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Sample records for repeated measures revealed

  1. Analysis of repeated measures data

    CERN Document Server

    Islam, M Ataharul

    2017-01-01

    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  2. Measurement-based quantum repeaters

    CERN Document Server

    Zwerger, M; Briegel, H J

    2012-01-01

    We introduce measurement-based quantum repeaters, where small-scale measurement-based quantum processors are used to perform entanglement purification and entanglement swapping in a long-range quantum communication protocol. In the scheme, pre-prepared entangled states stored at intermediate repeater stations are coupled with incoming photons by simple Bell-measurements, without the need of performing additional quantum gates or measurements. We show how to construct the required resource states, and how to minimize their size. We analyze the performance of the scheme under noise and imperfections, with focus on small-scale implementations involving entangled states of few qubits. We find measurement-based purification protocols with significantly improved noise thresholds. Furthermore we show that already resource states of small size suffice to significantly increase the maximal communication distance. We also discuss possible advantages of our scheme for different set-ups.

  3. Repeated measurements of cerebral blood flow in the left superior temporal gyrus reveal tonic hyperactivity in patients with auditory verbal hallucinations: A possible trait marker

    Directory of Open Access Journals (Sweden)

    Philipp eHoman

    2013-06-01

    Full Text Available Background: The left superior temporal gyrus (STG has been suggested to play a key role in auditory verbal hallucinations in patients with schizophrenia. Methods: Eleven medicated subjects with schizophrenia and medication-resistant auditory verbal hallucinations and 19 healthy controls underwent perfusion magnetic resonance imaging with arterial spin labeling. Three additional repeated measurements were conducted in the patients. Patients underwent a treatment with transcranial magnetic stimulation (TMS between the first 2 measurements. The main outcome measure was the pooled cerebral blood flow (CBF, which consisted of the regional CBF measurement in the left superior temporal gyrus (STG and the global CBF measurement in the whole brain.Results: Regional CBF in the left STG in patients was significantly higher compared to controls (p < 0.0001 and to the global CBF in patients (p < 0.004 at baseline. Regional CBF in the left STG remained significantly increased compared to the global CBF in patients across time (p < 0.0007, and it remained increased in patients after TMS compared to the baseline CBF in controls (p < 0.0001. After TMS, PANSS (p = 0.003 and PSYRATS (p = 0.01 scores decreased significantly in patients.Conclusions: This study demonstrated tonically increased regional CBF in the left STG in patients with schizophrenia and auditory hallucinations despite a decrease in symptoms after TMS. These findings were consistent with what has previously been termed a trait marker of auditory verbal hallucinations in schizophrenia.

  4. Multivariate linear models and repeated measurements revisited

    DEFF Research Database (Denmark)

    Dalgaard, Peter

    2009-01-01

    Methods for generalized analysis of variance based on multivariate normal theory have been known for many years. In a repeated measurements context, it is most often of interest to consider transformed responses, typically within-subject contrasts or averages. Efficiency considerations leads...

  5. On balanced minimal repeated measurements designs

    Directory of Open Access Journals (Sweden)

    Shakeel Ahmad Mir

    2014-10-01

    Full Text Available Repeated Measurements designs are concerned with scientific experiments in which each experimental unit is assigned more than once to a treatment either different or identical. This class of designs has the property that the unbiased estimators for elementary contrasts among direct and residual effects are obtainable. Afsarinejad (1983 provided a method of constructing balanced Minimal Repeated Measurements designs p < t , when t is an odd or prime power, one or more than one treatment may occur more than once in some sequences and  designs so constructed no longer remain uniform in periods. In this paper an attempt has been made to provide a new method to overcome this drawback. Specifically, two cases have been considered                RM[t,n=t(t-t/(p-1,p], λ2=1 for balanced minimal repeated measurements designs and  RM[t,n=2t(t-t/(p-1,p], λ2=2 for balanced  repeated measurements designs. In addition , a method has been provided for constructing              extra-balanced minimal designs for special case RM[t,n=t2/(p-1,p], λ2=1.

  6. Nonparametric additive regression for repeatedly measured data

    KAUST Repository

    Carroll, R. J.

    2009-05-20

    We develop an easily computed smooth backfitting algorithm for additive model fitting in repeated measures problems. Our methodology easily copes with various settings, such as when some covariates are the same over repeated response measurements. We allow for a working covariance matrix for the regression errors, showing that our method is most efficient when the correct covariance matrix is used. The component functions achieve the known asymptotic variance lower bound for the scalar argument case. Smooth backfitting also leads directly to design-independent biases in the local linear case. Simulations show our estimator has smaller variance than the usual kernel estimator. This is also illustrated by an example from nutritional epidemiology. © 2009 Biometrika Trust.

  7. Bayesian model selection of informative hypotheses for repeated measurements

    NARCIS (Netherlands)

    Mulder, Joris; Klugkist, I.G.; Schoot, Rens van de; Meeus, W.H.J.; Selfhout, Maarten; Hoijtink, Herbert

    2010-01-01

    When analyzing repeated measurements data, researchers often have expectations about the relations between the measurement means. The expectations can often be formalized using equality and inequality constraints between (i) the measurement means over time, (ii) the measurement means between

  8. Bayesian model selection of informative hypotheses for repeated measurements

    NARCIS (Netherlands)

    Mulder, J.|info:eu-repo/dai/nl/304823031; Klugkist, I.G.|info:eu-repo/dai/nl/27330089X; Van de Schoot, R.|info:eu-repo/dai/nl/304833207; Meeus, W.H.J.|info:eu-repo/dai/nl/070442215; van Zalk, M.H.W.|info:eu-repo/dai/nl/304836214; Hoijtink, H.J.A.|info:eu-repo/dai/nl/075184427

    2009-01-01

    When analyzing repeated measurements data, researchers often have expectations about the relations between the measurement means. The expectations can often be formalized using equality and inequality constraints between (i) the measurement means over time, (ii) the measurement means between groups,

  9. Analysis of repeated outcome measures from longitudinal studies

    Institute of Scientific and Technical Information of China (English)

    Yuanjia WANG; Naihua DUAN

    2011-01-01

    @@ In many clinical studies repeated measurements of an outcome are collected over time.For example,in an 8-week study of treatment for obsessive compulsive disorder,the severity of the disorder may be measured weekly using the Yale-Brown-Obsessive-Compulsive-Disorder-Scale (YBOCS).For each study participant who completes the study,there will be nine repeated measures of YBOCS (a baseline assessment plus eight assessments during the course of treatment).Such a study in which participants are followed and measured repeatedly over time is called a longitudinal study and the resulting data are called longitudinal data.

  10. Airborne Repeat Pass Interferometry for Deformation Measurements

    NARCIS (Netherlands)

    Groot, J.; Otten, M.; Halsema, E. van

    2000-01-01

    In ground engineering the need for deformation measurements is urgent. SAR interferometry can be used to measure small (sub-wavelength) deformations. An experiment to investigate this for dike deformations was set up, using the C-band SAR system PHARUS (PHased ARray Universal SAR). This paper descri

  11. Discriminant analysis for repeated measures data: a review

    Directory of Open Access Journals (Sweden)

    Lisa Lix

    2010-09-01

    Full Text Available Discriminant analysis (DA encompasses procedures for classifying observations into groups (i.e., predictive discriminative analysis and describing the relative importance of variables for distinguishing amongst groups (i.e., descriptive discriminative analysis. In recent years, a number of developments have occurred in DA procedures for the analysis of data from repeated measures designs. Specifically, DA procedures have been developed for repeated measures data characterized by missing observations and/or unbalanced measurement occasions, as well as high-dimensional data in which measurements are collected repeatedly on two or more variables. This paper reviews the literature on DA procedures for univariate and multivariate repeated measures data, focusing on covariance pattern and linear mixed-effects models. A numeric example illustrates their implementation using SAS software.

  12. Coseismic and postseismic velocity changes measured by repeating earthquakes

    Science.gov (United States)

    Schaff, David P.; Beroza, Gregory C.

    2004-10-01

    Repeating earthquakes that rupture approximately the same fault patch and have nearly identical waveforms are a useful tool for measuring temporal changes in wave propagation in the Earth's crust. Since source and path effects are common to all earthquakes in a repeating earthquake sequence (multiplet), differences in their waveforms can be attributed to changes in the characteristics of the medium. We have identified over 20 multiplets containing between 5 and 40 repeating events in the aftershock zones of the 1989 Loma Prieta and 1984 Morgan Hill, California, earthquakes. Postmain shock events reveal delays of phases in the early S wave coda of as much as 0.2 s relative to premain shock events. The delay amounts to a path-averaged coseismic velocity decrease of about 1.5% for P waves and 3.5% for S waves. Since most of the multiplets are aftershocks and follow Omori's law, we have excellent temporal sampling in the immediate postmain shock period. We find that the amplitude of the velocity decrease decays logarithmically in time following the main shock. In some cases it returns to the premain shock values, while in others it does not. Similar results are obtained for the Morgan Hill main shock. Because the fractional change in S wave velocity is greater than the fractional change in P wave velocity, it suggests that the opening or connection of fluid-filled fractures is the underlying cause. The magnitude of the velocity change implies that low effective pressures are present in the source region of the velocity change. Our results suggest that the changes are predominantly near the stations and shallow, but we cannot exclude the possibility that changes occur at greater depth as well. If the variations are shallow, we may be detecting the lingering effects of nonlinearity during main shock strong ground motion. If the variations are deep, it suggests that pore pressures at seismogenic depths are high, which would likely play a key role in the earthquake process.

