-3 (STP air). The concentrations observed with plant material at the same sampling site range between delta 14C (excess) = 0% and 120%, corresponding to 0 and 27 mBq (g carbon)-1. With the meteorological dispersion parameters actually measured at the nuclear power plants, the dispersion factors for the various sampling sites and for the individual periods of sampling were calculated on the basis of a one-dimensional Gaussian plume model. With the observed 14C excess concentrations and the dispersion factor, a "theoretical" (i.e. calculated) reactor 14C source strength is then determined. For the Philippsburg reactor, which is situated in the flat Rhine valley, the "theoretical" and the observed yearly mean 14C emissions compare rather well (within a factor of 2). A significant systematical deviation from the model was found in the concentration decrease with source distance: the decrease predicted between the 1.75-km and 3.25-km distances is steeper than actually observed. The 14C excess concentrations found in tree leaves around the Isar/Ohu reactor (907 MW electrical power) at 1-2 km distance fall into the same range as observed at Philippsburg. In the hilly terrain at this reactor site, the model calculations agree well with the observed values up to a distance of 1 km if the relative elevation of the sampling site is taken into account by introducing a "reduced stack height" in the model calculations. This method fails in predicting the concentrations at distances greater than 1 km from the source. PMID:3123421

  15. 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.

  16. Understanding and identifying amino acid repeats.

    PubMed

    Luo, Hong; Nijveen, Harm

    2014-07-01

    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

  17. 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

  18. Approaching improved adhesive bonding repeatability

    NASA Astrophysics Data System (ADS)

    Schlette, Christian; Müller, Tobias; Roβmann, Jürgen; Brecher, Christian

    2016-03-01

    Today, the precision of micro-optics assembly is mostly limited by the accuracy of the bonding process ― and in the case of adhesive bonding by the prediction and compensation of adhesive shrinkage during curing. In this contribution, we present a novel approach to address adhesive bonding based on hybrid control system theory. In hybrid control, dynamic systems are described as "plants" which produce discrete and/or continuous outputs from given discrete and/or continuous inputs, thus yielding a hybrid state space description of the system. The task of hybrid controllers is to observe the plant and to generate a discrete and/or continuous input sequence that guides or holds the plant in a desired target state region while avoiding invalid or unwanted intermediate states. Our approach is based on a series of experiments carried out in order to analyze, define and decouple the dependencies of adhesive shrinkage on multiple parameters, such as application geometries, fixture forces and UV intensities. As some of the dependencies describe continuous effects (e.g. shrinkage from UV intensity) and other dependencies describe discrete state transitions (e.g. fixture removal during curing), the resulting model of the overall bonding process is a hybrid dynamic system in the general case. For this plant model, we then propose a concept of sampling-based parameter search as a basis to design suitable hybrid controllers, which have the potential to optimize process control for a selection of assembly steps, thus improving the repeatability of related production steps like beam-shaping optics or mounting of turning mirrors for fiber coupling.

  19. All Repeats are Not Equal: A Module-Based Approach to Guide Repeat Protein Design

    PubMed Central

    Regan, Lynne

    2013-01-01

    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 3 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 armadillio repeat (ARM) 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. PMID:23434848

  20. 47 CFR 97.205 - Repeater station.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Special Operations § 97.205 Repeater station. (a) Any amateur station licensed to a holder of a Technician, General, Advanced or Amateur Extra Class operator license may be a repeater. A holder of...

  1. 47 CFR 97.205 - Repeater station.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Special Operations § 97.205 Repeater station. (a) Any amateur station licensed to a holder of a Technician, General, Advanced or Amateur Extra Class operator license may be a repeater. A holder of...

  2. 47 CFR 97.205 - Repeater station.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Special Operations § 97.205 Repeater station. (a) Any amateur station licensed to a holder of a Technician, General, Advanced or Amateur Extra Class operator license may be a repeater. A holder of...

  3. 47 CFR 97.205 - Repeater station.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Special Operations § 97.205 Repeater station. (a) Any amateur station licensed to a holder of a Technician, General, Advanced or Amateur Extra Class operator license may be a repeater. A holder of...

  4. 47 CFR 97.205 - Repeater station.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES AMATEUR RADIO SERVICE Special Operations § 97.205 Repeater station. (a) Any amateur station licensed to a holder of a Technician, General, Advanced or Amateur Extra Class operator license may be a repeater. A holder of...

  5. The Effects of Repeaters on Test Equating.

    ERIC Educational Resources Information Center

    Andrulis, Richard S.; And Others

    The purpose of this investigation was to establish the effects of repeaters on test equating. Since consideration was not given to repeaters in test equating, such as in the derivation of equations by Angoff (1971), the hypothetical effect needed to be established. A case study was examined which showed results on a test as expected; overall mean…

  6. The Effects of Repeaters on Test Equating.

    ERIC Educational Resources Information Center

    Andrulis, Richard S.; And Others

    1978-01-01

    The effects of repeaters (testees included in both administrations of two forms of a test) on the test equating process are examined. It is shown that repeaters do effect test equating and tend to lower the cutoff point for passing the test. (JKS)

  7. Evaluating a Group Repeated Reading Intervention

    ERIC Educational Resources Information Center

    Klubnik, Cynthia Adele

    2009-01-01

    Fluency has been identified as an important component of effective reading instruction, and repeated reading has been shown to improve oral reading fluency. In order to improve the efficiency of repeated reading interventions, more research is needed on the effectiveness of small group reading interventions. An alternating treatments, single…

  8. Laparoscopic repeat hepatectomy after right hepatopancreaticoduodenectomy.

    PubMed

    Igami, Tsuyoshi; Komaya, Kenichi; Hirose, Tomoaki; Ebata, Tomoki; Yokoyama, Yukihiro; Sugawara, Gen; Mizuno, Takashi; Yamaguchi, Junpei; Nagino, Masato

    2016-08-01

    Although laparoscopic hepatectomy is widely accepted for primary hepatectomy, the clinical value of laparoscopic hepatectomy for repeat hepatectomy is still challenging. We herein describe our experience with laparoscopic repeat hepatectomy after right hepatopancreaticoduodenectomy. A 72-year-old woman who had undergone right hepatopancreaticoduodenectomy for perihilar cholangiocarcinoma 31 months prior was diagnosed with liver metastasis in segment 3. We performed laparoscopic repeat hepatectomy. Because mild adhesions in the left side of the abdominal cavity were detected by laparoscopy, the planned procedure was accomplished. The operative time and intraoperative blood loss were 139 min and less than 1 mL, respectively. The patient was discharged at 6 days after surgery and was healthy with no evidence of recurrence at 21 months after laparoscopic repeat hepatectomy. Laparoscopic repeat hepatectomy is a suitable and safe procedure for minor hepatectomy, provided that careful technique is used after the working space is secured under pneumoperitoneum. PMID:27221034

  9. 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…

  10. Finding and Characterizing Repeats in Plant Genomes.

    PubMed

    Nicolas, Jacques; Peterlongo, Pierre; Tempel, Sébastien

    2016-01-01

    Plant genomes contain a particularly high proportion of repeated structures of various types. This chapter proposes a guided tour of available software that can help biologists to look for these repeats and check some hypothetical models intended to characterize their structures. Since transposable elements are a major source of repeats in plants, many methods have been used or developed for this large class of sequences. They are representative of the range of tools available for other classes of repeats and we have provided a whole section on this topic as well as a selection of the main existing software. In order to better understand how they work and how repeats may be efficiently found in genomes, it is necessary to look at the technical issues involved in the large-scale search of these structures. Indeed, it may be hard to keep up with the profusion of proposals in this dynamic field and the rest of the chapter is devoted to the foundations of the search for repeats and more complex patterns. The second section introduces the key concepts that are useful for understanding the current state of the art in playing with words, applied to genomic sequences. This can be seen as the first stage of a very general approach called linguistic analysis that is interested in the analysis of natural or artificial texts. Words, the lexical level, correspond to simple repeated entities in texts or strings. In fact, biologists need to represent more complex entities where a repeat family is built on more abstract structures, including direct or inverted small repeats, motifs, composition constraints as well as ordering and distance constraints between these elementary blocks. In terms of linguistics, this corresponds to the syntactic level of a language. The last section introduces concepts and practical tools that can be used to reach this syntactic level in biological sequence analysis. PMID:26519414

  11. Do gamma-ray burst sources repeat?

    NASA Technical Reports Server (NTRS)

    Meegan, C. A.; Hartmann, D. H.; Brainerd, J. J.; Briggs, M.; Paciesas, W. S.; Pendleton, G.; Kouveliotou, C.; Fishman, G.; Blumenthal, G.; Brock, M.

    1994-01-01

    The demonstration of repeated gamma-ray bursts from an individual source would severely constrain burst source models. Recent reports 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 ad 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 bursts cannot be excluded.

  12. 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

  13. Repeat radiosurgery for cerebral arteriovenous malformations.

    PubMed

    Awad, Ahmed J; Walcott, Brian P; Stapleton, Christopher J; Ding, Dale; Lee, 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. PMID:25913746

  14. 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. PMID:16421768

  15. Stalled DNA Replication Forks at the Endogenous GAA Repeats Drive Repeat Expansion in Friedreich's Ataxia Cells.

    PubMed

    Gerhardt, Jeannine; Bhalla, Angela D; Butler, Jill Sergesketter; Puckett, James W; Dervan, Peter B; Rosenwaks, Zev; Napierala, Marek

    2016-08-01

    Friedreich's ataxia (FRDA) is caused by the expansion of GAA repeats located in the Frataxin (FXN) gene. The GAA repeats continue to expand in FRDA patients, aggravating symptoms and contributing to disease progression. The mechanism leading to repeat expansion and decreased FXN transcription remains unclear. Using single-molecule analysis of replicated DNA, we detected that expanded GAA repeats present a substantial obstacle for the replication machinery at the FXN locus in FRDA cells. Furthermore, aberrant origin activation and lack of a proper stress response to rescue the stalled forks in FRDA cells cause an increase in 3'-5' progressing forks, which could enhance repeat expansion and hinder FXN transcription by head-on collision with RNA polymerases. Treatment of FRDA cells with GAA-specific polyamides rescues DNA replication fork stalling and alleviates expansion of the GAA repeats, implicating DNA triplexes as a replication impediment and suggesting that fork stalling might be a therapeutic target for FRDA. PMID:27425605

  16. 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.

  17. Variable efficacy of repeated annual influenza vaccination.

    PubMed

    Smith, D J; Forrest, S; Ackley, D H; Perelson, A S

    1999-11-23

    Conclusions have differed in studies that have compared vaccine efficacy in groups receiving influenza vaccine for the first time to efficacy in groups vaccinated more than once. For example, the Hoskins study [Hoskins, T. W., Davis, J. R., Smith, A. J., Miller, C. L. & Allchin, A. (1979) Lancet i, 33-35] concluded that repeat vaccination was not protective in the long term, whereas the Keitel study [Keitel, W. A., Cate, T. R., Couch, R. B., Huggins, L. L. & Hess, K. R. (1997) Vaccine 15, 1114-1122] concluded that repeat vaccination provided continual protection. We propose an explanation, the antigenic distance hypothesis, and test it by analyzing seven influenza outbreaks that occurred during the Hoskins and Keitel studies. The hypothesis is that variation in repeat vaccine efficacy is due to differences in antigenic distances among vaccine strains and between the vaccine strains and the epidemic strain in each outbreak. To test the hypothesis, antigenic distances were calculated from historical hemagglutination inhibition assay tables, and a computer model of the immune response was used to predict the vaccine efficacy of individuals given different vaccinations. The model accurately predicted the observed vaccine efficacies in repeat vaccinees relative to the efficacy in first-time vaccinees (correlation 0.87). Thus, the antigenic distance hypothesis offers a parsimonious explanation of the differences between and within the Hoskins and Keitel studies. These results have implications for the selection of influenza vaccine strains, and also for vaccination strategies for other antigenically variable pathogens that might require repeated vaccination. PMID:10570188

  18. Quantum key distribution over probabilistic quantum repeaters

    NASA Astrophysics Data System (ADS)

    Amirloo, Jeyran; Razavi, Mohsen; Majedi, A. Hamed

    2010-09-01

    A feasible route toward implementing long-distance quantum key distribution (QKD) systems relies on probabilistic schemes for entanglement distribution and swapping as proposed in the work of Duan, Lukin, Cirac, and Zoller (DLCZ) [Nature (London)NATUAS0028-083610.1038/35106500 414, 413 (2001)]. Here, we calculate the conditional throughput and fidelity of entanglement for DLCZ quantum repeaters by accounting for the DLCZ self-purification property in the presence of multiple excitations in the ensemble memories as well as loss and other sources of inefficiency in the channel and measurement modules. We then use our results to find the generation rate of secure key bits for QKD systems that rely on DLCZ quantum repeaters. We compare the key generation rate per logical memory employed in the two cases with and without a repeater node. We find the crossover distance beyond which the repeater system outperforms the nonrepeater one. That provides us with the optimum internode distancing in quantum repeater systems. We also find the optimal excitation probability at which the QKD rate peaks. Such an optimum probability, in most regimes of interest, is insensitive to the total distance.

  19. 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.

  20. 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.

  1. Nucleic acid recognition by tandem helical repeats.

    PubMed

    Rubinson, Emily H; Eichman, Brandt F

    2012-02-01

    Protein domains constructed from tandem α-helical repeats have until recently been primarily associated with protein scaffolds or RNA recognition. Recent crystal structures of human mitochondrial termination factor MTERF1 and Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA revealed two new superhelical tandem repeat architectures capable of wrapping around the double helix in unique ways. Unlike DNA sequence recognition motifs that rely mainly on major groove read-out, MTERF and ALK motifs locate target sequences and aberrant nucleotides within DNA by resculpting the double-helix through extensive backbone contacts. Comparisons between MTERF and ALK repeats, together with recent advances in ssRNA recognition by Pumilio/FBF (PUF) domains, provide new insights into the fundamental principles of protein-nucleic acid recognition. PMID:22154606

  2. 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.

  3. 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.

  4. 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.

  5. 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

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

    PubMed

    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

  7. Cumulative Intertrial Inhibition in Repeated Visual Search

    ERIC Educational Resources Information Center

    Takeda, Yuji

    2007-01-01

    In the present study the author examined visual search when the items remain visible across trials but the location of the target varies. Reaction times for inefficient search cumulatively increased with increasing numbers of repeated search trials, suggesting that inhibition for distractors carried over successive trials. This intertrial…

  8. 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

  9. 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. () 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. PMID:27012819

  10. 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…

  11. 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

  12. 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…

  13. Repeated Transmissions In Mobile/Satellite Communications

    NASA Technical Reports Server (NTRS)

    Yan, Tsun-Yee; Clare, Loren P.

    1988-01-01

    Repetition increases throughput and decreases delay. Paper discusses theoretical performance of communication system for land-mobile stations with satellite relay using ALOHA random-access protocol modified for repeated transimssions. Methods and conclusions contribute to general understanding of packet communications in fading channels.

  14. 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…

  15. 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. PMID:26733936

  16. 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…

  17. 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. PMID:25779755

  18. 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…

  19. 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.

  20. 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…

  1. Blood Donation by Elderly Repeat Blood Donors

    PubMed Central

    Zeiler, Thomas; Lander-Kox, Jutta; Alt, Timo

    2014-01-01

    Summary Background Upper age limits for blood donors are intended to protect elderly blood donors from donor reactions. However, due to a lack of data about adverse reactions in elderly blood donors, upper age limits are arbitrary and vary considerably between different countries. Methods Here we present data from 171,231 voluntary repeat whole blood donors beyond the age of 68 years. Results Blood donations from repeat blood donors beyond the age of 68 years increased from 2,114 in 2005 to 38,432 in 2012 (from 0,2% to 4.2% of all whole blood donations). Adverse donor reactions in repeat donors decreased with age and were lower than in the whole group (0.26%), even in donors older than 71 years (0.16%). However, from the age of 68 years, the time to complete recovery after donor reactions increased. Donor deferrals were highest in young blood donors (21.4%), but increased again in elderly blood donors beyond 71 years (12.6%). Conclusion Blood donation by regular repeat blood donors older than 71 years may be safely continued. However, due to a lack of data for donors older than 75 years, blood donation in these donors should be handled with great caution. PMID:25254019

  2. Accuracy of velocities from repeated GPS measurements

    NASA Astrophysics Data System (ADS)

    Akarsu, V.; Sanli, D. U.; Arslan, E.

    2015-04-01

    Today repeated GPS measurements are still in use, because we cannot always employ GPS permanent stations due to a variety of limitations. One area of study that uses velocities/deformation rates from repeated GPS measurements is the monitoring of crustal motion. This paper discusses the quality of the velocities derived using repeated GPS measurements for the aim of monitoring crustal motion. From a global network of International GNSS Service (IGS) stations, we processed GPS measurements repeated monthly and annually spanning nearly 15 years and estimated GPS velocities for GPS baseline components latitude, longitude and ellipsoidal height. We used web-based GIPSY for the processing. Assuming true deformation rates can only be determined from the solutions of 24 h observation sessions, we evaluated the accuracy of the deformation rates from 8 and 12 h sessions. We used statistical hypothesis testing to assess the velocities derived from short observation sessions. In addition, as an alternative control method we checked the accuracy of GPS solutions from short observation sessions against those of 24 h sessions referring to statistical criteria that measure the accuracy of regression models. Results indicate that the velocities of the vertical component are completely affected when repeated GPS measurements are used. The results also reveal that only about 30% of the 8 h solutions and about 40% of 12 h solutions for the horizontal coordinates are acceptable for velocity estimation. The situation is much worse for the vertical component in which none of the solutions from campaign measurements are acceptable for obtaining reliable deformation rates.

  3. Inhibition of breast cancer cell proliferation in repeated and non-repeated treatment with zoledronic acid

    PubMed Central

    2012-01-01

    Background Zoledronic acid is used to treat bone metastases and has been shown to reduce skeletal-related events and exert antitumor activity. The present in vitro study investigates the mechanism of action of Zoledronic Acid on breast cancer cell lines with different hormonal and HER2 patterns. Furthermore, we investigated the efficacy of repeated versus non-repeated treatments. Methods The study was performed on 4 breast cancer cell lines (BRC-230, SkBr3, MCF-7 and MDA-MB-231). Non-repeated treatment (single exposure of 168 hrs’ duration) with zoledronic acid was compared with repeated treatment (separate exposures, each of 48 hrs’ duration, for a total of 168 hrs) at different dosages. A dose–response profile was generated using sulforhodamine B assay. Apoptosis was evaluated by TUNEL assay and biomolecular characteristics were analyzed by western blot. Results Zoledronic acid produced a dose-dependent inhibition of proliferation in all cell lines. Anti-proliferative activity was enhanced with the repeated treatment, proving to be statistically significant in the triple-negative lines. In these lines repeated treatment showed a cytocidal effect, with apoptotic cell death caused by caspase 3, 8 and 9 activation and decreased RAS and pMAPK expression. Apoptosis was not observed in estrogen receptor-positive line: p21 overexpression suggested a slowing down of cell cycle. A decrease in RAS and pMAPK expression was seen in HER2-overexpressing line after treatment. Conclusions The study suggests that zoledronic acid has an antitumor activity in breast cancer cell lines. Its mechanism of action involves the decrease of RAS and RHO, as in osteoclasts. Repeated treatment enhances antitumor activity compared to non-repeated treatment. Repeated treatment has a killing effect on triple-negative lines due to apoptosis activation. Further research is warranted especially in the treatment of triple-negative breast cancer. PMID:23173568

  4. 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. PMID:25126053

  5. Interoperability in encoded quantum repeater networks

    NASA Astrophysics Data System (ADS)

    Nagayama, Shota; Choi, Byung-Soo; Devitt, Simon; Suzuki, Shigeya; Van Meter, Rodney

    2016-04-01

    The future of quantum repeater networking will require interoperability between various error-correcting codes. A few specific code conversions and even a generalized method are known, however, no detailed analysis of these techniques in the context of quantum networking has been performed. In this paper we analyze a generalized procedure to create Bell pairs encoded heterogeneously between two separate codes used often in error-corrected quantum repeater network designs. We begin with a physical Bell pair and then encode each qubit in a different error-correcting code, using entanglement purification to increase the fidelity. We investigate three separate protocols for preparing the purified encoded Bell pair. We calculate the error probability of those schemes between the Steane [[7,1,3

  6. 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.

  7. 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. PMID:24575886

  8. [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. PMID:26934788

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. A New Property of Repeating Decimals

    ERIC Educational Resources Information Center

    Arledge, Jane; Tekansik, Sarah

    2008-01-01

    As extended by Ginsberg, Midi's theorem says that if the repeated section of a decimal expansion of a prime is split into appropriate blocks and these are added, the result is a string of nines. We show that if the expansion of 1/p[superscript n+1] is treated the same way, instead of being a string of nines, the sum is related to the period of…

  14. 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. PMID:26208520

  15. Androgen receptor polymorphism (CAG repeats) and androgenicity.

    PubMed

    Canale, D; Caglieresi, C; Moschini, C; Liberati, C D; Macchia, E; Pinchera, A; Martino, E

    2005-09-01

    Objective Polymorphism of the androgen receptor (AR) has been related to various pathophysiological conditions, such as osteoporosis and infertility. The objectives of this study were to evaluate the frequency of distribution in a normal Italian population and to assess CAG repeats (CAGr) in other conditions, such as hypoandrogenism, potentially influenced by AR polymorphism. Patients and measurements CAGr polymorphism was determined in a group of 91 healthy normoandrogenized subjects, 29 hypoandrogenized patients (hypoplasia of prostate and seminal vesicles, reduced beard or body hair, etc.) and 29 infertile patients by direct sequencing. Results The mean (+/- SD) number of CAG repeats [(CAGr)n] was 21.5 (+/- 1.7) in the control group, 21.4 (+/- 2.0) in the infertile patients and 24.0 (+/- 2.9) in the hypoandrogenic males. The difference was statistically significant between this last group and the other two (P < 0.0001), while there was no difference between normal controls and infertile patients. The frequency distribution showed a shift towards higher CAG length in hypoandrogenized patients compared to controls and infertile patients. If we used a cut-off point of 24.9 (2 SD above the mean), the percentage of patients with 25 or more CAGr repeats was 38% among hypoandrogenized patients, 7% among infertile patients and 5% among the control group. In hypoandrogenized subjects (CAGr)n correlated slightly with testis and prostate volume. The number of CAG repeats was not associated with any of the hormonal parameters, including testosterone, evaluated in the three groups. Conclusions Our normal population, representing subjects from Central Italy, is superimposable on other European populations with regard to (CAGr)n distribution. Hypoandrogenic males have a shift in the frequency distribution towards longer (CAGr)n. Infertile patients are not statistically different from the control group. These findings suggest that, given the same amount of circulating

  16. 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.

  17. 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.

  18. Multiplexing schemes for quantum repeater networks

    NASA Astrophysics Data System (ADS)

    Aparicio, Luciano; Van Meter, Rodney

    2011-08-01

    When built, quantum repeaters will allow the distribution of entangled quantum states across large distances, playing a vital part in many proposed quantum technologies. Enabling multiple users to connect through the same network will be key to their real-world deployment. Previous work on repeater technologies has focussed only on simple entanglment production, without considering the issues of resource scarcity and competition that necessarily arise in a network setting. In this paper we simulated a thirteen-node network with up to five flows sharing different parts of the network, measuring the total throughput and fairness for each case. Our results suggest that the Internet-like approach of statistical multiplexing use of a congested link gives the highest aggregate throughput. Time division multiplexing and buffer space multiplexing were slightly less effective, but all three schemes allow the sum of multiple flows to substantially exceed that of any one flow, improving over circuit switching by taking advantage of resources that are forced to remain idle in circuit switching. All three schemes proved to have excellent fairness. The high performance, fairness and simplicity of implementation support a recommendation of statistical multiplexing for shared quantum repeater networks.

  19. 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

  20. Repeated buckling of composite shear panels

    NASA Technical Reports Server (NTRS)

    Singer, Josef; Weller, Tanchum

    1990-01-01

    Failures in service of aerospace structures and research at the Technion Aircraft Structures Laboratory have revealed that repeatedly buckled stiffened shear panels might be susceptible to premature fatigue failures. Extensive experimental and analytical studies have been performed at Technion on repeated buckling, far in excess of initial buckling, for both metal and composite shear panels with focus on the influence of the surrounding structure. The core of the experimental investigation consisted of repeated buckling and postbuckling tests on Wagner beams in a three-point loading system under realistic test conditions. The effects of varying sizes of stiffeners, of the magnitude of initial buckling loads, of the panel aspect ratio and of the cyclic shearing force, V sub cyc, were studied. The cyclic to critical shear buckling ratios, (V sub cyc/V sub cr) were on the high side, as needed for efficient panel design, yet all within possible flight envelopes. The experiments were supplemented by analytical and numerical analyses. For the metal shear panels the test and numerical results were synthesized into prediction formulas, which relate the life of the metal shear panels to two cyclic load parameters. The composite shear panels studied were hybrid beams with graphite/epoxy webs bonded to aluminum alloy frames. The test results demonstrated that composite panels were less fatigue sensitive than comparable metal ones, and that repeated buckling, even when causing extensive damage, did not reduce the residual strength by more than 20 percent. All the composite panels sustained the specified fatigue life of 250,000 cycles. The effect of local unstiffened holes on the durability of repeatedly buckled shear panels was studied for one series of the metal panels. Tests on 2024 T3 aluminum panels with relatively small unstiffened holes in the center of the panels demonstrated premature fatigue failure, compared to panels without holes. Preliminary tests on two graphite

  1. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    PubMed

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474

  2. 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. PMID:25774031

  3. Simple sequence repeats in Haemophilus influenzae.

    PubMed

    Power, Peter M; Sweetman, W A; Gallacher, N J; Woodhall, M R; Kumar, G A; Moxon, E R; Hood, D W

    2009-03-01

    Simple sequence repeat (SSRs) of DNA are subject to high rates of mutation and are important mediators of adaptation in Haemophilus influenzae. Previous studies of the Rd KW20 genome identified the primacy of tetranucleotide SSRs in mediating phase variation (the rapid reversible switching of gene expression) of surface exposed structures such as lipopolysaccharide. The recent sequencing of the genomes of multiple strains of H. influenzae allowed the comparison of the SSRs (repeat units of one to nine nucleotides in length) in detail across four complete H. influenzae genomes and then comparison with a further 12 genomes when they became available. The SSR loci were broadly classified into three groups: (1) those that did not vary; (2) those for which some variation between strains was observed but this could not be linked to variation of gene expression; and (3) those that both varied and were located in regions consistent with mediating phase variable gene expression. Comparative analysis of 988 SSR associated loci confirmed that tetranucleotide repeats were the major mediators of phase variation and extended the repertoire of known tetranucleotide SSR loci by identifying ten previously uncharacterised tetranucleotide SSR loci with the potential to mediate phase variation which were unequally distributed across the H. influenzae pan-genome. Further, analysis of non-tetranucleotide SSR in the 16 strains revealed a number of mononucleotide, dinucleotide, pentanucleotide, heptanucleotide, and octanucleotide SSRs which were consistent with these tracts mediating phase variation. This study substantiates previous findings as to the important role that tetranucleotide SSRs play in H. influenzae biology. Two Brazilian isolates showed the most variation in their complement of SSRs suggesting the possibility of geographic and phenotypic influences on SSR distribution. PMID:19095084

  4. Capping motifs stabilize the leucine-rich repeat protein PP32 and rigidify adjacent repeats.

    PubMed

    Dao, Thuy P; Majumdar, Ananya; Barrick, Doug

    2014-06-01

    Capping motifs are found to flank most β-strand-containing repeat proteins. To better understand the roles of these capping motifs in organizing structure and stability, we carried out folding and solution NMR studies on the leucine-rich repeat (LRR) domain of PP32, which is composed of five tandem LRR, capped by α-helical and β-hairpin motifs on the N- and C-termini. We were able to purify PP32 constructs lacking either cap and containing destabilizing substitutions. Removing the C-cap results in complete unfolding of PP32. Removing the N-cap has a much less severe effect, decreasing stability but retaining much of its secondary structure. In contrast, the dynamics and tertiary structure of the first two repeats are significantly perturbed, based on (1)H-(15)N relaxation studies, chemical shift perturbations, and residual dipolar couplings. However, more distal repeats (3 to C-cap) retain their native tertiary structure. In this regard, the N-cap drives the folding of adjacent repeats from what appears to be a molten-globule-like state. This interpretation is supported by extensive analysis using core packing substitutions in the full-length and N-cap-truncated PP32. This work highlights the importance of caps to the stability and structural integrity of β-strand-containing LRR proteins, and emphasizes the different contributions of the N- and C-terminal caps. PMID:24659532

  5. Cataractogenesis after Repeat Laser in situ Keratomileusis

    PubMed Central

    Mansour, Ahmad M.; Ghabra, Marwan

    2012-01-01

    There has been the unsubstantiated clinical impression that laser refractive surgery accelerates cataract development along with solid experimental data about the cataractogenic effects of excimer laser treatment. We present the first documented case of significant cataract formation in a young myope after repeat excimer laser ablation necessitating phacoemulsification with a posterior chamber implant. Proposed explanations include focusing of the ablation wave on the posterior capsule (acoustic wave lens epithelial damage), photooxidative stress of the lens (ultraviolet and inflammatory oxidative stress), and corticosteroid-induced cataract (lens toxicity). PMID:22949915

  6. Mars orbits with daily repeating ground traces

    NASA Technical Reports Server (NTRS)

    Noreen, Gary K.; Kerridge, Stuart; Diehl, Roger; neelon, Joseph; Ely, Todd; Turner, Andrew

    2003-01-01

    This paper derives orbits at Mars with ground traces that repeat at the same times every solar day (sol). A relay orbiter in such an orbit would pass over insitu probes at the same times every sol, ensuring consistent coverage and simplifying mission design and operations. 42 orbits in five classes are characteried: 14 cicular equatorial prograde orbits; 14 circular equatorial retrograde orbits; 11 circular sun synchrounous orbits; 2 eccentroc equatorial orbits; 1 eccentric critcally inclined orbit. the paper reports on the performance of a relay orbiter in some of the orbits.

  7. Innovative collaboration to prevent repeated adolescent pregnancies.

    PubMed

    Saunders, R B; Brown, H N

    1997-01-01

    Nurse educators from a university setting and staff from the county health department collaborated to establish an innovative program to prevent repeated pregnancy in adolescents. Called Dollar-A-Day and patterned after the original in Denver, CO, the program was operated jointly for 5 years and today continues to operate under the auspices of the health department. Success of the venture is attributed to use of skills in assessment, building, managing, and evaluating, as described by Loxley (1997). These elements were used to construct a context for collaboration. PMID:9397869

  8. Multifunctional protein: cardiac ankyrin repeat protein*

    PubMed Central

    Zhang, Na; Xie, Xiao-jie; Wang, Jian-an

    2016-01-01

    Cardiac ankyrin repeat protein (CARP) not only serves as an important component of muscle sarcomere in the cytoplasm, but also acts as a transcription co-factor in the nucleus. Previous studies have demonstrated that CARP is up-regulated in some cardiovascular disorders and muscle diseases; however, its role in these diseases remains controversial now. In this review, we will discuss the continued progress in the research related to CARP, including its discovery, structure, and the role it plays in cardiac development and heart diseases. PMID:27143260

  9. 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.

  10. Hypermnesia: the role of repeated testing.

    PubMed

    Roediger, H L; Payne, D G

    1982-01-01

    The present study was designed to determine whether the increased recall of pictures across repeated tests (hypermnesia) is due to increasing strength of imaginal traces during the retention interval or to increased retrieval practice from prior tests. Subjects studied 60 pictures and then recalled them after various delays that were filled with instructions and, in two cases, reading a passage. Recall on a first test showed no change with retention interval. With retention interval held constant, however, the number of pictures recalled varied directly with the number of prior tests subjects had been given. This finding points up the critical nature of retrieval factors in producing hypermnesia. PMID:6210744

  11. An investigation of electromagnetic launcher repeatability

    NASA Astrophysics Data System (ADS)

    Heyse, Mark W.; Cornette, James B.; Brown, Jere L.

    1992-07-01

    Electromagnetic launcher (EML) performance repeatability has been identified as a potential development issue for several years. Investigation of this issue has been difficult because an EML that is powered on a relatively continuous basis to provide long duration operation has not been available. A battery charged capacitor power system has enabled long duration, 6 to 7 seconds, EML experiments. This paper provides a summary of an experiment to investigate EML launch to launch performance consistency. A series of 8 ten-shot bursts, each separated by 15 to 30 minutes, performed in a single day using a single set of bore materials is the subject of this paper.

  12. An investigation of electromagnetic launch repeatability

    NASA Astrophysics Data System (ADS)

    Cornette, James B.; Heyse, Mark W.; Brown, Jere L.

    1993-01-01

    Electromagnetic launcher (EML) performance repeatability has been identified as a potential development issue for several years. Investigation of this issue has been difficult because an EML that is powered on a relatively continuous basis to provide long duration operation has not been available. A battery charged capacitor power system has enabled long duration, 6 to 7 seconds, EML experiments. This paper provides a summary of an experiment to investigate EML launch to launch performance consistency. A series of 8 ten-shot bursts, each separated by 15 to 30 minutes, performed in a single day using a single set of bore materials is the subject of this paper.

  13. 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.

  14. Entanglement replication via quantum repeated interactions

    NASA Astrophysics Data System (ADS)

    Wendenbaum, Pierre; Platini, Thierry; Karevski, Dragi

    2015-04-01

    We study entanglement creation between two independent XX chains, which are repeatedly coupled locally to spin-1/2 Bell pairs. We show analytically that in the steady state the entanglement of the Bell pairs is perfectly transferred to the chains, generating large-scale interchain pair correlations. However, before the steady state is reached, within a growing causal region around the interacting locus the chains are found in a current driven nonequilibrium steady state (NESS). In the NESS, the chains cross entanglement decays exponentially with respect to the distance to the boundary sites with a typical length scale which is inversely proportional to the driving current.

  15. Rapid automatic detection and alignment of repeats in protein sequences.

    PubMed

    Heger, A; Holm, L

    2000-11-01

    Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. We have developed an automatic algorithm, RADAR, for segmenting a query sequence into repeats. The segmentation procedure has three steps: (i) repeat length is determined by the spacing between suboptimal self-alignment traces; (ii) repeat borders are optimized to yield a maximal integer number of repeats, and (iii) distant repeats are validated by iterative profile alignment. The method identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in the query sequence. No manual intervention and no prior assumptions on the number and length of repeats are required. Comparison to the Pfam-A database indicates good coverage, accurate alignments, and reasonable repeat borders. Screening the Swissprot database revealed 3,000 repeats not annotated in existing domain databases. A number of these repeats had been described in the literature but most were novel. This illustrates how in times when curated databases grapple with ever increasing backlogs, automatic (re)analysis of sequences provides an efficient way to capture this important information. PMID:10966575

  16. Sequence analysis of Vicia faba repeated DNA, the FokI repeat element.

    PubMed Central

    Kato, A; Yakura, K; Tanifuji, S

    1984-01-01

    A type of highly repeated DNA sequences present in the genome of Vicia faba was detected by digestion its nuclear DNA with FokI endonuclease and fractionating the digests on polyacrylamide gels. Four fragments of 59, 108, 177 and 246 bp of the FokI repeated sequences were collected from the gels and their primary structures were determined by the method of Maxam and Gilbert. These repeated DNA sequences were shown to be a multiple tandem array of a 59 bp sequence element. And its nucleotide sequence was almost completely conserved among all the sequence members of each the size class and also among these classes. This sequence element consists of a duplet of an about the duplet has an incomplete dyad symmetrical structure. Images PMID:6089113

  17. Characteristics of repeatedly assaultive psychiatric inpatients.

    PubMed

    Convit, A; Isay, D; Otis, D; Volavka, J

    1990-10-01

    Investigations of assaults in psychiatric hospitals have found that a small proportion of inpatients are responsible for a large percentage of the violence that occurs. In a large state hospital patients who were repeatedly violent (recidivists) were compared with patients who were violent only once or twice (nonrecidivists), and the relationships between repeatedly violent behavior and gender, age, and diagnosis were examined. All reports of violent incidents over a six-month period for a population of 1,552 inpatients--a total of 497 incidents involving 313 patients--were reviewed. Seventy patients were involved in three or more incidents each and were responsible for 53 percent of all violence. Recidivist men inflicted serious injuries at a rate ten times higher than that for all the other violent patients. Recidivist women were significantly younger than nonrecidivist assaultive women and were about the same mean age as the assaultive men. Recidivist women were also more likely to have organic brain disorder or personality disorder. PMID:2242874

  18. 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

  19. 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.

  20. Dangling chain elastomers as repeatable fibrillar adhesives.

    PubMed

    Sitti, Metin; Cusick, Brian; Aksak, Burak; Nese, Alper; Lee, Hyung-il; Dong, Hongchen; Kowalewski, Tomasz; Matyjaszewski, Krzysztof

    2009-10-01

    This work reports on repeatable adhesive materials prepared by controlled grafting of dangling hetero chains from polymer elastomers. The dangling chain elastomer system was prepared by grafting poly(n-butyl acrylate) (PBA) chains from prefunctionalized polydimethylsiloxane (PDMS) elastomer networks using atom transfer radical polymerization. To study the effects of chain growth and network strain as they relate to network adhesion mechanics, various lengths of PBA chains with degree of polymerizations (DP) of 65, 281, 508, and 1200 were incorporated into the PDMS matrix. PBA chains with a DP value of 281 grafted from a flat PDMS substrate showed the highest (approximately 3.5-fold) enhancement of nano- and macroscale adhesion relative to a flat raw (ungrafted and not prefunctionalized) PDMS substrate. Moreover, to study the effect of PBA dangling chains on adhesion in fibrillar elastomer structures inspired by gecko foot hairs, a dip-transfer fabrication method was used to graft PBA chains with a DP value of 296 from the tip endings of mushroom-shaped PDMS micropillars. A PBA chain covered micropillar array showed macroscale adhesion enhancement up to approximately 7 times relative to the flat ungrafted prefunctionalized PDMS control substrate, showing additional nonoptimized approximately 2-fold adhesion enhancement due to fibrillar structuring and mushroom-shaped tip ending. These dangling hetero chains on elastomer micro-/nanofibrillar structures may provide a novel fabrication platform for multilength scale, repeatable, and high-strength fibrillar adhesives inspired by gecko foot hairs. PMID:20355863

  1. 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

  2. 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.

  3. 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.

  4. Distribution of repeat unit differences between alleles at tandem repeat microsatellite loci

    SciTech Connect

    Jin, L. |; Zhong, Y.; Chakraborty, R.

    1994-09-01

    PCR-based assays of tandemly repeated microsatellite loci detect genetic variation from which alleles may be scored by their repeat unit lengths. Comparison of allele sizes from such data yields a probability distribution (P{sub k}) of repeat unit differences (k) between alleles segregating in a population. We show that this distribution (P{sub k}; k = 0, 1,2,...) provides insight regarding the mechanism of production of new alleles at such loci and the demographic history of populations, far better than that obtained from other summary measures (e.g., heterozygosity, number of alleles, and the range of allele sizes). The distributions of P{sub k} under multi-step stepwise models of mutation are analytically derived, which show that when a population is at equilibrium under the mutation-drift balance, the distribution of repeat unit differences between alleles is positively skewed with a mode larger than zero. However, when the heterozygosity at a locus is low (say, less than 40%), P{sub k} is a monotonically decreasing function of k. Applications of this theory to data on repeat unit sizes at over 1,240 microsatellite loci from the Caucasians, categorized by the average heterozygosity of loci, indicate that at most microsatellite loci new alleles are produced by stepwise mutations, and this is consistent with the replication slippage mechanism of mutations. The repeat size changes of mutants are probably within one or two units of alleles from which the mutants arise. Distributions of P{sub k} at microsatellite loci located within genes show evidence of allele size constraints. No significant evidence of recent expansion of population sizes in the Caucasians is detected by the distribution of P{sub k}.

  5. New insights into the genetic instability in CCTG repeats.

    PubMed

    Guo, Pei; Lam, Sik Lok

    2015-10-01

    Tetranucleotide CCTG repeat expansion is associated with myotonic dystrophy type 2, which is an inherited and progressive muscle degeneration disease. Yet, no cure is available and the molecular mechanism of repeat expansion remains elusive. In this study, we used high-resolution nuclear magnetic resonance spectroscopy to reveal a mini-dumbbell structure formed by two CCTG repeats. Upon slippage in the nascent strand during DNA replication, the formation of the mini-dumbbell provides a possible pathway for a two-repeat expansion. In addition, fast exchange between two competing mini-dumbbells among three repeats results in a mini-loop structure that accounts for one-repeat expansion. These mini-dumbbell and mini-loop intermediates can also co-exist at multiple sites in CCTG repeats, leading to three or larger size repeat expansions. PMID:26384951

  6. 47 CFR 80.1179 - On-board repeater limitations.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 5 2012-10-01 2012-10-01 false On-board repeater limitations. 80.1179 Section... SERVICES STATIONS IN THE MARITIME SERVICES Voluntary Radio Installations On-Board Communications § 80.1179 On-board repeater limitations. When an on-board repeater is used, the following limitations must...

  7. 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…

  8. 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…

  9. 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…

  10. Aging and repeated thought suppression success.

    PubMed

    Lambert, Ann E; Smyth, Frederick L; Beadel, Jessica R; Teachman, Bethany A

    2013-01-01

    Intrusive thoughts and attempts to suppress them are common, but while suppression may be effective in the short-term, it can increase thought recurrence in the long-term. Because intentional suppression involves controlled processing, and many aspects of controlled processing decline with age, age differences in thought suppression outcomes may emerge, especially over repeated thought suppression attempts as cognitive resources are expended. Using multilevel modeling, we examined age differences in reactions to thought suppression attempts across four thought suppression sequences in 40 older and 42 younger adults. As expected, age differences were more prevalent during suppression than during free monitoring periods, with younger adults indicating longer, more frequent thought recurrences and greater suppression difficulty. Further, younger adults' thought suppression outcomes changed over time, while trajectories for older adults' were relatively stable. Results are discussed in terms of older adults' reduced thought recurrence, which was potentially afforded by age-related changes in reactive control and distractibility. PMID:23776442

  11. Semiconductor structures for repeated velocity overshoot

    NASA Astrophysics Data System (ADS)

    Cooper, J. A., Jr.; Capasso, F.; Thornber, K. K.

    1982-12-01

    The conditions required for obtaining repeated velocity overshoot in semiconductors are discussed. Two classes of structures that provide these conditions are considered. The structures are seen as holding promise for achieving average drift velocities well in excess of the maximum steady-state velocity over distances ranging from submicron to tens of microns. In structures of the first class, the stairstep in potential is achieved by using a graded bandgap that is similar to the avalanche photodetector described by Williams et al. (1982), where the composition is graded from GaAs to Al(0.2)Ga(0.8)As. The second class of structures uses alternating planar doped charge sheets, as described by Malik et al. (1980).

  12. [The repeat reliability of somatosensory evoked potentials].

    PubMed

    Strenge, H

    1989-09-01

    The test-immediate-retest reliability of latency and amplitude values of cervical and cortical somatosensory evoked potentials (SEP) to median nerve stimulation was assessed in 86 normal subjects aged 15 to 71 years. In addition to the stability of data between repeat trials within one test session the standard errors of measurement and the interpretable differences for SEP measures were calculated according to measurement theory. The study revealed retest correlations rtt greater than 0.80 for all latency measures of the cervical and cortical SEPs and all cortical amplitude parameters. The highest stability was found for the latency measures of the cervical components P10, N11, N13, the cortical components P16 and N20 and for the amplitude N20/P25. PMID:2507277

  13. 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. PMID:24491104

  14. Trochlear Nerve Schwannoma With Repeated Intratumoral Hemorrhage.

    PubMed

    Liu, Pengfei; Bao, Yuhai; Zhang, Wenchuan

    2016-09-01

    Trochlear nerve schwannoma is extremely rare, with only 35 pathologically confirmed patients being reported in the literature. Here, the authors report a patient of trochlear nerve schwannoma in the prepontine cistern manifesting as facial pain and double vision and presenting the image characteristics of repeated intratumoral hemorrhage, which has never been reported in the literature. Total tumor along with a portion of the trochlear nerve was removed by using a retrosigmoid approach. Facial pain disappeared after operation, and the diplopia remained. Follow-up studies have shown no tumor recurrence for 2 years and the simultaneous alleviation of diplopia. Information regarding the clinical presentation, radiological features and surgical outcomes of trochlear nerve schwannoma are discussed and reviewed in the paper. PMID:27607129

  15. 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

  16. The hidden price of repeated traumatic exposure.

    PubMed

    Levy-Gigi, Einat; Richter-Levin, Gal

    2014-07-01

    Neuroimaging studies have demonstrated reduced hippocampal volume in trauma-exposed individuals without posttraumatic stress disorder (PTSD). However, the implications of such a deficit in this non-clinical population are still unclear. Animal and human models of PTSD suggest that hippocampal deficit may result in impaired learning and use of associations between contextual information and aversive events. Previous study has shown that individuals with PTSD have a selective impairment in reversing the negative outcome of context-related information. The aim of this study was to test whether non-PTSD individuals who are repeatedly exposed to traumatic events display similar impairment. To that end, we compared the performance of active-duty firefighters who are frequently exposed to traumatic events as part of their occupational routine and civilian matched-controls with no history of trauma-exposure. We used a novel cue-context reversal paradigm, which separately evaluates reversal of negative and positive outcomes of cue and context-related information. As predicted, we found that while both trauma-exposed firefighters and unexposed matched-controls were able to acquire and retain stimulus-outcome associations, firefighters struggled to learn that a previously negative context is later associated with a positive outcome. This impairment did not correlate with levels of PTSD, anxiety or depressive symptoms. The results suggest that similar to individuals with PTSD, highly exposed individuals fail to associate traumatic outcomes with their appropriate context. This impairment may reflect a possible hidden price of repeated traumatic exposure, which is not necessarily associated with PTSD diagnosis, and may affect the way highly exposed individuals interpret and react to their environment. PMID:24810272

  17. 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. PMID:19396957

  18. 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.

  19. Analysis of separate isolates of Bordetella pertussis repeated DNA sequences.

    PubMed

    McPheat, W L; Hanson, J H; Livey, I; Robertson, J S

    1989-06-01

    Two independent isolates of a Bordetella pertussis repeated DNA unit were sequenced and shown to be an insertion sequence element with five nucleotide differences between the two copies. The sequences were 1053 bp in length with near-perfect terminal inverted repeats of 28 bp, had three open reading frames, and were each flanked by short direct repeats. The two insertion sequences showed considerable homology to two other B. pertussis repeated DNA sequences reported recently: IS481 and a 530 bp repeated DNA unit. The B. pertussis insertion sequence would appear to comprise a group of closely related sequences differing mainly in flanking direct repeats and the terminal inverted repeats. The two isolates reported here, which were from the adenylate cyclase and agglutinogen 2 regions of the genome, were numbered IS48lvl and IS48lv2 respectively. PMID:2559151

  20. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

    PubMed Central

    Parra, R. Gonzalo; Espada, Rocío; Verstraete, Nina; Ferreiro, Diego U.

    2015-01-01

    Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. PMID:26691182

  1. Detection of repeating and "anti-repeating" earthquakes in the Bucaramanga Nest

    NASA Astrophysics Data System (ADS)

    Barrett, S. A.; Prieto, G.; Beroza, G. C.

    2011-12-01

    The Bucaramanga Nest, beneath northern Colombia represents the densest concentration of intermediate-depth earthquakes in the world. The roughly 11 km3 volume produces approximately 15 events per day, yielding an active catalog of seismicity well separated from surrounding seismic activity. We correlate template-event waveforms from known earthquakes to continuous records from the Colombian National (RSNC) seismic network. Typical repeating events are identified as well as the more curious "anti-repeat" events for which seismograms show reversed polarity and nearly perfect anti-correlation. These events are of particular interest as they are not known for shallow, crustal earthquake populations. By compiling a more complete catalog of earthquakes, and by developing precise relative locations, we seek to understand the temporal and size variations of these recurring events in the Bucaramanga Nest.

  2. Comparison of simple sequence repeats in 19 Archaea.

    PubMed

    Trivedi, S

    2006-01-01

    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. PMID:17183484

  3. REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

    PubMed Central

    Chu, Chong; Nielsen, Rasmus; Wu, Yufeng

    2016-01-01

    Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo. PMID:26977803

  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. Repeating covalent structure of streptococcal M protein.

    PubMed Central

    Beachey, E H; Seyer, J M; Kang, A H

    1978-01-01

    We have attempted to identify the covalent structure of the M protein molecule of group A streptococci that is responsible for inducing type-specific, protective immunity. M protein was extracted from type 24 streptococci, purified, and cleaved with cyanogen bromide. Seven cyanogen bromide peptides were purified and further characterized. Together, the peptides account for the entire amino acid content of the M protein molecule. Each of the purified peptides possessed the type-specific determinant that inhibits opsonic antibodies for group A streptococci. The primary structures of the amino-terminal regions of each of the purified peptides was studied by automated Edman degradation. The partial sequences of two of the peptides were found to be identical to each other and to that of the uncleaved M protein molecule through at least the first 27 residues. The amino-terminal sequences of the remaining five peptides were identical to each other through the twentieth residue but completely different from the amino-terminal region of the other two peptides. However, the type-specific immunoreactivity and the incomplete analysis of the primary structure of the seven peptides suggest that the antiphagocytic determinant resides in a repeating amino acid sequence in the M protein molecule. PMID:80011

  6. [Pharmacokinetics of cefatrizine administered in repeated doses].

    PubMed

    Couet, W; Reigner, B G; Lefebvre, M A; Bizouard, J; Fourtillan, J B

    1988-05-01

    Twelve healthy volunteers received cefatrizine orally at doses equal to 500 mg every 12 h for 5 days. Cefatrizine was assayed by high performance liquid chromatography in plasma and urines collected after the first and/or the last administration. Cefatrizine absorption was rapid; its peak plasma level was reached at time 1.79 +/- 0.07 h following the first dose, it was equal to 7.37 +/- 0.31 micrograms.ml-1. Its apparent elimination half-life was equal to 1.50 +/- 0.05 h, it explains the lack of accumulation with time during multiple administrations every 12 hours. Comparisons between peak plasma concentration and area under curves following the first and last dosing showed significant (p less than 0.01) but weak (close to 15%) reduction of these 2 parameters with time which could be explained by a slight reduction of cefatrizine absorption with time. In conclusion, cefatrizine does not accumulate when administered repeatedly at a dose equal to 500 mg every 12 h in young adult, and its pharmacokinetics is virtually linear with time. PMID:3043350

  7. Repeated intravenous doxapram induces phrenic motor facilitation

    PubMed Central

    Sandhu, MS; Lee, KZ; Gonzalez-Rothi, EJ; Fuller, DD

    2013-01-01

    Doxapram is a respiratory stimulant used to treat hypoventilation. Here we investigated whether doxapram could also trigger respiratory neuroplasticity. Specifically, we hypothesized that intermittent delivery of doxapram at low doses would lead to long-lasting increases (i.e., facilitation) of phrenic motor output in anesthetized, vagotomized, and mechanically-ventilated rats. Doxapram was delivered intravenously in a single bolus (2 or 6 mg/kg) or as a series of 3 injections (2 mg/kg) at 5 min intervals. Control groups received pH-matched saline injections (vehicle) or no treatment (anesthesia time control). Doxapram evoked an immediate increase in phrenic output in all groups, but a persistent increase in burst amplitude only occurred after repeated dosing with 2 mg/kg. At 60 min following the last injection, phrenic burst amplitude was 168±24% of baseline (%BL) in the group receiving 3 injections (P < 0.05 vs. controls), but was 103±8%BL and 112±4%BL in the groups receiving a single dose of 2 or 6 mg/kg, respectively. Following bilateral section of the carotid sinus nerves, the acute phrenic response to doxapram (2 mg/kg) was reduced by 68% suggesting that at low doses the drug was acting primarily via the carotid chemoreceptors. We conclude that intermittent application of doxapram can trigger phrenic neuroplasticity, and this approach might be of use in the context of respiratory rehabilitation following neurologic injury. PMID:24013015

  8. 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.

  9. Global Seismic Oscillations in Soft Gamma Repeaters

    NASA Astrophysics Data System (ADS)

    Duncan, Robert C.

    1998-05-01

    There is evidence that soft gamma repeaters (SGRs) are neutron stars that experience frequent starquakes, possibly driven by an evolving, ultrastrong magnetic field. The empirical power-law distribution of SGR burst energies, analogous to the Gutenberg-Richter law for earthquakes, exhibits a turnover at high energies, consistent with a global limit on the crust fracture size. With such large starquakes occurring, the significant excitation of global seismic oscillations (GSOs) seems likely. Moreover, GSOs may be self-exciting in a stellar crust that is strained by many randomly oriented stresses. We explain why low-order toroidal modes, which preserve the shape of the star and have observable frequencies as low as ~30 Hz, may be especially susceptible to excitation. We estimate the eigenfrequencies as a function of stellar mass and radius, as well as their magnetic and rotational shiftings/splittings. We also describe ways in which these modes might be detected and damped. There is marginal evidence for 23 ms oscillations in the hard initial pulse of the 1979 March 5 event. This could be due to the 3t0 mode in a neutron star with B~1014 G or less, or it could be the fundamental toroidal mode if the field in the deep crust of SGR 0526-66 is ~4×1015 G, in agreement with other evidence. If confirmed, GSOs would give corroborating evidence for crust-fracturing magnetic fields in SGRs: B>~1014 G.

  10. Power Line Integrity Monitor and Repeater

    Energy Science and Technology Software Center (ESTSC)

    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 centralmore » 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.« less

  11. [Tandem repeats in rodents genome and their mapping].

    PubMed

    Ostromyshenskii, D I; Kuznetsova, L S; Komissarov, A S; Kartavtseva, I V; Podgornaya, L

    2015-01-01

    Tandemly-repeated sequences represent a unique class of eukaryotic DNA. Their content in the genome of higher eukaryotes mounts to tens of percents. However, the evolution of this class of sequences is poorly-studied. In our paper, 62 families of Mus musculus tandem repeats are analyzed by bioinformatic methods, and 7 of them are analyzed by fluorescence in situ hybridization. It is shown that the same tandem repeat sets co-occure only in closely related species of mice. But even in such species we observe differences in localization on the chromosomes and the number of individual tandem repeats. With increasing evolutionary distance only some of the tandem repeat families remain common for different species. It is shown, that the use of a combination of bioinformatics and molecular biology techniques is very perspective for further studies of the evolution of tandem repeats. PMID:26035967

  12. Function and evolution of local repeats in the Firre locus

    PubMed Central

    Hacisuleyman, Ezgi; Shukla, Chinmay J.; Weiner, Catherine L.; Rinn, John L.

    2016-01-01

    More than half the human and mouse genomes are comprised of repetitive sequences, such as transposable elements (TEs), which have been implicated in many biological processes. In contrast, much less is known about other repeats, such as local repeats that occur in multiple instances within a given locus in the genome but not elsewhere. Here, we systematically characterize local repeats in the genomic locus of the Firre long noncoding RNA (lncRNA). We find a conserved function for the RRD repeat as a ribonucleic nuclear retention signal that is sufficient to retain an otherwise cytoplasmic mRNA in the nucleus. We also identified a repeat, termed R0, that can function as a DNA enhancer element within the intronic sequences of Firre. Collectively, our data suggest that local repeats can have diverse functionalities and molecular modalities in the Firre locus and perhaps more globally in other lncRNAs. PMID:27009974

  13. 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. PMID:27382061

  14. 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

  15. Practical quantum repeaters with parametric down-conversion sources

    NASA Astrophysics Data System (ADS)

    Krovi, Hari; Guha, Saikat; Dutton, Zachary; Slater, Joshua A.; Simon, Christoph; Tittel, Wolfgang

    2016-03-01

    Conventional wisdom suggests that realistic quantum repeaters will require quasi-deterministic sources of entangled photon pairs. In contrast, we here study a quantum repeater architecture that uses simple parametric down-conversion sources, as well as frequency-multiplexed multimode quantum memories and photon-number-resolving detectors. We show that this approach can significantly extend quantum communication distances compared to direct transmission. This shows that important trade-offs are possible between the different components of quantum repeater architectures.

  16. 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.

  17. 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

  18. 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

  19. 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

  20. Diversity and evolution of centromere repeats in the maize genome.

    PubMed

    Bilinski, Paul; Distor, Kevin; Gutierrez-Lopez, Jose; Mendoza, Gabriela Mendoza; Shi, Jinghua; Dawe, R Kelly; Ross-Ibarra, Jeffrey

    2015-03-01

    Centromere repeats are found in most eukaryotes and play a critical role in kinetochore formation. Though centromere repeats exhibit considerable diversity both within and among species, little is understood about the mechanisms that drive centromere repeat evolution. Here, we use maize as a model to investigate how a complex history involving polyploidy, fractionation, and recent domestication has impacted the diversity of the maize centromeric repeat CentC. We first validate the existence of long tandem arrays of repeats in maize and other taxa in the genus Zea. Although we find considerable sequence diversity among CentC copies genome-wide, genetic similarity among repeats is highest within these arrays, suggesting that tandem duplications are the primary mechanism for the generation of new copies. Nonetheless, clustering analyses identify similar sequences among distant repeats, and simulations suggest that this pattern may be due to homoplasious mutation. Although the two ancestral subgenomes of maize have contributed nearly equal numbers of centromeres, our analysis shows that the majority of all CentC repeats derive from one of the parental genomes, with an even stronger bias when examining the largest assembled contiguous clusters. Finally, by comparing maize with its wild progenitor teosinte, we find that the abundance of CentC likely decreased after domestication, while the pericentromeric repeat Cent4 has drastically increased. PMID:25190528

  1. Intragenic tandem repeat variation between Legionella pneumophila strains

    PubMed Central

    Coil, David A; Vandersmissen, Liesbeth; Ginevra, Christophe; Jarraud, Sophie; Lammertyn, Elke; Anné, Jozef

    2008-01-01

    Background Bacterial genomes harbour a large number of tandem repeats, yet the possible phenotypic effects of those found within the coding region of genes are only beginning to be examined. Evidence exists from other organisms that these repeats can be involved in the evolution of new genes, gene regulation, adaptation, resistance to environmental stresses, and avoidance of the immune system. Results In this study, we have investigated the presence and variability in copy number of intragenic tandemly repeated sequences in the genome of Legionella pneumophila, the etiological agent of a severe pneumonia known as Legionnaires' disease. Within the genome of the Philadelphia strain, we have identified 26 intragenic tandem repeat sequences using conservative selection criteria. Of these, seven were "polymorphic" in terms of repeat copy number between a large number of L. pneumophila serogroup 1 strains. These strains were collected from a wide variety of environments and patients in several geographical regions. Within this panel of strains, all but one of these seven genes exhibited statistically different patterns in repeat copy number between samples from different origins (environmental, clinical, and hot springs). Conclusion These results support the hypothesis that intragenic tandem repeats could play a role in virulence and adaptation to different environments. While tandem repeats are an increasingly popular focus of molecular typing studies in prokaryotes, including in L. pneumophila, this study is the first examining the difference in tandem repeat distribution as a function of clinical or environmental origin. PMID:19077205

  2. 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

  3. [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. PMID:24388944

  4. 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.

  5. Continental-scale enrichment of atmospheric 14CO2 from the nuclear power industry: potential impact on the estimation of fossil fuel-derived CO2

    NASA Astrophysics Data System (ADS)

    Graven, H. D.; Gruber, N.

    2011-12-01

    The 14C-free fossil carbon added to atmospheric CO2 by combustion dilutes the atmospheric 14C/C ratio (Δ14C), potentially providing a means to verify fossil CO2 emissions calculated using economic inventories. However, sources of 14C from nuclear power generation and spent fuel reprocessing can counteract this dilution and may bias 14C/C-based estimates of fossil fuel-derived CO2 if these nuclear influences are not correctly accounted for. Previous studies have examined nuclear influences on local scales, but the potential for continental-scale influences on Δ14C has not yet been explored. We estimate annual 14C emissions from each nuclear site in the world and conduct an Eulerian transport modeling study to investigate the continental-scale, steady-state gradients of Δ14C caused by nuclear activities and fossil fuel combustion. Over large regions of Europe, North America and East Asia, nuclear enrichment may offset at least 20% of the fossil fuel dilution in Δ14C, corresponding to potential biases of more than -0.25 ppm in the CO2 attributed to fossil fuel emissions, larger than the bias from plant and soil respiration in some areas. Model grid cells including high 14C-release reactors or fuel reprocessing sites showed much larger nuclear enrichment, despite the coarse model resolution of 1.8°×1.8°. The recent growth of nuclear 14C emissions increased the potential nuclear bias over 1985-2005, suggesting that changing nuclear activities may complicate the use of Δ14C observations to identify trends in fossil fuel emissions. The magnitude of the potential nuclear bias is largely independent of the choice of reference station in the context of continental-scale Eulerian transport and inversion studies, but could potentially be reduced by an appropriate choice of reference station in the context of local-scale assessments.

  6. Preliminary Constraints on Fossil-fuel CO2: Comparison of Tracers CO and SF6 With Measurements of 14CO2

    NASA Astrophysics Data System (ADS)

    Turnbull, J. C.; Miller, J. B.; Lehman, S. J.; Sparks, R. J.; Tans, P. P.

    2004-12-01

    CO2 derived from the combustion of fossil fuels is a significant component of the carbon balance of North America. However, on the sub-continental spatial scales and sub-annual time scales relevant to the objectives of the North American Carbon Program, estimates of combustion CO2 from traditional economic inventories are unlikely to be accurate, and may contribute to biases in the interpretation of atmospheric CO2 measurements. Indirect estimates of the combustion CO2 component can also be obtained from measured CO:CO2 ratios and SF6:CO2 ratios. The low cost and ease of measurement allow the application of these methods in intensive measurement campaigns. However, the accuracy of the combustion CO2 detection capability relies on accurately determining the emission ratio of CO:CO2 or SF6:CO2 at relevant time and space scales. In the case of CO, atmospheric chemical biases and non fossil fuel sources must also be understood. CO2 derived from fossil fuels contains no 14C, whereas other sources have a 14C content close to that of ambient air. Measurement of the 14C content in CO2 thus provides a direct tracer for fossil fuel derived CO2, without the biases associated with the indirect tracer methods. We used high-precision accelerator mass spectrometry to determine the 14C content of CO2 at several North American sites (Niwot Ridge, CO, Harvard Forest, MA and New Hampshire) during 2003 and 2004, and calculate the fossil fuel CO2 contribution in each case. We compare these results with CO:CO2 and SF6:CO2 measurements on the same samples to evaluate the indirect tracer methods at these sites. Preliminary results for wintertime measurements (when biological CO2 exchange fluxes are small) support the accuracy of the 14C method. The back-calculated emission ratios for SF6:CO2 vary significantly and consistently underestimate the global average. While the back-calculated CO:CO2 ratios are more consistent, they also underestimate the predicted values from emissions inventories.

  7. 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.

  8. Development of simple sequence repeat markers in cymbopogon species.

    PubMed

    Kumar, Jitendra; Verma, Vijeshwar; Shahi, Ashok Kumar; Qazi, Gulam Nab; Balyan, Harindra Singh

    2007-03-01

    The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8%) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8%) and other higher order repeat motifs. Eighteen (81.8%) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2%) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1-18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding. PMID:17318781

  9. Reduced hnRNPA3 increases C9orf72 repeat RNA levels and dipeptide-repeat protein deposition.

    PubMed

    Mori, Kohji; Nihei, Yoshihiro; Arzberger, Thomas; Zhou, Qihui; Mackenzie, Ian R; Hermann, Andreas; Hanisch, Frank; Kamp, Frits; Nuscher, Brigitte; Orozco, Denise; Edbauer, Dieter; Haass, Christian

    2016-09-01

    Intronic hexanucleotide (G4C2) repeat expansions in C9orf72 are genetically associated with frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). The repeat RNA accumulates within RNA foci but is also translated into disease characterizing dipeptide repeat proteins (DPR). Repeat-dependent toxicity may affect nuclear import. hnRNPA3 is a heterogeneous nuclear ribonucleoprotein, which specifically binds to the G4C2 repeat RNA We now report that a reduction of nuclear hnRNPA3 leads to an increase of the repeat RNA as well as DPR production and deposition in primary neurons and a novel tissue culture model that reproduces features of the C9orf72 pathology. In fibroblasts derived from patients carrying extended C9orf72 repeats, nuclear RNA foci accumulated upon reduction of hnRNPA3. Neurons in the hippocampus of C9orf72 patients are frequently devoid of hnRNPA3. Reduced nuclear hnRNPA3 in the hippocampus of patients with extended C9orf72 repeats correlates with increased DPR deposition. Thus, reduced hnRNPA3 expression in C9orf72 cases leads to increased levels of the repeat RNA as well as enhanced production and deposition of DPR proteins and RNA foci. PMID:27461252

  10. Telomeric Repeat Mutagenicity in Human Somatic Cells is Modulated by Repeat Orientation and G-Quadruplex Stability

    PubMed Central

    Damerla, Rama Rao; Knickelbein, Kelly E.; Kepchia, Devin; Jackson, Abbe; Armitage, Bruce A.; Eckert, Kristin A.; Opresko, Patricia L.

    2010-01-01

    Telomeres consisting of tandem guanine-rich repeats can form secondary DNA structures called G-quadruplexes that represent potential targets for DNA repair enzymes. While G-quadruplexes interfere with DNA synthesis in vitro, the impact of G-quadruplex formation on telomeric repeat replication in human cells is not clear. We investigated the mutagenicity of telomeric repeats as a function of G-quadruplex folding opportunity and thermal stability using a shuttle vector mutagenesis assay. Since single stranded DNA during lagging strand replication increases the opportunity for G-quadruplex folding, we tested vectors with G-rich sequences on the lagging versus the leading strand. Contrary to our prediction, vectors containing human [TTAGGG]10 repeats with a G-rich lagging strand were significantly less mutagenic than vectors with a G-rich leading strand, after replication in normal human cells. We show by UV melting experiments that G-quadruplexes from ciliates [TTGGGG]4 and [TTTTGGGG]4 are thermally more stable compared to human [TTAGGG]4. Consistent with this, replication of vectors with ciliate [TTGGGG]10 repeats yielded a 3-fold higher mutant rate compared to the human [TTAGGG]10 vectors. Furthermore, we observed significantly more mutagenic events in the ciliate repeats compared to the human repeats. Our data demonstrate that increased G-quadruplex opportunity (repeat orientation) in human telomeric repeats decreased mutagenicity, while increased thermal stability of telomeric G-qaudruplexes was associated with increased mutagenicity. PMID:20800555

  11. 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…

  12. Measurement Precision for Repeat Examinees on a Standardized Patient Examination

    ERIC Educational Resources Information Center

    Raymond, Mark R.; Swygert, Kimberly A.; Kahraman, Nilufer

    2012-01-01

    Examinees who initially fail and later repeat an SP-based clinical skills exam typically exhibit large score gains on their second attempt, suggesting the possibility that examinees were not well measured on one of those attempts. This study evaluates score precision for examinees who repeated an SP-based clinical skills test administered as part…

  13. The Effects of Repeated Experience on Children's Suggestibility.

    ERIC Educational Resources Information Center

    Powell, Martine B.; Roberts, Kim P.; Ceci, Stephen J.; Hembrooke, Helene

    1999-01-01

    Examined effect of suggestive questions on 3- to 5-year-olds' and 6- to 8-year-olds' recall of the final occurrence of repeated event. Found that relative to reports of children experiencing single occurrence, reports about fixed items of repeated events were less contaminated by false suggestions. Children's age and delay of interview were…

  14. Repeat users of crisis resolution and home treatment team.

    PubMed

    Lunawat, Vinod Kumar; Karale, Milind

    2014-11-01

    CRHT services have reduced admissions to psychiatric hospitals. Some patients use CRHT services repeatedly. We reviewed the first 30 patients who were repeat users of the CRHT services, Luton, between 1 August 2010 and 31 July 2011. The repeat users were a small group of patients needing disproportionately large amounts of resources from the CRHT service. The factors associated with repeat use of CRHT were past psychiatric admission and the diagnoses of emotionally unstable personality disorder, self-harm behaviour and substance misuse. Identifying the factors leading to repeat CRHT use could lead to providing a more tailored service and reduce repeat use of these services. It appears that repeat CRHT service use might be the result of the interaction of a wide range of factors relating to underlying disorder, substance misuse, self harm behaviour, employment status and social support. It is also important to note that many of the patients are liable to relapse as they go through stressful life situations, despite adequate medication and psychosocial intervention. It can be difficult to identify all the factors that contribute to a pattern of repeat presentation to CRHT services. However, identification of such factors might help clinicians to offer more targeted services and might also assist commissioners in focusing resources effectively. They might need more intensive community-based programs to identify and treat the relapses. The CRHT teams should include all the appropriate professional disciplines required to provide community care for these challenging service users. PMID:25413503

  15. 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…

  16. Repeatable mechanochemical activation of dynamic covalent bonds in thermoplastic elastomers.

    PubMed

    Imato, Keiichi; Kanehara, Takeshi; Nojima, Shiki; Ohishi, Tomoyuki; Higaki, Yuji; Takahara, Atsushi; Otsuka, Hideyuki

    2016-08-18

    Repeated mechanical scission and recombination of dynamic covalent bonds incorporated in segmented polyurethane elastomers are demonstrated by utilizing a diarylbibenzofuranone-based mechanophore and by the design of the segmented polymer structures. The repeated mechanochemical reactions can accompany clear colouration and simultaneous fading. PMID:27424868

  17. 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…

  18. 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.