  13. Stability of parameters in repeated TVA measures

    DEFF Research Database (Denmark)

    Sørensen, Thomas Alrik

    Several recent studies have explored the limitations of human visual short-term memory or VSTM (e.g. Luck & Vogel, 1997; Wheeler & Treisman, 2002; Alvarez & Cavanagh, 2004). Usually researchers agree that VSTM is limited to a capacity of about 3 to 4 objects at any given moment (Cowan, 2001......). Capacity of short-term memory is measured in a range of studies often using the change detection paradigm (CD). However, the whole report paradigm (WR) may be a more reliable paradigm (Cusack, Lehmann, Veldsman, & Mitchell, 2009). Moreover, each individual WR trial yield more information compared to a CD...

  14. Correct use of repeated measures analysis of variance.

    Science.gov (United States)

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

    2009-02-01

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

  15. Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

    Directory of Open Access Journals (Sweden)

    Hua Wan

    2016-01-01

    Full Text Available TAL effectors (TALEs contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.

  16. Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study

    Science.gov (United States)

    Wan, Hua; Chang, Shan; Hu, Jian-ping; Tian, Xu-hong

    2016-01-01

    TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE. PMID:27803930

  17. Repeated measurement sampling in genetic association analysis with genotyping errors.

    Science.gov (United States)

    Lai, Renzhen; Zhang, Hong; Yang, Yaning

    2007-02-01

    Genotype misclassification occurs frequently in human genetic association studies. When cases and controls are subject to the same misclassification model, Pearson's chi-square test has the correct type I error but may lose power. Most current methods adjusting for genotyping errors assume that the misclassification model is known a priori or can be assessed by a gold standard instrument. But in practical applications, the misclassification probabilities may not be completely known or the gold standard method can be too costly to be available. The repeated measurement design provides an alternative approach for identifying misclassification probabilities. With this design, a proportion of the subjects are measured repeatedly (five or more repeats) for the genotypes when the error model is completely unknown. We investigate the applications of the repeated measurement method in genetic association analysis. Cost-effectiveness study shows that if the phenotyping-to-genotyping cost ratio or the misclassification rates are relatively large, the repeat sampling can gain power over the regular case-control design. We also show that the power gain is not sensitive to the genetic model, genetic relative risk and the population high-risk allele frequency, all of which are typically important ingredients in association studies. An important implication of this result is that whatever the genetic factors are, the repeated measurement method can be applied if the genotyping errors must be accounted for or the phenotyping cost is high.

  18. Assessment of bone loss with repeated bone mineral measurements: Application to measurements on the individual patient

    Energy Technology Data Exchange (ETDEWEB)

    Wahner, H.W.

    1987-02-01

    Longitudinal measurements on lumbar spine and mid-radius were made by bone absorptiometry techniques in 139 normal women. Bone mineral was measured every 6 months over an median interval of 2.1 years. The results revealed that bone loss at different skeletal sites is non-uniform with equal bone loss patterns in all patients and relatively small variations in bone loss rate between normal women. For achieving these results there is strong demand on high precision and properly spaced measuring intervals for long-term rate of loss measurements. For exclusion of progressive degenerative disease a radiographic evaluation of the spine in the beginning and at the end of the study is mandatory as compression fractures or trauma reveal bone mineral changes independent from the agerelated bone loss. These repeated bone mineral measurements are useful for monitoring and follow-up studies during different therapeutic regimens.

  19. Assessing agreement with repeated measures for random observers.

    Science.gov (United States)

    Chen, Chia-Cheng; Barnhart, Huiman X

    2011-12-30

    Agreement studies are often concerned with assessing whether different observers for measuring responses on the same subject or sample can produce similar results. The concordance correlation coefficient (CCC) is a popular index for assessing the closeness among observers for quantitative measurements. Usually, the CCC is used for data without and with replications based on subject and observer effects only. However, we cannot use this methodology if repeated measurements rather than replications are collected. Although there exist some CCC-type indices for assessing agreement with repeated measurements, there is no CCC for random observers and random time points. In this paper, we propose a new CCC for repeated measures where both observers and time points are treated as random effects. A simulation study demonstrates our proposed methodology, and we use vertebral body data and image data for illustrations.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Conservative Sample Size Determination for Repeated Measures Analysis of Covariance.

    Science.gov (United States)

    Morgan, Timothy M; Case, L Douglas

    2013-07-05

    In the design of a randomized clinical trial with one pre and multiple post randomized assessments of the outcome variable, one needs to account for the repeated measures in determining the appropriate sample size. Unfortunately, one seldom has a good estimate of the variance of the outcome measure, let alone the correlations among the measurements over time. We show how sample sizes can be calculated by making conservative assumptions regarding the correlations for a variety of covariance structures. The most conservative choice for the correlation depends on the covariance structure and the number of repeated measures. In the absence of good estimates of the correlations, the sample size is often based on a two-sample t-test, making the 'ultra' conservative and unrealistic assumption that there are zero correlations between the baseline and follow-up measures while at the same time assuming there are perfect correlations between the follow-up measures. Compared to the case of taking a single measurement, substantial savings in sample size can be realized by accounting for the repeated measures, even with very conservative assumptions regarding the parameters of the assumed correlation matrix. Assuming compound symmetry, the sample size from the two-sample t-test calculation can be reduced at least 44%, 56%, and 61% for repeated measures analysis of covariance by taking 2, 3, and 4 follow-up measures, respectively. The results offer a rational basis for determining a fairly conservative, yet efficient, sample size for clinical trials with repeated measures and a baseline value.

  2. Measurement and repeatability of interrupter resistance in unsedated newborn infants.

    Science.gov (United States)

    Adams, A M; Olden, C; Wertheim, D; Ives, A; Bridge, P D; Lenton, J; Seddon, P

    2009-12-01

    Interrupter resistance (R(int)) is a useful measure of airway caliber in young children, but has not been well characterized in infants-in whom there are concerns about the accurate measurement of driving pressure. This study aimed to assess the feasibility and repeatability of measuring R(int) in unsedated newborn infants, and to explore alternative algorithms for calculating driving pressure. R(int) measurement was attempted in 28 healthy term newborn infants during natural sleep using the MicroRint device. Paired R(int) measurements were achieved in 24 infants, but after screening of waveforms only 15 infants had at least 5 technically acceptable waveforms on both measurements. R(int) values obtained were comparable with reported values for airflow resistance in newborns using other methods. However, the repeatability coefficient (CR) was much higher than reported values in preschool children using standard back-extrapolation algorithms, with CR 2.47 KPa L(-1) sec (unscreened) and 2.93 KPa L(-1) sec (screened). Other algorithms gave only marginally better repeatability, with all CR values over 50% of the mean R(int) value. Using current commercially available equipment, R(int) is too poorly repeatable to be a reliable measurement of airflow resistance in newborn infants. Lower deadspace equipment is needed, but anatomical and physiological factors in the infant are also important.

  3. Modeling repeated measurement data for occupational exposure assessment and epidemiology

    NARCIS (Netherlands)

    Peretz, Chava

    2004-01-01

    Repeated measurements designs, occur frequently in the assessment of exposure to toxic chemicals. This thesis deals with the possibilities of using mixed effects models for occupational exposure assessment and in the analysis of exposure response relationships. The model enables simultaneous estima

  4. Applying the General Linear Model to Repeated Measures Problems.

    Science.gov (United States)

    Pohlmann, John T.; McShane, Michael G.

    The purpose of this paper is to demonstrate the use of the general linear model (GLM) in problems with repeated measures on a dependent variable. Such problems include pretest-posttest designs, multitrial designs, and groups by trials designs. For each of these designs, a GLM analysis is demonstrated wherein full models are formed and restrictions…

  5. Positional Repeatability Measurements Of Stepper Motors At Cryogenic Temperatures

    Science.gov (United States)

    Pompea, Stephen M.; Hall, Michael S.; Bartko, Frank; Houck, James R.

    1983-08-01

    Stepper motors operating at liquid helium temperature have multiple applications in cryogenically-cooled telescopes such as the Shuttle Infrared Telescope Facility (SIRTF). These SIRTF applications include driving cryogen flow valves, operating the Multiple Instrument Chamber (MIC) beam splitter mechanism, and operating filters and grating wheel mechanisms in the scientific instruments. The positional repeatability of the beam splitter drive mechanism is especially critical since it feeds the optical beam to the scien-tific instruments. Despite these important applications, no significant data on the positional repeatability of stepper motors at cryogenic temperatures has been available. Therefore, we conducted a series of measurements to determine the positional repeatability of a modified, off-the-shelf Berger/Lahr stepper motor (model RDM 253/25, step angle 3.6°) which had demonstrated excellent performance in previous endurance testing at LHe temperature. These test results indicated that the positional repeatability of the motor was excellent at all temperatures, with somewhat better performance at cryogenic temperatures. Another important result was that the motor could be repeatedly turned off and on while still accurately retaining its rotor position.

  6. Repeatability of OCT lens thickness measures with age and accommodation.

    Science.gov (United States)

    Doyle, Lesley; Little, Julie-Anne; Saunders, Kathryn J

    2013-12-01

    To investigate crystalline lens thickness (LT) across a range of ages and accommodative demands and to evaluate the repeatability of LT measurements using the Visante Anterior Segment Optical Coherence Tomographer (AS-OCT) (Zeiss Meditec, Germany) under non-cycloplegic conditions. Participants were 98 visually normal adults aged 18-75 years, stratified into age groups of 18-29, 30-39, 40-49, 50-59, and 60-75 years of age. Images of the crystalline lens were taken using the Visante AS-OCT during stimulation of accommodation at demands of 0, 1, 2, 3, 4, 5, and 8 D with accommodative response measured in a subgroup of participants. Images were analyzed and LT measured assuming a refractive index of 1.42. Repeat measures were taken from 86 participants for each accommodative demand at a second visit. The mean unaccommodated LT for all participants was 4.07 ± 0.40 mm. An average increase in LT of 20 μm per year was calculated (linear regression, R² = 0.61, F(1,89) = 143.92, p report the repeatability of LT measures using the Visante AS-OCT in the non-cyclopleged eye. It has also demonstrated the ability of the Visante AS-OCT to detect small changes in lens thickness with accommodation.