  19. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Mobile repeater stations. 90.247 Section 90.247... MOBILE RADIO SERVICES Non-Voice and Other Specialized Operations § 90.247 Mobile repeater stations. A mobile station authorized to operate on a mobile service frequency above 25 MHz may be used as a...

  20. Simple Sequence Repeats in Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total o...

  1. Vocabulary Learning through Assisted and Unassisted Repeated Reading

    ERIC Educational Resources Information Center

    Webb, Stuart; Chang, Anna C-S.

    2012-01-01

    Previous research investigating the effects of unassisted and assisted repeated reading has primarily focused on how each approach may contribute to improvement in reading comprehension and fluency. Incidental learning of the form and meaning of unknown or partially known words encountered through assisted and unassisted repeated reading has yet…

  2. 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. PMID:23906673

  3. Mechanisms of RNA-induced toxicity in CAG repeat disorders.

    PubMed

    Nalavade, R; Griesche, N; Ryan, D P; Hildebrand, S; Krauss, S

    2013-01-01

    Several inherited neurodegenerative disorders are caused by CAG trinucleotide repeat expansions, which can be located either in the coding region or in the untranslated region (UTR) of the respective genes. Polyglutamine diseases (polyQ diseases) are caused by an expansion of a stretch of CAG repeats within the coding region, translating into a polyQ tract. The polyQ tract expansions result in conformational changes, eventually leading to aggregate formation. It is widely believed that the aggregation of polyQ proteins is linked with disease development. In addition, in the last couple of years, it has been shown that RNA-mediated mechanisms also have a profound role in neurotoxicity in both polyQ diseases and diseases caused by elongated CAG repeat motifs in their UTRs. Here, we review the different molecular mechanisms assigned to mRNAs with expanded CAG repeats. One aspect is the mRNA folding of CAG repeats. Furthermore, pathogenic mechanisms assigned to CAG repeat mRNAs are discussed. First, we discuss mechanisms that involve the sequestration of the diverse proteins to the expanded CAG repeat mRNA molecules. As a result of this, several cellular mechanisms are aberrantly regulated. These include the sequestration of MBNL1, leading to misregulated splicing; sequestration of nucleolin, leading to reduced cellular rRNA; and sequestration of proteins of the siRNA machinery, resulting in the production of short silencing RNAs that affect gene expression. Second, we discuss the effect of expanded CAG repeats on the subcellular localization, transcription and translation of the CAG repeat mRNA itself. Here we focus on the MID1 protein complex that triggers an increased translation of expanded CAG repeat mRNAs and a mechanism called repeat-associated non-ATG translation, which leads to proteins aberrantly translated from CAG repeat mRNAs. In addition, therapeutic approaches for CAG repeat disorders are discussed. Together, all the findings summarized here show that

  4. Mechanisms of RNA-induced toxicity in CAG repeat disorders

    PubMed Central

    Nalavade, R; Griesche, N; Ryan, D P; Hildebrand, S; Krauß, S

    2013-01-01

    Several inherited neurodegenerative disorders are caused by CAG trinucleotide repeat expansions, which can be located either in the coding region or in the untranslated region (UTR) of the respective genes. Polyglutamine diseases (polyQ diseases) are caused by an expansion of a stretch of CAG repeats within the coding region, translating into a polyQ tract. The polyQ tract expansions result in conformational changes, eventually leading to aggregate formation. It is widely believed that the aggregation of polyQ proteins is linked with disease development. In addition, in the last couple of years, it has been shown that RNA-mediated mechanisms also have a profound role in neurotoxicity in both polyQ diseases and diseases caused by elongated CAG repeat motifs in their UTRs. Here, we review the different molecular mechanisms assigned to mRNAs with expanded CAG repeats. One aspect is the mRNA folding of CAG repeats. Furthermore, pathogenic mechanisms assigned to CAG repeat mRNAs are discussed. First, we discuss mechanisms that involve the sequestration of the diverse proteins to the expanded CAG repeat mRNA molecules. As a result of this, several cellular mechanisms are aberrantly regulated. These include the sequestration of MBNL1, leading to misregulated splicing; sequestration of nucleolin, leading to reduced cellular rRNA; and sequestration of proteins of the siRNA machinery, resulting in the production of short silencing RNAs that affect gene expression. Second, we discuss the effect of expanded CAG repeats on the subcellular localization, transcription and translation of the CAG repeat mRNA itself. Here we focus on the MID1 protein complex that triggers an increased translation of expanded CAG repeat mRNAs and a mechanism called repeat-associated non-ATG translation, which leads to proteins aberrantly translated from CAG repeat mRNAs. In addition, therapeutic approaches for CAG repeat disorders are discussed. Together, all the findings summarized here show that

  5. 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.

  6. Repeated positive fighting experience in male inbred mice.

    PubMed

    Kudryavtseva, Natalia N; Smagin, Dmitry A; Kovalenko, Irina L; Vishnivetskaya, Galina B

    2014-11-01

    Repeated aggression is a frequent symptom of many psychiatric and neurological disorders, including obsessive-compulsive and attention deficit hyperactivity disorders, bipolar and post-traumatic stress disorders, epilepsy, autism, schizophrenia and drug abuse. However, repeated aggression is insufficiently studied because there is a lack of adequate models in animals. The sensory contact model (SCM), widely used to study the effects of chronic social defeat stress, can also be used to investigate the effects of repeated aggression. Mice with repeated positive fighting experience in daily agonistic interactions in this model develop pronounced aggressiveness, anxiety and impulsivity, disturbances in motivated and cognitive behaviors, and impairments of sociability; they also demonstrate hyperactivity, attention-deficit behavior, motor dysfunctions and repetitive stereotyped behaviors, such as jerks, rotations and head twitches. In this protocol, we describe how to apply the SCM to study repeated aggression in mice. Severe neuropathology develops in male mice after 20-21 d of agonistic interactions. PMID:25340443

  7. 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

  8. 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

    2015-01-01

    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. PMID:26782581

  9. 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. PMID:25775519

  10. The repeatability of behaviour: a meta-analysis

    PubMed Central

    Bell, Alison M.; Hankison, Shala J.; Laskowski, Kate L.

    2014-01-01

    There is increasing interest in individual differences in animal behaviour. Recent research now suggests that an individual’s behaviour, once considered to be plastic, may be more predictable than previously thought. Here, we take advantage of the large number of studies that have estimated the repeatability of various behaviours to evaluate whether there is good evidence for consistent individual differences in behaviour and to answer some outstanding questions about possible factors that can influence repeatability. Specifically, we use meta-analysis to ask whether different types of behaviours were more repeatable than others, and if repeatability estimates depended on taxa, sex, age, field versus laboratory, the number of measures and the interval between measures. Some of the overall patterns that were revealed by this analysis were that repeatability estimates were higher in the field compared to the laboratory and repeatability was higher when the interval between observations was short. Mate preference behaviour was one of the best studied but least repeatable behaviours. Our findings prompt new insights into the relative flexibility of different types of behaviour and offer suggestions for the design and analysis of future research. PMID:24707058

  11. 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

  12. RNA FISH for detecting expanded repeats in human diseases.

    PubMed

    Urbanek, Martyna O; Krzyzosiak, Wlodzimierz J

    2016-04-01

    RNA fluorescence in situ hybridization (FISH) is a widely used technique for detecting transcripts in fixed cells and tissues. Many variants of RNA FISH have been proposed to increase signal strength, resolution and target specificity. The current variants of this technique facilitate the detection of the subcellular localization of transcripts at a single molecule level. Among the applications of RNA FISH are studies on nuclear RNA foci in diseases resulting from the expansion of tri-, tetra-, penta- and hexanucleotide repeats present in different single genes. The partial or complete retention of mutant transcripts forming RNA aggregates within the nucleoplasm has been shown in multiple cellular disease models and in the tissues of patients affected with these atypical mutations. Relevant diseases include, among others, myotonic dystrophy type 1 (DM1) with CUG repeats, Huntington's disease (HD) and spinocerebellar ataxia type 3 (SCA3) with CAG repeats, fragile X-associated tremor/ataxia syndrome (FXTAS) with CGG repeats, myotonic dystrophy type 2 (DM2) with CCUG repeats, amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) with GGGGCC repeats and spinocerebellar ataxia type 32 (SCA32) with GGCCUG. In this article, we summarize the results obtained with FISH to examine RNA nuclear inclusions. We provide a detailed protocol for detecting RNAs containing expanded CAG and CUG repeats in different cellular models, including fibroblasts, lymphoblasts, induced pluripotent stem cells and murine and human neuronal progenitors. We also present the results of the first single-molecule FISH application in a cellular model of polyglutamine disease. PMID:26615955

  13. 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

  14. Repeated, but Not Acute, Stress Suppresses Inflammatory Plasma Extravasation

    NASA Astrophysics Data System (ADS)

    Strausbaugh, Holly J.; Dallman, Mary F.; Levine, Jon D.

    1999-12-01

    Clinical findings suggest that inflammatory disease symptoms are aggravated by ongoing, repeated stress, but not by acute stress. We hypothesized that, compared with single acute stressors, chronic repeated stress may engage different physiological mechanisms that exert qualitatively different effects on the inflammatory response. Because inhibition of plasma extravasation, a critical component of the inflammatory response, has been associated with increased disease severity in experimental arthritis, we tested for a potential repeated stress-induced inhibition of plasma extravasation. Repeated, but not single, exposures to restraint stress produced a profound inhibition of bradykinin-induced synovial plasma extravasation in the rat. Experiments examining the mechanism of inhibition showed that the effect of repeated stress was blocked by adrenalectomy, but not by adrenal medullae denervation, suggesting that the adrenal cortex mediates this effect. Consistent with known effects of stress and with mediation by the adrenal cortex, restraint stress evoked repeated transient elevations of plasma corticosterone levels. This elevated corticosterone was necessary and sufficient to produce inhibition of plasma extravasation because the stress-induced inhibition was blocked by preventing corticosterone synthesis and, conversely, induction of repeated transient elevations in plasma corticosterone levels mimicked the effects of repeated stress. These data suggest that repetition of a mild stressor can induce changes in the physiological state of the animal that enable a previously innocuous stressor to inhibit the inflammatory response. These findings provide a potential explanation for the clinical association between repeated stress and aggravation of inflammatory disease symptoms and provide a model for study of the biological mechanisms underlying the stress-induced aggravation of chronic inflammatory diseases.

  15. 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

  16. Sequence conservation of an avian centromeric repeated DNA component.

    PubMed

    Madsen, C S; Brooks, J E; de Kloet, E; de Kloet, S R

    1994-06-01

    The approximately 190-bp centromeric repeat monomers of the spur-winged lapwing (Vanellus spinosus, Charadriidae), the Chilean flamingo (Phoenicopterus chilensis, Phoenicopteridae), the sarus crane (Grus antigone, Gruidae), parrots (Psittacidae), waterfowl (Anatidae), and the merlin (Falco columbarius, Falconidae) contain elements that are interspecifically highly variable, as well as elements (trinucleotides and higher order oligonucleotides) that are highly conserved in sequence and relative location within the repeat. Such conservation suggests that the centromeric repeats of these avian species have evolved from a common ancestral sequence that may date from very early stages of avian radiation. PMID:8034177

  17. Repeatability observations from a time-lapse seismic survey

    USGS Publications Warehouse

    Walters, S.L.; Miller, R.D.; Raef, A.E.

    2006-01-01

    Time-lapse seismic surveys have proven extremely valuable in recent years, having numerous economical and environmental applications. To fully utilize this monitoring technique, problems associated with recording repeatability must be minimized. Much work has been done to equalize data from one survey to the next via processing techniques (Huang et al., 1998). The purpose of this study is to investigate the potential for minimized processing, allowing study of extremely small changes in subsurface characteristics. The goal is to evaluate source and receiver terrain combination to optimize signal repeatability, and to improve deconvolution with the ground force to suppress different types of noise and increase repeatability. ?? 2005 Society of Exploration Geophysicists.

  18. 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

  19. Secure quantum network coding for controlled repeater networks

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    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.

  20. On the error analysis of quantum repeaters with encoding

    NASA Astrophysics Data System (ADS)

    Epping, Michael; Kampermann, Hermann; Bruß, Dagmar

    2016-03-01

    Losses of optical signals scale exponentially with the distance. Quantum repeaters are devices that tackle these losses in quantum communication by splitting the total distance into shorter parts. Today two types of quantum repeaters are subject of research in the field of quantum information: Those that use two-way communication and those that only use one-way communication. Here we explain the details of the performance analysis for repeaters of the second type. Furthermore we compare the two different schemes. Finally we show how the performance analysis generalizes to large-scale quantum networks.

  1. The repeatability of fluctuating asymmetry: a revision and extension

    PubMed Central

    Whitlock, M.

    1998-01-01

    Fluctuating asymmetry (FA) is an imperfect measure of the developmental stability of an individual. Estimates of the heritability of FA will underestimate the heritability of developmental stability; the extent of this bias can be estimated and corrected by estimating the repeatability of developmental stability. This note corrects an error in a previous derivation of this repeatability using the absolute value of the difference between sides as the measure of FA, and derives the repeatability of developmental stability for another common measure of FA, the variance among sides within an individual.

  2. 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.

  3. Bovine gall-bladder mucin contains two distinct tandem repeating sequences: evidence for scavenger receptor cysteine-rich repeats.

    PubMed Central

    Nunes, D P; Keates, A C; Afdhal, N H; Offner, G D

    1995-01-01

    Gall-bladder mucin is a densely glycosylated macromolecule which is the primary secretory product of the gall-bladder epithelium. It has been shown to bind cholesterol and other biliary lipids and to promote cholesterol crystal nucleation in vitro. In order to understand the molecular basis for mucin-lipid interactions, bovine gall-bladder mucin cDNAs were identified by expression cloning and were isolated and sequenced. The nucleotide sequences of these cDNAs revealed two distinct tandem repeating domains. One of these domains contained a 20-amino acid tandem repeating sequence enriched in threonine, serine and proline. This sequence was similar to, but not identical with, the short tandem repeating sequences identified previously in other mammalian mucins. The other domain contained a 127-amino acid tandem repeating sequence enriched in cysteine and glycine. This repeat displayed considerable sequence similarity to a family of receptor- and ligand-binding proteins containing scavenger receptor cysteine-rich repeats. By analogy with other proteins containing these cysteine-rich repeats, it is possible that, in gall-bladder mucin, this domain serves as a binding site for hydrophobic ligands such as bilirubin, cholesterol and other biliary lipids. Images Figure 4 Figure 5 Figure 6 PMID:7646470

  4. Bidirectional transcripts of the expanded C9orf72 hexanucleotide repeat are translated into aggregating dipeptide repeat proteins.

    PubMed

    Mori, Kohji; Arzberger, Thomas; Grässer, Friedrich A; Gijselinck, Ilse; May, Stephanie; Rentzsch, Kristin; Weng, Shih-Ming; Schludi, Martin H; van der Zee, Julie; Cruts, Marc; Van Broeckhoven, Christine; Kremmer, Elisabeth; Kretzschmar, Hans A; Haass, Christian; Edbauer, Dieter

    2013-12-01

    Massive GGGGCC repeat expansion in the first intron of the gene C9orf72 is the most common known cause of familial frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Despite its intronic localization and lack of an ATG start codon, the repeat region is translated in all three reading frames into aggregating dipeptide-repeat (DPR) proteins, poly-(Gly-Ala), poly-(Gly-Pro) and poly-(Gly-Arg). We took an antibody-based approach to further validate the translation of DPR proteins. To test whether the antisense repeat RNA transcript is also translated, we raised antibodies against the predicted products, poly-(Ala-Pro) and poly-(Pro-Arg). Both antibodies stained p62-positive neuronal cytoplasmic inclusions throughout the cerebellum and hippocampus indicating that not only sense but also antisense strand repeats are translated into DPR proteins in the absence of ATG start codons. Protein products of both strands co-aggregate suggesting concurrent translation of both strands. Moreover, an antibody targeting the putative carboxyl terminus of DPR proteins can detect inclusion pathology in C9orf72 repeat expansion carriers suggesting that the non-ATG translation continues through the entire repeat and beyond. A highly sensitive monoclonal antibody against poly-(Gly-Arg), visualized abundant inclusion pathology in all cortical regions and some inclusions also in motoneurons. Together, our data show that the GGGGCC repeat is bidirectionally translated into five distinct DPR proteins that co-aggregate in the characteristic p62-positive TDP-43 negative inclusions found in FTLD/ALS cases with C9orf72 repeat expansion. Novel monoclonal antibodies against poly-(Gly-Arg) will facilitate pathological diagnosis of C9orf72 FTLD/ALS. PMID:24132570

  5. 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

  6. 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.

  7. 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.

  8. Network synthesis localization of two soft gamma repeaters

    NASA Technical Reports Server (NTRS)

    Hurley, Kevin; Sommer, M.; Kouveliotou, C.; Fishman, G.; Meegan, C.; Cline, T.; Boer, M.; Niel, M.

    1994-01-01

    We introduce the method of 'network synthesis,' which allows the detection of very weak gamma-ray transient signals in the data of the Ulysses gamma-ray burst (GRB) experiment from repeating sources. It consists of defining a grid of alpha, delta values, and for each BATSE detection of a burst from a soft gamma repeater, predicting the arrival time of the burst at Ulysses and co-adding the Ulysses data rephased so that the burst signals are aligned in time and produce a detectable pulse. We demonstrate that this method identifies the position of the soft repeater SGR 1806-20, and apply it to the repeater B1900+14. We show that the counterpart to this burst source is probably in or in the vicinity of the Galactic supernova remnant G42.8+0.6.

  9. Lack of Stem Cells May Be Key to Repeat Miscarriages

    MedlinePlus

    ... gov/medlineplus/news/fullstory_157663.html Lack of Stem Cells May Be Key to Repeat Miscarriages Potential ... March 8, 2016 (HealthDay News) -- A lack of stem cells in the lining of the uterus may ...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  11. A general computational approach for repeat protein design.

    PubMed

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

    2015-01-30

    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 1Å 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

  12. Quantitation of Leishmania lipophosphoglycan repeat units by capillary electrophoresis.

    PubMed

    Barron, Tamara L; Turco, Salvatore J

    2006-04-01

    The glycosylphosphatidylinositol (GPI)-anchored lipophosphoglycan (LPG) of Leishmania is the dominant cell surface glycoconjugate of these pathogenic parasites. LPG is structurally characterized by a series of phosphoglycan repeat units. Determining the number of repeat units per LPG molecule has proven difficult using current technologies, such as mass spectrometry. As an alternative method to quantitate the number of repeat units in LPG, a procedure based on capillary electrophoretic analysis of the proportion of mannose to 2,5-anhydromannose (derived from the nonacetylated glucosamine of the GPI anchor of LPG) was developed. The CE-based technique is sensitive and relatively rapid compared to GC-MS-based protocols. Its application was demonstrated in quantitating the number of LPG repeat units from several species of Leishmania as well as from two life-cycle stages of these organisms. PMID:16310310

  13. 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

  14. 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.

  15. Are major repeater patients addicted to suicidal behavior?

    PubMed

    Blasco-Fontecilla, Hilario; Artieda-Urrutia, Paula; Berenguer-Elias, Nuria; Garcia-Vega, Juan Manuel; Fernandez-Rodriguez, Monica; Rodriguez-Lomas, Cesar; Gonzalez-Villalobos, Isabel; Iruela-Cuadrado, Luis; de Leon, José

    2014-01-01

    The literature provides support for the hypothesis that some major repeaters (individuals with >=5 lifetime suicide attempts) are addicted to suicidal behavior (SB). This study explores whether major repeaters are addicted to SB or not using 7 criteria: tolerance (Criterion 1), withdrawal (Criterion 2), loss of control (Criterion 3), problems in quitting/cutting down (Criterion 4), much time spent using (Criterion 5), substantial reduction in activities (Criterion 6), and adverse physiological/physical consequences (Criterion 7). Total dependence on SB was indicated by the presence of 3 or more of the 7 criteria in the last 12 months. This cross-sectional study at Puerta de Hierro University Hospital (Madrid, Spain) recruited 118 suicide attempters including 8 major repeaters (7%, 8/118), who were all females. The association between each SB addiction criterion, physiological dependence and total dependence with major repeater status was tested for significance and for effect size with odds ratios (ORs) and their 95% confidence intervals. As hypothesized, major repeaters met significantly higher frequency of criteria for total dependence on SB, OR=62.9 (6.4-615). A backward stepwise logistic regression model was used to provide an OR between major repeater status and total dependence status corrected by confounding variables. Age, panic disorder without agoraphobia, borderline personality disorder, history of psychiatric inpatient admission, and total dependence on SB were introduced as independent variables with major repeater status as the dependent variable. The model selected total dependence and age as the remaining significant variables in the last step. Accordingly, major repeaters appear to be addicted to SB. PMID:25580865

  16. 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.

  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. 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

  19. 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.

  20. Community Protection Policies and Repeat Sexual Offenses in Florida.

    PubMed

    Levenson, Jill S; Zgoba, Kristen M

    2016-08-01

    The purpose of this study was to investigate the impact of sexual offender management policies on sex crime repeat arrest rates in Florida. Aggregate data for the period 1990 to 2010 were provided by the Florida Department of Law Enforcement. The repeat offense rate was defined as the proportion of arrests each year that were committed by individuals with a previous conviction in the same crime category. The average yearly repeat offense rate for sex crimes was 6.5%, which was consistently and significantly lower than rates for other crimes: 8.3% for non-sex assaults, 15.1% for robbery, 29.8% for drug offenses, and 11.6% for DUI. The average annual sexual repeat arrest rate prior to and after the implementation of sexual offender registration laws in 1997 was 4.9% and 7.5%, respectively, indicating a statistically significant increase. The average annual repeat arrest rates for non-sex assaults, robberies, drug crimes, and DUIs also increased after 1997. No significant differences were found when comparing the average annual percent change for sexual re-arrest (+3.47%) with non-sexual assault (+3.93%), robbery (-.73%), drug offenses (+1.59%), and DUI (+1.14). Sex crime repeat arrests in Florida do not appear to show a decline attributable to sex offender management policies implemented since 1997. PMID:25759428

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

    PubMed

    Millership, C; Phillips, J J; Main, E R G

    2016-05-01

    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. PMID:26947150

  2. 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.

  3. Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

    PubMed

    Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

    1997-12-01

    Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R. PMID:9451957

  4. 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. PMID:26465749

  5. Poisson process approximation for sequence repeats, and sequencing by hybridization.

    PubMed

    Arratia, R; Martin, D; Reinert, G; Waterman, M S

    1996-01-01

    Sequencing by hybridization is a tool to determine a DNA sequence from the unordered list of all l-tuples contained in this sequence; typical numbers for l are l = 8, 10, 12. For theoretical purposes we assume that the multiset of all l-tuples is known. This multiset determines the DNA sequence uniquely if none of the so-called Ukkonen transformations are possible. These transformations require repeats of (l-1)-tuples in the sequence, with these repeats occurring in certain spatial patterns. We model DNA as an i.i.d. sequence. We first prove Poisson process approximations for the process of indicators of all leftmost long repeats allowing self-overlap and for the process of indicators of all left-most long repeats without self-overlap. Using the Chen-Stein method, we get bounds on the error of these approximations. As a corollary, we approximate the distribution of longest repeats. In the second step we analyze the spatial patterns of the repeats. Finally we combine these two steps to prove an approximation for the probability that a random sequence is uniquely recoverable from its list of l-tuples. For all our results we give some numerical examples including error bounds. PMID:8891959

  6. Considerations on repeated repairing of weldments in Inconel 718 alloy

    NASA Technical Reports Server (NTRS)

    Bayless, E. O.; Lovoy, C. V.; Mcilwain, M. C.; Munafo, P.

    1981-01-01

    The effects of repeated weld repairs on the metallurgical characteristics, high cycle fatigue (HCF), and tensile properties of Inconel 718 butt weld joints were determined. A 1/4 in thick plate and a 1/2 in thick plate were used as well as tungsten inert gas welding, and Inconel 718 filler wire. Weld panels were subjected to 2, 6, and 12 repeated repairs and were made in a highly restrained condition. Post weld heat treatments were also conducted with the welded panel in the highly restrained condition. Results indicate that no significant metallurgical anomaly is evident as a result of up to twelve repeated weld repairs. No degradation in fatigue life is noted for up to twelve repeated repairs. Tensile results from specimens which contained up to twelve repeated weld repairs revealed no significant degradation in UTS and YS. However, a significant decrease in elongation is evident with specimens (solution treated and age hardened after welding) which contained twelve repeated repairs. The elongation loss is attributed to the presence of a severe notch on each side (fusion line) of the repair weld bead reinforcement.

  7. Who Repeats Algebra I, and How Does Initial Performance Relate to Improvement When the Course Is Repeated? REL 2015-059

    ERIC Educational Resources Information Center

    Fong, Anthony B.; Jaquet, Karina; Finkelstein, Neal

    2014-01-01

    This REL West study explores the prevalence of students repeating Algebra I, who is most likely to repeat the course, and the level of improvement for students who repeat. Using six years of data from a cohort of 3,400 first-time seventh grade students in a California school district, authors found that 44 percent of students repeated algebra I.…

  8. Excision of plastid marker genes using directly repeated DNA sequences.

    PubMed

    Mudd, Elisabeth A; Madesis, Panagiotis; Avila, Elena Martin; Day, Anil

    2014-01-01

    Excision of marker genes using DNA direct repeats makes use of the predominant homologous recombination pathways present in the plastids of algae and plants. The method is simple, efficient, and widely applicable to plants and microalgae. Marker excision frequency is dependent on the length and number of directly repeated sequences. When two repeats are used a repeat size of greater than 600 bp promotes efficient excision of the marker gene. A wide variety of sequences can be used to make the direct repeats. Only a single round of transformation is required, and there is no requirement to introduce site-specific recombinases by retransformation or sexual crosses. Selection is used to maintain the marker and ensure homoplasmy of transgenic plastid genomes. Release of selection allows the accumulation of marker-free plastid genomes generated by marker excision, which is spontaneous, random, and a unidirectional process. Positive selection is provided by linking marker excision to restoration of the coding region of an herbicide resistance gene from two overlapping but incomplete coding regions. Cytoplasmic sorting allows the segregation of cells with marker-free transgenic plastids. The marker-free shoots resulting from direct repeat-mediated excision of marker genes have been isolated by vegetative propagation of shoots in the T0 generation. Alternatively, accumulation of marker-free plastid genomes during growth, development and flowering of T0 plants allows the collection of seeds that give rise to a high proportion of marker-free T1 seedlings. The simplicity and convenience of direct repeat excision facilitates its widespread use to isolate marker-free crops. PMID:24599849

  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. PMID:21756130

  10. Intra-Genomic Variation in the Ribosomal Repeats of Nematodes

    PubMed Central

    Bik, Holly M.; Fournier, David; Sung, Way; Bergeron, R. Daniel; Thomas, W. Kelley

    2013-01-01

    Ribosomal loci represent a major tool for investigating environmental diversity and community structure via high-throughput marker gene studies of eukaryotes (e.g. 18S rRNA). Since the estimation of species’ abundance is a major goal of environmental studies (by counting numbers of sequences), understanding the patterns of rRNA copy number across species will be critical for informing such high-throughput approaches. Such knowledge is critical, given that ribosomal RNA genes exist within multi-copy repeated arrays in a genome. Here we measured the repeat copy number for six nematode species by mapping the sequences from whole genome shotgun libraries against reference sequences for their rRNA repeat. This revealed a 6-fold variation in repeat copy number amongst taxa investigated, with levels of intragenomic variation ranging from 56 to 323 copies of the rRNA array. By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function. We find that the dramatic variation in repeat copy number among these six nematode genomes would limit the use of rRNA in estimates of organismal abundance. In addition, the unique pattern of variation within a single genome was uncorrelated with patterns of divergence between species, reflecting a strong signature of natural selection for rRNA function. A better understanding of the factors that control or affect copy number in these arrays, as well as their rates and patterns of evolution, will be

  11. Repeat Sequences and Base Correlations in Human Y Chromosome Palindromes

    NASA Astrophysics Data System (ADS)

    Jin, Neng-zhi; Liu, Zi-xian; Qi, Yan-jiao; Qiu, Wen-yuan

    2009-06-01

    On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes. The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.

  12. Rapid evolution of simple sequence repeat induced by allopolyploidization.

    PubMed

    Tang, Zongxiang; Fu, Shulan; Ren, Zhenglong; Zou, Yuting

    2009-09-01

    Microsatellite evolution normally occurs in diploids. Until now, there has been a lack of direct experimental evidence for microsatellite evolution following allopolyploidization. In the present study, F(1) hybrids and newly synthesized allopolyploids were derived from Triticum aestivum Chinese Spring x Secale cereale Jinzhou-heimai. One hundred and sixty-three wheat simple sequence repeat (SSR) markers were used to investigate the variation of wheat microsatellites after allopolyploidization and variation of the PCR products of 29 of the SSR markers was observed. Of these 29 SSR markers, 15 were unable to produce products from amphiploids. The other 14 SSR markers did produce products from parental wheat, F(1) hybrids and amphiploids. However, the length of the products amplified from amphiploids was different from the length of the products amplified from parental wheat and F(1) hybrids. Sequencing indicated that the length variation of the 14 microsatellites stemmed mainly from variation in the number of repeat units. The alteration of repeat units occurred in both perfect and compound repeats. In some compound SSR loci, one motif was observed to expand whereas another to contract. Almost all the microsatellite evolution observed in this study could be explained by the slipped-strand mispairing model. The results of this study seem to indicate that stress caused by allopolyploidization might be one of the factors that induce microsatellite evolution. In addition, the findings of present study provided an instance of how simple sequence repeats evolved after allopolyploidization. PMID:19688286

  13. 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.

  14. 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.

  15. 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

  16. The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes

    PubMed Central

    Siozios, Stefanos; Ioannidis, Panagiotis; Klasson, Lisa; Andersson, Siv G. E.; Braig, Henk R.; Bourtzis, Kostas

    2013-01-01

    Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions. PMID:23390535

  17. 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. PMID:11256821

  18. 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

  19. Coevolution between simple sequence repeats (SSRs) and virus genome size

    PubMed Central

    2012-01-01

    Background Relationship between the level of repetitiveness in genomic sequence and genome size has been investigated by making use of complete prokaryotic and eukaryotic genomes, but relevant studies have been rarely made in virus genomes. Results In this study, a total of 257 viruses were examined, which cover 90% of genera. The results showed that simple sequence repeats (SSRs) is strongly, positively and significantly correlated with genome size. Certain repeat class is distributed in a certain range of genome sequence length. Mono-, di- and tri- repeats are widely distributed in all virus genomes, tetra- SSRs as a common component consist in genomes which more than 100 kb in size; in the range of genome < 100 kb, genomes containing penta- and hexa- SSRs are not more than 50%. Principal components analysis (PCA) indicated that dinucleotide repeat affects the differences of SSRs most strongly among virus genomes. Results showed that SSRs tend to accumulate in larger virus genomes; and the longer genome sequence, the longer repeat units. Conclusions We conducted this research standing on the height of the whole virus. We concluded that genome size is an important factor in affecting the occurrence of SSRs; hosts are also responsible for the variances of SSRs content to a certain degree. PMID:22931422

  20. Recent social conditions affect boldness repeatability in individual sticklebacks

    PubMed Central

    Jolles, Jolle Wolter; Aaron Taylor, Benjamin; Manica, Andrea

    2016-01-01

    Animal personalities are ubiquitous across the animal kingdom and have been shown both to influence individual behaviour in the social context and to be affected by it. However, little attention has been paid to possible carryover effects of social conditions on personality expression, especially when individuals are alone. Here we investigated how the recent social context affected the boldness and repeatability of three-spined sticklebacks, Gasterosteus aculeatus, during individual assays. We housed fish either solitarily, solitarily part of the time or socially in groups of four, and subjected them twice to a risk-taking task. The social conditions had a large effect on boldness repeatability, with fish housed solitarily before the trials showing much higher behavioural repeatability than fish housed socially, for which repeatability was not significant. Social conditions also had a temporal effect on the boldness of the fish, with only fish housed solitarily taking more risks during the first than the second trial. These results show that recent social conditions can thus affect the short-term repeatability of behaviour and obfuscate the expression of personality even in later contexts when individuals are alone. This finding highlights the need to consider social housing conditions when designing personality studies and emphasizes the important link between animal personality and the social context by showing the potential role of social carryover effects. PMID:26949265

  1. 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.

  2. 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.

  3. 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.

  4. Effects of repeated production on vowel distinctiveness within nonwords

    PubMed Central

    Sasisekaran, Jayanthi; Munson, Benjamin

    2012-01-01

    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. PMID:22502490

  5. Control of repeat protein curvature by computational protein design

    PubMed Central

    Park, Keunwan; Shen, Betty W.; Parmeggiani, Fabio; Huang, Po-Ssu; Stoddard, Barry L.; Baker, David

    2014-01-01

    Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat protein scaffolds, and apply it to leucine rich repeat proteins. First, a set of self-compatible building block modules are designed that when polymerized each generate surfaces with unique but constant curvatures. Second, a set of junction modules that connect the different building blocks are designed. Finally, new proteins with custom designed shapes are generated by appropriately combining building block and junction modules. Crystal structures of the designs illustrate the power of the approach in controlling repeat protein curvature. PMID:25580576

  6. 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

  7. 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.

  8. Evaluating post-Katrina recovery in Mississippi using repeat photography.

    PubMed

    Burton, Christopher; Mitchell, Jerry T; Cutter, Susan L

    2011-07-01

    Hurricane Katrina of August 2005 had extensive consequences for the state of Mississippi in the United States. Widespread infrastructure and property damage, massive social dislocation, and ecological loss remain among the many challenges faced by communities as they work towards 'normalcy'. This study employs repeat photography to understand differential recovery from Hurricane Katrina in Mississippi. Revealing change with conventional landscape photography, a process known as repeat photography, is common in the natural sciences. Simply stated, repeat photography is the practice of re-photographing the same scene as it appears in an earlier photograph. Photographs were taken at 131 sites every six months over a three-year period. Each photograph was assigned a recovery score and a spatially interpolated recovery surface was generated for each time period. The mapped and graphed results show disparities in the progression of recovery: some communities quickly entered the rebuilding process whereas others have lagged far behind. PMID:21272057

  9. 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. PMID:26119259

  10. Repetition is easy: Why repeated referents have reduced prominence

    PubMed Central

    Lam, Tuan Q.; Watson, Duane G.

    2011-01-01

    The repetition and predictability of a word in a conversation are two factors that are believed to affect whether or not it is emphasized: predictable, repeated words are less acoustically prominent than unpredictable, new words. However, because predictability and repetition are correlated, it is unclear whether speakers lengthen unpredictable words to facilitate comprehension or whether this lengthening is the result of difficulties in accessing a new (non-repeated) lexical item. In this paper, we investigate the relationship between acoustic prominence, repetition, and predictability in a description task. In Experiment 1, we find that repeated referents are produced with reduced prominence, even when these referents are unexpected. In Experiment 2, we find that predictability and repetition both have independent effects on duration and intensity. However, word duration was primarily determined by repetition, and intensity was primarily determined by predictability. The data are most consistent with an account in which multiple cognitive factors influence the acoustic prominence of a word. PMID:21156876

  11. Repeat rape and multiple offending among undetected rapists.

    PubMed

    Lisak, David; Miller, Paul M

    2002-02-01

    Pooling data from four samples in which 1,882 men were assessed for acts of interpersonal violence, we report on 120 men whose self-reported acts met legal definitions of rape or attempted rape, but who were never prosecuted by criminal justice authorities. A majority of these undetected rapists were repeat rapists, and a majority also committed other acts of interpersonal violence. The repeat rapists averaged 5.8 rapes each. The 120 rapists were responsible for 1,225 separate acts of interpersonal violence, including rape, battery, and child physical and sexual abuse. These findings mirror those from studies of incarcerated sex offenders (Abel, Becker, Mittelman, Cunningham-Rathner, Rouleau, & Murphy, 1987; Weinrott and Saylor, 1991), indicating high rates of both repeat rape and multiple types of offending. Implications for the investigation and prosecution of this so-called "hidden" rape are discussed. PMID:11991158

  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. 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

  14. Characteristics of LGV repeaters: analysis of LGV surveillance data

    PubMed Central

    Rönn, Minttu; Hughes, Gwenda; White, Peter; Simms, Ian; Ison, Catherine; Ward, Helen

    2014-01-01

    Objectives A number of individuals have acquired lymphogranuloma venereum (LGV) infection multiple times since its re-emergence. We describe the characteristics of reinfections and those who acquire them. Methods The LGV Enhanced Surveillance system collected detailed information on LGV episodes in the UK from 2004 to 2010. Using logistic regression we compared the baseline characteristics of men who have sex with men (MSM) who had a repeat LGV episode (‘repeaters’) to MSM with a single reported episode (‘non-repeaters’). Results There were 66 individuals among the 1281 MSM (5.2%) with LGV episode who had a recorded reinfection during the data collection period. Those who acquired LGV reinfection were more likely to be HIV positive (97% vs 79%), visit a clinic in London (OR 2.0, 95% CI 1.1 to 3.8), and have hepatitis C (OR 2.2, 95% CI 1.1 to 4.6) or concurrent gonorrhoea (OR 2.2, 95% CI 1.2 to 3.8) on their first recorded LGV episode. Repeaters reported higher levels of unprotected sex, but behavioural variables were not significantly different between repeaters and non-repeaters. Conclusions Among LGV repeaters, risk behaviour alone did not explain subsequent reinfection. LGV repeaters have a high level of other sexually transmitted infections (STIs) which may be linked to their central position in the sexual network that contributes to their heightened risk of STI acquisition. Given the low prevalence of LGV in the general MSM population, momentary increases in incidence in subsets of the population may be an important factor for LGV risk where the overall level of sexual risk behaviour is higher. Validating this would require research into sexual network structures. PMID:24431182

  15. 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.

  16. Formation of the Arabidopsis Pentatricopeptide Repeat Family1[W

    PubMed Central

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

    2006-01-01

    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. PMID:16825340

  17. Cortical Activation Changes During Simple Motor Task over Repeated Sessions

    NASA Astrophysics Data System (ADS)

    Matsuzaki, Shuichi; Yamada, Taro; Wada, Yasuhiro

    Recent fMRI studies of human motor function and learning have reported that the magnitude of brain activity involves a decreasing trend over repeated tasks in the absence of improvements in task performance, probably suggesting the effect of habituation. Here we show that similar effect can be detected by NIRS. In experiments, oxygenated hemoglobin (HbO) changes were monitored during a finger tapping task over repeated sessions. Results showed that task-related brain activity exhibited a decreasing trend on motor-related areas over the sessions. These suggest that measurements of NIRS may exhibit the brain-induced trends over repetition of simple motor tasks.

  18. Evaluation of pulsed RFI effects on digital satellite repeaters

    NASA Technical Reports Server (NTRS)

    Huang, T. C.; Braun, W. R.

    1980-01-01

    This paper presents an analytical approach for assessing the effect of pulsed RFI on the error probability of a coherent phase-shift keyed signal through a nonlinear satellite repeater. The RFI is assumed to affect the uplink channel and to consist of CW pulses with random power levels and arriving randomly in time with a Poisson distribution. A model to approximate the effect of intermodulation products is introduced and the error probability conditioned on the output of the satellite repeater is computed. The classical moment technique is then used as an efficient method of averaging the conditional error probability over the numerous random parameters associated with the uplink signal.

  19. Repeatability and oblique flow response characteristics of current meters

    USGS Publications Warehouse

    Fulford, Janice M.; Thibodeaux, Kirk G.; Kaehrle, William R.

    1993-01-01

    Laboratory investigation into the precision and accuracy of various mechanical-current meters are presented. Horizontal-axis and vertical-axis meters that are used for the measurement of point velocities in streams and rivers were tested. Meters were tested for repeatability and response to oblique flows. Both horizontal- and vertical-axis meters were found to under- and over-register oblique flows with errors generally increasing as the velocity and angle of flow increased. For the oblique flow tests, magnitude of errors were smallest for horizontal-axis meters. Repeatability of all meters tested was good, with the horizontal- and vertical-axis meters performing similarly.

  20. Layered Architectures for Quantum Computers and Quantum Repeaters

    NASA Astrophysics Data System (ADS)

    Jones, Nathan C.

    This chapter examines how to organize quantum computers and repeaters using a systematic framework known as layered architecture, where machine control is organized in layers associated with specialized tasks. The framework is flexible and could be used for analysis and comparison of quantum information systems. To demonstrate the design principles in practice, we develop architectures for quantum computers and quantum repeaters based on optically controlled quantum dots, showing how a myriad of technologies must operate synchronously to achieve fault-tolerance. Optical control makes information processing in this system very fast, scalable to large problem sizes, and extendable to quantum communication.

  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. N170 adaptation effect for repeated faces and words.

    PubMed

    Cao, X; Ma, X; Qi, C

    2015-05-21

    Using ERP adaptation paradigms, studies have shown that the N170 adaptation effect is a stable phenomenon for both faces and words. However, the N170 adaptation effect for repeated identity remains unclear, so we have addressed this with two experiments. In Experiment 1, we investigated the face-related N170 repeated adaptation effect in a short interstimulus interval (ISI) and found that the N170 response elicited by faces was smaller when preceded by a same face adaptor than by another face adaptor. Experiment 2 addressed whether this repeated N170 adaptation effect generalizes to words. For the first time, the results indicated that the N170 response elicited by words was larger with a different word as an adaptor relative to the same word as an adaptor. Our results demonstrate that the face-related N170 response is sensitive to visual face features and extend the characteristics of N170 with the sensitivity to repeated items to other familiar objects of expertise (i.e. words). The results also suggest that there are some common characteristics between faces and words in the early perceptual processing. PMID:25772788

  4. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... continuous access signal, the absence of which will de-activate the mobile transmitter. The continuous access signal is not required when the mobile unit is equipped with a switch that activates the automatic mode... 47 Telecommunication 5 2011-10-01 2011-10-01 false Mobile repeater stations. 90.247 Section...

  5. 47 CFR 90.247 - Mobile repeater stations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... continuous access signal, the absence of which will de-activate the mobile transmitter. The continuous access signal is not required when the mobile unit is equipped with a switch that activates the automatic mode... 47 Telecommunication 5 2014-10-01 2014-10-01 false Mobile repeater stations. 90.247 Section...

  6. Simple sequence repeat markers that identify Claviceps species and strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  7. 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…

  8. Prospective Teachers' Understanding of Decimals with Single Repeating Digits

    ERIC Educational Resources Information Center

    Burroughs, Elizabeth A.; Yopp, David

    2010-01-01

    This article investigates prospective elementary teachers' conceptions of the repeating decimal 0.999... Five students from a first-semester undergraduate course "Mathematics for Elementary School Teachers" were interviewed to ascertain their conceptions about the mathematical statement 0.999... = 1. All of the students indicated they do not…

  9. Repeated blast exposures cause brain DNA fragmentation in mice.

    PubMed

    Wang, Ying; Arun, Peethambaran; Wei, Yanling; Oguntayo, Samuel; Gharavi, Robert; Valiyaveettil, Manojkumar; Nambiar, Madhusoodana P; Long, Joseph B

    2014-03-01

    The pathophysiology of blast-induced traumatic brain injury (TBI) and subsequent behavioral deficits are not well understood. Unraveling the mechanisms of injury is critical to derive effective countermeasures against this form of neurotrauma. Preservation of the integrity of cellular DNA is crucial for the function and survival of cells. We evaluated the effect of repeated blast exposures on the integrity of brain DNA and tested the utility of cell-free DNA (CFD) in plasma as a biomarker for the diagnosis and prognosis of blast-induced polytrauma. The results revealed time-dependent breakdown in cellular DNA in different brain regions, with the maximum damage at 24 h post-blast exposures. CFD levels in plasma showed a significant transient increase, which was largely independent of the timing and severity of brain DNA damage; maximum levels were recorded at 2 h after repeated blast exposure and returned to baseline at 24 h. A positive correlation was observed between the righting reflex time and CFD level in plasma at 2 h after blast exposure. Brain DNA damage subsequent to repeated blast was associated with decreased mitochondrial membrane potential, increased release of cytochrome C, and up-regulation of caspase-3, all of which are indicative of cellular apoptosis. Shock-wave-induced DNA damage and initiation of mitochondrial-driven cellular apoptosis in the brain after repeated blast exposures indicate that therapeutic strategies directed toward inhibition of DNA damage or instigation of DNA repair may be effective countermeasures. PMID:24074345

  10. 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:…

  11. 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

  12. 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

  13. Evolutionary Footprints of Short Tandem Repeats in Avian Promoters

    PubMed Central

    Abe, Hideaki; Gemmell, Neil J.

    2016-01-01

    Short tandem repeats (STRs) or microsatellites are well-known sequence elements that may change the spacing between transcription factor binding sites (TFBSs) in promoter regions by expansion or contraction of repetitive units. Some of these mutations have the potential to contribute to phenotypic diversity by altering patterns of gene expression. To explore how repetitive sequence motifs within promoters have evolved in avian lineages under mutation-selection balance, more than 400 evolutionary conserved STRs (ecSTRs) were identified in this study by comparing the 2 kb upstream promoter sequences of chicken against those of other birds (turkey, duck, zebra finch, and flycatcher). The rate of conservation was significantly higher in AG dinucleotide repeats than in AC or AT repeats, with the expansion of AG motifs being noticeably constrained in passerines. Analysis of the relative distance between ecSTRs and TFBSs revealed a significantly higher rate of conserved TFBSs in the vicinity of ecSTRs in both chicken-duck and chicken-passerine comparisons. Our comparative study provides a novel insight into which intrinsic factors have influenced the degree of constraint on repeat expansion/contraction during avian promoter evolution. PMID:26766026

  14. 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.

  15. Physiological responses to repeated transportation of gestating Brahman cows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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,...

  16. A survey of FRB fields: limits on repeatability

    NASA Astrophysics Data System (ADS)

    Petroff, E.; Johnston, S.; Keane, E. F.; van Straten, W.; Bailes, M.; Barr, E. D.; Barsdell, B. R.; Burke-Spolaor, S.; Caleb, M.; Champion, D. J.; Flynn, C.; Jameson, A.; Kramer, M.; Ng, C.; Possenti, A.; Stappers, B. W.

    2015-11-01

    Several theories exist to explain the source of the bright, millisecond duration pulses known as fast radio bursts (FRBs). If the progenitors of FRBs are non-cataclysmic, such as giant pulses from pulsars, pulsar-planet binaries, or magnetar flares, FRB emission may be seen to repeat. We have undertaken a survey of the fields of eight known FRBs from the High Time Resolution Universe survey to search for repeating pulses. Although no repeat pulses were detected the survey yielded the detection of a new FRB, described in Petroff et al. (2015a). From our observations we rule out periodic repeating sources with periods P ≤ 8.6 h and rule out sources with periods 8.6 < P < 21 h at the 90 per cent confidence level. At P ≥ 21 h our limits fall off as ˜1/P. Dedicated and persistent observations of FRB source fields are needed to rule out repetition on longer time-scales, a task well-suited to next generation wide-field transient detectors.

  17. Comparative Analysis of Alu Repeats in Primate Genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. 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 desire.…

  19. DURABILITY AND BREAKAGE OF FEED PELLETS DURING REPEATED ELEVATOR HANDLING

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pelleting of animal feeds is important for improved feeding efficiency and for convenience of handling. Pellet quality impacts the feeding benefits for the animals and pellet integrity during handling. To determine the effect of repeated handling on feed pellet breakage and durability, a 22.6-t (100...

  20. 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.

  1. Continuity of care. Opportunity for residents to see repeat patients.

    PubMed Central

    Bell, N. R.; Szafran, O.

    1995-01-01

    OBJECTIVE: To examine the opportunity for first-year family medicine residents to experience continuity of care during family medicine block time and half-day returns. DESIGN: Retrospective analysis of patient encounter data during the 1987-1988 and 1991-1992 academic years to determine how much contact residents had with repeat patients. SETTING: Two family medicine teaching centres in Edmonton. PARTICIPANTS: First-year family medicine residents: 24 residents during 1987-1988 and 24 during 1991-1992. MAIN OUTCOME MEASURES: Number of patient-resident contacts and number of repeat contacts. RESULTS: During the 4-month block time and half-day return, residents had repeat contact with 25.9% and 20.3% of the patients seen. These patients provided 48.3% and 37.7% of all visits at Centres A and B, respectively. CONCLUSION: Increasing block time from 2 to 4 months resulted in only a slight increase in repeat contact with patients. Half-day returns did not appear to enhance the opportunity for continuity of care. PMID:8563505

  2. 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…

  3. WDSPdb: a database for WD40-repeat proteins

    PubMed Central

    Wang, Yang; Hu, Xue-Jia; Zou, Xu-Dong; Wu, Xian-Hui; Ye, Zhi-Qiang; Wu, Yun-Dong

    2015-01-01

    WD40-repeat proteins, as one of the largest protein families, often serve as platforms to assemble functional complexes through the hotspot residues on their domain surfaces, and thus play vital roles in many biological processes. Consequently, it is highly required for researchers who study WD40 proteins and protein–protein interactions to obtain structural information of WD40 domains. Systematic identification of WD40-repeat proteins, including prediction of their secondary structures, tertiary structures and potential hotspot residues responsible for protein–protein interactions, may constitute a valuable resource upon this request. To achieve this goal, we developed a specialized database WDSPdb (http://wu.scbb.pkusz.edu.cn/wdsp/) to provide these details of WD40-repeat proteins based on our recently published method WDSP. The WDSPdb contains 63 211 WD40-repeat proteins identified from 3383 species, including most well-known model organisms. To better serve the community, we implemented a user-friendly interactive web interface to browse, search and download the secondary structures, 3D structure models and potential hotspot residues provided by WDSPdb. PMID:25348404

  4. Cis-elements governing trinucleotide repeat instability in Saccharomyces cerevisiae.

    PubMed Central

    Rolfsmeier, M L; Dixon, M J; Pessoa-Brandão, L; Pelletier, R; Miret, J J; Lahue, R S

    2001-01-01

    Trinucleotide repeat (TNR) instability in humans is governed by unique cis-elements. One element is a threshold, or minimal repeat length, conferring frequent mutations. Since thresholds have not been directly demonstrated in model systems, their molecular nature remains uncertain. Another element is sequence specificity. Unstable TNR sequences are almost always CNG, whose hairpin-forming ability is thought to promote instability by inhibiting DNA repair. To understand these cis-elements further, TNR expansions and contractions were monitored by yeast genetic assays. A threshold of approximately 15--17 repeats was observed for CTG expansions and contractions, indicating that thresholds function in organisms besides humans. Mutants lacking the flap endonuclease Rad27p showed little change in the expansion threshold, suggesting that this element is not altered by the presence or absence of flap processing. CNG or GNC sequences yielded frequent mutations, whereas A-T rich sequences were substantially more stable. This sequence analysis further supports a hairpin-mediated mechanism of TNR instability. Expansions and contractions occurred at comparable rates for CTG tract lengths between 15 and 25 repeats, indicating that expansions can comprise a significant fraction of mutations in yeast. These results indicate that several unique cis-elements of human TNR instability are functional in yeast. PMID:11290713

  5. Repeated Interactive Read-Alouds in Preschool and Kindergarten

    ERIC Educational Resources Information Center

    McGee, Lea M.; Schickedanz, Judith A.

    2007-01-01

    Repeated interactive read-alouds, a systematic method of reading aloud, allow teachers to scaffold children's understanding of the book being read, model strategies for making inferences and explanations, and teach vocabulary and concepts. A storybook is read three times in slightly different ways in order to increase the amount and quality of…

  6. Promoting Reading amidst Repeated Failure: Meeting the Challenges

    ERIC Educational Resources Information Center

    Warrican, S. Joel

    2006-01-01

    This article reports a project undertaken in a Caribbean high school among 17 students in a low stream Year 3 class of reluctant readers (mostly boys) who had been experiencing repeated failure. The project, aimed at promoting leisure reading among the adolescents, ran for 16 weeks. During this period, reading materials--mostly those in which the…

  7. Amino acid repeats and the structure and evolution of proteins.

    PubMed

    Albà, M M; Tompa, P; Veitia, R A

    2007-01-01

    Many proteins have repeats or runs of single amino acids. The pathogenicity of some repeat expansions has fueled proteomic, genomic and structural explorations of homopolymeric runs not only in human but in a wide variety of other organisms. Other types of amino acid repetitive structures exhibit more complex patterns than homopeptides. Irrespective of their precise organization, repetitive sequences are defined as low complexity or simple sequences, as one or a few residues are particularly abundant. Prokaryotes show a relatively low frequency of simple sequences compared to eukaryotes. In the latter the percentage of proteins containing homopolymeric runs varies greatly from one group to another. For instance, within vertebrates, amino acid repeat frequency is much higher in mammals than in amphibians, birds or fishes. For some repeats, this is correlated with the GC-richness of the regions containing the corresponding genes. Homopeptides tend to occur in disordered regions of transcription factors or developmental proteins. They can trigger the formation of protein aggregates, particularly in 'disease' proteins. Simple sequences seem to evolve more rapidly than the rest of the protein/gene and may have a functional impact. Therefore, they are good candidates to promote rapid evolutionary changes. All these diverse facets of homopolymeric runs are explored in this review. PMID:18753788

  8. Increasing Positive Perceptions of Counseling: The Importance of Repeated Exposures

    ERIC Educational Resources Information Center

    Kaplan, Scott A.; Vogel, David L.; Gentile, Douglas A.; Wade, Nathaniel G.

    2012-01-01

    This study assesses the effectiveness of repeated exposures to a video intervention based on the Elaboration Likelihood Model. The video was designed to increase help-seeking attitudes and perceptions of peer norms and to decrease the stigma associated with seeking counseling. Participants were 290 undergraduates who were randomly assigned to a…

  9. Single and repeated elective abortions in Japan: a psychosocial study.

    PubMed

    Kitamura, T; Toda, M A; Shima, S; Sugawara, M

    1998-09-01

    Despite its social, legal and medical importance, termination of pregnancy (TOP) (induced abortion) has rarely been the focus of psychosocial research. Of a total of 1329 women who consecutively attended the antenatal clinic of a general hospital in Japan, 635 were expecting their first baby. Of these 635 women, 103 (16.2%) had experienced TOP once previously (first aborters), while 47 (7.4%) had experienced TOP two or more times (repeated aborters). Discriminant function analysis was performed using psychosocial variables found to be significantly associated with either first abortion or repeated abortion in bivariate analyses. This revealed that both first and repeated aborters could be predicted by smoking habits and an unwanted current pregnancy while the repeated aborters appear to differ from first aborters in having a longer pre-marital dating period, non-arranged marriages, smoking habits, early maternal loss experience or a low level of maternal care during childhood. These findings suggest that both the frequency of abortion and its repetition have psychosocial origins. PMID:9844843

  10. Genome Wide Characterization of Simple Sequence Repeats in Cucumber

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  11. 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

  12. Relationship between uterine natural killer cells and unexplained repeated miscarriage

    PubMed Central

    Farghali, Mohamed M.; El-kholy, Abdel-Latif G.; Swidan, Khaled H.; Abdelazim, Ibrahim A.; Rashed, Ahmed R.; El-Sobky, Ezzat; Goma, Mostafa F.

    2015-01-01

    Objective To evaluate the relation between uterine killer (uK) cells and unexplained repeated miscarriage (RM). Material and Methods Eighty women with unexplained repeated miscarriage and missed miscarriage of current pregnancy were studied. Fetal viability and gestational age of the current pregnancy were confirmed by ultrasound, followed by suction evacuation to collect abortion specimens and uterine wall curettage to collect decidua specimens. Abortion specimens were collected for long-term monolayer cell culture and subsequent chromosome analysis using conventional G-banding. Decidua specimens were subjected to immunohistochemical staining using monoclonal antibodies specific to CD56+ and CD16+ expressed by uK cells. Results CD56+ CD16+ uK cells were found in 85% [68/80] of the studied decidua specimens of women with unexplained repeated miscarriage; 88.5% [54/61] had normal abortion karyotyping and 73.7% [14/19] had abnormal abortion karyotyping. Moreover, 73.75% [59/80] of the studied women with a past history of early miscarriage had CD56+ CD16+ uK cells in their decidua specimens, and 66.25% [53/80] of studied women with a past history of late miscarriage had CD56+ CD16+ uK cells in their decidua specimens; the association between early and late miscarriage and CD56+ CD16+ uK cells in decidua specimens was significant. Conclusion CD56+CD16+ uK cells were predominant in the decidua specimens of the studied women with repeated miscarriage. A significant association was found between the presence of CD56+ CD16+ uK cells in the studied decidua specimens and unexplained repeated miscarriage. PMID:26692771

  13. Evolution Analysis of Simple Sequence Repeats in Plant Genome

    PubMed Central

    Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

    2015-01-01

    Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1–3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution. PMID:26630570

  14. [Repeated action of hyperbaria on rat blood system].

    PubMed

    Maslova, M N; Klimova, V K

    2014-01-01

    There are considered reactions of male Wistar rat blood system to repeated action of nitrogen-oxygen hyperbaria (pressure 0.5 MPa, density of gas medium 6 g/l, pO2 = 0.02-0.03 MPa). Rats were placed into a barochamber for 5 h 24, 72, and 120 h after the first exposition (control in air without the increased pressure). Parameters of red blood were studied and the general state of the animals was estimated. It has been established that after the first hyperbaria séance the stress-reaction develops in rats with all objective stress parameters (level of corticosteroids and content of ascorbic acid in adrenals). At repeated exposure after 24 h the almost complete normalization of all stress parameters was observed, except for the increased hemoglobin content in plasma as a result of impair of permeability of erythrocytic membranes. After repeated actions 72 and 120 h later, the stress parameters manifested again. After exposure 120 h later, the general state of animals was sharply deteriorated they did not move in the "open" field, could not be hold on a horizontal bar, and mainly were lying. The performed control with the immobilization stress showed that after the initial stress-reaction the rats were recovered completely and at repeated exposures no changes were observed in the blood system and in the general state of the animals. We belive that the hyperbaria-produced stress is connected with difficult breathing under pressure. Thereby, the repeated action of hyperbaria is a harmful factor and habituation to it does not occur. PMID:25782286

  15. 47 CFR 80.469 - Maritime mobile repeater stations in Alaska.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 5 2014-10-01 2014-10-01 false Maritime mobile repeater stations in Alaska. 80... Maritime mobile repeater stations in Alaska. (a) Maritime mobile repeater stations are authorized to extend...) On a secondary basis, maritime mobile repeater stations may be authorized to extend the range of...

  16. 47 CFR 80.469 - Maritime mobile repeater stations in Alaska.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Maritime mobile repeater stations in Alaska. 80... Maritime mobile repeater stations in Alaska. (a) Maritime mobile repeater stations are authorized to extend...) On a secondary basis, maritime mobile repeater stations may be authorized to extend the range of...

  17. 30 CFR 250.522 - When do I have to repeat casing diagnostic testing?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 2 2011-07-01 2011-07-01 false When do I have to repeat casing diagnostic... repeat casing diagnostic testing? Casing diagnostic testing must be repeated according to the following table: When * * * you must repeat diagnostic testing * * * (a) your casing pressure request...

  18. Simple sequence repeat markers useful for sorghum downy mildew (Peronosclerospora sorghi) and related species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55%) with dinucleotide repeats and 6 (11%) with trinucleotide repeats. A total of 22 microsatellites with CA/AC or GT/TG repeats were the most abund...

  19. 47 CFR 80.469 - Maritime mobile repeater stations in Alaska.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Maritime mobile repeater stations in Alaska. 80... Maritime mobile repeater stations in Alaska. (a) Maritime mobile repeater stations are authorized to extend...) On a secondary basis, maritime mobile repeater stations may be authorized to extend the range of...

  20. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CR1 repeats are the most abundant family of repeats in the chicken genome, with more than 200,000 copies accounting for ~80% of the chicken interspersed repeats. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to the 22 CR1 su...

  1. Fully integrated, fully automated generation of short tandem repeat profiles

    PubMed Central

    2013-01-01

    Background The generation of short tandem repeat profiles, also referred to as ‘DNA typing,’ is not currently performed outside the laboratory because the process requires highly skilled technical operators and a controlled laboratory environment and infrastructure with several specialized instruments. The goal of this work was to develop a fully integrated system for the automated generation of short tandem repeat profiles from buccal swab samples, to improve forensic laboratory process flow as well as to enable short tandem repeat profile generation to be performed in police stations and in field-forward military, intelligence, and homeland security settings. Results An integrated system was developed consisting of an injection-molded microfluidic BioChipSet cassette, a ruggedized instrument, and expert system software. For each of five buccal swabs, the system purifies DNA using guanidinium-based lysis and silica binding, amplifies 15 short tandem repeat loci and the amelogenin locus, electrophoretically separates the resulting amplicons, and generates a profile. No operator processing of the samples is required, and the time from swab insertion to profile generation is 84 minutes. All required reagents are contained within the BioChipSet cassette; these consist of a lyophilized polymerase chain reaction mix and liquids for purification and electrophoretic separation. Profiles obtained from fully automated runs demonstrate that the integrated system generates concordant short tandem repeat profiles. The system exhibits single-base resolution from 100 to greater than 500 bases, with inter-run precision with a standard deviation of ±0.05 - 0.10 bases for most alleles. The reagents are stable for at least 6 months at 22°C, and the instrument has been designed and tested to Military Standard 810F for shock and vibration ruggedization. A nontechnical user can operate the system within or outside the laboratory. Conclusions The integrated system represents the

  2. Tandemly repeated DNA families in the mouse genome

    PubMed Central

    2011-01-01

    Background Functional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies. Results Using a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites. To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions. Conclusions Chromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report

  3. C9orf72 repeat expansions cause neurodegeneration in Drosophila through arginine-rich proteins

    PubMed Central

    Ridler, Charlotte E.; Clayton, Emma L.; Devoy, Anny; Moens, Thomas; Norona, Frances E.; Woollacott, Ione O.C.; Pietrzyk, Julian; Cleverley, Karen; Nicoll, Andrew J.; Pickering-Brown, Stuart; Dols, Jacqueline; Cabecinha, Melissa; Hendrich, Oliver; Fratta, Pietro; Fisher, Elizabeth M.C.; Partridge, Linda; Isaacs, Adrian M.

    2016-01-01

    An expanded GGGGCC repeat in C9orf72 is the most common genetic cause of frontotemporal dementia and amyotrophic lateral sclerosis. A fundamental question is whether toxicity is driven by the repeat RNA itself and/or by dipeptide repeat proteins generated by repeat-associated, non-ATG translation. To address this question we developed in vitro and in vivo models to dissect repeat RNA and dipeptide repeat protein toxicity. Expression of pure repeats in Drosophila caused adult-onset neurodegeneration attributable to poly-(glycine-arginine) proteins. Thus expanded repeats promoted neurodegeneration through neurotoxic proteins. Expression of individual dipeptide repeat proteins with a non-GGGGCC RNA sequence showed both poly-(glycine-arginine) and poly-(proline-arginine) proteins caused neurodegeneration. These findings are consistent with a dual toxicity mechanism, whereby both arginine-rich proteins and repeat RNA contribute to C9orf72-mediated neurodegeneration. PMID:25103406

  4. Identification of repetitive elements in the genome of Oreochromis niloticus: Tilapia repeat-masker

    PubMed Central

    Shirak, A.; Grabherr, M.; Di Palma, F.; Lindblad-Toh, K.; Hulata, G.; Ron, M.; Kocher, TD.

    2011-01-01

    The large-scale BAC end-sequencing project of Nile tilapia (Oreochromis niloticus) has generated extensive sequence data that allowed the examination of the repeat content in this fish genome and building of a repeat library specific for this species. This library was established based on Tilapiini repeat sequences from GenBank; sequences orthologous to the repeat library of zebrafish in Repbase; and novel repeats detected by genome analysis using MIRA assembler. We estimate that repeats constitute about 14% of the tilapia genome and also give estimates for the occurrence of the different repeats based on the BLAST searches within the database of known tilapia sequences. The frequent occurrence of novel repeats in the tilapia genome indicates the importance of using the species-specific repeat masker prior to sequence analyses. A web tool based on the RepeatMasker software was designed to assist tilapia genomics. PMID:19936833

  5. Repeated Witnessing of Conspecifics in Pain: Effects on Emotional Contagion.

    PubMed

    Carrillo, Maria; Migliorati, Filippo; Bruls, Rune; Han, Yingying; Heinemans, Mirjam; Pruis, Ilanah; Gazzola, Valeria; Keysers, Christian

    2015-01-01

    Witnessing of conspecifics in pain has been shown to elicit socially triggered freezing in rodents. It is unknown how robust this response is to repeated exposure to a cage-mate experiencing painful stimulation. To address this question, shock-experienced Observer rats repeatedly witnessed familiar Demonstrators receive painful footshocks (six sessions). Results confirm that Observers freeze during the first testing session. The occurrence of this behaviour however gradually diminished as the experimental sessions progressed, reaching minimal freezing levels by the end of the experiments. In contrast, the appearance and continuous increase in the frequency of yawning, a behavior that was inhibited by metyrapone (i.e,. a glucocorticoid synthesis blocker), might represent an alternative coping strategy, suggesting that the observer's reduced freezing does not necessarily indicate a disappearance in the affective response to the Demonstrator's distress. PMID:26356506

  6. A high stability and repeatability electrochemical scanning tunneling microscope

    SciTech Connect

    Xia, Zhigang; Wang, Jihao; Lu, Qingyou; Hou, Yubin

    2014-12-15

    We present a home built electrochemical scanning tunneling microscope (ECSTM) with very high stability and repeatability. Its coarse approach is driven by a closely stacked piezo motor of GeckoDrive type with four rigid clamping points, which enhances the rigidity, compactness, and stability greatly. It can give high clarity atomic resolution images without sound and vibration isolations. Its drifting rates in XY and Z directions in solution are as low as 84 pm/min and 59 pm/min, respectively. In addition, repeatable coarse approaches in solution within 2 mm travel distance show a lateral deviation less than 50 nm. The gas environment can be well controlled to lower the evaporation rate of the cell, thus reducing the contamination and elongating the measurement time. Atomically resolved SO{sub 4}{sup 2−} image on Au (111) work electrode is demonstrated to show the performance of the ECSTM.

  7. Repeated games and direct reciprocity under active linking

    PubMed Central

    Pacheco, Jorge M.; Traulsen, Arne; Ohtsuki, Hisashi; Nowak, Martin A.