  7. Measuring Repeatability of the Focus-variable Lenses

    Directory of Open Access Journals (Sweden)

    Jan Řezníček

    2014-12-01

    Full Text Available In the field of photogrammetry, the optical system, usually represented by the glass lens, is used for metric purposes. Therefore, the aberration characteristics of such a lens, inducing deviations from projective imaging, has to be well known. However, the most important property of the metric lens is the stability of its glass and mechanical elements, ensuring long-term reliability of the measured parameters. In case of a focus-variable lens, the repeatability of the lens setup is important as well. Lenses with a fixed focal length are usually considered as “fixed” though, in fact, most of them contain one or more movable glass elements, providing the focusing function. In cases where the lens is not equipped with fixing screws, the repeatability of the calibration parameters should be known. This paper derives simple mathematical formulas that can be used for measuring the repeatability of the focus-variable lenses, and gives a demonstrative example of such measuring. The given procedure has the advantage that only demanded parameters are estimated, hence, no unwanted correlations with the additional parameters exist. The test arrangement enables us to measure each demanded magnification of the optical system, which is important in close-range photogrammetry.

  8. Capturing learning effects on eye movements in repeated measures experiments

    DEFF Research Database (Denmark)

    Bagger, Martin; Orquin, Jacob Lund; Fiedler, Susann

    We propose and illustrate that repeated exposure to stimuli sets increases the size of the saccade amplitudes. Saccadic amplitudes are closely related to the perceptual span and therefore used as a measure for the information intake in an experiment. Studies on expertise have shown that experts...... experiment in which 68 participants made choices between four alternatives with three different between subject conditions varying in presentation format (verbal matrix, a pictorial matrix, and a realistic product representation). The results consistently demonstrate an increase of the saccade amplitude over...... the course of the experiment independent of condition. We conclude by discussing our results in the light of the possible increase of the perceptual span and its implications for the research procedure in eye-tracking experiments with a repeated measurement design....

  9. Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin

    Science.gov (United States)

    Fogl, Claudia; Mohammed, Fiyaz; Al-Jassar, Caezar; Jeeves, Mark; Knowles, Timothy J.; Rodriguez-Zamora, Penelope; White, Scott A.; Odintsova, Elena; Overduin, Michael; Chidgey, Martyn

    2016-03-01

    Plakin proteins form critical connections between cell junctions and the cytoskeleton; their disruption within epithelial and cardiac muscle cells cause skin-blistering diseases and cardiomyopathies. Envoplakin has a single plakin repeat domain (PRD) which recognizes intermediate filaments through an unresolved mechanism. Herein we report the crystal structure of envoplakin's complete PRD fold, revealing binding determinants within its electropositive binding groove. Four of its five internal repeats recognize negatively charged patches within vimentin via five basic determinants that are identified by nuclear magnetic resonance spectroscopy. Mutations of the Lys1901 or Arg1914 binding determinants delocalize heterodimeric envoplakin from intracellular vimentin and keratin filaments in cultured cells. Recognition of vimentin is abolished when its residues Asp112 or Asp119 are mutated. The latter slot intermediate filament rods into basic PRD domain grooves through electrosteric complementarity in a widely applicable mechanism. Together this reveals how plakin family members form dynamic linkages with cytoskeletal frameworks.

  10. Modeling intraindividual variability with repeated measures data methods and applications

    CERN Document Server

    Hershberger, Scott L

    2013-01-01

    This book examines how individuals behave across time and to what degree that behavior changes, fluctuates, or remains stable.It features the most current methods on modeling repeated measures data as reported by a distinguished group of experts in the field. The goal is to make the latest techniques used to assess intraindividual variability accessible to a wide range of researchers. Each chapter is written in a ""user-friendly"" style such that even the ""novice"" data analyst can easily apply the techniques.Each chapter features:a minimum discussion of mathematical detail;an empirical examp

  11. Unitarity, Feedback, Interactions -- Dynamics Emergent from Repeated Measurements

    CERN Document Server

    Altamirano, Natacha; Mann, Robert B; Zych, Magdalena

    2016-01-01

    Motivated by the recent efforts to describe the gravitational interaction as a classical channel arising from continuous quantum measurements, we study what types of dynamics can emerge from a model of repeated short interactions of a system with a set of ancillae. We show that contingent on the model parameters the resulting dynamics ranges from exact unitarity to arbitrary fast decoherence (quantum Zeno effect). For a series of measurements the effective dynamics includes feedback-control, which for a composite system yields effective interactions between the subsystems. We quantify the amount of decoherence accompanying such induced interactions, generalizing the lower bound of the gravitational example. However, by allowing multipartite measurements, the interactions can be induced with arbitrary low decoherence. Our results have implications for gravity-inspired decoherence models and the simple framework used in the present study can find applications in devising novel quantum control protocols, or quan...

  12. Repeated High-Precision Gravity and GPS Measurement Techniques

    Science.gov (United States)

    Gettings, P.; Harris, R. N.; Allis, R.; Chapman, D. S.

    2003-12-01

    Repeated high-precision gravity and GPS measurements are becoming a common tool for tracking changes in subsurface reservoirs. Despite this, there is little literature which discusses measurement techniques and the expected errors. Our research has focused on improving measurement techniques to be applied to ground water and geothermal steam reservoirs, including quantifying the minimum error levels with modern equipment. We applied these methods in two studies: ground water monitoring of the southern Salt Lake valley, Utah, USA, and steam monitoring of The Geysers geothermal field, California, USA. Gravity measurements using modern relative high-precision meters, such as Scintrex CG-3Ms or L&R E series, can now be routinely made to an accuracy of 5 μ Gal. Such accuracy requires the use of time series analysis at each station, and non-linear instrument drift functions. Modern computerized meters are capable of internally storing a time series of measurements for each station; older meters can often be fitted to log such data to a field computer. This time series, typically of 10-15 minute duration in our work, can then be analyzed in several ways to produce stable estimates of the gravity reading. In particular, our research has emphasized using a weighted arithmetic average (for long occupations), or a Thiele extrapolation scheme (for shorter station occupations). Instrument drift is removed through a superposition of a linear long-term drift function, and an empirical staircase function formed from differences between repeated station occupations. To achieve high-accuracy GPS measurements while maximizing the number of field stations in a survey, rapid-static measurements are necessary. We have tested the effect of occupation time and processing schemes on the absolute accuracy of the resulting GPS position. Using a post-processing differential method with a fixed (but not necessarily continuous) base station within 15 km, positioning error of <4 cm vertical is

  13. Quasar Variability Measurements With SDSS Repeated Imaging and POSS Data

    CERN Document Server

    Ivezic, Z; Juric, M; Anderson, S; Hall, P B; Richards, G T; Rockosi, C M; Vanden Berk, Daniel E; Turner, E L; Knapp, G R; Gunn, J E; Schlegel, D J; Strauss, M A; Schneider, D P

    2004-01-01

    We analyze the properties of quasar variability using repeated SDSS imaging data in five UV-to-far red photometric bands, accurate to 0.02 mag, for 13,000 spectroscopically confirmed quasars. The observed time lags span the range from 3 hours to over 3 years, and constrain the quasar variability for rest-frame time lags of up to two years, and at rest-frame wavelengths from 1000 Ang. to 6000 Ang. We demonstrate that 66,000 SDSS measurements of magnitude differences can be described within the measurement noise by a simple function of only three free parameters. The addition of POSS data constrains the long-term behavior of quasar variability and provides evidence for a turn-over in the structure function. This turn-over indicates that the characteristic time scale for optical variability of quasars is of the order 1 year.

  14. Dispersion Measure Variation of Repeating Fast Radio Burst Sources

    Science.gov (United States)

    Yang, Yuan-Pei; Zhang, Bing

    2017-09-01

    The repeating fast radio burst (FRB) 121102 was recently localized in a dwarf galaxy at a cosmological distance. The dispersion measure (DM) derived for each burst from FRB 121102 so far has not shown significant evolution, even though an apparent increase was recently seen with newly detected VLA bursts. It is expected that more repeating FRB sources may be detected in the future. In this work, we investigate a list of possible astrophysical processes that might cause DM variation of a particular FRB source. The processes include (1) cosmological scale effects such as Hubble expansion and large-scale structure fluctuations; (2) FRB local effects such as gas density fluctuation, expansion of a supernova remnant (SNR), a pulsar wind nebula, and an H ii region; and (3) the propagation effect due to plasma lensing. We find that the DM variations contributed by the large-scale structure are extremely small, and any observable DM variation is likely caused by the plasma local to the FRB source. In addition to mechanisms that decrease DM over time, we suggest that an FRB source in an expanding SNR around a nearly neutral ambient medium during the deceleration (Sedov–Taylor and snowplow) phases or in a growing H ii region can increase DM. Some effects (e.g., an FRB source moving in an H ii region or plasma lensing) can produce either positive or negative DM variations. Future observations of DM variations of FRB 121102 and other repeating FRB sources can provide important clues regarding the physical origin of these sources.