    2008-01-01

    Direct reciprocity relies on repeated encounters between the same two individuals. Here we examine the evolution of cooperation under direct reciprocity in dynamically structured populations. Individuals occupy the vertices of a graph, undergoing repeated interactions with their partners via the edges of the graph. Unlike the traditional approach to evolutionary game theory, where individuals meet at random and have no control over the frequency or duration of interactions, we consider a model in which individuals differ in the rate at which they seek new interactions. Moreover, once a link between two individuals has formed, the productivity of this link is evaluated. Links can be broken off at different rates. Whenever the active dynamics of links is sufficiently fast, population structure leads to a simple transformation of the payoff matrix, effectively changing the game under consideration, and hence paving the way for reciprocators to dominate defectors.We derive analytical conditions for evolutionary stability. PMID:18076911

  8. Versatile communication strategies among tandem WW domain repeats

    PubMed Central

    Dodson, Emma Joy; Fishbain-Yoskovitz, Vered; Rotem-Bamberger, Shahar

    2015-01-01

    Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands. PMID:25710931

  9. CRISPRdigger: detecting CRISPRs with better direct repeat annotations

    PubMed Central

    Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Manli; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems’ fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/. PMID:27596864

  10. Repeated early thrombolysis in cervical spinal cord ischemia.

    PubMed

    Etgen, Thorleif; Höcherl, Constanze

    2016-07-01

    Specific therapy of acute spinal ischemia is not established. We report the first case of an MRI-verified cervical spinal ischemia treated by thrombolysis and review the literature. A 72-year old woman with right-sided motor hemiparesis and trunk ataxia was treated by intravenous thrombolysis with full recovery. Three days later she developed again a severe right-sided sensorimotor hemiparesis and a second off-label intravenous thrombolysis was repeated. Magnetic resonance imaging revealed a right-sided posterior-lateral cervical spinal ischemia. Spinal ischemia may clinically present with a cerebral-stroke-like picture challenging diagnostic and therapeutic procedure. Systemic thrombolysis might be a treatment option in acute spinal ischemia. In addition, early repeated systemic thrombolysis may be considered in selected strokes. PMID:26762860

  11. The first crystal structure of an archaeal helical repeat protein

    PubMed Central

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-01-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-­helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein. PMID:16511116

  12. The strength of laminated composite materials under repeated impact loading

    NASA Technical Reports Server (NTRS)

    Rotem, Assa

    1988-01-01

    When low velocity and energy impact is exerted on a laminated composite material, in a perpendicular direction to the plane of the laminate, invisible damage may develop. It is shown analytically and experimentally that the invisible damage occurs during the first stage of contact between the impactor and the laminate and is a result of the contact stresses. However, the residual flexural strength changes only slightly, because it depends mainly on the outer layers, and these remain undamaged. Repeated impact intensifies the damage inside the laminate and causes larger bending under equivalent impact load. Finally, when the damage is most severe, even though it is still invisible, the laminate fails because of bending on the tension side. If the repeated impact is halted before final fracture occurs the residual strength and modulus would decrease by a certain amount.

  13. The recovery of blocked memories in repeated recall tests.

    PubMed

    Gunawan, Kris; Gerkens, David R

    2011-08-01

    There is continued controversy over the possibility of blocked and subsequently recovered accurate memories. Memory blocking produced by a retrieval biasing procedure followed by recovery through repeated testing was demonstrated in two experiments. Predictions derived from the retrieval bias explanation and from the level of cumulative recall (LOCR) concerning hypermnesia for blocked material were tested. Expt 1 disconfirmed the retrieval bias hypothesis that the blocked material would remain blocked. However, there was no accelerated recovery despite the lower rate of recall for the bias group compared to the control group as predicted based on LOCR. Expt 2 replicated the Expt 1 findings and used metamemory tasks to further explore the recovery process. The data led the authors to conclude that accurate recovery of memory with corresponding high confidence is possible through repeated testing provided suggestive questioning and misinformation are not presented. PMID:21751995

  14. Roles for RNA in Telomerase Nucleotide and Repeat Addition Processivity

    PubMed Central

    Lai, Cary K.; Miller, Michael C.; Collins, Kathleen

    2010-01-01

    Summary Telomerase is a ribonucleoprotein reverse transcriptase with two subunits critical for catalytic activity, the protein telomerase reverse transcriptase (TERT) and telomerase RNA. In this study, we establish additional roles of the telomerase RNA subunit by demonstrating that RNA motifs stimulate the processivity of nucleotide and repeat addition. These functions are both functionally and physically separable from the roles of other RNA motifs in establishing a properly defined template. Binding of Tetrahymena telomerase RNA stem IV to TERT enhances nucleotide addition processivity, while a cooperation of the RNA pseudoknot and stem IV promotes repeat addition processivity. The low processivity of DNA synthesis by telomerase ribonucleoproteins lacking the pseudoknot and/or stem IV can be rescued by addition of the deleted region in trans. These findings demonstrate RNA elements with roles in telomerase elongation processivity that are distinct from RNA elements that specify the internal template. PMID:12820978

  15. Mechanisms of trinucleotide repeat instability during human development

    PubMed Central

    McMurray, Cynthia T.

    2011-01-01

    Trinucleotide expansion underlies several human diseases. Expansion occurs during multiple stages of human development in different cell types, and is sensitive to the gender of the parent who transmits the repeats. Repair and replication models for expansions have been described, but we do not know whether the pathway involved is the same under all conditions and for all repeat tract lengths, which differ among diseases. Currently, researchers rely on bacteria, yeast and mice to study expansion, but these models differ substantially from humans. We need now to connect the dots among human genetics, pathway biochemistry and the appropriate model systems to understand the mechanism of expansion as it occurs in human disease. PMID:20953213

  16. Apnea diving: long-term neurocognitive sequelae of repeated hypoxemia.

    PubMed

    Ridgway, Lynne; McFarland, Ken

    2006-02-01

    This article examines the neurocognitive sequelae of repeated exposure to hypoxemia in apnea (breath-hold) divers. A brief review of the literature on the physiological and neurological adaptations involved in the "human diving reflex" is presented. The results from a neuropsychological investigation of N = 21 elite apnea divers are evaluated. Standard neuropsychological tests, with known sensitivity to mild brain insults, included speed of visuo-motor responding, speed of language comprehension, response inhibition, and visual and verbal attention and recall tasks. Results indicated that the breath-hold divers performed tasks within the average range compared to norms on all tests, suggesting that 1-20 years of repeated exposure to hypoxemia including multiple adverse neurological events did not impact on performance on standard neuropsychological tasks. The results are discussed in relation to implications for clinical conditions such as sleep apnea, respiratory disorders, altitude sickness, and recreational apnea activities. PMID:16410228

  17. Gel permeation chromatography (GPC) of repeatedly extruded polyethylene terephthalate (PET).

    PubMed

    Milana, M R; Denaro, M; Arrivabene, L; Maggio, A; Gramiccioni, L

    1998-04-01

    The paper deals with gel permeation chromatography (GPC) monitoring of the behaviour of PET (polyethylene terephthalate) after repeated extrusions. Virgin PET was submitted to three successive extrusion/drying cycles and then the samples were swelled with hexafluoroisopropanol and treated with chloroform. GPC analysis was carried out at room temperature on a B.C.S. Serial LC 2000 GPC system equipped with a series of four GPC columns with UV detection at 254 nm and chloroform as eluent. GPC results showed that after each extrusion step the molecular weight distribution of the PET was different and Mw, Mn and Mz decreased. These findings suggest that during each extrusion degradation occurs and that repeated extrusions, as in the case of the recycling PET, may cause an alteration of the molecular weight distribution of the original PET. PMID:9666895

  18. Protocols and prospects for building a quantum repeater

    NASA Astrophysics Data System (ADS)

    van Loock, Peter

    2013-10-01

    An overview will be given of various approaches to implementing a quantum repeater for quantum communication over large distances. This includes a discussion of systems and protocols that are experimentally feasible and thus realizable in the midterm in order to go beyond the current limit of a few hundred km given by direct quantum-state transmissions. At the same time, these schemes should be, in principle, scalable to arbitrary distances. In this context, the influence of various elements and strategies in a quantum repeater protocol on the final fidelities and rates shall be addressed: initial entanglement distribution, Bell measurements, multiplexing, postselection, quantum memories, and quantum error detection/correction. Solely on the hardware side, the differences in using just single quanta or instead employing many quanta for the flying (photons) and the stationary (atoms) qubits will be pointed out.

  19. Activating frataxin expression by repeat-targeted nucleic acids

    PubMed Central

    Li, Liande; Matsui, Masayuki; Corey, David R.

    2016-01-01

    Friedreich's ataxia is an incurable genetic disorder caused by a mutant expansion of the trinucleotide GAA within an intronic FXN RNA. This expansion leads to reduced expression of frataxin (FXN) protein and evidence suggests that transcriptional repression is caused by an R-loop that forms between the expanded repeat RNA and complementary genomic DNA. Synthetic agents that increase levels of FXN protein might alleviate the disease. We demonstrate that introducing anti-GAA duplex RNAs or single-stranded locked nucleic acids into patient-derived cells increases FXN protein expression to levels similar to analogous wild-type cells. Our data are significant because synthetic nucleic acids that target GAA repeats can be lead compounds for restoring curative FXN levels. More broadly, our results demonstrate that interfering with R-loop formation can trigger gene activation and reveal a new strategy for upregulating gene expression. PMID:26842135

  20. CRISPRdigger: detecting CRISPRs with better direct repeat annotations.

    PubMed

    Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Manli; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems' fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/. PMID:27596864

  1. Repeated Witnessing of Conspecifics in Pain: Effects on Emotional Contagion

    PubMed Central

    Bruls, Rune; Han, Yingying; Heinemans, Mirjam; Pruis, Ilanah; Gazzola, Valeria; Keysers, Christian

    2015-01-01

    Witnessing of conspecifics in pain has been shown to elicit socially triggered freezing in rodents. It is unknown how robust this response is to repeated exposure to a cage-mate experiencing painful stimulation. To address this question, shock-experienced Observer rats repeatedly witnessed familiar Demonstrators receive painful footshocks (six sessions). Results confirm that Observers freeze during the first testing session. The occurrence of this behaviour however gradually diminished as the experimental sessions progressed, reaching minimal freezing levels by the end of the experiments. In contrast, the appearance and continuous increase in the frequency of yawning, a behavior that was inhibited by metyrapone (i.e,. a glucocorticoid synthesis blocker), might represent an alternative coping strategy, suggesting that the observer’s reduced freezing does not necessarily indicate a disappearance in the affective response to the Demonstrator’s distress. PMID:26356506

  2. Highly repeatable all-solid-state polarization-state generator

    NASA Astrophysics Data System (ADS)

    Yao, X. Steve; Yan, Lianshan; Shi, Yongqiang

    2005-06-01

    We report an all solid-state polarization-state generator that uses magneto-optic polarization rotators. The device can generate either five or six distinctive polarization states uniformly across a Poincaré sphere with repeatability better than 0.1°. It is ideal for polarization analysis, swept-wavelength measurement, and monitoring of polarization-related parameters and signal-to-noise ratios of optical networks.

  3. Repeatability in the assessment of multi-segment foot kinematics.

    PubMed

    Deschamps, Kevin; Staes, Filip; Bruyninckx, Herman; Busschots, Ellen; Jaspers, Ellen; Atre, Ameya; Desloovere, Kaat

    2012-02-01

    A recently published systematic review on 3D multi-segment foot models has illustrated the lack of repeatability studies providing evidence for appropriate clinical decision making. The aim of the current study was to assess the repeatability of the recently published model developed by Leardini et al. [10]. Foot kinematics of six healthy adults were analyzed through a repeated-measures design including two therapists with different levels of experience and four test sessions. For the majority of the parameters moderate or good repeatability was observed for the within-day and between-day sessions. A trend towards consistently higher within- and between-day variability was observed for the junior compared to the senior clinician. The mean inter-session variability of the relative 3D rotations ranged between 0.9-4.2° and 1.6-5.0° for respectively the senior and junior clinician whereas for the absolute angles this variability increased to respectively 2.0-6.2° and 2.6-7.8°. Mean inter-therapist standard deviations ranged between 2.2° and 6.5° for the relative 3D rotations and between 2.8° and 7.6° for the absolute 3D rotations. The ratio of inter-therapist to inter-trial errors ranged between 1.8 and 5.5 for the relative 3D rotations and between 2.4 and 9.7 for the absolute 3D rotations. Absolute angle representation of the planar angles was found to be more difficult. Observations from the current study indicate that an adequate normative database can be installed in gait laboratories, however, it should be stressed that experience of therapists is important and gait laboratories should therefore be encouraged to put effort in training their clinicians. PMID:22100210

  4. Perioperative Challenges in Repeat Bladder Exstrophy Repair - Case Report

    PubMed Central

    Etta, Otu Enenyi; Ituen, Monday

    2015-01-01

    Bladder exstrophy is a rare congenital malformation. It presents as leakage of urine in the anterior abdominal wall following defects in midline anterior abdominal wall skin and bladder. We report the use of combined general anaesthesia and caudal epidural analgesia in a 4yr old boy for repeat bladder exstrophy repair. Problems of prolonged surgery and the challenges of pain and sedation management in the post operative period are discussed. PMID:27275265

  5. NTRFinder: a software tool to find nested tandem repeats.

    PubMed

    Matroud, Atheer A; Hendy, M D; Tuffley, C P

    2012-02-01

    We introduce the software tool NTRFinder to search for a complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that NTRs can be used as phylogenetic and population markers. We have tested our algorithm on both real and simulated data, and present some real NTRs of interest. NTRFinder can be downloaded from http://www.maths.otago.ac.nz/~aamatroud/. PMID:22121222

  6. Repeated hydrocephalus in recurrent intraventricular neurocysticercosis: An uncommon presentation

    PubMed Central

    Joshi, Krishna C; Singh, Hukum; Sakhuja, Puja; Singh, Daljit

    2013-01-01

    A rare case of a 42-years old man presented with repeated hydrocephalus due to the neurocysticercosis cyst (NCC) in the lateral ventricle. Patient was operated previously 2½ years back for a similar lesion at same site. Both times he was treated endoscopically with removal of the cyst. Interestingly there was no parenchymatous lesion at any stage of follow up. Isolated recurrent intraventricular NCC is a rare condition that has never been reported in the literature. PMID:23546368

  7. Strategies to Improve Repeat Fecal Occult Blood Testing Cancer Screening

    PubMed Central

    Davis, Terry C.; Arnold, Connie L.; Bennett, Charles L.; Wolf, Michael S.; Reynolds, Cristalyn; Liu, Dachao; Rademaker, Alfred

    2013-01-01

    Background A comparative effectiveness intervention by this team improved initial fecal occult blood testing (FOBT) rates from 3% to 53% among community clinic patients. The purpose of this study was to evaluate the effectiveness and costs associated with a literacy-informed intervention on repeat FOBT testing. Methods Between 2008 and 2011, a three-arm quasi-experiential comparative effectiveness evaluation was conducted in 8 community clinics in Louisiana. Clinics were randomly assigned to receive: enhanced care, a screening recommendation and FOBT kit annually; a brief educational intervention where patients additionally received a literacy appropriate pamphlet and simplified FOBT instructions; or nurse support where a nurse manager provided the education and followed up with phone support. In year 2 all materials were mailed. The study consisted of 461 patients, ages 50–85, with a negative initial FOBT. Results Repeat FOBT rates were 38% enhanced care, 33% education, and 59% with nurse support (p=0.017). After adjusting for age, race, gender, and literacy, patients receiving nurse support were 1.46 times more likely to complete repeat FOBT screening than those receiving education (95% CI 1.14–1.06, p=0.002) and 1.45 times more likely than those in enhanced care but this was not significant (95% CI 0.93–2.26 p=0.10). The incremental cost per additional person screened was $2,450 for nurse over enhanced care. Conclusion A mailed pamphlet and FOBT with simplified instructions did not improve annual screening. Impact Telephone outreach by a nurse manager was effective in improving rates of repeat FOBT yet this may be too costly for community clinics. PMID:24192009

  8. Photodynamic therapy repeated without reinjection of Photofrin (porfimer sodium)

    NASA Astrophysics Data System (ADS)

    McCaughan, James S.

    1998-05-01

    Background and objective: To compare the effectiveness in decreasing the amount of obstruction caused by endobronchial tumors when they are retreated with photodynamic therapy (PDT) several weeks after injection of PhotofrinR (porfimer sodium). Study design, materials and methods: The percentage of endobronchial obstruction from tumors before PDT and at the end of toilet bronchoscopy of 91 sites with PDT performed within 4 days after injection of porfimer sodium was compared to that obtained when PDT was repeated without re-injection of porfimer sodium in the time frames 2 - 4 weeks after injection to 11 sites and the period 4 - 8 weeks after injection to 17 sites. All patients were injected intravenously with 60 mg of PhotofrinR per square meter of body surface and all treatments were done with a power density of 500 mW/CF and a light dose of 400 J/CF delivered from cylinder diffusing fibers. Results: Paired Student's t tests and Wilcoxon signed ranks tests showed significant decreases in the percentage of endobronchial obstruction regardless of whether the PDT was first performed or repeated. Unpaired Student's t tests and Mann-Whitney U statistical comparisons showed a significant difference between the decrease of obstruction when treatment was performed within the first 4 days after injection (mean 41%) as compared to the repeated group 2 to 4 weeks after injection (mean 16%) and the group treated 4 to 8 weeks after injection (mean 19%). However there was no significant difference in the amount of decrease of obstruction between the 2 - 4 week group and the 4 - 8 week group. Conclusions: Photodynamic therapy to relieve endobronchial obstruction can be repeated without reinjection of PhotofrinR up to 8 weeks after injection with a significant decrease in the amount of obstruction. However, it will only be about 1/3 as effective as the initial treatment performed within the first four days of injection.

  9. (Efficient identification and analysis of low and medium frequency repeats)

    SciTech Connect

    Jurka, J.

    1991-08-28

    The effective starting date of this grant was May 15. In the first three months of this project we focused primarily on organizational and technical aspects of our research which included: organization of the database of repeats in primates; preparation of software for rapid and sensitive search of novel repetitive elements in GenBank; purchase and installation of the Sun workstation; and research on the mammal-specific MAR1 family of repetitive elements (to be communicated in October).

  10. Dynamical semigroup for unbounded repeated perturbation of an open system

    NASA Astrophysics Data System (ADS)

    Tamura, Hiroshi; Zagrebnov, Valentin A.

    2016-02-01

    We consider a dynamical semigroup for unbounded Kossakowski-Lindblad-Davies generator corresponding to evolution of an open system for a tuned repeated harmonic perturbation. For this evolution, we prove the existence of uniquely determined minimal trace-preserving strongly continuous dynamical semigroups on the space of states. The corresponding dual W∗-dynamical system is shown to be unital quasi-free and completely positive automorphisms of the canonical commutation relation-algebra.

  11. Dynamics of an Open System for Repeated Harmonic Perturbation

    NASA Astrophysics Data System (ADS)

    Tamura, Hiroshi; Zagrebnov, Valentin A.

    2016-05-01

    We use the Kossakowski-Lindblad-Davies formalism to study an open dynamical system defined as Markovian extension of the one-mode quantum resonator S, perturbed by repeated harmonic interaction with a chain of multi-level harmonic atoms C. The long-time asymptotic behaviour and correlations of various subsystems of the system S + C are treated in the framework of the W^*-dynamical system approach.

  12. Psychological and Physiological Responses following Repeated Peer Death

    PubMed Central

    Andersen, Judith Pizarro; Silver, Roxane Cohen; Stewart, Brandon; Koperwas, Billie; Kirschbaum, Clemens

    2013-01-01

    Objective Undergraduates at a university in the United States were exposed – directly and indirectly – to 14 peer deaths during one academic year. We examined how individual and social factors were associated with psychological (e.g., anxiety, depression, somatization) and physiological (i.e., cortisol) distress responses following this unexpected and repeated experience with loss. Method Two to three months after the final peer death, respondents (N = 122, 61% female, 18–23 years, M = 20.13, SD = 1.14) reported prior adverse experiences, degree of closeness with the deceased, acute responses to the peer deaths, ongoing distress responses, social support, support seeking, and media viewing. A subset (n = 24) returned hair samples for evaluation of cortisol responses during the previous 3 months. Results Ongoing psychological distress was associated with a) prior interpersonal trauma, b) fewer social supports, and c) media exposure to news of the deaths (p's<.05). Participants who had no prior bereavements showed, on average, high cortisol (>25 p/mg) compared to individuals with one or two prior bereavement experiences (who were, on average, within the normal range, 10 to 25 p/mg) (p<.05). Only 8% of the sample utilized available university psychological or physical health resources and support groups. Conclusions Limited research has examined the psychological and physiological impact of exposure to chronic, repeated peer loss, despite the fact that there are groups of individuals (e.g., police, military soldiers) that routinely face such exposures. Prior adversity appears to play a role in shaping psychological and physiological responses to repeated loss. This topic warrants further research given the health implications of repeated loss for individuals in high-risk occupations and university settings. PMID:24086655

  13. Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins.

    PubMed

    Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P; Zhao, Zhendong; Wang, Yejun

    2016-08-01

    Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

  14. Striatal patch compartment lesions reduce stereotypy following repeated cocaine administration.

    PubMed

    Murray, Ryan C; Logan, Mary C; Horner, Kristen A

    2015-08-27

    Stereotypy can be characterized as inflexible, repetitive behaviors that occur following repeated exposure to psychostimulants, such as cocaine (COC). Stereotypy may be related to preferential activation of the patch (striosome) compartment of striatum, as enhanced relative activation of the patch compartment has been shown to positively correlate with the emergence of stereotypy following repeated psychostimulant treatment. However, the specific contribution of the patch compartment to COC-induced stereotypy following repeated exposure is unknown. To elucidate the involvement of the patch compartment to the development of stereotypy following repeated COC exposure, we determined if destruction of this sub-region altered COC-induced behaviors. The neurons of the patch compartment were ablated by bilateral infusion of the neurotoxin dermorphin-saporin (DERM-SAP; 17 ng/μl) into the striatum. Animals were allowed to recover for eight days following the infusion, and then were given daily injections of COC (25mg/kg) or saline for one week, followed by a weeklong drug-free period. Animals were then given a challenge dose of saline or COC, observed for 2h in activity chambers and sacrificed. The number of mu-labeled patches in the striatum were reduced by DERM-SAP pretreatment. In COC-treated animals DERM-SAP pretreatment significantly reduced the immobilization and intensity of stereotypy but increased locomotor activity. DERM-SAP pretreatment attenuated COC-induced c-Fos expression in the patch compartment, while enhancing COC-induced c-Fos expression in the matrix compartment. These data indicate that the patch compartment contributes to repetitive behavior and suggests that alterations in activity in the patch vs matrix compartments may underlie to this phenomenon. PMID:26100338

  15. Feasibility, Accuracy, and Repeatability of Suprathreshold Saccadic Vector Optokinetic Perimetry

    PubMed Central

    Murray, Ian C.; Cameron, Lorraine A.; McTrusty, Alice D.; Perperidis, Antonios; Brash, Harry M.; Fleck, Brian W.; Minns, Robert A.

    2016-01-01

    Purpose To evaluate feasibility, accuracy, and repeatability of suprathreshold Saccadic Vector Optokinetic Perimetry (SVOP) by comparison with Humphrey Field Analyzer (HFA) perimetry. Methods The subjects included children with suspected field defects (n = 10, age 5–15 years), adults with field defects (n = 33, age 39–78 years), healthy children (n = 12, age 6–14 years), and healthy adults (n = 30, age 16–61 years). The test protocol comprised repeat suprathreshold SVOP and HFA testing with the C-40 test pattern. Feasibility was assessed by protocol completeness. Sensitivity, specificity, and accuracy of SVOP was established by comparison with reliable HFA tests in two ways: (1) visual field pattern results (normal/abnormal), and (2) individual test point outcomes (seen/unseen). Repeatability of each test type was assessed using Cohen's kappa coefficient. Results Of subjects, 82% completed a full protocol. Poor reliability of HFA testing in child patients limited the robustness of comparisons in this group. Sensitivity, specificity, and accuracy across all groups when analyzing the visual field pattern results was 90.9%, 88.5%, and 89.0%, respectively, and was 69.1%, 96.9%, and 95.0%, respectively, when analyzing the individual test points. Cohen's kappa coefficient for repeatability of SVOP and HFA was excellent (0.87 and 0.88, respectively) when assessing visual field pattern results, and substantial (0.62 and 0.74, respectively) when assessing test point outcomes. Conclusions SVOP was accurate in this group of adults. Further studies are required to assess SVOP in child patient groups. Translational Relevance SVOP technology is still in its infancy but is used in a number of centers. It will undergo iterative improvements and this study provides a benchmark for future iterations. PMID:27617181

  16. Repeat triage in disaster relief: questions from haiti.

    PubMed

    Eyal, Nir; Firth, Paul

    2012-01-01

    During a mass casualty disaster, the acute imbalance between need for treatment and capacity to supply care poses difficult rationing problems. It is common to assume that such disasters call for "utilitarian" procedures that deliberately prioritize saving the most lives over other considerations. A group of medical responders to the 2010 Haitian earthquake faced particular challenges in determining how to allocate limited treatment, time and other resources between existing patients and potential patients not yet under care. We identified that rationing dilemmas points occurred at three points: when care had to be limited, when care had to be completed prematurely, and when care had to be withdrawn. "Repeat triage" refers to rationing challenges occurring at all these points, where the allocation of care is between existing and potential patients. By contrast, "initial triage" designates the allocation of access to treatment among new arrivals, all of whom are potential patients. Repeat and initial triage differ significantly. Several considerations make repeat triage special by supporting limited priority to existing patients, in transgression of pure "utilitarian" procedures: (1) Pragmatically, often it is more efficient to complete treatment on existing patients, for whom prognosis can be established with greater certainty and without added time, than to attempt to save new patients; (2) A fiduciary trust relationship has been formed between care-giver and existing patients, which may make the moral obligation towards them somewhat stronger than the one to potential patients; (3) Existing patients will have often arrived earlier, so when needs are equal, the "first come, first served" principle prioritizes them for care; (4) Withdrawal of care during repeat triage may constitute active rather than passive harm, and more often a serious transgression of patient autonomy; (5) Health providers should normally not be asked to behave in ways that profoundly violate

  17. Repeat prescribing — a study in one practice

    PubMed Central

    Parker, E. John C.; Schrieber, Victor

    1980-01-01

    A survey of the prescribing habits of a group practice of 10,500 patients was conducted during a three-month period to compare the pattern of repeat prescribing with that practised during consultations. Further analysis into therapeutic groups and categories depending on the length of treatment prescribed was performed. The results obtained were compared with annual prescribing rates and it was found that monthly figures could not be accurately extrapolated. ImagesFigure 1.Figure 2.Figure 3. PMID:6779000

  18. Analysis of Flow Angularity Repeatability Tests in the NTF

    NASA Technical Reports Server (NTRS)

    Hemsch, Michael J.

    2006-01-01

    An extensive data base of flow angularity repeatability measurements from four NTF check standard model tests is analyzed for statistical consistency and to characterize the results for prediction of angle-of-attack uncertainty for customer tests. A procedure for quality assurance for flow angularity measurements during customer tests is also presented. The efficacy of the procedure is tested using results from a customer test.

  19. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants.

    PubMed

    Sharma, Manisha; Pandey, Girdhar K

    2015-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  20. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants

    PubMed Central

    Sharma, Manisha; Pandey, Girdhar K.

    2016-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein–protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  1. The evolutionary origin of insect telomeric repeats, (TTAGG)n.

    PubMed

    Vítková, Magda; Král, Jirí; Traut, Walther; Zrzavý, Jan; Marec, Frantisek

    2005-01-01

    The (TTAGG)n sequence is supposed to be an ancestral DNA motif of telomeres in insects. Here we examined the occurrence of TTAGG telomeric repeats in other arthropods and their close relatives by Southern hybridization of genomic DNAs and fluorescence in-situ hybridization (FISH) of chromosomes with (TTAGG)n probes or, alternatively, with the 'vertebrate' telomeric probe, (TTAGGG)n. Our results show that the (TTAGG)n motif is conserved in entognathous hexapods (Diplura and Collembola), crustaceans (Malacostraca, Branchiura, Pentastomida, and Branchiopoda), myriapods (Diplopoda and Chilopoda), pycnogonids, and most chelicerates (Palpigradi, Amblypygi, Acari, Opiliones, Scorpiones, Pseudoscorpiones, and Solifugae) but not in spiders (Araneae). The presence of TTAGG repeats in these groups suggests that the sequence is an ancestral motif of telomeres not only in insects but in Arthropoda. We failed, however, to detect the TTAGG repeats in close relatives of the arthropods, Tardigrada and Onychophora. But while Onychophora had the 'vertebrate' (TTAGGG)n motif instead, the Tardigrada did not. The (TTAGG)n motif probably evolved from the (TTAGGG)n motif. Based on our and compiled data, we presume that the 'vertebrate' motif (TTAGGG)n is an ancestral motif of telomeres in bilaterian animals and possibly also in the superclade including animals, fungi and amoebozoans. PMID:15861304

  2. CAG repeat expansions in bipolar and unipolar disorders

    SciTech Connect

    Oruc, L.; Verheyen, G.R.; Raeymaekers, P.; Van Broeckhoven, C.

    1997-03-01

    Family, twin, and adoption studies consistently have indicated that the familial aggregation of bipolar (BP) disorder and unipolar recurrent major depression (UPR) is accounted for largely by genetic factors. However, the mode of inheritance is complex. One of the possible explanations could be that a gene with variable penetrance and variable expression is involved. Recently there have been reports on a new class of genetic diseases caused by an abnormal trinucleotide-repeat expansion (TRE). In a number of genetic disorders, these dynamic mutations were proved to be the biological basis for the clinically observed phenomenon of anticipation. DNA consisting of repeated triplets of nucleotides becomes unstable and increases in size over generations within families, giving rise to an increased severity and/or an earlier onset of the disorder. It has been recognized for a long time that anticipation occurs in multiplex families transmitting mental illness. More recent studies also suggest that both BP disorder and UPR show features that are compatible with anticipation. Although the findings of anticipation in BP disorders and in UPR must be interpreted with caution because of the possible presence of numerous ascertainment biases, they support the hypothesis that pathological TREs are implicated in the transmission of these disorders. TRE combined with variable penetrance of expression could explain the complex transmission pattern observed in BP disorder. In view of this, the recent reports of an association between CAG-repeat length and BP disorder in a Belgian, Swedish, and British population are promising. 14 refs., 1 fig., 1 tab.

  3. The role of oxytocin antagonists in repeated implantation -failure.

    PubMed

    Decleer, W; Osmanagaoglu, K; Devroey, P

    2012-01-01

    A prospective cohort study has been performed to find out if the administration of an oxytocin antagonist (Atosiban) at the occasion of embryo transfer has an effect on the pregnancy rate in patients with repeated failure of implantation. A total of 52 women with repeated failure of implantation after IVF/ICSI were included in this study. The ongoing pregnancy rate (OPR) in the total group of patients was 12 out of 52 (23.1%). Based on embryo quality all cases were categorized in two groups. One with good embryo quality (Group A) and one with poor quality embryos (Group B). Of all patients who became pregnant, 11 belonged to the group of 26 patients with good quality embryos (OPR 42.3 %) and only one to the group of 26 patients with poor quality embryos (OPR 3.8 %). Our results indicate that when good quality embryos can be obtained, the use of Atosiban at the occasion of embryo transfer might offer a significant better implantation rate in women with repeated implantation failure after IVF/ICSI. PMID:24753913

  4. Alu repeats as markers for forensic DNA analyses

    SciTech Connect

    Batzer, M.A.; Alegria-Hartman, M.; Kass, D.H.

    1994-01-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 98.9% nucleotide identity with the HS subfamily consensus sequence, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 inch and 3 inch unique flanking DNA sequences from each HS Alu that allow the locus to be assayed for the presence or absence of the Alu repeat. The dimorphic HS Alu sequences probably inserted in the human genome after the radiation of modem humans (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project. HS Alu family member insertions differ from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) in that polymorphisms due to Alu insertions arise as a result of a unique event which has occurred only one time in the human population and spread through the population from that point. Therefore, individuals that share HS Alu repeats inherited these elements from a common ancestor. Most VNTR and RFLP polymorphisms may arise multiple times in parallel within a population.

  5. Predicting repeat DUI offenses with the alcohol interlock recorder.

    PubMed

    Marques, P R; Tippetts, A S; Voas, R B; Beirness, D J

    2001-09-01

    The aim of this report has been to use information contained in the alcohol ignition interlock recorder to determine whether systematic analysis of it can be used to predict which DUI offenders will recidivate during the first 2 years after the interlock is removed. The interlock record was accumulated during a 4-year intervention study in Alberta, Canada. Data from more than 5.5 million breath tests collected during interlock use were analyzed retrospectively after allowing repeat DUI offenses to accumulate for up to 2 years post-interlock. The rate of interlock warns at low BAC (0.02-0.04%) and fails at higher BAC ( > 0.04%) were found to be predictive of later repeat DUI. The interlock record was used along with selected driver record variables and questionnaire data to identify predictor sets. CHAID segmentation analysis was used to identify combinations of predictor variables; these were joined with sensitivity analysis to compare different predictor combinations. Several variables, but primarily more prior DUIs and more interlock warns and fails logged during the first 5 months of interlock usage predict greater than 60% of repeat DUI with a false positive rate of less than 10%. PMID:11491241

  6. Repeatability of nest morphology in African weaver birds.

    PubMed

    Walsh, Patrick T; Hansell, Mike; Borello, Wendy D; Healy, Susan D

    2010-04-23

    It is generally assumed that birds build nests according to a genetic 'template', little influenced by learning or memory. One way to confirm the role of genetics in nest building is to assess the repeatability of nest morphology with repeated nest attempts. Solitary weaver birds, which build multiple nests in a single breeding season, are a useful group with which to do this. Here we show that repeatability of nest morphology was low, but significant, in male Southern Masked weaver birds and not significant in the Village weavers. The larger bodied Village weavers built larger nests than did Southern Masked weavers, but body size did not explain variation in Southern Masked weaver nest dimensions. Nests built by the same male in both species got shorter and lighter as more nests were constructed. While these data demonstrate the potential for a genetic component of variation in nest building in solitary weavers, it is also clear that there remains plenty of scope in both of these species for experience to shape nest construction. PMID:19846449

  7. Highly Repeatable Dissolution Dynamic Nuclear Polarization for Heteronuclear NMR Metabolomics.

    PubMed

    Bornet, Aurélien; Maucourt, Mickaël; Deborde, Catherine; Jacob, Daniel; Milani, Jonas; Vuichoud, Basile; Ji, Xiao; Dumez, Jean-Nicolas; Moing, Annick; Bodenhausen, Geoffrey; Jannin, Sami; Giraudeau, Patrick

    2016-06-21

    At natural (13)C abundance, metabolomics based on heteronuclear NMR is limited by sensitivity. We have recently demonstrated how hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) assisted by cross-polarization (CP) provides a reliable way of enhancing the sensitivity of heteronuclear NMR in dilute mixtures of metabolites. In this Technical Note, we evaluate the precision of this experimental approach, a critical point for applications to metabolomics. The higher the repeatability, the greater the likelihood that one can detect small biologically relevant differences between samples. The average repeatability of our state-of-the-art D-DNP NMR equipment for samples of metabolomic relevance (20 mg dry weight tomato extracts) is 3.6% for signals above the limit of quantification (LOQ) and 6.4% when all the signals above the limit of detection (LOD) are taken into account. This first report on the repeatability of D-DNP highlights the compatibility of the technique with the requirements of metabolomics and confirms its potential as an analytical tool for such applications. PMID:27253320

  8. Biokinetics in repeated-dosing in vitro drug toxicity studies.

    PubMed

    Kramer, Nynke I; Di Consiglio, Emma; Blaauboer, Bas J; Testai, Emanuela

    2015-12-25

    The aim of the EU FP7 Predict-IV project was to improve the predictivity of in vitro assays for unwanted effects of drugs after repeated dosing. The project assessed the added benefit of integrating long-lived in vitro organotypic cell systems with 'omics' technologies and in silico modelling, including systems biology and pharmacokinetic assessments. RPTEC/TERT1 kidney cells, primary rat and human hepatocytes, HepaRG liver cells and 2D and 3D primary brain cultures were dosed daily or every other day for 14 days to a selection of drugs varying in their mechanism of pharmacological action. Since concentration-effect relationships not only depend on the activity of the drug or the sensitivity of the target, but also on the distribution of compounds in the in vitro system, the concentration of a selection of drugs in cells, microtitre plate plastic and medium was measured over time. Results, reviewed in this paper, indicate that lipophilic drugs bind significantly to plastic labware. A few drugs, including less lipophilic drugs, bind to cell-attachment matrices. Chemicals that reach high concentrations in cells, including cyclosporin A and amiodarone, significantly accumulate over time after repeated dosing, partly explaining their increased toxicity after repeated dosing, compared to a single dose. PMID:26362508

  9. Simulation of between Repeat Variability in Real Time PCR Reactions

    PubMed Central

    Lievens, Antoon; Van Aelst, Stefan; Van den Bulcke, Marc; Goetghebeur, Els

    2012-01-01

    While many decisions rely on real time quantitative PCR (qPCR) analysis few attempts have hitherto been made to quantify bounds of precision accounting for the various sources of variation involved in the measurement process. Besides influences of more obvious factors such as camera noise and pipetting variation, changing efficiencies within and between reactions affect PCR results to a degree which is not fully recognized. Here, we develop a statistical framework that models measurement error and other sources of variation as they contribute to fluorescence observations during the amplification process and to derived parameter estimates. Evaluation of reproducibility is then based on simulations capable of generating realistic variation patterns. To this end, we start from a relatively simple statistical model for the evolution of efficiency in a single PCR reaction and introduce additional error components, one at a time, to arrive at stochastic data generation capable of simulating the variation patterns witnessed in repeated reactions (technical repeats). Most of the variation in values was adequately captured by the statistical model in terms of foreseen components. To recreate the dispersion of the repeats' plateau levels while keeping the other aspects of the PCR curves within realistic bounds, additional sources of reagent consumption (side reactions) enter into the model. Once an adequate data generating model is available, simulations can serve to evaluate various aspects of PCR under the assumptions of the model and beyond. PMID:23189123

  10. Synthesis of hybrid bacterial plasmids containing highly repeated satellite DNA.

    PubMed

    Brutlag, D; Fry, K; Nelson, T; Hung, P

    1977-03-01

    Hybrid plasmid molecules containing tandemly repeated Drosophila satellite DNA were constructed using a modification of the (dA)-(dT) homopolymer procedure of Lobban and Kaiser (1973). Recombinant plasmids recovered after transformation of recA bacteria contained 10% of the amount of satellite DNA present in the transforming molecules. The cloned plasmids were not homogenous in size. Recombinant plasmids isolated from a single colony contained populations of circular molecules which varied both in the length of the satellite region and in the poly(dA)-(dt) regions linking satellite and vector. While subcloning reduced the heterogeneity of these plasmid populations, continued cell growth caused further variations in the size of the repeated regions. Two different simple sequence satellites of Drosophila melanogaster (1.672 and 1.705 g/cm3) were unstable in both recA and recBC hosts and in both pSC101 and pCR1 vectors. We propose that this recA-independent instability of tandemly repeated sequences is due to unequal intramolecular recombination events in replicating DNA molecules, a mechanism analogous to sister chromatid exchange in eucaryotes. PMID:403010

  11. Nociceptive Reactions in Rats during Repeated Stress Exposure.

    PubMed

    Kozlov, A Yu; Abramova, A Yu; Chekhlov, V V; Grigorchuk, O S; Pertsov, S S

    2015-10-01

    Changes in nociceptive sensitivity of rats with various behavioral patterns in the open-field test were studied after repeated stress exposure on the model of daily 4-h immobilization for 8 days. The tail-flick latency in response to light-heat stimulation in passive and active specimens decreased most significantly on days 2 and 7, respectively. However, this parameter did not differ from the baseline on day 8 of observations. Vocalization threshold during electrocutaneous stimulation in behaviorally active animals did not change over the first 7 days of repeated stress exposure, but increased significantly on day 8 of the study. The emotional component of nociception in passive animals increased on day 3, but decreased on days 4 and 6 of the experiment. Therefore, repeated stress exposure in rats is mainly accompanied by an increase in the perceptual component of nociception. Variations in the emotional component of nociceptive sensitivity after stress loads are manifested in the initial increase and subsequent decrease in this parameter. The observed changes are more pronounced in behaviorally passive rats than in active animals. These data illustrate the specifics of stress-induced changes in nociception of specimens with various individual and typological characteristics. Our results hold much promise for the development of new individual approaches to modulation of pain sensitivity in humans under conditions of negative emotiogenic exposures. PMID:26519267

  12. Hippocampal ER stress and learning deficits following repeated pyrethroid exposure.

    PubMed

    Hossain, Muhammad M; DiCicco-Bloom, Emanuel; Richardson, Jason R

    2015-01-01

    Endoplasmic reticulum (ER) stress is implicated as a significant contributor to neurodegeneration and cognitive dysfunction. Previously, we reported that the widely used pyrethroid pesticide deltamethrin causes ER stress-mediated apoptosis in SK-N-AS neuroblastoma cells. Whether or not this occurs in vivo remains unknown. Here, we demonstrate that repeated deltamethrin exposure (3 mg/kg every 3 days for 60 days) causes hippocampal ER stress and learning deficits in adult mice. Repeated exposure to deltamethrin caused ER stress in the hippocampus as indicated by increased levels of C/EBP-homologous protein (131%) and glucose-regulated protein 78 (96%). This was accompanied by increased levels of caspase-12 (110%) and activated caspase-3 (50%). To determine whether these effects resulted in learning deficits, hippocampal-dependent learning was evaluated using the Morris water maze. Deltamethrin-treated animals exhibited profound deficits in the acquisition of learning. We also found that deltamethrin exposure resulted in decreased BrdU-positive cells (37%) in the dentate gyrus of the hippocampus, suggesting potential impairment of hippocampal neurogenesis. Collectively, these results demonstrate that repeated deltamethrin exposure leads to ER stress, apoptotic cell death in the hippocampus, and deficits in hippocampal precursor proliferation, which is associated with learning deficits. PMID:25359175

  13. Repeat-containing protein effectors of plant-associated organisms

    PubMed Central

    Mesarich, Carl H.; Bowen, Joanna K.; Hamiaux, Cyril; Templeton, Matthew D.

    2015-01-01

    Many plant-associated organisms, including microbes, nematodes, and insects, deliver effector proteins into the apoplast, vascular tissue, or cell cytoplasm of their prospective hosts. These effectors function to promote colonization, typically by altering host physiology or by modulating host immune responses. The same effectors however, can also trigger host immunity in the presence of cognate host immune receptor proteins, and thus prevent colonization. To circumvent effector-triggered immunity, or to further enhance host colonization, plant-associated organisms often rely on adaptive effector evolution. In recent years, it has become increasingly apparent that several effectors of plant-associated organisms are repeat-containing proteins (RCPs) that carry tandem or non-tandem arrays of an amino acid sequence or structural motif. In this review, we highlight the diverse roles that these repeat domains play in RCP effector function. We also draw attention to the potential role of these repeat domains in adaptive evolution with regards to RCP effector function and the evasion of effector-triggered immunity. The aim of this review is to increase the profile of RCP effectors from plant-associated organisms. PMID:26557126

  14. Repeatability of nest morphology in African weaver birds

    PubMed Central

    Walsh, Patrick T.; Hansell, Mike; Borello, Wendy D.; Healy, Susan D.

    2010-01-01

    It is generally assumed that birds build nests according to a genetic ‘template’, little influenced by learning or memory. One way to confirm the role of genetics in nest building is to assess the repeatability of nest morphology with repeated nest attempts. Solitary weaver birds, which build multiple nests in a single breeding season, are a useful group with which to do this. Here we show that repeatability of nest morphology was low, but significant, in male Southern Masked weaver birds and not significant in the Village weavers. The larger bodied Village weavers built larger nests than did Southern Masked weavers, but body size did not explain variation in Southern Masked weaver nest dimensions. Nests built by the same male in both species got shorter and lighter as more nests were constructed. While these data demonstrate the potential for a genetic component of variation in nest building in solitary weavers, it is also clear that there remains plenty of scope in both of these species for experience to shape nest construction. PMID:19846449

  15. Nanoparticle role on the repeatability of stimuli-responsive nanocomposites

    PubMed Central

    Ahn, Sungsook; Lee, Sang Joon

    2014-01-01

    Repeatability of the responsiveness with time is one important concern for effective durable functions of stimuli-responsive materials. Although the increase in the yield and tensile strength of the hybrid composite materials by nanoparticle (NP) incorporation has been reported, exact NP effect on stimuli-responsiveness is rarely reported. In this study, a set of nanoscale actuating system is demonstrated by a thermo-sensitive process operated by polyethylene glycol (PEG) linked by gold nanoparticle (AuNP). This designed nanocomposite exclusively provides an artificial on/off gate function for selective passages of permeate molecules. The results demonstrate high repetition efficiency with sharp responding in a timely manner. In terms of the morphology changes induced by repeated swelling-deswelling mechanics, the nanocomposite exhibits phase separation between AuNP clusters and PEG domains. This leads to a delay in responsiveness in a cumulative way with time. Acting as stable junction points in the nanocomposite network structures, the incorporated AuNPs contribute to maintain repeatability in responsiveness. This study contributes to new-concept smart material design and fundamental understanding on the hybrid nanomaterials for various applications in terms of a dynamic mechanical behavior. PMID:25315841

  16. Phenotypic Characterization of Individuals with 30–40 CAG Repeats in the Huntington Disease (HD) Gene Reveals HD Cases with 36 Repeats and Apparently Normal Elderly Individuals with 36–39 Repeats

    PubMed Central

    Rubinsztein, David C.; Leggo, Jayne; Coles, Rhian; Almqvist, Elisabeth; Biancalana, Valerie; Cassiman, Jean-Jacques; Chotai, Kokila; Connarty, Margaret; Craufurd, David; Curtis, Anne; Curtis, Diana; Davidson, Mark J.; Differ, Anne-Marie; Dode, Catherine; Dodge, Alan; Frontali, Marina; Ranen, Neal G.; Stine, O. Colin; Sherr, Meeia; Abbott, Margaret H.; Franz, Mary L.; Graham, Colin A.; Harper, Peter S.; Hedreen, John C.; Jackson, Anthony; Kaplan, Jean-Claude; Losekoot, Monique; MacMillan, John C.; Morrison, Patrick; Trottier, Yvon; Novelletto, Andrea; Simpson, Sheila A.; Theilmann, Jane; Whittaker, Joanne L.; Folstein, Susan E.; Ross, Christopher A.; Hayden, Michael R.

    1996-01-01

    Abnormal CAG expansions in the IT-15 gene are associated with Huntington disease (HD). In the diagnostic setting it is necessary to define the limits of the CAG size ranges on normal and HD-associated chromosomes. Most large analyses that defined the limits of the normal and pathological size ranges employed PCR assays, which included the CAG repeats and a CCG repeat tract that was thought to be invariant. Many of these experiments found an overlap between the normal and disease size ranges. Subsequent findings that the CCG repeats vary by 8 trinucleotide lengths suggested that the limits of the normal and disease size ranges should be reevaluated with assays that exclude the CCG polymorphism. Since patients with between 30 and 40 repeats are rare, a consortium was assembled to collect such individuals. All 178 samples were reanalyzed in Cambridge by using assays specific for the CAG repeats. We have optimized methods for reliable sizing of CAG repeats and show cases that demonstrate the dangers of using PCR assays that include both the CAG and CCG polymorphisms. Seven HD patients had 36 repeats, which confirms that this allele is associated with disease. Individuals without apparent symptoms or signs of HD were found at 36 repeats (aged 74, 78, 79, and 87 years), 37 repeats (aged 69 years), 38 repeats (aged 69 and 90 years), and 39 repeats (aged 67, 90, and 95 years). The detailed case histories of an exceptional case from this series will be presented: a 95-year-old man with 39 repeats who did not have classical features of HD. The apparently healthy survival into old age of some individuals with 36–39 repeats suggests that the HD mutation may not always be fully penetrant. ImagesFigure 1Figure 2 PMID:8659522

  17. Spatial and waveform relationships of repeating and anti-repeating earthquake clusters at intermediate-depths in the Bucaramanga nest, Colombia

    NASA Astrophysics Data System (ADS)

    Barrett, S. A.; Prieto, G.; Beroza, G. C.

    2012-12-01

    The Bucaramanga Nest beneath Northern Colombia is the densest concentration of intermediate depth seismicity in the world. It includes large groups of repeating earthquakes, as well as anti-repeating (or repeating with reverse polarity) earthquakes. We seek to understand the spatial relationship of these repeating and anti-repeating events with respect to each other as well as with respect to the surrounding seismicity. We accomplish this first through precise relocations of events in the Colombian national catalog (RSNC) using double-difference relocation. Preliminary results using only catalog times indicate that repeating and anti-repeating earthquakes occur in the core of the nest among a cloud of non-correlating seismicity. Further improvements on initial relocations will be made using cross-correlation measurements. Once we have precise locations, we will use a combination of waveform similarity and possibly moment tensor inversion to develop a mechanical model for the occurrence of these events.

  18. SMRT Sequencing of Long Tandem Nucleotide Repeats in SCA10 Reveals Unique Insight of Repeat Expansion Structure

    PubMed Central

    Landrian, Ivette; Godiska, Ronald; Shanker, Savita; Yu, Fahong; Farmerie, William G.; Ashizawa, Tetsuo

    2015-01-01

    A large, non-coding ATTCT repeat expansion causes the neurodegenerative disorder, spinocerebellar ataxia type 10 (SCA10). In a subset of SCA10 patients, interruption motifs are present at the 5’ end of the expansion and strongly correlate with epileptic seizures. Thus, interruption motifs are a predictor of the epileptic phenotype and are hypothesized to act as a phenotypic modifier in SCA10. Yet, the exact internal sequence structure of SCA10 expansions remains unknown due to limitations in current technologies for sequencing across long extended tracts of tandem nucleotide repeats. We used the third generation sequencing technology, Single Molecule Real Time (SMRT) sequencing, to obtain full-length contiguous expansion sequences, ranging from 2.5 to 4.4 kb in length, from three SCA10 patients with different clinical presentations. We obtained sequence spanning the entire length of the expansion and identified the structure of known and novel interruption motifs within the SCA10 expansion. The exact interruption patterns in expanded SCA10 alleles will allow us to further investigate the potential contributions of these interrupting sequences to the pathogenic modification leading to the epilepsy phenotype in SCA10. Our results also demonstrate that SMRT sequencing is useful for deciphering long tandem repeats that pose as “gaps” in the human genome sequence. PMID:26295943

  19. DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica.

    PubMed

    Wang, Rui; Li, Ming; Gong, Luyao; Hu, Songnian; Xiang, Hua

    2016-05-19

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) acquire new spacers to generate adaptive immunity in prokaryotes. During spacer integration, the leader-preceded repeat is always accurately duplicated, leading to speculations of a repeat-length ruler. Here in Haloarcula hispanica, we demonstrate that the accurate duplication of its 30-bp repeat requires two conserved mid-repeat motifs, AACCC and GTGGG. The AACCC motif was essential and needed to be ∼10 bp downstream from the leader-repeat junction site, where duplication consistently started. Interestingly, repeat duplication terminated sequence-independently and usually with a specific distance from the GTGGG motif, which seemingly served as an anchor site for a molecular ruler. Accordingly, altering the spacing between the two motifs led to an aberrant duplication size (29, 31, 32 or 33 bp). We propose the adaptation complex may recognize these mid-repeat elements to enable measuring the repeat DNA for spacer integration. PMID:27085805

  20. DNA motifs determining the accuracy of repeat duplication during CRISPR adaptation in Haloarcula hispanica

    PubMed Central

    Wang, Rui; Li, Ming; Gong, Luyao; Hu, Songnian; Xiang, Hua

    2016-01-01

    Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) acquire new spacers to generate adaptive immunity in prokaryotes. During spacer integration, the leader-preceded repeat is always accurately duplicated, leading to speculations of a repeat-length ruler. Here in Haloarcula hispanica, we demonstrate that the accurate duplication of its 30-bp repeat requires two conserved mid-repeat motifs, AACCC and GTGGG. The AACCC motif was essential and needed to be ∼10 bp downstream from the leader-repeat junction site, where duplication consistently started. Interestingly, repeat duplication terminated sequence-independently and usually with a specific distance from the GTGGG motif, which seemingly served as an anchor site for a molecular ruler. Accordingly, altering the spacing between the two motifs led to an aberrant duplication size (29, 31, 32 or 33 bp). We propose the adaptation complex may recognize these mid-repeat elements to enable measuring the repeat DNA for spacer integration. PMID:27085805

  1. GFP-Based Fluorescence Assay for CAG Repeat Instability in Cultured Human Cells

    PubMed Central

    Santillan, Beatriz A.; Moye, Christopher; Mittelman, David; Wilson, John H.

    2014-01-01

    Trinucleotide repeats can be highly unstable, mutating far more frequently than point mutations. Repeats typically mutate by addition or loss of units of the repeat. CAG repeat expansions in humans trigger neurological diseases that include myotonic dystrophy, Huntington disease, and several spinocerebellar ataxias. In human cells, diverse mechanisms promote CAG repeat instability, and in mice, the mechanisms of instability are varied and tissue-dependent. Dissection of mechanistic complexity and discovery of potential therapeutics necessitates quantitative and scalable screens for repeat mutation. We describe a GFP-based assay for screening modifiers of CAG repeat instability in human cells. The assay exploits an engineered intronic CAG repeat tract that interferes with expression of an inducible GFP minigene. Like the phenotypes of many trinucleotide repeat disorders, we find that GFP function is impaired by repeat expansion, in a length-dependent manner. The intensity of fluorescence varies inversely with repeat length, allowing estimates of repeat tract changes in live cells. We validate the assay using transcription through the repeat and engineered CAG-specific nucleases, which have previously been reported to induce CAG repeat instability. The assay is relatively fast and should be adaptable to large-scale screens of chemical and shRNA libraries. PMID:25423602

  2. Hyperventilation as a strategy for improved repeated sprint performance.

    PubMed

    Sakamoto, Akihiro; Naito, Hisashi; Chow, Chin-Moi

    2014-04-01

    Repeated high-intensity sprints incur substantial anaerobic metabolic challenges and create an acidic muscle milieu that is unfavorable for subsequent performance. Hyperventilation, resulting in respiratory alkalosis, acts as a compensatory mechanism for metabolic acidosis. This study tested the hypothesis that hyperventilation performed during recovery intervals would attenuate performance decrement in repeated sprint pedaling. Thirteen male university athletes performed 10 sets of 10-second maximal pedaling on a cycle ergometer with a 60-second recovery between sets under control (spontaneous breathing) and hyperventilation conditions in a crossover counter-balanced manner. Pedaling load was set at 0.075 × body mass. Peak and mean power outputs were documented for each set to compare performance decrements for 10 sets between conditions. Hyperventilation (60 breaths per minute and end-tidal partial pressure of CO2 maintained at 20-25 mm Hg) was performed 30 seconds before each sprint set. This intervention successfully increased blood pH by 0.03-0.07 but lowered P(CO2) by 1.2-8.4 mm Hg throughout exercise (p < 0.001). The peak and mean power outputs, and blood [La] accumulation were not significantly different between the conditions. However, a significant condition × time interaction existed for peak power (p = 0.035) and mean power (p = 0.023), demonstrating an attenuation in power decrement in later sprint sets with hyperventilation. In conclusion, hyperventilation implemented during recovery intervals of repeated sprint pedaling attenuated performance decrements in later exercise bouts that was associated with substantial metabolic acidosis. The practical implication is that hyperventilation may have a strategic role for enhancing training effectiveness and may give an edge in performance outcomes. PMID:23838981

  3. TRStalker: an efficient heuristic for finding fuzzy tandem repeats

    PubMed Central

    Pellegrini, Marco; Renda, M. Elena; Vecchio, Alessio

    2010-01-01

    Motivation: Genomes in higher eukaryotic organisms contain a substantial amount of repeated sequences. Tandem Repeats (TRs) constitute a large class of repetitive sequences that are originated via phenomena such as replication slippage and are characterized by close spatial contiguity. They play an important role in several molecular regulatory mechanisms, and also in several diseases (e.g. in the group of trinucleotide repeat disorders). While for TRs with a low or medium level of divergence the current methods are rather effective, the problem of detecting TRs with higher divergence (fuzzy TRs) is still open. The detection of fuzzy TRs is propaedeutic to enriching our view of their role in regulatory mechanisms and diseases. Fuzzy TRs are also important as tools to shed light on the evolutionary history of the genome, where higher divergence correlates with more remote duplication events. Results: We have developed an algorithm (christened TRStalker) with the aim of detecting efficiently TRs that are hard to detect because of their inherent fuzziness, due to high levels of base substitutions, insertions and deletions. To attain this goal, we developed heuristics to solve a Steiner version of the problem for which the fuzziness is measured with respect to a motif string not necessarily present in the input string. This problem is akin to the ‘generalized median string’ that is known to be an NP-hard problem. Experiments with both synthetic and biological sequences demonstrate that our method performs better than current state of the art for fuzzy TRs and that the fuzzy TRs of the type we detect are indeed present in important biological sequences. Availability: TRStalker will be integrated in the web-based TRs Discovery Service (TReaDS) at bioalgo.iit.cnr.it. Contact: marco.pellegrini@iit.cnr.it Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20529928

  4. Neck-cooling improves repeated sprint performance in the heat

    PubMed Central

    Sunderland, Caroline; Stevens, Ryan; Everson, Bethan; Tyler, Christopher J.

    2015-01-01

    The present study evaluated the effect of neck-cooling during exercise on repeated sprint ability in a hot environment. Seven team-sport playing males completed two experimental trials involving repeated sprint exercise (5 × 6 s) before and after two 45 min bouts of a football specific intermittent treadmill protocol in the heat (33.0 ± 0.2°C; 53 ± 2% relative humidity). Participants wore a neck-cooling collar in one of the trials (CC). Mean power output and peak power output declined over time in both trials but were higher in CC (540 ± 99 v 507 ± 122 W, d = 0.32; 719 ± 158 v 680 ± 182 W, d = 0.24 respectively). The improved power output was particularly pronounced (d = 0.51–0.88) after the 2nd 45 min bout but the CC had no effect on % fatigue. The collar lowered neck temperature and the thermal sensation of the neck (P < 0.001) but had no effect on heart rate, fluid loss, fluid consumption, lactate, glucose, plasma volume change, cortisol, or thermal sensation (P > 0.05). There were no trial differences but interaction effects were demonstrated for prolactin concentration and rating of perceived exertion (RPE). Prolactin concentration was initially higher in the collar cold trial and then was lower from 45 min onwards (interaction trial × time P = 0.04). RPE was lower during the football intermittent treadmill protocol in the collar cold trial (interaction trial × time P = 0.01). Neck-cooling during exercise improves repeated sprint performance in a hot environment without altering physiological or neuroendocrinological responses. RPE is reduced and may partially explain the performance improvement. PMID:26594177

  5. IMHEX fuel cell repeat component manufacturing continuous improvement accomplishments

    SciTech Connect

    Jakaitis, L.A.; Petraglia, V.J.; Bryson, E.S.

    1996-12-31

    M-C Power is taking a power generation technology that has been proven in the laboratory and is making it a commercially competitive product. There are many areas in which this technology required scale up and refinement to reach the market entry goals for the IMHEX{reg_sign} molten carbonate fuel cell power plant. One of the primary areas that needed to be addressed was the manufacturing of the fuel cell stack. Up to this point, the fuel cell stack and associated components were virtually hand made for each system to be tested. M-C Power has now continuously manufactured the repeat components for three 250 kW stacks. M-C Power`s manufacturing strategy integrated both evolutionary and revolutionary improvements into its comprehensive commercialization effort. M-C Power`s objectives were to analyze and continuously improve stack component manufacturing and assembly techniques consistent with established specifications and commercial scale production requirements. Evolutionary improvements are those which naturally occur as the production rates are increased and experience is gained. Examples of evolutionary (learning curve) improvements included reducing scrap rates and decreasing raw material costs by buying in large quantities. Revolutionary improvements result in significant design and process changes to meet cost and performance requirements of the market entry system. Revolutionary changes often involve identifying new methods and developing designs to accommodate the new process. Based upon our accomplishments, M-C Power was able to reduce the cost of continuously manufactured fuel cell repeat components from the first to third 250 kW stack by 63%. This paper documents the continuous improvement accomplishments realized by M-C Power during IMHEX{reg_sign} fuel cell repeat component manufacturing.

  6. Repeating Earthquakes on the Queen Charlotte Plate Boundary

    NASA Astrophysics Data System (ADS)

    Hayward, T. W.; Bostock, M. G.

    2015-12-01

    The Queen Charlotte Fault (QCF) is a major plate boundary located off the northwest coast of North America that has produced large earthquakes in 1949 (M8.1) and more recently in October, 2012 (M7.8). The 2012 event was dominated by thrusting despite the fact that plate motions at the boundary are nearly transcurrent. It is now widely believed that the plate boundary comprises the QCF (i.e., a dextral strike-slip fault) as well as an element of subduction of the Pacific Plate beneath the North American Plate. Repeating earthquakes and seismic tremor have been observed in the vicinity of the QCF; providing insight into the spatial and temporal characteristics of repeating earthquakes is the goal of this research. Due to poor station coverage and data quality, traditional methods of locating earthquakes are not applicable to these events. Instead, we have implemented an algorithm to locate local (i.e., < 100 km distance to epicenter) earthquakes using a single, three-component seismogram. This algorithm relies on the P-wave polarization and, through comparison with larger local events in the Geological Survey of Canada catalogue, is shown to yield epicentral locations accurate to within 5-10 km. A total of 24 unique families of repeating earthquakes has been identified, and 4 of these families have been located with high confidence. Their epicenters locate directly on the trace of the QCF and their depths are shallow (i.e., 5-15 km), consistent with the proposed depth of the QCF. Analysis of temporal recurrence leading up to the 2012 M7.8 event reveals a non-random pattern, with an approximately 15 day periodicity. Further analysis is planned to study whether this behaviour persists after the 2012 event and to gain insight into the effects of the 2012 event on the stress field and frictional properties of the plate boundary.

  7. Alu repeats as markers for human population genetics

    SciTech Connect

    Batzer, M.A.; Alegria-Hartman, M.; Bazan, H.

    1993-09-01

    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  8. Repeating sources of classical gamma-ray bursts

    NASA Technical Reports Server (NTRS)

    Wang, V. C.; Lingenfelter, R. E.

    1995-01-01

    From an analysis of the first catalog of the Burst and Transient Source Experiment (BATSE) experiment (Fishman et al. 1993, 1994a) on the Compton Gamma Ray Observatory (CGRO), we find an excessive number of pairs of gamma-ray bursts which are clustered in both a space and time . The angular separation between the two bursts in each pair is less than their positional uncertainties, and the interval between their occurrence times is within several days. Optimizing the signal, we find that the probability of observing such a clustered excess froma Poisson ensemble is approximately 2 x 10(exp -5). We suggest that these bursts arise from repeating sources. A detailed study of the most prolific source, GBS 0855-00, is presented in a separate paper (Wang & Lingenfelter 1993a, b). Unlike most of the 'soft' gamma-ray repeaters, these repeating bursts have relatively hard spectra, complex light curves, and widely varying durations, that are indistinguishable from classical gamma-ray bursts. Although the significance of the clustered excess was optimized a posteriori, because it depends on temporal and spatial bin sized that could not be defined a priori, we can use the optimizations from the first catalog to test subsequent BATSE data sets. Unfortunately, the failure of the on-board tape recorders during the second catalog period seriously reduced the number of accurately positioned bursts (Fishman et al. 1994b), so that we can neither confirm, nor refute, the predicted repitition in that sample, and we must await the results of the third catalog.

  9. Oligomerization of the hydrophobic heptad repeat of gp41.

    PubMed Central

    Bernstein, H B; Tucker, S P; Kar, S R; McPherson, S A; McPherson, D T; Dubay, J W; Lebowitz, J; Compans, R W; Hunter, E

    1995-01-01

    The transmembrane protein of human immunodeficiency virus type 1 (HIV-1) contains a leucine zipper-like (hydrophobic heptad) repeat which has been predicted to form an amphipathic alpha helix. To evaluate the potential of the hydrophobic heptad repeat to induce protein oligomerization, this region of gp41 has been cloned into the bacterial expression vector pRIT2T. The resulting plasmid, pRIT3, expresses a fusion protein consisting of the Fc binding domain of monomeric protein A, a bacterial protein, and amino acids 538 to 593 of HIV-1 gp41. Gel filtration chromatography demonstrated the presence of oligomeric forms of the fusion protein, and analytical centrifugation studies confirmed that the chimeric protein formed a higher-order multimer that was greater than a dimer. Thus, we have identified a region of HIV-1 gp41 which is capable of directing the oligomerization of a fusion protein containing monomeric protein A. Point mutations, previously shown to inhibit the biological activity of the HIV-1 envelope glycoprotein, have been engineered into the segment of gp41 contained in the fusion protein, and expressed mutant proteins were purified and analyzed via fast protein liquid chromatography. A point mutation in the heptad repeat, which changed the central isoleucine to an alanine, caused a significant (> 60%) decrease in oligomerization, whereas changing the central isoleucine to aspartate or proline resulted in almost a complete loss of oligomerization. Deletions of one, two, or three amino acids following the first isoleucine also resulted in a profound decrease in oligomerization. The inhibitory effects of the mutations on oligomer formation correlated with the effects of the same mutations on envelope glycoprotein-mediated fusion. A possible role of the leucine zipper-like region in the fusion process and in an oligomerization event distinct from assembly of the envelope glycoprotein complex is discussed. PMID:7707497

  10. Assessments of recent tundra change based on repeated vegetation surveys

    NASA Astrophysics Data System (ADS)

    Elmendorf, S.; Henry, G.; Thetundra Vegetation Change Group

    2010-12-01

    Results from experimental warming studies suggest tundra vegetation will respond rapidly and dramatically to climate warming, and indeed, NDVI data from remote sensing and repeat aerial photography suggest such changes may already be occurring. NDVI changes, however, may reflect responses to a variety of processes. Repeat measurements of permanently marked plots offer an invaluable opportunity to monitor detailed changes in vegetation composition and abundance. Here, we report results from a synthesis of repeat measurements of 195 permanent plots in Arctic and alpine tundra plant communities in North America (90 plots), Europe (82 plots), Asia (10 plots), Australia (12 plots), and Antarctica (1 plot) that were revisited at least twice between 1980 and 2010, with an average timespan of 13 years between first and last sampling periods. Annual air-temperature warming over the sampling period varied considerably among sites, ranging from slight cooling to increases of nearly 2°C per decade. In our preliminary analyses, we found significant tundra-wide increases in vegetation height as well as abundance of evergreen shrubs and graminoids, but declines in mosses. We anticipated that changes in vegetation height, abundance of deciduous shrubs, and percent of vegetated ground would be highest in areas where climate warming is occurring most rapidly, but found no support for these predictions in our observational dataset. It is possible that local vegetation dynamics in these areas are affected more by other longer-term non-equilibrium processes such as recovery from glaciation, or an alternative suite of local drivers, such as snow cover, precipitation, disturbance or herbivory.

  11. Use of passive repeaters for tunnel surface communications

    SciTech Connect

    Capista, D.; McDowell, D.

    1996-04-01

    Many times there is a need to establish ratio communication between the surface and a beam enclosure. When one solicits communication companies for solutions, the answer is often to purchase expensive communication equipment such as repeaters or radiax type cable which can cost in the tens of thousands of dollars. This TM will describe an inexpensive solution to this problem and the results that can be expected. The cost of a passive repeater is $100--$200 depending on how elaborate one wants to be. A passive repeater system consists of two antennas connected together with a transmission line. When using VHF or UHF transceivers, one can use 5/8 wave mobile antennas, such as the Larson NMO406-CK for the 400--420 MHz range, with the antenna connected to a 19 inch square piece of aluminum to act as a ground plane. This type of antenna has reasonably good gain, seems to be adequate, and is inexpensive. Another antenna choice is to cut a dipole out of bus wire and solder this wire to a female N connector. Using a dipole seems to work OK in the tunnel and avoids the problem of having a wire sticking down for people to poke their eye with. The cable connecting the antennas should be of good quality so that the signal lost in the cable is minimal. The authors chose Belden 9913 coax. This cable has a characteristic impedance of 50 ohms and has 2.7 dB/100 ft. of attenuation at 400 MHz.