  15. Bayesian Concordance Correlation Coefficient with Application to Repeatedly Measured Data

    Directory of Open Access Journals (Sweden)

    Atanu BHATTACHARJEE

    2015-10-01

    Full Text Available Objective: In medical research, Lin's classical concordance correlation coefficient (CCC is frequently applied to evaluate the similarity of the measurements produced by different raters or methods on the same subjects. It is particularly useful for continuous data. The objective of this paper is to propose the Bayesian counterpart to compute CCC for continuous data. Material and Methods: A total of 33 patients of astrocytoma brain treated in the Department of Radiation Oncology at Malabar Cancer Centre is enrolled in this work. It is a continuous data of tumor volume and tumor size repeatedly measured during baseline pretreatment workup and post surgery follow-ups for all patients. The tumor volume and tumor size are measured separately by MRI and CT scan. The agreement of measurement between MRI and CT scan is calculated through CCC. The statistical inference is performed through Markov Chain Monte Carlo (MCMC technique. Results: Bayesian CCC is found suitable to get prominent evidence for test statistics to explore the relation between concordance measurements. The posterior mean estimates and 95% credible interval of CCC on tumor size and tumor volume are observed with 0.96(0.87,0.99 and 0.98(0.95,0.99 respectively. Conclusion: The Bayesian inference is adopted for development of the computational algorithm. The approach illustrated in this work provides the researchers an opportunity to find out the most appropriate model for specific data and apply CCC to fulfill the desired hypothesis.

  16. A Simple and Transparent Alternative to Repeated Measures ANOVA

    Directory of Open Access Journals (Sweden)

    James W. Grice

    2015-09-01

    Full Text Available Observation Oriented Modeling is a novel approach toward conceptualizing and analyzing data. Compared with traditional parametric statistics, Observation Oriented Modeling is more intuitive, relatively free of assumptions, and encourages researchers to stay close to their data. Rather than estimating abstract population parameters, the overarching goal of the analysis is to identify and explain distinct patterns within the observations. Selected data from a recent study by Craig et al. were analyzed using Observation Oriented Modeling; this analysis was contrasted with a traditional repeated measures ANOVA assessment. Various pitfalls in traditional parametric analyses were avoided when using Observation Oriented Modeling, including the presence of outliers and missing data. The differences between Observation Oriented Modeling and various parametric and nonparametric statistical methods were finally discussed.

  17. Matrix-based concordance correlation coefficient for repeated measures.

    Science.gov (United States)

    Hiriote, Sasiprapa; Chinchilli, Vernon M

    2011-09-01

    In many clinical studies, Lin's concordance correlation coefficient (CCC) is a common tool to assess the agreement of a continuous response measured by two raters or methods. However, the need for measures of agreement may arise for more complex situations, such as when the responses are measured on more than one occasion by each rater or method. In this work, we propose a new CCC in the presence of repeated measurements, called the matrix-based concordance correlation coefficient (MCCC) based on a matrix norm that possesses the properties needed to characterize the level of agreement between two p× 1 vectors of random variables. It can be shown that the MCCC reduces to Lin's CCC when p= 1. For inference, we propose an estimator for the MCCC based on U-statistics. Furthermore, we derive the asymptotic distribution of the estimator of the MCCC, which is proven to be normal. The simulation studies confirm that overall in terms of accuracy, precision, and coverage probability, the estimator of the MCCC works very well in general cases especially when n is greater than 40. Finally, we use real data from an Asthma Clinical Research Network (ACRN) study and the Penn State Young Women's Health Study for demonstration.

  18. [Analysis of binary classification repeated measurement data with GEE and GLMMs using SPSS software].

    Science.gov (United States)

    An, Shengli; Zhang, Yanhong; Chen, Zheng

    2012-12-01

    To analyze binary classification repeated measurement data with generalized estimating equations (GEE) and generalized linear mixed models (GLMMs) using SPSS19.0. GEE and GLMMs models were tested using binary classification repeated measurement data sample using SPSS19.0. Compared with SAS, SPSS19.0 allowed convenient analysis of categorical repeated measurement data using GEE and GLMMs.

  19. REPEATED MEASURES ANALYSIS OF CHANGES IN PHOTOSYNTHETIC EFFICIENCY IN SOUR CHERRY DURING WATER DEFICIT

    Directory of Open Access Journals (Sweden)

    Marija Viljevac

    2012-06-01

    Full Text Available The objective of this study was to investigate changes in photosynthetic efficiency applying repeated measures ANOVA using the photosynthetic performance index (PIABS of the JIP-test as a vitality parameter in seven genotypes of sour cherry (Prunus cerasus, L. during 10 days of continuous water deficit. Both univariate and multivariate ANOVA repeated measures revealed highly significant time effect (Days and its subsequent interactions with genotype and water deficit. However, the multivariate Pillai’s trace test detected the interaction Time × Genotype × Water deficit as not significant. According to the Tukey’s Studentized Range (HSD test, differences between the control and genotypes exposed to water stress became significant on the fourth day of the experiment, indicating that the plants on the average, began to lose their photosynthetic efficiency four days after being exposed to water shortage. It corroborates previous findings in other species that PIABS is very sensitive tool for detecting drought stress.

  20. Rank-Based Analysis of Unbalanced Repeated Measures Data

    Directory of Open Access Journals (Sweden)

    M. Mushfiqur Rashid

    2012-07-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";} In this article, we have developed a rank (intra-subject based analysis of clinical trials with unbalanced repeated measures data. We assume that the errors within each patient are exchangeable and continuous random variables. This rank-based inference is valid when the unbalanced data are missing either completely at random or by design. A drop in dispersion test is developed for general linear hypotheses. A numerical example is given to illustrate the procedure.

  1. Individual and population variation in invertebrates revealed by Inter-simple Sequence Repeats (ISSRs

    Directory of Open Access Journals (Sweden)

    Patrick Abbot

    2001-08-01

    Full Text Available PCR-based molecular markers are well suited for questions requiring large scale surveys of plant and animal populations. Inter-simple Sequence Repeats or ISSRs are analyzed by a recently developed technique based on the amplification of the regions between inverse-oriented microsatellite loci with oligonucleotides anchored in microsatellites themselves. ISSRs have shown much promise for the study of the population biology of plants, but have not yet been explored for similar studies of animals. The value of ISSRs is demonstrated for the study of animal species with low levels of within-population variation. Sets of primers are identified which reveal variation in two aphid species, Acyrthosiphon pisum and Pemphigus obesinymphae, in the yellow fever mosquito Aedes aegypti, and in a rotifer in the genus Philodina.

  2. Antarctic Ice Sheet Slope and Aspect Based on Icesat's Repeat Orbit Measurement

    Science.gov (United States)

    Yuan, L.; Li, F.; Zhang, S.; Xie, S.; Xiao, F.; Zhu, T.; Zhang, Y.

    2017-09-01

    Accurate information of ice sheet surface slope is essential for estimating elevation change by satellite altimetry measurement. A study is carried out to recover surface slope of Antarctic ice sheet from Ice, Cloud and land Elevation Satellite (ICESat) elevation measurements based on repeat orbits. ICESat provides repeat ground tracks within 200 meters in cross-track direction and 170 meters in along-track direction for most areas of Antarctic ice sheet. Both cross-track and along-track surface slopes could be obtained by adjacent repeat ground tracks. Combining those measurements yields a surface slope model with resolution of approximately 200 meters. An algorithm considering elevation change is developed to estimate the surface slope of Antarctic ice sheet. Three Antarctic Digital Elevation Models (DEMs) were used to calculate surface slopes. The surface slopes from DEMs are compared with estimates by using in situ GPS data in Dome A, the summit of Antarctic ice sheet. Our results reveal an average surface slope difference of 0.02 degree in Dome A. High resolution remote sensing images are also used in comparing the results derived from other DEMs and this paper. The comparison implies that our results have a slightly better coherence with GPS observation than results from DEMs, but our results provide more details and perform higher accuracy in coastal areas because of the higher resolution for ICESat measurements. Ice divides are estimated based on the aspect, and are weakly consistent with ice divides from other method in coastal regions.

  3. [Analysis of variance of repeated data measured by water maze with SPSS].

    Science.gov (United States)

    Qiu, Hong; Jin, Guo-qin; Jin, Ru-feng; Zhao, Wei-kang

    2007-01-01

    To introduce the method of analyzing repeated data measured by water maze with SPSS 11.0, and offer a reference statistical method to clinical and basic medicine researchers who take the design of repeated measures. Using repeated measures and multivariate analysis of variance (ANOVA) process of the general linear model in SPSS and giving comparison among different groups and different measure time pairwise. Firstly, Mauchly's test of sphericity should be used to judge whether there were relations among the repeatedly measured data. If any (PSPSS statistical package is available to fulfil this process.

  4. Detecting tropical forest biomass dynamics from repeated airborne lidar measurements

    Directory of Open Access Journals (Sweden)

    V. Meyer

    2013-08-01

    census data, differences of approximately one year between the ground census and lidar measurements, and differences in sensor characteristics. Our results indicate that the 50 ha BCI plot lost a significant amount of biomass (−0.8 Mg ha−1 yr−1 ± 2.2(SD over the past decade (2000–2010. Over the entire island and during the same period, mean AGB change was 0.2 ± 2.4 Mg ha−1 yr−1 with old growth forests losing −0.7 Mg ha−1 yr−1 ± 2.2 (SD, and secondary forests gaining +1.8 Mg ha yr−1 ± 3.4 (SD biomass. Our analysis suggests that repeated lidar surveys, despite taking measurement with different sensors, can estimate biomass changes in old-growth tropical forests at landscape scales (>10 ha.

  5. [Repeated measurement of memory with valenced test items: verbal memory, working memory and autobiographic memory].

    Science.gov (United States)

    Kuffel, A; Terfehr, K; Uhlmann, C; Schreiner, J; Löwe, B; Spitzer, C; Wingenfeld, K

    2013-07-01

    A large number of questions in clinical and/or experimental neuropsychology require the multiple repetition of memory tests at relatively short intervals. Studies on the impact of the associated exercise and interference effects on the validity of the test results are rare. Moreover, hardly any neuropsychological instruments exist to date to record the memory performance with several parallel versions in which the emotional valence of the test material is also taken into consideration. The aim of the present study was to test whether a working memory test (WST, a digit-span task with neutral or negative distraction stimuli) devised by our workgroup can be used with repeated measurements. This question was also examined in parallel versions of a wordlist learning paradigm and an autobiographical memory test (AMT). Both tests contained stimuli with neutral, positive and negative valence. Twenty-four participants completed the memory testing including the working memory test and three versions of a wordlist and the AMT at intervals of a week apiece (measuring points 1. - 3.). The results reveal consistent performances across the three measuring points in the working and autobiographical memory test. The valence of the stimulus material did not influence the memory performance. In the delayed recall of the wordlist an improvement in memory performance over time was seen. The tests on working memory presented and the parallel versions for the declarative and autobiographical memory constitute informal economic instruments within the scope of the measurement repeatability designs. While the WST and AMT are appropriate for study designs with repeated measurements at relatively short intervals, longer intervals might seem more favourable for the use of wordlist learning paradigms. © Georg Thieme Verlag KG Stuttgart · New York.

  6. Sequencing analysis of the spinal bulbar muscular atrophy CAG expansion reveals absence of repeat interruptions.

    Science.gov (United States)

    Fratta, Pietro; Collins, Toby; Pemble, Sally; Nethisinghe, Suran; Devoy, Anny; Giunti, Paola; Sweeney, Mary G; Hanna, Michael G; Fisher, Elizabeth M C

    2014-02-01

    Trinucleotide repeat disorders are a heterogeneous group of diseases caused by the expansion, beyond a pathogenic threshold, of unstable DNA tracts in different genes. Sequence interruptions in the repeats have been described in the majority of these disorders and may influence disease phenotype and heritability. Spinal bulbar muscular atrophy (SBMA) is a motor neuron disease caused by a CAG trinucleotide expansion in the androgen receptor (AR) gene. Diagnostic testing and previous research have relied on fragment analysis polymerase chain reaction to determine the AR CAG repeat size, and have therefore not been able to assess the presence of interruptions. We here report a sequencing study of the AR CAG repeat in a cohort of SBMA patients and control subjects in the United Kingdom. We found no repeat interruptions to be present, and we describe differences between sequencing and traditional sizing methods.

  7. Using repeated measures of sleep disturbances to predict future diagnosis-specific work disability

    DEFF Research Database (Denmark)

    Salo, Paula; Vahtera, Jussi; Hall, Martica

    2012-01-01

    It is unknown whether or not measuring sleep disturbances repeatedly, rather than at only one point in time, improves prediction of work disability.......It is unknown whether or not measuring sleep disturbances repeatedly, rather than at only one point in time, improves prediction of work disability....

  8. Intelligence Is in the Eye of the Beholder: Investigating Repeated IQ Measurements in Forensic Psychiatry

    Science.gov (United States)

    Habets, Petra; Jeandarme, Inge; Uzieblo, Kasia; Oei, Karel; Bogaerts, Stefan

    2015-01-01

    Background: A stable assessment of cognition is of paramount importance for forensic psychiatric patients (FPP). The purpose of this study was to compare repeated measures of IQ scores in FPPs with and without intellectual disability. Methods: Repeated measurements of IQ scores in FPPs (n = 176) were collected. Differences between tests were…

  9. Intelligence Is in the Eye of the Beholder: Investigating Repeated IQ Measurements in Forensic Psychiatry

    Science.gov (United States)

    Habets, Petra; Jeandarme, Inge; Uzieblo, Kasia; Oei, Karel; Bogaerts, Stefan

    2015-01-01

    Background: A stable assessment of cognition is of paramount importance for forensic psychiatric patients (FPP). The purpose of this study was to compare repeated measures of IQ scores in FPPs with and without intellectual disability. Methods: Repeated measurements of IQ scores in FPPs (n = 176) were collected. Differences between tests were…

  10. Genome-wide analysis of tandem repeats in Tribolium castaneum genome reveals abundant and highly dynamic tandem repeat families with satellite DNA features in euchromatic chromosomal arms.

    Science.gov (United States)

    Pavlek, Martina; Gelfand, Yevgeniy; Plohl, Miroslav; Meštrović, Nevenka

    2015-12-01

    Although satellite DNAs are well-explored components of heterochromatin and centromeres, little is known about emergence, dispersal and possible impact of comparably structured tandem repeats (TRs) on the genome-wide scale. Our bioinformatics analysis of assembled Tribolium castaneum genome disclosed significant contribution of TRs in euchromatic chromosomal arms and clear predominance of satellite DNA-typical 170 bp monomers in arrays of ≥5 repeats. By applying different experimental approaches, we revealed that the nine most prominent TR families Cast1-Cast9 extracted from the assembly comprise ∼4.3% of the entire genome and reside almost exclusively in euchromatic regions. Among them, seven families that build ∼3.9% of the genome are based on ∼170 and ∼340 bp long monomers. Results of phylogenetic analyses of 2500 monomers originating from these families show high-sequence dynamics, evident by extensive exchanges between arrays on non-homologous chromosomes. In addition, our analysis shows that concerted evolution acts more efficiently on longer than on shorter arrays. Efficient genome-wide distribution of nine TR families implies the role of transposition only in expansion of the most dispersed family, and involvement of other mechanisms is anticipated. Despite similarities in sequence features, FISH experiments indicate high-level compartmentalization of centromeric and euchromatic tandem repeats.

  11. Variable Number Tandem Repeat (VNTR) analysis reveals genetic diversity within Mycoplasma mycoides mycoides small colony isolates from Nigeria.

    Science.gov (United States)

    Nwankpa, N D; Manso-silvan, L; Lorenzon, S; Yaya, A; Lombin, L H; Thiaucourt, F

    2010-12-15

    A Variable Number Tandem Repeat (VNTR) analysis was conducted on thirteen (13) M. mycoides mycoides Small Colony isolates from Nigeria using Tandem Repeat (TR) 34 which is a predicted lipoprotein located within the hypothetical protein MAG6170. The analysis revealed diversity within the M. mycoides mycoides Small Colony isolates with five different VNTR types indicated. Some correlation was determined between the VNTR types and their geographical origin. VNTR analysis may represent a useful, rapid first-line test for use in molecular epidemiological analysis of M. mycoides mycoides Small Colony for possible outbreak tracing and disease control.

  12. Significance of satellite DNA revealed by conservation of a widespread repeat DNA sequence among angiosperms.

    Science.gov (United States)

    Mehrotra, Shweta; Goel, Shailendra; Raina, Soom Nath; Rajpal, Vijay Rani

    2014-08-01

    The analysis of plant genome structure and evolution requires comprehensive characterization of repetitive sequences that make up the majority of plant nuclear DNA. In the present study, we analyzed the nature of pCtKpnI-I and pCtKpnI-II tandem repeated sequences, reported earlier in Carthamus tinctorius. Interestingly, homolog of pCtKpnI-I repeat sequence was also found to be present in widely divergent families of angiosperms. pCtKpnI-I showed high sequence similarity but low copy number among various taxa of different families of angiosperms analyzed. In comparison, pCtKpnI-II was specific to the genus Carthamus and was not present in any other taxa analyzed. The molecular structure of pCtKpnI-I was analyzed in various unrelated taxa of angiosperms to decipher the evolutionary conserved nature of the sequence and its possible functional role.

  13. Genomic and polyploid evolution in genus Avena as revealed by RFLPs of repeated DNA sequences.

    Science.gov (United States)

    Morikawa, Toshinobu; Nishihara, Miho

    2009-06-01

    Phylogenetic relationships and genome affinities were investigated by utilizing all the biological Avena species consisting of 11 diploid species (15 accessions), 8 tetraploid species (9 accessions) and 4 hexaploid species (5 accessions). Genomic DNA regions of As120a, avenin, and globulin were amplified by PCR. A total of 130 polymorphic fragments were detected out of 156 fragments generated by digesting the PCR-amplified fragments with 11 restriction enzymes. The number of fragments generated by PCR-amplification followed by digestion with restriction enzymes was almost the same as those among the three repeated DNA sequences. A high level of genetic distance was detected between A. damascena (Ad) and A. canariensis (Ac) genomes, which reflected their different morphology and reproductive isolation. The A. longiglumis (Al) and A. prostrata (Ap) genomes were closely related to the As genome group. The AB genome species formed a cluster with the AsAs genome artificial autotetraploid and the As genome diploids indicating near-autotetraploid origin. The A. macrostachya is an outbreeding autotetraploid closely related with the C genome diploid and the AC genome tetraploid species. The differences of genetic distances estimated from the repeated DNA sequence divergence among the Avena species were consistent with genome divergences and it was possible to compare the genetic intra- and inter-ploidy relationships produced by RFLPs. These results suggested that the PCR-mediated analysis of repeated DNA polymorphism can be used as a tool to examine genomic relationships of polyploidy species.

  14. Repeated Structural Imaging Reveals Nonlinear Progression of Experience-Dependent Volume Changes in Human Motor Cortex.

    Science.gov (United States)

    Wenger, Elisabeth; Kühn, Simone; Verrel, Julius; Mårtensson, Johan; Bodammer, Nils Christian; Lindenberger, Ulman; Lövdén, Martin

    2017-05-01

    Evidence for experience-dependent structural brain change in adult humans is accumulating. However, its time course is not well understood, as intervention studies typically consist of only 2 imaging sessions (before vs. after training). We acquired up to 18 structural magnetic resonance images over a 7-week period while 15 right-handed participants practiced left-hand writing and drawing. After 4 weeks, we observed increases in gray matter of both left and right primary motor cortices relative to a control group; 3 weeks later, these differences were no longer reliable. Time-series analyses revealed that gray matter in the primary motor cortices expanded during the first 4 weeks and then partially renormalized, in particular in the right hemisphere, despite continued practice and increasing task proficiency. Similar patterns of expansion followed by partial renormalization are also found in synaptogenesis, cortical map plasticity, and maturation, and may qualify as a general principle of structural plasticity. Research on human brain plasticity needs to encompass more than 2 measurement occasions to capture expansion and potential renormalization processes over time. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Repeatability of gait pattern variables measured by use of extremity-mounted inertial measurement units in nonlame horses during trotting.