  12. Accuracy and Repeatability of Refractive Error Measurements by Photorefractometry

    PubMed Central

    Rajavi, Zhale; Sabbaghi, Hamideh; Baghini, Ahmad Shojaei; Yaseri, Mehdi; Sheibani, Koroush; Norouzi, Ghazal

    2015-01-01

    Purpose: To determine the accuracy of photorefraction and autorefraction as compared to cycloautorefraction and to detect the repeatability of photorefraction. Methods: This diagnostic study included the right eyes of 86 children aged 7-12 years. Refractive status was measured using photorefraction (PlusoptiX SO4, GmbH, Nürnberg, Germany) and autorefraction (Topcon RM800, USA) with and without cycloplegia. Photorefraction for each eye was performed three times to assess repeatability. Results: The overall agreement between photorefraction and cycloautorefraction was over 81% for all refractive errors. Photorefractometry had acceptable sensitivity and specificity for myopia and astigmatism. There was no statistically significant difference considering myopia and astigmatism in all comparisons, while the difference was significant for hyperopia using both amblyogenic (P = 0.006) and nonamblyogenic criteria (P = 0.001). A myopic shift of 1.21 diopter (D) and 1.58 D occurred with photorefraction in nonamblyogenic and amblyogenic hyperopia, respectively. Using revised cut-off points of + 1.12 D and + 2.6 D instead of + 2.00 D and + 3.50 D improved the sensitivity of photorefractometry to 84.62% and 69.23%, respectively. The repeatability of photorefraction for measurement of myopia, astigmatism and hyperopia was acceptable (intra-cluster correlation [ICC]: 0.98, 0.94 and 0.77, respectively). Autorefraction results were significantly different from cycloautorefraction in hyperopia (P < 0.0001), but comparable in myopia and astigmatism. Also, noncycloglegic autorefraction results were similar to photorefraction in this study. Conclusion: Although photorefraction was accurate for measurement of myopia and astigmatism, its sensitivity for hyperopia was low which could be improved by considering revised cut-off points. Considering cut-off points, photorefraction can be used as a screening method. PMID:26730305

  13. Neck-cooling improves repeated sprint performance in the heat.

    PubMed

    Sunderland, Caroline; Stevens, Ryan; Everson, Bethan; Tyler, Christopher J

    2015-01-01

    The present study evaluated the effect of neck-cooling during exercise on repeated sprint ability in a hot environment. Seven team-sport playing males completed two experimental trials involving repeated sprint exercise (5 × 6 s) before and after two 45 min bouts of a football specific intermittent treadmill protocol in the heat (33.0 ± 0.2°C; 53 ± 2% relative humidity). Participants wore a neck-cooling collar in one of the trials (CC). Mean power output and peak power output declined over time in both trials but were higher in CC (540 ± 99 v 507 ± 122 W, d = 0.32; 719 ± 158 v 680 ± 182 W, d = 0.24 respectively). The improved power output was particularly pronounced (d = 0.51-0.88) after the 2nd 45 min bout but the CC had no effect on % fatigue. The collar lowered neck temperature and the thermal sensation of the neck (P < 0.001) but had no effect on heart rate, fluid loss, fluid consumption, lactate, glucose, plasma volume change, cortisol, or thermal sensation (P > 0.05). There were no trial differences but interaction effects were demonstrated for prolactin concentration and rating of perceived exertion (RPE). Prolactin concentration was initially higher in the collar cold trial and then was lower from 45 min onwards (interaction trial × time P = 0.04). RPE was lower during the football intermittent treadmill protocol in the collar cold trial (interaction trial × time P = 0.01). Neck-cooling during exercise improves repeated sprint performance in a hot environment without altering physiological or neuroendocrinological responses. RPE is reduced and may partially explain the performance improvement. PMID:26594177

  14. A quick telemanipulator calibration and repeatability method with applications

    SciTech Connect

    Jansen, J.F.; Haley, D.C.

    1994-09-01

    This paper will present a methodology that was used to calibrate and measure the repeatability of two telemanipulators at Oak Ridge National Laboratory. The global accuracy of the method was 0.05 in. ({approx_equal} 1.3 mm), and the orientation accuracy was approximately 6 min ({approx_equal} 0.002 rads). For most teleoperator systems, these accuracies are more than adequate because of the construction of the mechanism and sensor capabilities (e.g., typically 12 bits of resolution). Although industrial robots require accuracies of about 0.05 mm or better, telemanipulators do not.

  15. Repeatability and Precision of Laser Diffraction Measurements of Small Objects

    NASA Astrophysics Data System (ADS)

    Dudley, Scott C.; Mudry, R.

    2006-12-01

    In this poster we’ll present results of using diffraction measurements to infer the size of small objects such as the diameter of a human hair. We’ll compare the diffraction results with visual measurements through a microscope, and we’ll discuss repeatability of the diffraction measurements across semesters, which can enable the use of hair samples as an unknown in a diffraction laboratory. Finally, we’ll show that there are large variations in the diameter of human hair even from a single spot of an individual’s head.

  16. Repeated observation of an uncertain signal. [sensory adaptation

    NASA Technical Reports Server (NTRS)

    Swets, J. A.; Birdsall, T. G.

    1978-01-01

    The focus here is on sensory adaptation, or progressively more appropriate attention, as repeated observations yield more information about a signal with an uncertain parameter. The signal was a brief sinusoid; its uncertain parameter was frequency. Detection performance is predicted from data on a signal of known and constant frequency, as a function of the number of frequencies the uncertain signal could assume. A comparison condition presented a signal that varied in a manner not permitting adaptation. Models derived from signal detection theory describe the ideal observation processes for the three signal conditions, and supply quantitative predictions of relative performances. The models are generally supported by the data.

  17. Preservice science teachers' experiences with repeated, guided inquiry

    NASA Astrophysics Data System (ADS)

    Slack, Amy B.

    The purpose of this study was to examine preservice science teachers' experiences with repeated scientific inquiry (SI) activities. The National Science Education Standards (National Research Council, 1996) stress students should understand and possess the abilities to do SI. For students to meet these standards, science teachers must understand and be able to perform SI; however, previous research demonstrated that many teachers have naive understandings in this area. Teacher preparation programs provide an opportunity to facilitate the development of inquiry understandings and abilities. In this study, preservice science teachers had experiences with two inquiry activities that were repeated three times each. The research questions for this study were (a) How do preservice science teachers' describe their experiences with repeated, guided inquiry activities? (b) What are preservice science teachers' understandings and abilities of SI? This study was conducted at a large, urban university in the southeastern United States. The 5 participants had bachelor's degrees in science and were enrolled in a graduate science education methods course. The researcher was one of the course instructors but did not lead the activities. Case study methodology was used. Data was collected from a demographic survey, an open-ended questionnaire with follow-up interviews, the researcher's observations, participants' lab notes, personal interviews, and participants' journals. Data were coded and analyzed through chronological data matrices to identify patterns in participants' experiences. The five domains identified in this study were understandings of SI, abilities to conduct SI, personal feelings about the experience, science content knowledge, and classroom implications. Through analysis of themes identified within each domain, the four conclusions made about these preservice teachers' experiences with SI were that the experience increased their abilities to conduct inquiry

  18. UAVSAR: Airborne L-band Radar for Repeat Pass Interferometry

    NASA Technical Reports Server (NTRS)

    Moes, Timothy R.

    2009-01-01

    The primary objectives of the UAVSAR Project were to: a) develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for use on an unmanned aerial vehicle (UAV) or piloted vehicle. b) develop the associated processing algorithms for repeat-pass differential interferometric measurements using a single antenna. c) conduct measurements of geophysical interest, particularly changes of rapidly deforming surfaces such as volcanoes or earthquakes. Two complete systems were developed. Operational Science Missions began on February 18, 2009 ... concurrent development and testing of the radar system continues.

  19. Design and performance of a repeater for optical satellite communication

    NASA Astrophysics Data System (ADS)

    Ohm, G.; Wiesmann, Th.; Hieber, E.

    General design aspects of optical inter-satellite and inter-orbit links and the choice of technology for data relay applications are described. A first step toward optical links is the ESA in-orbit experiment SILEX which is briefly reviewed with emphasis on the communication subsystem. All relevant equipments of the communication subsystem, which is based on 0.85-micron laser diodes, QPPM data format, and direct detection, have been developed and tested. Using the equipment developed, an experimental repeater was assembled and investigated. Measured and simulated results are in close agreement, and no major critical events occurred during the development and test activities.

  20. Data-adaptive algorithms for calling alleles in repeat polymorphisms.

    PubMed

    Stoughton, R; Bumgarner, R; Frederick, W J; McIndoe, R A

    1997-01-01

    Data-adaptive algorithms are presented for separating overlapping signatures of heterozygotic allele pairs in electrophoresis data. Application is demonstrated for human microsatellite CA-repeat polymorphisms in LiCor 4000 and ABI 373 data. The algorithms allow overlapping alleles to be called correctly in almost every case where a trained observer could do so, and provide a fast automated objective alternative to human reading of the gels. The algorithm also supplies an indication of confidence level which can be used to flag marginal cases for verification by eye, or as input to later stages of statistical analysis. PMID:9059812

  1. Spiculated Bladder Calculi: The Culprit for Repeated Catheter Failure

    PubMed Central

    Wek, C.; Fox, T. P.; Muir, G. H.

    2013-01-01

    We report on the case of a frustrated 90-year-old gentleman who was seen in the Accident and Emergency department for the third time in four days with failure of his long-term urethral catheter. He reported that the catheter simply “fell out” with the balloon deflated. On each occasion previously, the catheter had been reinserted in A&E and the patient discharged home. These repeated visits to A&E were understandably a source of much frustration for the patient and his family. On the third presentation, plain abdominal radiography demonstrated a large spiculated bladder calculus. PMID:23984173

  2. Repeater in the sky. [public service communications satellite program

    NASA Technical Reports Server (NTRS)

    Cote, C. E.; Brown, J. P.

    1977-01-01

    The Public Service Communications Satellite (PSCS) program is intended to develop and demonstrate a space system aimed at stimulating future commercial markets in fixed and mobile applications. The services are envisioned for rural areas, regions beyond access to terrestrial systems, or for continuous cross-country applications. The system incorporates a UHF repeater for mobile voice and data experiments; 8 MHz of spectrum is specified for serving 70 channels. This paper describes the PSCS program and discusses some demonstration experiments. A future concept based on large structure multibeam antennas is also discussed.

  3. Characteristics of cloned repeated DNA sequences in the barley genome

    SciTech Connect

    Anan'ev, E.V.; Bochkanov, S.S.; Ryzhik, M.V.; Sonina, N.V.; Chernyshev, A.I.; Shchipkova, N.I.; Yakovleva, E.Yu.

    1986-12-01

    A partial clone library of barley DNA fragments based on plasmid pBR325 was created. The cloned EcoRI-fragments of chromosomal DNA are from 2 to 14 kbp in length. More than 95% of the barley DNA inserts comprise repeated sequences of different complexity and copy number. Certain of these DNA sequences are from families comprising at least 1% of the barley genome. A significant proportion of the clones hybridize with numerous sets of restriction fragments of genome DNA and they are dispersed throughout the barley chromosomes.

  4. A model of nonautonomous dynamics driven by repeated harmonic interaction

    NASA Astrophysics Data System (ADS)

    Zagrebnov, V. A.; Tamura, H.

    2016-06-01

    We consider an exactly solvable model of nonautonomous W*-dynamics driven by repeated harmonic interaction. The dynamics is Hamiltonian and quasifree. Because of inelastic interaction in the large-time limit, it leads to relaxation of initial states to steady states. We derive the explicit entropy production rate accompanying this relaxation. We also study the evolution of different subsystems to elucidate their eventual correlations and convergence to equilibriums. In conclusion, we prove that the W*-dynamics manifests a universal stationary behavior in a short-time interaction limit.

  5. Repeatability and heritability of response to superovulation in Holstein cows.

    PubMed

    Tonhati, H; Lôbo, R B; Oliveira, H N

    1999-04-15

    The objective of this study was to estimate the relative effects of genetic and phenotypic factors on the efficacy and efficiency of superovulation for Holstein-Friesian cows reared in Brazil. A database, established by the Associacao Brasileira de Criadores de Bovinos da Raca Holandesa, consisting of a total of 5387 superovulations of 2941 cows distributed over 473 herds and sired by 690 bulls was used for the analysis. The records were analyzed by MTDFREML (Multiple Trait Derivative-Free Restricted Maximum Likelihood), using a repeatability animal model. The fixed effects included in the model were contemporaneous group (veterinarian, herd, year and season of the superovulation); number of semen doses; cow age; and superovulation order. The estimated repeatability of the number of the transferable embryos was low (0.13), and the estimated heritability was 0.03. These results indicate that environmental factors play a critical role in the response of a cow to a superovulation treatment. There is little evidence that future responses to superovulation by individual females can be predicted by previous treatment(s) or that superovulation response is an heritable trait. PMID:10729033

  6. Effects of Hypohydration on Repeated 40-yd Sprint Performance.

    PubMed

    Gann, Joshua J; Green, James M; OʼNeal, Eric K; Renfroe, Lee G; Andre, Thomas L

    2016-04-01

    This study examined the effects of hypohydration on repeated 40-yd sprint performance. Anaerobically fit current and former Division II male athletes (n = 12) completed 2 bouts of 10 × 40-yd sprints followed by an agility test, dehydrated (∼3% body weight [DT]), or hydrated trial (HT). Statistical analysis of group means indicated that hypohydration had little effect on sprint times for either the first (DT= 5.38 ± 0.37; HT = 5.35 ± 0.34) or second (DT = 5.47 ± 0.39; HT = 5.42 ± 0.39) bout of 10 sprints with only sprint number 2, 5, and 6 of bout 2 reaching statistical significance. However, when individual sprint performance was considered, a greater effect was seen. In all, 83% (10 of 12) of subjects experienced a meaningful change (≥0.1 seconds) (positive or negative) in mean sprint time (DT vs. HT) for one or more bout of 10 sprints. Ratings of perceived exertion was significantly higher (∼1 unit on a 10 point scale) for DT in all sprints during bout 1 and the first 2 sprints of bout 2. These results indicate that the effect of hypohydration on repeated sprint performance varies among individuals. Some improved performance with hypohydration, while others experienced detrimental effects. Hypohydration also resulted in a particularly notable negative impact on perceptual measures of exertion even when performance was similar. PMID:26349041

  7. Cybersickness Following Repeated Exposure to DOME and HMD Virtual Environments

    NASA Technical Reports Server (NTRS)

    Taylor, Laura C.; Harm, Deborah L.; Kennedy, Robert S.; Reschke, Millard F.; Loftin, R. Bowen

    2011-01-01

    Virtual environments (VE) offer unique training opportunities, including training astronauts to preadapt them to the novel sensory conditions of microgravity. However, one unresolved issue with VE use is the occurrence of cybersickness during and following exposure to VE systems. Most individuals adapt and become less ill with repeated interaction with VEs. The goal of this investigation was to compare motion sickness symptoms (MSS) produced by dome and head-mounted (HMD) displays and to examine the effects of repeated exposures on MSS. Sixty-one subjects participated in the study. Three experimental sessions were performed each separated by one day. The subjects performed a navigation and pick and place task in either a dome or HMD VE. MSS were measured using a Simulator Sickness Questionnaire before, immediately after, and at 1, 2, 4 and 6 hours following exposure to the VEs. MSS data were normalized by calculating the natural log of each score and an analysis of variance was performed. We observed significant main effects for day and time and a significant day by time interaction for total sickness and for each of the subscales, nausea, oculomotor and disorientation. However, there was no significant main effect for device. In conclusion, subjects reported a large increase in MSS immediately following exposure to both the HMD and dome, followed by a rapid recovery across time. Sickness severity also decreased over days, which suggests that subjects become dual-adapted over time making VE training a viable pre-flight countermeasure for space motion sickness.

  8. Repeatability of Marine CSEM Imaging for Reservoir Monitoring

    NASA Astrophysics Data System (ADS)

    Black, N.; Wilson, G. A.; Zhdanov, M. S.

    2011-12-01

    Recent studies have inferred the feasibility of time-lapse controlled-source electromagnetic (CSEM) methods for the monitoring of offshore oil and gas fields. However, survey repeatability is difficult as transmitter and receiver positions will vary, and the resistivity of the water column may vary with season. Moreover, cultural noise due to sub-sea infrastructure may increase as the field is developed. These effects will influence the CSEM data. Using Archie's Law, rock and fluid properties from dynamic reservoir simulations of the Harding field in the North Sea were converted to resistivity, from preproduction in 1996 to decommissioning in 2016. CSEM data were simulated for each state, where the transmitters and receivers were varied within the tolerance of today's best practice. Even with imperfect survey repeatability, we demonstrate how 3D imaging can be used for monitoring the oil-water contact from preproduction to the end of oil production in 2011, and for monitoring of the gas-water contact from 2011 to 2016 during gas production.

  9. The role of variable DNA tandem repeats in bacterial adaptation.

    PubMed

    Zhou, Kai; Aertsen, Abram; Michiels, Chris W

    2014-01-01

    DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date. PMID:23927439

  10. Analysis of quantum network coding for realistic repeater networks

    NASA Astrophysics Data System (ADS)

    Satoh, Takahiko; Ishizaki, Kaori; Nagayama, Shota; Van Meter, Rodney

    2016-03-01

    Quantum repeater networks have attracted attention for the implementation of long-distance and large-scale sharing of quantum states. Recently, researchers extended classical network coding, which is a technique for throughput enhancement, into quantum information. The utility of quantum network coding (QNC) has been shown under ideal conditions, but it has not been studied previously under conditions of noise and shortage of quantum resources. We analyzed QNC on a butterfly network, which can create end-to-end Bell pairs at twice the rate of the standard quantum network repeater approach. The joint fidelity of creating two Bell pairs has a small penalty for QNC relative to entanglement swapping. It will thus be useful when we care more about throughput than fidelity. We found that the output fidelity drops below 0.5 when the initial Bell pairs have fidelity F <0.90 , even with perfect local gates. Local gate errors have a larger impact on quantum network coding than on entanglement swapping.

  11. A WD-repeat protein stabilizes ORC binding to chromatin.

    PubMed

    Shen, Zhen; Sathyan, Kizhakke M; Geng, Yijie; Zheng, Ruiping; Chakraborty, Arindam; Freeman, Brian; Wang, Fei; Prasanth, Kannanganattu V; Prasanth, Supriya G

    2010-10-01

    Origin recognition complex (ORC) plays critical roles in the initiation of DNA replication and cell-cycle progression. In metazoans, ORC associates with origin DNA during G1 and with heterochromatin in postreplicated cells. However, what regulates the binding of ORC to chromatin is not understood. We have identified a highly conserved, leucine-rich repeats and WD40 repeat domain-containing protein 1 (LRWD1) or ORC-associated (ORCA) in human cells that interacts with ORC and modulates chromatin association of ORC. ORCA colocalizes with ORC and shows similar cell-cycle dynamics. We demonstrate that ORCA efficiently recruits ORC to chromatin. Depletion of ORCA in human primary cells and embryonic stem cells results in loss of ORC association to chromatin, concomitant reduction of MCM binding, and a subsequent accumulation in G1 phase. Our results suggest ORCA-mediated association of ORC to chromatin is critical to initiate preRC assembly in G1 and chromatin organization in post-G1 cells. PMID:20932478

  12. Repeated mobility testing for later artificial visual function evaluation

    NASA Astrophysics Data System (ADS)

    Velikay-Parel, M.; Ivastinovic, D.; Koch, M.; Hornig, R.; Dagnelie, G.; Richard, G.; Langmann, A.

    2007-03-01

    The study investigates the utility of a newly designed mobility test for repeated testing of visual function in patients with severe visual impairment and future application in evaluating functional progress in patients with artificial vision. Ten subjects divided into three groups based on visual acuity (VA) ranging from light perception to 20/200 and reduced visual field (VF) were included in the study. The mobility test consisted of using a set of four different but structurally similar and relatively short mazes having a constant number of obstacles of various sizes. The subjects, divided into three groups by acuity, passed through each course several times. In general, the patients with better VA had a larger extent of VF. Average speed and number of contacts were recorded as measures of performance. The average passing times of the groups through the courses were significantly different (p = 0.03), which was influenced by VA and VF. There was no significant difference in average number of contacts between the groups (p = 0.15). The mobility test proved to be appropriate for gaining statistically relevant results in repeated individual testing of patients with severe vision impairment. Results show promise for use this mobility test as a tool for assessing visual function of patients undergoing implantation of a visual prosthesis for artificial vision.

  13. Labor union members play an OLG repeated game

    PubMed Central

    Kandori, Michihiro; Obayashi, Shinya

    2014-01-01

    Humans are capable of cooperating with one another even when it is costly and a deviation provides an immediate gain. An important reason is that cooperation is reciprocated or rewarded and deviations are penalized in later stages. For cooperation to be sustainable, not only must rewards and penalties be strong enough but individuals should also have the right incentives to provide rewards and punishments. Codes of conduct with such properties have been studied extensively in game theory (as repeated game equilibria), and the literature on the evolution of cooperation shows how equilibrium behavior might emerge and proliferate in society. We found that community unions, a subclass of labor unions that admits individual affiliations, are ideal to corroborate these theories with reality, because (i) their activities are simple and (ii) they have a structure that closely resembles a theoretical model, the overlapping generations repeated game. A detailed case study of a community union revealed a possible equilibrium that can function under the very limited observability in the union. The equilibrium code of conduct appears to be a natural focal point based on simple heuristic reasoning. The union we studied was created out of necessity for cooperation, without knowing or anticipating how cooperation might be sustained. The union has successfully resolved about 3,000 labor disputes and created a number of offspring. PMID:25024211

  14. Maximum likelihood decoding analysis of Accumulate-Repeat-Accumulate Codes

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    Repeat-Accumulate (RA) codes are the simplest turbo-like codes that achieve good performance. However, they cannot compete with Turbo codes or low-density parity check codes (LDPC) as far as performance is concerned. The Accumulate Repeat Accumulate (ARA) codes, as a subclass of LDPC codes, are obtained by adding a pre-coder in front of RA codes with puncturing where an accumulator is chosen as a precoder. These codes not only are very simple, but also achieve excellent performance with iterative decoding. In this paper, the performance of these codes with (ML) decoding are analyzed and compared to random codes by very tight bounds. The weight distribution of some simple ARA codes is obtained, and through existing tightest bounds we have shown the ML SNR threshold of ARA codes approaches very closely to the performance of random codes. We have shown that the use of precoder improves the SNR threshold but interleaving gain remains unchanged with respect to RA code with puncturing.

  15. Protein landscape at Drosophila melanogaster telomere-associated sequence repeats.

    PubMed

    Antão, José M; Mason, James M; Déjardin, Jérôme; Kingston, Robert E

    2012-06-01

    The specific set of proteins bound at each genomic locus contributes decisively to regulatory processes and to the identity of a cell. Understanding of the function of a particular locus requires the knowledge of what factors interact with that locus and how the protein composition changes in different cell types or during the response to internal and external signals. Proteomic analysis of isolated chromatin segments (PICh) was developed as a tool to target, purify, and identify proteins associated with a defined locus and was shown to allow the purification of human telomeric chromatin. Here we have developed this method to identify proteins that interact with the Drosophila telomere-associated sequence (TAS) repeats. Several of the purified factors were validated as novel TAS-bound proteins by chromatin immunoprecipitation, and the Brahma complex was confirmed as a dominant modifier of telomeric position effect through the use of a genetic test. These results offer information on the efficacy of applying the PICh protocol to loci with sequence more complex than that found at human telomeres and identify proteins that bind to the TAS repeats, which might contribute to TAS biology and chromatin silencing. PMID:22493064

  16. Repeat-based Sequence Typing of Carnobacterium maltaromaticum.

    PubMed

    Rahman, Abdur; El Kheir, Sara M; Back, Alexandre; Mangavel, Cécile; Revol-Junelles, Anne-Marie; Borges, Frédéric

    2016-06-01

    Carnobacterium maltaromaticum is a Lactic Acid Bacterium (LAB) of technological interest for the food industry, especially the dairy as bioprotection and ripening flora. The industrial use of this LAB requires accurate and resolutive typing tools. A new typing method for C. maltaromaticum inspired from MLVA analysis and called Repeat-based Sequence Typing (RST) is described. Rather than electrophoresis analysis, our RST method is based on sequence analysis of multiple loci containing Variable-Number Tandem-Repeats (VNTRs). The method described here for C. maltaromaticum relies on the analysis of three VNTR loci, and was applied to a collection of 24 strains. For each strain, a PCR product corresponding to the amplification of each VNTR loci was sequenced. Sequence analysis allowed delineating 11, 11, and 12 alleles for loci VNTR-A, VNTR-B, and VNTR-C, respectively. Considering the allele combination exhibited by each strain allowed defining 15 genotypes, ending in a discriminatory index of 0.94. Comparison with MLST revealed that both methods were complementary for strain typing in C. maltaromaticum. PMID:26998709

  17. Repeatability and reproducibility of aquatic testing with zinc dithiophosphate

    SciTech Connect

    Hooter, D.L.; Hoke, D.I.; Kraska, R.C.; Wojewodka, R.A.

    1994-12-31

    This testing program was designed to characterize the repeatability and reproducibility of aquatic screening studies with a water insoluble chemical substance. Zinc dithiophosphate was selected for its limited water solubility and moderate aquatic toxicity. Acute tests were conducted using fathead minnows and Daphnia magna, according to guidelines developed to minimize random sources of non-repeatability. Zinc dithiosphosphate was exposed to the organisms in static tests using an oil-water dispersion method for the fathead minnows, and a water-accommodated-fraction method for the Daphnia magna. Testing was conducted in moderately hard water with pre-determined nominal concentrations of 0. 1, 1.0, 10.0, 100.00, and 1000.0 ppm or ppm WAF. 24 studies were contracted among 3 separate commercial contract laboratories. The program results demonstrate the diverse range of intralaboratory and interlaboratory variability based on the organism type, and emphasize the need for further study and caution in the design, and implementation of aquatic testing for insoluble materials.

  18. The evolution and function of protein tandem repeats in plants.

    PubMed

    Schaper, Elke; Anisimova, Maria

    2015-04-01

    Sequence tandem repeats (TRs) are abundant in proteomes across all domains of life. For plants, little is known about their distribution or contribution to protein function. We exhaustively annotated TRs and studied the evolution of TR unit variations for all Ensembl plants. Using phylogenetic patterns of TR units, we detected conserved TRs with unit number and order preserved during evolution, and those TRs that have diverged via recent TR unit gains/losses. We correlated the mode of evolution of TRs to protein function. TR number was strongly correlated with proteome size, with about one-half of all TRs recognized as common protein domains. The majority of TRs have been highly conserved over long evolutionary distances, some since the separation of red algae and green plants c. 1.6 billion yr ago. Conversely, recurrent recent TR unit mutations were rare. Our results suggest that the first TRs by far predate the first plants, and that TR appearance is an ongoing process with similar rates across the plant kingdom. Interestingly, the few detected highly mutable TRs might provide a source of variation for rapid adaptation. In particular, such TRs are enriched in leucine-rich repeats (LRRs) commonly found in R genes, where TR unit gain/loss may facilitate resistance to emerging pathogens. PMID:25420631

  19. Mechanism of deflagration-to-detonation transitions above repeated obstacles

    NASA Astrophysics Data System (ADS)

    Obara, T.; Kobayashi, T.; Ohyagi, S.

    2012-11-01

    Experiments are carried out to investigate the mechanism of the deflagration-to-detonation transition (DDT). Because, this mechanism has relevance to safety issues in industries, where combustible premixed gases are in general use. A stoichiometric gas of oxygen and hydrogen (oxy-hydrogen) is ignited in a tube, repeated obstacles are installed, and the DDT behaviours are visualized using a high-speed video camera. The pitch and height of the repeated obstacles and the initial pressure of the oxy-hydrogen premixed gas are varied in an attempt to obtain the optimum conditions that cause DDT a short distance from the ignition source. The experiments identified DDT as being essentially caused by one of the following mechanisms: (1) A deflagration wave is accelerated in terms of a vortex, which is generated behind the obstacle, and the flame acceleration induces a secondary shock wave. Eventually, the shock-flame interaction ahead of the obstacle causes DDT via a very strong local explosion. (2) Each shock wave generated by relatively weak local explosions between the obstacles is not sufficient to cause DDT directly, but DDT results from an accumulation of shock waves. The detonation induction distance is also examined, taking into account the physical and chemical parameters of the obstacles and the oxy-hydrogen premixed gas.

  20. The C9orf72 repeat expansion disrupts nucleocytoplasmic transport.

    PubMed

    Zhang, Ke; Donnelly, Christopher J; Haeusler, Aaron R; Grima, Jonathan C; Machamer, James B; Steinwald, Peter; Daley, Elizabeth L; Miller, Sean J; Cunningham, Kathleen M; Vidensky, Svetlana; Gupta, Saksham; Thomas, Michael A; Hong, Ingie; Chiu, Shu-Ling; Huganir, Richard L; Ostrow, Lyle W; Matunis, Michael J; Wang, Jiou; Sattler, Rita; Lloyd, Thomas E; Rothstein, Jeffrey D

    2015-09-01

    The hexanucleotide repeat expansion (HRE) GGGGCC (G4C2) in C9orf72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent studies support an HRE RNA gain-of-function mechanism of neurotoxicity, and we previously identified protein interactors for the G4C2 RNA including RanGAP1. A candidate-based genetic screen in Drosophila expressing 30 G4C2 repeats identified RanGAP (Drosophila orthologue of human RanGAP1), a key regulator of nucleocytoplasmic transport, as a potent suppressor of neurodegeneration. Enhancing nuclear import or suppressing nuclear export of proteins also suppresses neurodegeneration. RanGAP physically interacts with HRE RNA and is mislocalized in HRE-expressing flies, neurons from C9orf72 ALS patient-derived induced pluripotent stem cells (iPSC-derived neurons), and in C9orf72 ALS patient brain tissue. Nuclear import is impaired as a result of HRE expression in the fly model and in C9orf72 iPSC-derived neurons, and these deficits are rescued by small molecules and antisense oligonucleotides targeting the HRE G-quadruplexes. Nucleocytoplasmic transport defects may be a fundamental pathway for ALS and FTD that is amenable to pharmacotherapeutic intervention. PMID:26308891

  1. Evidence for a Creative Dilemma Posed by Repeated Collaborations.

    PubMed

    Inoue, Hiroyasu

    2015-01-01

    We focused on how repeat collaborations in projects for inventions affect performance. Repeat collaborations have two contradictory aspects. A positive aspect is team development or experience, and a negative aspect is team degeneration or decline. Since both contradicting phenomena are observed, inventors have a dilemma as to whether they should keep collaborating in a team or not. The dilemma has not previously been quantitatively analyzed. We provide quantitative and extensive analyses of the dilemma in creative projects by using patent data from Japan and the United States. We confirm three predictions to quantitatively validate the existence of the dilemma. The first prediction is that the greater the patent a team achieves, the longer the team will work together. The second prediction is that the impact of consecutive patents decreases after a team makes a remarkable invention, which is measured by the impact of patents. The third prediction is that the expectation of impact with new teams is greater than that with the same teams successful in the past. We find these predictions are validated in patents published in Japan and the United States. On the basis of these three predictions, we can quantitatively validate the dilemma in creative projects. We also propose preventive strategies for degeneration. One is developing technological diversity, and another is developing inventor diversity in teams. We find the two strategies are both effective by validating with the data. PMID:26340441

  2. Evaluation of polyglutamine repeats in autosomal dominant Parkinson's disease.

    PubMed

    Yamashita, Chikara; Tomiyama, Hiroyuki; Funayama, Manabu; Inamizu, Saeko; Ando, Maya; Li, Yuanzhe; Yoshino, Hiroyo; Araki, Takehisa; Ichikawa, Tadashi; Ehara, Yoshiro; Ishikawa, Kinya; Mizusawa, Hidehiro; Hattori, Nobutaka

    2014-07-01

    We evaluated the contributions of various polyglutamine (polyQ) disease genes to Parkinson's disease (PD). We compared the distributions of polyQ repeat lengths in 8 common genes (ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, ATN1, and HTT) in 299 unrelated patients with autosomal dominant PD (ADPD) and 329 normal controls. We also analyzed the possibility of genetic interactions between ATXN1 and ATXN2, ATXN2 and ATXN3, and ATXN2 and CACNA1A. Intermediate-length polyQ expansions (>24 Qs) of ATXN2 were found in 7 ADPD patients and no controls (7/299 = 2.34% and 0/329 = 0%, respectively; p = 0.0053 < 0.05/8 after Bonferroni correction). These patients showed typical L-DOPA-responsive PD phenotypes. Conversely, no significant differences in polyQ repeat lengths were found between the ADPD patients and the controls for the other 7 genes. Our results may support the hypothesis that ATXN2 polyQ expansion is a specific predisposing factor for multiple neurodegenerative diseases. PMID:24534762

  3. Pattern mixture models for the analysis of repeated attempt designs.

    PubMed

    Daniels, Michael J; Jackson, Dan; Feng, Wei; White, Ian R

    2015-12-01

    It is not uncommon in follow-up studies to make multiple attempts to collect a measurement after baseline. Recording whether these attempts are successful or not provides useful information for the purposes of assessing the missing at random (MAR) assumption and facilitating missing not at random (MNAR) modeling. This is because measurements from subjects who provide this data after multiple failed attempts may differ from those who provide the measurement after fewer attempts. This type of "continuum of resistance" to providing a measurement has hitherto been modeled in a selection model framework, where the outcome data is modeled jointly with the success or failure of the attempts given these outcomes. Here, we present a pattern mixture approach to model this type of data. We re-analyze the repeated attempt data from a trial that was previously analyzed using a selection model approach. Our pattern mixture model is more flexible and is more transparent in terms of parameter identifiability than the models that have previously been used to model repeated attempt data and allows for sensitivity analysis. We conclude that our approach to modeling this type of data provides a fully viable alternative to the more established selection model. PMID:26149119

  4. Repeated Pesticide Exposure among North Carolina Migrant and Seasonal Farmworkers

    PubMed Central

    Arcury, Thomas A.; Grzywacz, Joseph G.; Talton, Jennifer W.; Chen, Haiying; Vallejos, Quirina M.; Galvan, Leonardo; Barr, Dana B.; Quandt, Sara A.