    Science.gov (United States)

    Cruz, Antonio M; Maninchedda, Ugo E; Burger, Dominik; Wanda, Sabine; Vidondo, Beatriz

    2017-09-01

    OBJECTIVE To determine repeatability of gait variables measured by use of extremity-mounted inertial measurement units (IMUs) in nonlame horses during trotting under controlled conditions of treadmill exercise. ANIMALS 10 horses. PROCEDURES Six IMUs were strapped to the metacarpal, metatarsal, and distal tibial regions of each horse. Data were collected in a standardized manner (3 measurements/d on 3 d/wk over a 3-week period) while each horse was trotted on a treadmill. Every measurement consisted of a minimum of 20 strides from which a minimum of 10 strides was selected for analysis. Spatial and temporal variables were derived from the IMUs. Repeatability coefficients based on the within-subject SD were computed for each gait analysis variable at each week. RESULTS Most of the temporal and spatial variables had high repeatability (repeatability coefficients variables, specifically the symmetry variables (which were calculated from other variables), had somewhat higher repeatability coefficients (ie, lower repeatability) only in the last week. CONCLUSIONS AND CLINICAL RELEVANCE With the exceptions of some symmetry variables, which may reflect individual variations during movement, the extremity-mounted IMUs provided data with high repeatability for nonlame horses trotting under controlled conditions of treadmill exercise. Repeatability was achieved for each instrumented limb segment with regard to the spatial relationship between 2 adjacent segments (joint angles) and the temporal relationship among all segments (limb phasing). Extremity-mounted IMUs could have the potential to become a method for gait analysis in horses.

  16. Analysis of repeated measurements from medical research when observations are missing

    OpenAIRE

    Walker, K.

    2007-01-01

    Subject dropout is a common problem in repeated measurements health stud ies. Where dropout is related to the response, the results obtained can be substantially biased. The research in this thesis is motivated by a repeated measurements asthma clinical trial with substantial patient dropout. In practice the extent to which missing observations affect parameter esti mates and their efficiency is not clear. Through extensive simulation studies under various scenarios and missing data mechanism...

  17. Repeated FcεRI triggering reveals modified mast cell function related to chronic allergic responses in tissue.

    Science.gov (United States)

    Suurmond, Jolien; Habets, Kim L L; Tatum, Zuotian; Schonkeren, Joris J; Hoen, Peter A C 't; Huizinga, Tom W J; Laros, Jeroen F J; Toes, René E M; Kurreeman, Fina

    2016-09-01

    Activation of mast cells through FcεRI plays an important role in acute allergic reactions. However, little is known about the function of mast cells in patients with chronic allergic inflammation or the effect of repeated FcεRI triggering occurring in such responses. We aimed to identify changes in mast cell function after repeated FcεRI triggering and to correlate these changes to chronic allergic responses in tissue. Human cord blood-derived mast cells were treated for 2 weeks with anti-IgE. The function of naive or treated mast cells was analyzed by means of RNA sequencing, quantitative RT-PCR, flow cytometry, and functional assays. Protein secretion was measured with ELISAs and multiplex assays. We observed several changes in mast cell function after repeated anti-IgE triggering. Although the acute response was dampened, we identified 289 genes significantly upregulated after repeated anti-IgE. Most of these genes (84%) were not upregulated after a single anti-IgE stimulus, indicating a significantly different response mode characterized by increased antigen presentation, response to bacteria, and chemotaxis. Changes in mast cell function were related to changes in expression of the transcription factors RXRA and BATF and others. Importantly, we found a substantial overlap between genes upregulated after repeated anti-IgE triggering and genes upregulated in tissue from patients with chronic allergy, in particular those of patients with chronic rhinosinusitis. Our study provides evidence for intrinsic modulation of mast cell function on repeated FcεRI-mediated activation. The overlap with gene expression in tissues is suggestive of a direct link between repeated IgE-mediated activation of mast cells and chronic allergy. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  18. Repeatability of Ocular Measurements with a Dual-Scheimpflug Analyzer in Healthy Eyes

    Directory of Open Access Journals (Sweden)

    Carmen Lopez de la Fuente

    2014-01-01

    Full Text Available Purpose. To assess the repeatability of the Galilei dual Scheimpflug analyzer (GDSA in anterior segment examination. Methods. Fifty-two eyes from 52 healthy volunteers were prospectively and consecutively recruited. Anatomic, axial, refractive, and instantaneous parameters were measured with GDSA to provide a complete characterization of the anterior segment. Repeatability was assessed calculating intraclass correlation coefficient (ICC, and coefficient of variation (COV. Results. Correlation among repeated measurements showed almost perfect reliability (ICC > 0.81 for all parameters except thinnest central corneal thickness (CCT (0.78, corneal thickness average out (0.79, and posterior axial curvature average out (0.60. Repeatability was excellent (COV < 10% for all parameters except anterior chamber volume and, superior iridocorneal angle and eccentricities. In these last three parameters, repeatability limits were excessively high compared to the mean. Conclusions. GDSA in healthy young persons had an almost perfect correlation in measuring anatomic, axial, instantaneous, and refractive parameters with greater variability for peripheral terms. Repeatability of anatomical parameters like pachymetry, anterior chamber, or iridocorneal angle and eccentricity were limited. In healthy young persons, the other evaluated parameters had very good repeatability and their limits of agreement showed excellent clinical results for this device.

  19. Heterogeneity among Mycobacterium ulcerans from French Guiana revealed by multilocus variable number tandem repeat analysis (MLVA).

    Science.gov (United States)

    Reynaud, Yann; Millet, Julie; Couvin, David; Rastogi, Nalin; Brown, Christopher; Couppié, Pierre; Legrand, Eric

    2015-01-01

    Buruli ulcer is an emerging and neglected tropical disease caused by Mycobacterium ulcerans. Few cases have been reported so far in the Americas. With 250 cases reported since 1969, French Guiana is the only Buruli ulcer endemic area in the continent. Thus far, no genetic diversity studies of strains of M. ulcerans from French Guiana have been reported. Our goal in the present study was to examine the genetic diversity of M. ulcerans strains in this region by using the Multilocus Variable Number Tandem Repeat Analysis (MLVA) approach. A total of 23 DNA samples were purified from ulcer biopsies or derived from pure cultures. MVLA was used in the study of six previously-described Variable Number of Tandem Repeat (VNTR) markers. A total of three allelic combinations were characterized in our study: genotype I which has been described previously, genotype III which is very similar to genotype I, and genotype II which has distinctly different characteristics in comparison with the other two genotypes. This high degree of genetic diversity appears to be uncommon for M. ulcerans. Further research based on complete genome sequencing of strains belonging to genotypes I and II is in progress and should lead soon to a better understanding of genetic specificities of M. ulcerans strains from French Guiana.

  20. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rong [Yale Univ., New Haven, CT (United States); Li, Xiaofeng [Yale Univ., New Haven, CT (United States); Boggon, Titus J. [Yale Univ., New Haven, CT (United States)

    2015-10-14

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/ TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is also an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD–FERM module. It resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD–FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  1. Structural analysis of the KRIT1 ankyrin repeat and FERM domains reveals a conformationally stable ARD-FERM interface.

    Science.gov (United States)

    Zhang, Rong; Li, Xiaofeng; Boggon, Titus J

    2015-12-01

    Cerebral cavernous malformations (CCM) are vascular dysplasias that usually occur in the brain and are associated with mutations in the KRIT1/CCM1, CCM2/MGC4607/OSM/Malcavernin, and PDCD10/CCM3/TFAR15 genes. Here we report the 2.9 Å crystal structure of the ankyrin repeat domain (ARD) and FERM domain of the protein product of KRIT1 (KRIT1; Krev interaction trapped 1). The crystal structure reveals that the KRIT1 ARD contains 4 ankyrin repeats. There is an unusual conformation in the ANK4 repeat that is stabilized by Trp-404, and the structure reveals a solvent exposed ankyrin groove. Domain orientations of the three copies within the asymmetric unit suggest a stable interaction between KRIT1 ARD and FERM domains, indicating a globular ARD-FERM module. This resembles the additional F0 domain found N-terminal to the FERM domain of talin. Structural analysis of KRIT1 ARD-FERM highlights surface regions of high evolutionary conservation, and suggests potential sites that could mediate interaction with binding partners. The structure therefore provides a better understanding of KRIT1 at the molecular level.

  2. Interrogation of the protein-protein interactions between human BRCA2 BRC repeats and RAD51 reveals atomistic determinants of affinity.

    Directory of Open Access Journals (Sweden)

    Daniel J Cole

    2011-07-01

    Full Text Available The breast cancer suppressor BRCA2 controls the recombinase RAD51 in the reactions that mediate homologous DNA recombination, an essential cellular process required for the error-free repair of DNA double-stranded breaks. The primary mode of interaction between BRCA2 and RAD51 is through the BRC repeats, which are ∼35 residue peptide motifs that interact directly with RAD51 in vitro. Human BRCA2, like its mammalian orthologues, contains 8 BRC repeats whose sequence and spacing are evolutionarily conserved. Despite their sequence conservation, there is evidence that the different human BRC repeats have distinct capacities to bind RAD51. A previously published crystal structure reports the structural basis of the interaction between human BRC4 and the catalytic core domain of RAD51. However, no structural information is available regarding the binding of the remaining seven BRC repeats to RAD51, nor is it known why the BRC repeats show marked variation in binding affinity to RAD51 despite only subtle sequence variation. To address these issues, we have performed fluorescence polarisation assays to indirectly measure relative binding affinity, and applied computational simulations to interrogate the behaviour of the eight human BRC-RAD51 complexes, as well as a suite of BRC cancer-associated mutations. Our computational approaches encompass a range of techniques designed to link sequence variation with binding free energy. They include MM-PBSA and thermodynamic integration, which are based on classical force fields, and a recently developed approach to computing binding free energies from large-scale quantum mechanical first principles calculations with the linear-scaling density functional code onetep. Our findings not only reveal how sequence variation in the BRC repeats directly affects affinity with RAD51 and provide significant new insights into the control of RAD51 by human BRCA2, but also exemplify a palette of computational and

  3. A Novel Signal Processing Measure to Identify Exact and Inexact Tandem Repeat Patterns in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Ravi Gupta

    2007-03-01

    Full Text Available The identification and analysis of repetitive patterns are active areas of biological and computational research. Tandem repeats in telomeres play a role in cancer and hypervariable trinucleotide tandem repeats are linked to over a dozen major neurodegenerative genetic disorders. In this paper, we present an algorithm to identify the exact and inexact repeat patterns in DNA sequences based on orthogonal exactly periodic subspace decomposition technique. Using the new measure our algorithm resolves the problems like whether the repeat pattern is of period P or its multiple (i.e., 2P, 3P, etc., and several other problems that were present in previous signal-processing-based algorithms. We present an efficient algorithm of O(NLw logLw, where N is the length of DNA sequence and Lw is the window length, for identifying repeats. The algorithm operates in two stages. In the first stage, each nucleotide is analyzed separately for periodicity, and in the second stage, the periodic information of each nucleotide is combined together to identify the tandem repeats. Datasets having exact and inexact repeats were taken up for the experimental purpose. The experimental result shows the effectiveness of the approach.

  4. Worldwide widespread decadal-scale decrease of glacier speed revealed using repeat optical satellite images

    Directory of Open Access Journals (Sweden)

    T. Heid

    2011-10-01

    Full Text Available Matching of repeat optical satellite images to derive glacier velocities is an approach that is much used within glaciology. Lately, focus has been put into developing, improving, automating and comparing different image matching methods. This makes it now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have decreased their speeds over the last decades, Pamir by 43 % in average per decade, Caucasus by 8 % in average per decade, Penny Ice Cap by 25 % in average per decade, Alaska Range by 11 % in average per decade and Patagonia by 20 % in average per decade. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area.

  5. Repeat optical satellite images reveal widespread and long term decrease in land-terminating glacier speeds

    Directory of Open Access Journals (Sweden)

    T. Heid

    2012-04-01

    Full Text Available By matching of repeat optical satellite images it is now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have over the last decades decreased their velocity at an average rate per decade of: 43 % in the Pamir, 8 % in the Caucasus, 25 % on Penny Ice Cap, 11 % in the Alaska Range and 20 % in Patagonia. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area. Therefore the calculated average speed change is not representative for this area.

  6. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    OpenAIRE

    Zulhairil Ariffin; Muhammad Shafie Md Sah; Salma Idris; Nuradni Hashim

    2015-01-01

    ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah), Bukit Gantang (Perak), Sibuti (Sarawak), and Papar (Sabah). A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.5...

  7. The concordance correlation coefficient for repeated measures estimated by variance components.

    Science.gov (United States)

    Carrasco, Josep L; King, Tonya S; Chinchilli, Vernon M

    2009-01-01

    The concordance correlation coefficient (CCC) is an index that is commonly used to assess the degree of agreement between observers on measuring a continuous characteristic. Here, a CCC for longitudinal repeated measurements is developed through the appropriate specification of the intraclass correlation coefficient from a variance components linear mixed model. A case example and the results of a simulation study are provided.

  8. Measurement repeatability of tibial tuberosity-trochlear groove offset distance in red fox (Vulpes vulpes) cadavers

    NARCIS (Netherlands)

    Miles, J.E.; Jensen, B.R.; Kirpensteijn, J.; Svalastoga, E.L.; Eriksen, T.

    2013-01-01

    Abstract OBJECTIVE: To describe CT image reconstruction criteria for measurement of the tibial tuberosity-trochlear groove (TT-TG) offset distance, evaluate intra- and inter-reconstruction repeatability, and identify key sources of error in the measurement technique, as determined in vulpine hind li

  9. Hierarchical linear model: thinking outside the traditional repeated-measures analysis-of-variance box.

    Science.gov (United States)

    Lininger, Monica; Spybrook, Jessaca; Cheatham, Christopher C

    2015-04-01

    Longitudinal designs are common in the field of athletic training. For example, in the Journal of Athletic Training from 2005 through 2010, authors of 52 of the 218 original research articles used longitudinal designs. In 50 of the 52 studies, a repeated-measures analysis of variance was used to analyze the data. A possible alternative to this approach is the hierarchical linear model, which has been readily accepted in other medical fields. In this short report, we demonstrate the use of the hierarchical linear model for analyzing data from a longitudinal study in athletic training. We discuss the relevant hypotheses, model assumptions, analysis procedures, and output from the HLM 7.0 software. We also examine the advantages and disadvantages of using the hierarchical linear model with repeated measures and repeated-measures analysis of variance for longitudinal data.

  10. Hierarchical Linear Model: Thinking Outside the Traditional Repeated-Measures Analysis-of-Variance Box

    Science.gov (United States)

    Lininger, Monica; Spybrook, Jessaca; Cheatham, Christopher C.

    2015-01-01

    Longitudinal designs are common in the field of athletic training. For example, in the Journal of Athletic Training from 2005 through 2010, authors of 52 of the 218 original research articles used longitudinal designs. In 50 of the 52 studies, a repeated-measures analysis of variance was used to analyze the data. A possible alternative to this approach is the hierarchical linear model, which has been readily accepted in other medical fields. In this short report, we demonstrate the use of the hierarchical linear model for analyzing data from a longitudinal study in athletic training. We discuss the relevant hypotheses, model assumptions, analysis procedures, and output from the HLM 7.0 software. We also examine the advantages and disadvantages of using the hierarchical linear model with repeated measures and repeated-measures analysis of variance for longitudinal data. PMID:25875072

  11. [Pyelovenous fistula revealed by repeated thromboembolic events after emergency peripartum hysterectomy].

    Science.gov (United States)

    Sauvanaud, C; Boillot, B; Sergent, F; Long, J A; Pernod, G; Rambeaud, J J

    2014-04-01

    We report the case of a 51-year old woman presenting pyelovenous fistula revealed by recurrent and serious thromboembolic events after ureteral ligation during emergency peripartum hysterectomy. Imaging reported a complete left ureteral obstruction, a fistula between the upper calix and the left renal vein and a renal function preserved. Uretero-vesical reimplantation was performed. The patient was well doing after 12 months. The authors wonder if pyelovenous fistula is responsible for prothrombotic state and maintaining renal function. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  12. Accuracy and repeatability of a new method for measuring facet loads in the lumbar spine.

    Science.gov (United States)

    Wilson, Derek C; Niosi, Christina A; Zhu, Qingan A; Oxland, Thomas R; Wilson, David R

    2006-01-01

    We assessed the repeatability and accuracy of a relatively new, resistance-based sensor (Tekscan 6900) for measuring lumbar spine facet loads, pressures, and contact areas in cadaver specimens. Repeatability of measurements in the natural facet joint was determined for five trials of four specimens loaded in pure moment (+/- 7.5 N m) flexibility tests in axial rotation and flexion-extension. Accuracy of load measurements in four joints was assessed by applying known compressive loads of 25, 50, and 100 N to the natural facet joint in a materials testing machine and comparing the known applied load to the measured load. Measurements of load were obtained using two different calibration approaches: linear and two-point calibrations. Repeatability for force, pressure, and area (average of standard deviation as a percentage of the mean for all trials over all specimens) was 4-6% for axial rotation and 7-10% for extension. Peak resultant force in axial rotation was 30% smaller when calculated using the linear calibration method. The Tekscan sensor overestimated the applied force by 18 +/- 9% (mean+/-standard deviation), 35 +/- 7% and 50 +/- 9% for compressive loads of 100, 50, and 25 N, respectively. The two-point method overestimated the loads by 35 +/- 16%, 45 +/- 7%, and 56 +/- 10% for the same three loads. Our results show that the Tekscan sensor is repeatable. However, the sensor measurement range is not optimal for the small loads transmitted by the facets and measurement accuracy is highly dependent on calibration protocol.

  13. Genome wide analysis of acute myeloid leukemia reveal leukemia specific methylome and subtype specific hypomethylation of repeats.

    Directory of Open Access Journals (Sweden)

    Marwa H Saied

    Full Text Available Methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq has the potential to identify changes in DNA methylation important in cancer development. In order to understand the role of epigenetic modulation in the development of acute myeloid leukemia (AML we have applied MeDIP-seq to the DNA of 12 AML patients and 4 normal bone marrows. This analysis revealed leukemia-associated differentially methylated regions that included gene promoters, gene bodies, CpG islands and CpG island shores. Two genes (SPHKAP and DPP6 with significantly methylated promoters were of interest and further analysis of their expression showed them to be repressed in AML. We also demonstrated considerable cytogenetic subtype specificity in the methylomes affecting different genomic features. Significantly distinct patterns of hypomethylation of certain interspersed repeat elements were associated with cytogenetic subtypes. The methylation patterns of members of the SINE family tightly clustered all leukemic patients with an enrichment of Alu repeats with a high CpG density (P<0.0001. We were able to demonstrate significant inverse correlation between intragenic interspersed repeat sequence methylation and gene expression with SINEs showing the strongest inverse correlation (R(2 = 0.7. We conclude that the alterations in DNA methylation that accompany the development of AML affect not only the promoters, but also the non-promoter genomic features, with significant demethylation of certain interspersed repeat DNA elements being associated with AML cytogenetic subtypes. MeDIP-seq data were validated using bisulfite pyrosequencing and the Infinium array.