    2010-01-01

    Background Limited data document the multiple and repeated pesticide absorption experienced by farmworkers in an agricultural season or their risk factors. Methods Data were collected from 196 farmworkers 4 times at monthly intervals in 2007. Urine samples were tested for 12 pesticide urinary metabolites. Questionnaire data provided measures of exposure risks. Results Farmworkers had at least one detection for many pesticide urinary metabolites; e.g. 84.2% had at least one detection for acephate, 88.8% for 3,5,6-trichloro-2-pyridinol. Most farmworkers had multiple detections for specific metabolites; e.g., 64.8% had 2 or more detections for acephate, 64.8% for 3,5,6-trichloro-2-pyridinol, 79.1% for 3-phenoxybenzoic acid, and 86.7% for 2,4-dichlorophenoxyacetic acid. Housing type had a consistent significant association with metabolite detections. Conclusions Farmworkers are exposed to multiple pesticides across an agricultural season, and they experience repeated exposures to the same pesticides. Reducing farmworker pesticide exposure and delineating the health outcomes of this exposure require more detailed data. PMID:20623661

  5. Notch Ankyrin Repeat Domain Variation Influences Leukemogenesis and Myc Transactivation

    PubMed Central

    Aster, Jon C.; Bodnar, Nick; Xu, Lanwei; Karnell, Fredrick; Milholland, John M.; Maillard, Ivan; Histen, Gavin; Nam, Yunsun; Blacklow, Stephen C.; Pear, Warren S.

    2011-01-01

    Background The functional interchangeability of mammalian Notch receptors (Notch1-4) in normal and pathophysiologic contexts such as cancer is unsettled. We used complementary in vivo, cell-based and structural analyses to compare the abilities of activated Notch1-4 to support T cell development, induce T cell acute lymphoblastic leukemia/lymphoma (T-ALL), and maintain T-ALL cell growth and survival. Principal Findings We find that the activated intracellular domains of Notch1-4 (ICN1-4) all support T cell development in mice and thymic organ culture. However, unlike ICN1-3, ICN4 fails to induce T-cell acute lymphoblastic leukemia/lymphoma (T-ALL) and is unable to rescue the growth of Notch1-dependent T-ALL cell lines. The ICN4 phenotype is mimicked by weak gain-of-function forms of Notch1, suggesting that it stems from a failure to transactivate one or more critical target genes above a necessary threshold. Experiments with chimeric receptors demonstrate that the Notch ankyrin repeat domains differ in their leukemogenic potential, and that this difference correlates with activation of Myc, a direct Notch target that has an important role in Notch-associated T-ALL. Conclusions/Significance We conclude that the leukemogenic potentials of Notch receptors vary, and that this functional difference stems in part from divergence among the highly conserved ankyrin repeats, which influence the transactivation of specific target genes involved in leukemogenesis. PMID:22022427

  6. Labor union members play an OLG repeated game.

    PubMed

    Kandori, Michihiro; Obayashi, Shinya

    2014-07-22

    Humans are capable of cooperating with one another even when it is costly and a deviation provides an immediate gain. An important reason is that cooperation is reciprocated or rewarded and deviations are penalized in later stages. For cooperation to be sustainable, not only must rewards and penalties be strong enough but individuals should also have the right incentives to provide rewards and punishments. Codes of conduct with such properties have been studied extensively in game theory (as repeated game equilibria), and the literature on the evolution of cooperation shows how equilibrium behavior might emerge and proliferate in society. We found that community unions, a subclass of labor unions that admits individual affiliations, are ideal to corroborate these theories with reality, because (i) their activities are simple and (ii) they have a structure that closely resembles a theoretical model, the overlapping generations repeated game. A detailed case study of a community union revealed a possible equilibrium that can function under the very limited observability in the union. The equilibrium code of conduct appears to be a natural focal point based on simple heuristic reasoning. The union we studied was created out of necessity for cooperation, without knowing or anticipating how cooperation might be sustained. The union has successfully resolved about 3,000 labor disputes and created a number of offspring. PMID:25024211

  7. Source-monitoring accuracy across repeated tests following directed forgetting.

    PubMed

    Goernert, Phillip N

    2005-05-01

    The repeated recall of items from lists that participants were earlier instructed to either remember or to forget was examined in two experiments. RR participants (those instructed to remember both lists they were presented) tended to recall more List 1 items than FR participants (those instructed to forget the first list and to remember the second list). FR participants recalled more List 2 items than did RR participants, but only when directed to report those items (Experiment 1), not when directed to report items from both lists (Experiment 2). Participants experienced difficulty correctly reporting the list source of items they recalled and incorrect source recall increased across tests, showing hypermnesia. This later result underscores the need for caution when assessing the accuracy of information retrieved from multiple sources across repeated tests. Together, the data patterns provide support for the retrieval dynamics account of hypermnesia, the context-change account of directed forgetting, and limited support for the retrieval inhibition view of directed forgetting. PMID:15969833

  8. Novel mutational mechanism in man: Expansion of trinucleotide repeats

    SciTech Connect

    Ilarioshkin, S.N.; Ivanova-Smolenskaya, I.A.; Markova, E.D.

    1995-11-01

    An analysis of a novel, recently discovered class of mutations in man - an expansion, i.e., an increase of the copy number of intragenic unstable trinucleotide repeats - is presented. The expansion of trinucleotide X chromosome syndrome (two separate variants of the disease - FRAXA and FRAXE), myotonic dystrophy, spinal and bulbar Kennedy`s amyotrophy, Huntington`s chorea, type 1 spinocerebellar ataxia, and dentatorubral-pallidolyusian atrophy. The discovery of triplet expansion allows a satisfactory explanation on the molecular level of a series of unusual clinical genetic phenomena, such as anticipation, the {open_quotes}paternal transmission{close_quotes} effect, the {open_quotes}Sherman paradox,{close_quotes} and others. The common properties and the distinctions of unstable trinucleotide mutations in the nosologic forms mentioned above are analyzed comprehensively. These features include the mechanism by which these mutations cause disease, the time of their appearance in ontogenesis, and various clinical genetic correlations. The evolutionary origin of this class of mutations and, in particular, the role of alleles with an {open_quotes}intermediate{close_quotes} triplet number, which are the persistent reservoir of mutations arising de novo in a population, are also discussed. The possible implication of unstable trinucleotide repeats for a series of other hereditary diseases, such as type 2, spinocerebellar ataxia, Machado-Joseph disease, hereditary spastic paraplegia, essential tremor, schizophrenia, and others, is also suggested. 108 refs., 1 tab.

  9. Towards highly multimode optical quantum memory for quantum repeaters

    NASA Astrophysics Data System (ADS)

    Jobez, Pierre; Timoney, Nuala; Laplane, Cyril; Etesse, Jean; Ferrier, Alban; Goldner, Philippe; Gisin, Nicolas; Afzelius, Mikael

    2016-03-01

    Long-distance quantum communication through optical fibers is currently limited to a few hundreds of kilometres due to fiber losses. Quantum repeaters could extend this limit to continental distances. Most approaches to quantum repeaters require highly multimode quantum memories in order to reach high communication rates. The atomic frequency comb memory scheme can in principle achieve high temporal multimode storage, without sacrificing memory efficiency. However, previous demonstrations have been hampered by the difficulty of creating high-resolution atomic combs, which reduces the efficiency for multimode storage. In this article we present a comb preparation method that allows one to increase the multimode capacity for a fixed memory bandwidth. We apply the method to a 3+151Eu -doped Y2SiO5 crystal, in which we demonstrate storage of 100 modes for 51 μ s using the AFC echo scheme (a delay-line memory) and storage of 50 modes for 0.541 ms using the AFC spin-wave memory (an on-demand memory). We also briefly discuss the ultimate multimode limit imposed by the optical decoherence rate, for a fixed memory bandwidth.

  10. The C9ORF72 repeat expansion disrupts nucleocytoplasmic transport

    PubMed Central

    Haeusler, Aaron R.; Grima, Jonathan C.; Machamer, James B.; Steinwald, Peter; Daley, Elizabeth L.; Miller, Sean J.; Cunningham, Kathleen M.; Vidensky, Svetlana; Gupta, Saksham; Thomas, Michael A.; Hong, Ingie; Chiu, Shu-Ling; Huganir, Richard L.; Ostrow, Lyle W.; Matunis, Michael J.; Wang, Jiou; Sattler, Rita

    2016-01-01

    A GGGGCC (G4C2) hexanucleotide repeat expansion (HRE) in C9ORF72 is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent studies support an HRE RNA gain-of-function mechanism of neurotoxicity, and we previously identified protein interactors for the G4C2 RNA including RanGAP1. A candidate-based genetic screen in Drosophila expressing 30 G4C2 repeats identified RanGAP (Drosophila ortholog of human RanGAP1), a key regulator of nucleocytoplasmic transport, as a potent suppressor of neurodegeneration. Enhancing nuclear import or suppressing nuclear export of proteins also suppresses neurodegeneration. RanGAP physically interacts with HRE RNA and is mislocalized in HRE-expressing flies, neurons from C9ORF72 ALS patient-derived induced pluripotent stem cells (iPSNs), and in C9ORF72 patient brain tissue. Nuclear import is impaired as a result of HRE expression in the fly model and in C9ORF72 iPSNs, and these deficits are rescued by small molecules and antisense oligonucleotides targeting the HRE G-quadruplexes. Nucleocytoplasmic transport defects may be a fundamental pathway for ALS and FTD amenable to pharmacotherapeutic intervention. PMID:26308891

  11. Evidence for a Creative Dilemma Posed by Repeated Collaborations

    PubMed Central

    Inoue, Hiroyasu

    2015-01-01

    We focused on how repeat collaborations in projects for inventions affect performance. Repeat collaborations have two contradictory aspects. A positive aspect is team development or experience, and a negative aspect is team degeneration or decline. Since both contradicting phenomena are observed, inventors have a dilemma as to whether they should keep collaborating in a team or not. The dilemma has not previously been quantitatively analyzed. We provide quantitative and extensive analyses of the dilemma in creative projects by using patent data from Japan and the United States. We confirm three predictions to quantitatively validate the existence of the dilemma. The first prediction is that the greater the patent a team achieves, the longer the team will work together. The second prediction is that the impact of consecutive patents decreases after a team makes a remarkable invention, which is measured by the impact of patents. The third prediction is that the expectation of impact with new teams is greater than that with the same teams successful in the past. We find these predictions are validated in patents published in Japan and the United States. On the basis of these three predictions, we can quantitatively validate the dilemma in creative projects. We also propose preventive strategies for degeneration. One is developing technological diversity, and another is developing inventor diversity in teams. We find the two strategies are both effective by validating with the data. PMID:26340441

  12. Repeated dose toxicity of alfa-cypermethrin in rats.

    PubMed

    Manna, S; Bhattacharyya, D; Mandal, T K; Das, S

    2004-09-01

    The present study was performed to investigate the subacute effect of alpha-cypermethrin (alpha-CP) in rats. Alfacypermethrin a synthetic pyrethroid insecticide, dissolved in dimethyl sulfoxide (DMSO) and oral LD50 was investigated after administering orally different doses in rats and was determined as 145 mg/kg. Other groups of rats were given repeated daily oral dose (1/10 LD50) of alpha-CP for 30 days. The animals were sacrificed on 31st day. Activities of various enzymes, cytochrome P450 and b5 contents in liver, hepatic antioxidant status, tissue residue concentration, haemogram and pathological changes were studied. It increased the serum aminotransaminases (AST, ALT), alkaline phosphatase (ALP), lactate dehydrogenase (LDH) activities and blood glucose level significantly. alpha-CP decreased RBC count, PCV and Hb level significantly. It significantly decreased cytochrome P450 in liver. Residues were present in different tissues. It increased malondialdehyde (MDA) level, while decreased the activities of catalase (CAT), superoxide dismutase (SOD) and glycogen level in liver significantly. Mild to moderate histological alterations were observed in lungs, liver, stomach, kidneys, testes and cerebellum. So repeated daily oral doses of alpha-CP at 1/10LD50 altered the biochemical parameters, decreased cytochrome P450 content, antioxidant status, which correlated with histopathological changes of tissues. PMID:15365239

  13. Backward estimation of exposure to organochlorines using repeated measurements.

    PubMed Central

    Karmaus, Wilfried; Fussman, Christopher; Muttineni, Jyotsna; Zhu, Xiaobei

    2004-01-01

    Great Lakes sport-caught fish are contaminated with various organochlorines (OCs) such as polychlorinated biphenyls (PCBs). Through consumption of these fish, humans are subject to continuing levels of OC contamination. To assess potential adverse effects of past exposure, we compared three different backward extrapolation models. The data originated from OC determinations in a cohort of anglers and their families. Repeated PCB measurements collected in the 1970s, 1980s, and 1990s were used when testing the backward extrapolations. We applied a simple and a complex decay model based on assumptions used in previous studies; a third was a regression model incorporating markers of OC intake and loss. These techniques provided past exposure estimates. Intraclass correlation coefficients (ICCs) were calculated comparing measured and estimated PCB values. ICC values for the regression model equations were 0.77 and 0.89; ICC values for the simple and complex decay models were significantly lower, with ranges of 0.07-0.45 and -0.14-0.69, respectively. Plots showing trends of OC concentrations in fish and humans indicate comparable increases and decreases of PCB in fish and humans, with fish concentrations peaking approximately 10 years before that in humans. Our findings suggest that one should be cautious when using simple backward extrapolation techniques to estimate OC exposure in situations involving changing environmental exposures. Whenever repeated measurements are available, regression analyses seem to produce more accurate backward estimations of exposure. PMID:15121515

  14. Genomic distribution of simple sequence repeats in Brassica rapa.

    PubMed

    Hong, Chang Pyo; Piao, Zhong Yun; Kang, Tae Wook; Batley, Jacqueline; Yang, Tae-Jin; Hur, Yoon-Kang; Bhak, Jong; Park, Beom-Seok; Edwards, David; Lim, Yong Pyo

    2007-06-30

    Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa. PMID:17646709

  15. A designed repeat protein as an affinity capture reagent.

    PubMed

    Speltz, Elizabeth B; Brown, Rebecca S H; Hajare, Holly S; Schlieker, Christian; Regan, Lynne

    2015-10-01

    Repeat proteins are an attractive target for protein engineering and design. We have focused our attention on the design and engineering of one particular class: tetratricopeptide repeat (TPR) proteins. In previous work, we have shown that the structure and stability of TPR proteins can be manipulated in a rational fashion [Cortajarena (2011) Prot. Sci. 20: , 1042-1047; Main (2003) Structure 11: , 497-508]. Building on those studies, we have designed and characterized a number of different peptide-binding TPR modules and we have also assembled these modules into supramolecular arrays [Cortajarena (2009) ACS Chem. Biol. 5: , 545-552; Cortajarena (2008) ACS Chem. Biol. 3: , 161-166; Jackrel (2009) Prot. Sci. 18: , 762-774; Kajander (2007) Acta Crystallogr. D Biol. Crystallogr. 63: , 800-811]. Here we focus on the development of one such TPR-peptide interaction for a practical application, affinity purification. We illustrate the general utility of our designed protein interaction. Furthermore, this example highlights how basic research on protein-peptide interactions can lead to the development of novel reagents with important practical applications. PMID:26517897

  16. Brokering as a framework for hydrological model repeatability

    NASA Astrophysics Data System (ADS)

    Fuka, Daniel; Collick, Amy; MacAlister, Charlotte; Braeckel, Aaron; Wright, Dawn; Jodha Khalsa, Siri; Boldrini, Enrico; Easton, Zachary

    2015-04-01

    Data brokering aims to provide those in the the sciences with quick and repeatable access to data that represents physical, biological, and chemical characteristics; specifically to accelerate scientific discovery. Environmental models are useful tools to understand the behavior of hydrological systems. Unfortunately, parameterization of these hydrological models requires many different data, from different sources, and from different disciplines (e.g., atmospheric, geoscience, ecology). In basin scale 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, or more suitable data products will exist. An added complexity is that various science communities have differing data formats, storage protocols, and manipulation methods, which makes use by a non native user exceedingly difficult and time consuming. We demonstrate 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 can increase the efficiency with which data are obtained, models are initialized, and results are analyzed. As an added benefit, it appears brokering can significantly increase the repeatability of a given study.

  17. Large Torque Variations in Two Soft Gamma Repeaters

    NASA Technical Reports Server (NTRS)

    Woods, Peter M.; Kouveliotou, Chryssa; Gogus, Ersin; Finger, Mark H.; Swank, Jean; Markwardt, Craig B.; Hurley, Kevin; vanderKlis, Michiel

    2002-01-01

    We have monitored the pulse frequencies of the two soft gamma repeaters SGR 1806-20 and SGR 1900+14 through the beginning of year 2001 using primarily Rossi X-Ray Timing Explorer Proportional Counter Array observations. In both sources, we observe large changes in the spin-down torque up to a factor of approximately 4, which persist for several months. Using long-baseline phase-connected timing solutions as well as the overall frequency histories, we construct torque noise power spectra for each SGR (Soft Gamma Repeater). The power spectrum of each source is very red (power-law slope is approximately -3.5). The torque noise power levels are consistent with some accreting systems on timescales of approximately 1 yr, yet the full power spectrum is much steeper in frequency than any known accreting source. To the best of our knowledge, torque noise power spectra with a comparably steep frequency dependence have been seen only in young, glitching radio pulsars (e.g., Vela). The observed changes in spin-down rate do not correlate with burst activity; therefore, the physical mechanisms behind each phenomenon are also likely unrelated. Within the context of the magnetar model, seismic activity can not account for both the bursts and the long-term torque changes unless the seismically active regions are decoupled from one another.

  18. Gibbs motif sampling: detection of bacterial outer membrane protein repeats.

    PubMed Central

    Neuwald, A. F.; Liu, J. S.; Lawrence, C. E.

    1995-01-01

    The detection and alignment of locally conserved regions (motifs) in multiple sequences can provide insight into protein structure, function, and evolution. A new Gibbs sampling algorithm is described that detects motif-encoding regions in sequences and optimally partitions them into distinct motif models; this is illustrated using a set of immunoglobulin fold proteins. When applied to sequences sharing a single motif, the sampler can be used to classify motif regions into related submodels, as is illustrated using helix-turn-helix DNA-binding proteins. Other statistically based procedures are described for searching a database for sequences matching motifs found by the sampler. When applied to a set of 32 very distantly related bacterial integral outer membrane proteins, the sampler revealed that they share a subtle, repetitive motif. Although BLAST (Altschul SF et al., 1990, J Mol Biol 215:403-410) fails to detect significant pairwise similarity between any of the sequences, the repeats present in these outer membrane proteins, taken as a whole, are highly significant (based on a generally applicable statistical test for motifs described here). Analysis of bacterial porins with known trimeric beta-barrel structure and related proteins reveals a similar repetitive motif corresponding to alternating membrane-spanning beta-strands. These beta-strands occur on the membrane interface (as opposed to the trimeric interface) of the beta-barrel. The broad conservation and structural location of these repeats suggests that they play important functional roles. PMID:8520488

  19. Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility.

    PubMed

    Voineagu, Irina; Surka, Christine F; Shishkin, Alexander A; Krasilnikova, Maria M; Mirkin, Sergei M

    2009-02-01

    Expanded CGG repeats cause chromosomal fragility and hereditary neurological disorders in humans. Replication forks stall at CGG repeats in a length-dependent manner in primate cells and in yeast. Saccharomyces cerevisiae proteins Tof1 and Mrc1 facilitate replication fork progression through CGG repeats. Remarkably, the fork-stabilizing role of Mrc1 does not involve its checkpoint function. Thus, chromosomal fragility might occur when forks stalled at expanded CGG repeats escape the S-phase checkpoint. PMID:19136957

  20. Replisome stalling and stabilization at CGG repeats that are responsible for chromosomal fragility

    PubMed Central

    Voineagu, Irina; Surka, Christine F.; Shishkin, Alexander A.; Krasilnikova, Maria M.; Mirkin, Sergei M.

    2010-01-01

    Expanded CGG repeats cause chromosomal fragility and hereditary neurological disorders in humans. Replication forks stall at CGG repeats in a length-dependent manner in primate cells and in yeast. Yeast Tof1 and Mrc1 proteins facilitate replication fork progression through CGG repeats. Remarkably, the fork-stabilizing role of Mrc1 does not involve its checkpoint function. Thus, chromosomal fragility might occur when forks stalled at expanded CGG repeats escape the S-phase checkpoint. PMID:19136957

  1. A Test for a Neglected Source of Variation: The Individual Difference by Repeated Measures Interaction.

    ERIC Educational Resources Information Center

    Draper, John F.; Porter, Andrew C.

    The repeated measures design is of importance to those interested in doing learning studies concerned with repeated trials on a single type of task, repeated trials on different tasks, or both together crossed with and following different treatments. In doing analysis of variance with such data it is assumed that the data fits an additive model.…

  2. Psychometric Equivalence of Ratings for Repeat Examinees on a Performance Assessment for Physician Licensure

    ERIC Educational Resources Information Center

    Raymond, Mark R.; Swygert, Kimberly A.; Kahraman, Nilufer

    2012-01-01

    Although a few studies report sizable score gains for examinees who repeat performance-based assessments, research has not yet addressed the reliability and validity of inferences based on ratings of repeat examinees on such tests. This study analyzed scores for 8,457 single-take examinees and 4,030 repeat examinees who completed a 6-hour clinical…

  3. Exposing Students to Repeat Photography: Increasing Cultural Understanding on a Short-Term Study Abroad

    ERIC Educational Resources Information Center

    Lemmons, Kelly K.; Brannstrom, Christian; Hurd, Danielle

    2014-01-01

    Traditionally, repeat photography has been used to analyze land cover change. This paper describes how repeat photography may be used as a tool to enhance the short-term study abroad experience by facilitating cultural interaction and understanding. We present evidence from two cases and suggest a five-step repeat photography method for educators…

  4. 47 CFR 22.573 - Use of base transmitters as repeaters.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 2 2011-10-01 2011-10-01 false Use of base transmitters as repeaters. 22.573... of base transmitters as repeaters. As an additional function, base transmitters may be used as repeaters. Licensees must be able to turn the base transmitter on or off from the control point...

  5. 47 CFR 25.263 - Information sharing requirements for SDARS terrestrial repeater operators.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... terrestrial repeater operators. 25.263 Section 25.263 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... requirements for SDARS terrestrial repeater operators. This section requires SDARS licensees in the 2320-2345 MHz band to share information regarding the location and operation of terrestrial repeaters with...

  6. 47 CFR 25.263 - Information sharing requirements for SDARS terrestrial repeater operators.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... terrestrial repeater operators. 25.263 Section 25.263 Telecommunication FEDERAL COMMUNICATIONS COMMISSION... requirements for SDARS terrestrial repeater operators. This section requires SDARS licensees in the 2320-2345 MHz band to share information regarding the location and operation of terrestrial repeaters with...

  7. 30 CFR 250.523 - When do I have to repeat casing diagnostic testing?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 2 2013-07-01 2013-07-01 false When do I have to repeat casing diagnostic... diagnostic testing? Casing diagnostic testing must be repeated according to the following table: When . . . you must repeat diagnostic testing . . . (a) your casing pressure request approved term has...

  8. 30 CFR 250.523 - When do I have to repeat casing diagnostic testing?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 2 2014-07-01 2014-07-01 false When do I have to repeat casing diagnostic... diagnostic testing? Casing diagnostic testing must be repeated according to the following table: When . . . you must repeat diagnostic testing . . . (a) your casing pressure request approved term has...

  9. 30 CFR 250.522 - When do I have to repeat casing diagnostic testing?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 2 2012-07-01 2012-07-01 false When do I have to repeat casing diagnostic... diagnostic testing? Casing diagnostic testing must be repeated according to the following table: When . . . you must repeat diagnostic testing . . . (a) your casing pressure request approved term has...

  10. Fluency in Learning to Read for Meaning: Going beyond Repeated Readings

    ERIC Educational Resources Information Center

    Nichols, William Dee; Rupley, William H.; Rasinski, Timothy

    2009-01-01

    The purpose of this article is to provide an overview of fluency development and focus on instructional approaches that are intended to improve fluency that go beyond the most frequently recommended strategy of repeated readings. Repeated reading is the most recognized approach for developing fluency, and although repeated readings have shown…

  11. Impact of repeated chlorotoluron application on its degradation in soil

    NASA Astrophysics Data System (ADS)

    Kocarek, Martin; Kodesova, Radka; Drabek, Ondrej; Kozak, Josef

    2010-05-01

    The effect of repeated chlorotoluron application on its degradation was studied under the field condition in Haplic Chernozem. Chlorotoluron was applied repeatedly (dose of 0.025 mg.m-2) on the top of the soil profile in years 2006, 2008 and 2009. Climatic data as a daily minimal and maximal temperature and daily rainfall were collected during the experiment. Pressure heads at 4 depths (10, 25, 50, 80 cm) were measured using tensiometers. Soil-water contents and temperatures at 5 depths (5, 10, 25, 50, 80 cm) were monitored using the ECH20 EC-TE sensors. The suction cups were used to take soil-water samples at various depths (5, 10, 25, 50 cm) to indentify presence of the herbicide during 140 days period. In addition, soil samples were taken from layers 2 cm thick (to the depth of 50 cm) 35, 50 and 140 day after the herbicide application to measure a total content of the applied herbicide in each layer within the soil profile. Herbicide concentrations in soil extracts and soil water samples were analyzed using the HPLC technology. The total chlorotoluron content within the monitored soil profile was evaluated, and the herbicide field degradation rate and half-life were calculated. Chlorotoluron was not detected below the depth of 32 cm during the entire experimental periods. Chlorotoluron field half-lives estimated in this study were 28.4, 33.4 and 32.3 days in 2006, 2008 and 2009, respectively. The herbicide half-lives were also measured in the laboratory under the controlled soil-water content and temperature conditions: 20.6 days (28 C, 40% soil-water content per mass), 33.16 days (28 C, 20% soil-water content per mass); 27.76 days (20 C, 40% soil-water content per mass); 39.85 days (20 C, 20% soil-water content per mass); 32.27 days (10 C, 40% soil-water content per mass); 45.7 days (10 C, 20% soil-water content per mass). The field herbicide half-lives (obtained under the similar average temperature and soil-water content conditions) corresponded to half

  12. Artificial corneas versus donor corneas for repeat corneal transplants

    PubMed Central

    Akpek, Esen K; Alkharashi, Majed; Hwang, Frank S; Ng, Sueko M; Lindsley, Kristina

    2014-01-01

    Background Individuals who have failed one or more full thickness penetrating keratoplasties (PKs) may be offered repeat corneal surgery using an artificial or donor cornea. An artificial or prosthetic cornea is known as a keratoprosthesis. Both donor and artificial corneal transplantations involve removal of the diseased and opaque recipient cornea (or the previously failed cornea) and replacement with another donor or prosthetic cornea. Objectives To assess the effectiveness of artificial versus donor corneas in individuals who have had one or more failed donor corneal transplantations. Search methods We searched CENTRAL (which contains the Cochrane Eyes and Vision Group Trials Register) (2013, Issue 10), Ovid MEDLINE, Ovid MEDLINE In-Process and Other Non-Indexed Citations, Ovid MEDLINE Daily, Ovid OLDMEDLINE (January 1946 to November 2013), EMBASE (January 1980 to November 2013), Latin American and Caribbean Health Sciences Literature Database (LILACS) (January 1982 to November 2013), the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com), ClinicalTrials.gov (www.clinicaltrials.gov) and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) (www.who.int/ictrp/search/en). We did not use any date or language restrictions in the electronic searches for trials. We last searched the electronic databases on 27 November 2013. Selection criteria Two review authors independently assessed reports from the electronic searches to identify randomized controlled trials (RCTs) or controlled clinical trials (CCTs). We resolved discrepancies by discussion or consultation with a third review author. Data collection and analysis For discussion purposes, we assessed findings from observational cohort studies and non-comparative case series. No data synthesis was performed. Main results We did not identify any RCTs or CCTs comparing artificial corneas with donor corneas for repeat corneal transplantations. Authors

  13. Common mechanism underlies repeated evolution of extreme pollution tolerance

    PubMed Central

    Whitehead, Andrew; Pilcher, Whitney; Champlin, Denise; Nacci, Diane

    2012-01-01

    Human alterations to the environment can exert strong evolutionary pressures, yet contemporary adaptation to human-mediated stressors is rarely documented in wildlife populations. A common-garden experimental design was coupled with comparative transcriptomics to discover evolved mechanisms enabling three populations of killifish resident in urban estuaries to survive normally lethal pollution exposure during development, and to test whether mechanisms are unique or common across populations. We show that killifish populations from these polluted sites have independently converged on a common adaptive mechanism, despite variation in contaminant profiles among sites. These populations are united by a similarly profound desensitization of aryl-hydrocarbon receptor-mediated transcriptional activation, which is associated with extreme tolerance to the lethal effects of toxic dioxin-like pollutants. The rapid, repeated, heritable and convergent nature of evolved tolerance suggests that ancestral killifish populations harboured genotypes that enabled adaptation to twentieth-century industrial pollutants. PMID:21733895

  14. Fuel cell repeater unit including frame and separator plate

    DOEpatents

    Yamanis, Jean; Hawkes, Justin R; Chiapetta, Jr., Louis; Bird, Connie E; Sun, Ellen Y; Croteau, Paul F

    2013-11-05

    An example fuel cell repeater includes a separator plate and a frame establishing at least a portion of a flow path that is operative to communicate fuel to or from at least one fuel cell held by the frame relative to the separator plate. The flow path has a perimeter and any fuel within the perimeter flow across the at least one fuel cell in a first direction. The separator plate, the frame, or both establish at least one conduit positioned outside the flow path perimeter. The conduit is outside of the flow path perimeter and is configured to direct flow in a second, different direction. The conduit is fluidly coupled with the flow path.

  15. Repeat laparotomy in ovarian carcinoma after primary surgery.

    PubMed

    Archer, J C; Soeters, R P; Bloch, B; Dehaeck, C M; Levin, W

    1991-09-21

    Thirty-two patients with malignant ovarian disease were referred after primary surgery to the Gynaecological Oncology Unit of Groote Schuur Hospital, Cape Town. All 32 patients underwent a re-laparotomy with a view to accurate staging and possible cytoreductive surgery. On referral, 24 patients (75%) had stage I or II disease and the remaining 8 patients (25%) had stage III and IV disease. Twenty-seven patients (81%) had ovarian malignant disease of epithelial origin while the remaining 5 patients (19%) had ovarian disease of nonepithelial origin. Five (20.8%) of a total of 24 patients with stage I or II disease had their disease stage raised after repeat laparotomy. The overall success rate of cytoreductive surgery, i.e. less than 2 cm residual disease, was 58%. PMID:1925822

  16. Repeated Training with Augmentative Vibrotactile Feedback Increases Object Manipulation Performance

    PubMed Central

    Stepp, Cara E.; An, Qi; Matsuoka, Yoky

    2012-01-01

    Most users of prosthetic hands must rely on visual feedback alone, which requires visual attention and cognitive resources. Providing haptic feedback of variables relevant to manipulation, such as contact force, may thus improve the usability of prosthetic hands for tasks of daily living. Vibrotactile stimulation was explored as a feedback modality in ten unimpaired participants across eight sessions in a two-week period. Participants used their right index finger to perform a virtual object manipulation task with both visual and augmentative vibrotactile feedback related to force. Through repeated training, participants were able to learn to use the vibrotactile feedback to significantly improve object manipulation. Removal of vibrotactile feedback in session 8 significantly reduced task performance. These results suggest that vibrotactile feedback paired with training may enhance the manipulation ability of prosthetic hand users without the need for more invasive strategies. PMID:22384283

  17. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role.

    PubMed

    Pellegrini, Marco

    2015-01-01

    Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR. PMID:26442257

  18. Overcoming lossy channel bounds using a single quantum repeater node

    NASA Astrophysics Data System (ADS)

    Luong, D.; Jiang, L.; Kim, J.; Lütkenhaus, N.

    2016-04-01

    We propose a scheme for performing quantum key distribution (QKD) which has the potential to beat schemes based on the direct transmission of photons between the communicating parties. In our proposal, the communicating parties exchange photons with two quantum memories placed between them. This is a very simple quantum repeater scheme and can be implemented with currently available technology. Ideally, its secret key rate scales as the square root of the transmittivity of the optical channel, which is superior to QKD schemes based on direct transmission because key rates for the latter scale at best linearly with transmittivity. Taking into account various imperfections in each component of our setup, we present parameter regimes in which our protocol outperforms protocols based on direct transmission.

  19. Repeatable reference for positioning sensors and transducers in drill pipe

    DOEpatents

    Hall, David R.; Fox, Joe; Pixton, David S.; Hall, Jr., H. Tracy

    2005-05-03

    A drill pipe having a box end having a tapered thread, and an internal shoulder and an external face for engagement with a drill pipe pin end having a tapered mating thread, and an external shoulder and an external face adapted for data acquisition or transmission. The relative dimensions of the box and pin ends are precisely controlled so that when the tool joint is made up, a repeatable reference plane is established for transmitting power and tuning downhole sensors, transducers, and means for sending and receiving data along the drill string. When the power or data acquisition and transmission means are located in the tool joint, the dimensions of the tool joint are further proportioned to compensate for the loss of cross-sectional area in order maintain the joints ability to sustain nominal makeup torque.

  20. Characterization of transcriptional regulatory domains of ankyrin repeat cofactor-1

    SciTech Connect

    Zhang, Aihua; Li, Chia-Wei; Chen, J. Don . E-mail: chenjd@umdnj.edu

    2007-07-13

    The ankyrin repeats cofactor-1 (ANCO-1) was recently identified as a p160 coactivator-interacting protein that may inhibit transcriptional activity of nuclear receptors. Here, we have characterized the transcriptional regulatory domains of ANCO-1. Two intrinsic repression domains (RD) were identified: an N-terminal RD1 at residues 318-611 and a C-terminal RD2 at 2369-2663. ANCO-1 also contains an activation domain (AD) capable of stimulating transcription in both mammalian and yeast cells. The minimal AD was delimited to a 70-amino acid region at residues 2076-2145. Overall, full-length ANCO-1 exhibited transcriptional repressor activity, suggesting that RD domains may suppress the AD activity. We further demonstrated that ANCO-1 silencing by siRNA enhanced progesterone receptor-mediated transcription. Together, these results indicate that the transcriptional potential of ANCO-1 may be modulated by a combination of repression and activation signals.