  14. Power analysis for multivariate and repeated measures designs: a flexible approach using the SPSS MANOVA procedure.

    Science.gov (United States)

    D'Amico, E J; Neilands, T B; Zambarano, R

    2001-11-01

    Although power analysis is an important component in the planning and implementation of research designs, it is often ignored. Computer programs for performing power analysis are available, but most have limitations, particularly for complex multivariate designs. An SPSS procedure is presented that can be used for calculating power for univariate, multivariate, and repeated measures models with and without time-varying and time-constant covariates. Three examples provide a framework for calculating power via this method: an ANCOVA, a MANOVA, and a repeated measures ANOVA with two or more groups. The benefits and limitations of this procedure are discussed.

  15. Repeated quantitative perfusion and contrast permeability measurement in the MRI examination of a CNS tumor

    Energy Technology Data Exchange (ETDEWEB)

    Vonken, E.P.A.; Osch, M.J.P. van; Willems, P.W.A.; Zwan, A. van der; Bakker, C.J.G.; Viergever, M.A.; Mali, W.P.T.M. [University Hospital Utrecht (Netherlands)

    2000-09-01

    This study reports on the results of quantitative MRI perfusion and contrast permeability measurement on two occasions in one patient. The measurements were separated 81 days in time. The tumor grew considerably in this period, but no change was found with respect to perfusion and contrast permeability. Non-involved white matter values were reproduced to demonstrate repeatability. The presented approach to dynamic susceptibility contrast MRI allows fast and repeatable quantitative assessment of perfusion and is easily integrated in a conventional brain tumor protocol. (orig.)

  16. Intraexaminer repeatability and agreement in stereoacuity measurements made in young adults

    Directory of Open Access Journals (Sweden)

    Beatriz Antona

    2015-04-01

    Full Text Available AIM: To determine the repeatability and agreement of stereoacuity measurements made using some of the most widely used clinical tests: Frisby, TNO, Randot and Titmus. METHODS: Stereoacuity was measured in two different sessions separated by a time interval of at least 24h but no longer than 1wk in 74 subjects of mean age 20.6y using the four methods. The study participants were divided into two groups: subjects with normal binocular vision and subjects with abnormal binocular vision. RESULTS: Best repeatability was shown by the Frisby and Titmus [coefficient of repeatability (COR: ±13 and ±12s arc respectively] in the subjects with normal binocular vision though a clear ceiling effect was noted. In the subjects with abnormal binocular vision, best repeatability was shown by the Frisby (COR: ±69s arc and Randot (COR: ±72s arc. In both groups, the TNO test showed poorest agreement with the other tests. CONCLUSION: The repeatability of stereoacuity measures was low in subjects with poor binocular vision yet fairly good in subjects with normal binocular vision with the exception of the TNO test. The reduced agreement detected between the tests indicates they cannot be used interchangeably.

  17. A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae

    Directory of Open Access Journals (Sweden)

    Renner Susanne S

    2011-01-01

    Full Text Available Abstract Background Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. Results Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. Conclusions The most surprising findings of this study are the frequent biome shifts (in a relatively small clade over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain

  18. Repeatability of the modified Thorington card used to measure far heterophoria.

    Science.gov (United States)

    Cebrian, Jose Luis; Antona, Beatriz; Barrio, Ana; Gonzalez, Enrique; Gutierrez, Angel; Sanchez, Isabel

    2014-07-01

    To determine the interexaminer and intraexaminer repeatability of the modified Thorington test (TH) for distance vision in young adults and to compare these results with those observed for the heterophoria tests most commonly used in clinical practice. Agreement among tests was also assessed. Distance heterophoria was quantified on two separate occasions by two examiners in 110 subjects aged 18 to 32 years (mean, 19.74 years; SD, 2.5 years) using four different tests: cover test (CT) Von Graefe, Maddox rod, and modified TH. The repeatability of the tests and agreement between them was estimated by the Bland and Altman method whereby the mean difference and the 95% limits of agreement were determined as the coefficient of repeatability (COR) and coefficient of agreement. The Thorington test showed best interexaminer repeatability (COR = ±1.43Δ), followed closely by CT (COR = ±1.65Δ), whereas best intraexaminer repeatability was observed for CT (COR = ±1.28Δ) followed by TH (COR = ±1.51Δ). Among the different combinations of tests, TH and CT showed best agreement indicated by the lowest coefficient of agreement (±2.23Δ) and a low mean difference (-0.63Δ) between measurements. Good interexaminer and intraexaminer repeatability was observed for both TH and CT, and agreement between the two tests was also good. Given the simple administration of the TH, we recommend its clinical use to quantify distance horizontal heterophoria.

  19. Australian House Prices: A Comparison of Hedonic and Repeat-sales Measures

    OpenAIRE

    James Hansen

    2006-01-01

    House prices are intrinsically difficult to measure due to changes in the composition of properties sold through time and changes in the quality of housing. I provide an overview of the theoretical nature of these issues and consider how regression-based measures of house prices – hedonic and repeat-sales measures – can control for compositional and quality change. I then explore whether these regression-based alternatives can provide accurate estimates of pure house price changes in the Aust...

  20. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    Directory of Open Access Journals (Sweden)

    Zulhairil Ariffin

    2015-01-01

    Full Text Available ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah, Bukit Gantang (Perak, Sibuti (Sarawak, and Papar (Sabah. A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.50. Analysis on 18 Mangifera indica accessions also showed high degree of polymorphism of 99% and mean Shannon index, H0=5.74. Dice index of genetic similarity ranged from 0.0938 to 0.8046 among the Mangifera species. The dendrogram showed that the Mangifera species were grouped into three main divergent clusters. Cluster 1 comprised 14 accessions from Kedah and Perak. Cluster II and cluster III comprised 14 accessions from Sarawak and Sabah. Meanwhile, the Dice index of genetic similarity for 18 accessions of Mangifera indica ranged from 0.2588 to 0.7742. The dendrogram also showed the 18 accessions of Mangifera indica were grouped into three main clusters. Cluster I comprised 10 landraces of Mangifera indica from Kedah. Cluster II comprised 7 landraces of Mangifera indica followed by Chokanan to form Cluster III.

  1. Concordance correlation coefficients estimated by generalized estimating equations and variance components for longitudinal repeated measurements.

    Science.gov (United States)

    Tsai, Miao-Yu

    2017-04-15

    The concordance correlation coefficient (CCC) is a commonly accepted measure of agreement between two observers for continuous responses. This paper proposes a generalized estimating equations (GEE) approach allowing dependency between repeated measurements over time to assess intra-agreement for each observer and inter- and total agreement among multiple observers simultaneously. Furthermore, the indices of intra-, inter-, and total agreement through variance components (VC) from an extended three-way linear mixed model (LMM) are also developed with consideration of the correlation structure of longitudinal repeated measurements. Simulation studies are conducted to compare the performance of the GEE and VC approaches for repeated measurements from longitudinal data. An application of optometric conformity study is used for illustration. In conclusion, the GEE approach allowing flexibility in model assumptions and correlation structures of repeated measurements gives satisfactory results with small mean square errors and nominal 95% coverage rates for large data sets, and when the assumption of the relationship between variances and covariances for the extended three-way LMM holds, the VC approach performs outstandingly well for all sample sizes. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  2. Repeatability of cardiac-MRI-measured right ventricular size and function in congenital heart disease

    Energy Technology Data Exchange (ETDEWEB)

    Walsh, Rowan; Salem, Yishay [Mount Sinai School of Medicine, Division of Pediatric Cardiology, New York, NY (United States); Shah, Amee; Lai, Wyman W. [Morgan Stanley Children' s Hospital of New York Presbyterian, New York, NY (United States); Nielsen, James C. [Mount Sinai School of Medicine, Division of Pediatric Cardiology, New York, NY (United States); Mount Sinai Children' s Heart Center, Box 1201, New York, NY (United States)

    2011-08-15

    The measurement error for right ventricular (RV) size and function assessed by cardiac MRI (CMRI) in congenital heart disease has not been fully characterized. As CMRI parameters are being increasingly utilized to make clinical decisions, defining error in the clinical setting is critical. This investigation examines the repeatability of CMRI for RV size and function. Forty consecutive people with congenital heart disease involving the RV were retrospectively identified. Contouring of RV volumes was performed by two expert CMRI clinicians. The coefficient of variability and repeatability coefficients were calculated. Repeatability coefficients were multiplied by the mean value for each group studied to define a threshold beyond which measurement error was unlikely to be responsible. The variability for indexed RV end-diastolic volume = 3.2% and 3.3% for intra- and interobserver comparisons, respectively. The repeatability coefficients were 13.2% and 14.9% for intra- and interobserver comparisons, which yielded threshold values of 15.1 ml/m{sup 2} and 20.2 ml/m{sup 2}, respectively. For RV ejection fraction (EF), the repeatability coefficients for intra- and interobserver comparisons were 5.0% and 6.0%, which resulted in threshold values of 2.6 EF% and 3.0 EF%. The threshold values generated can be used during serial assessment of RV size and function. (orig.)

  3. Accuracy and repeatability of an optical motion analysis system for measuring small deformations of biological tissues.

    Science.gov (United States)

    Liu, Helen; Holt, Cathy; Evans, Sam

    2007-01-01

    Optical motion analysis techniques have been widely used in biomechanics for measuring large-scale motions such as gait, but have not yet been significantly explored for measuring smaller movements such as the tooth displacements under load. In principle, very accurate measurements could be possible and this could provide a valuable tool in many engineering applications. The aim of this study was to evaluate accuracy and repeatability of the Qualisys ProReflex-MCU120 system when measuring small displacements, as a step towards measuring tooth displacements to characterise the properties of the periodontal ligament. Accuracy and repeatability of the system was evaluated using a wedge comparator with a resolution of 0.25 microm to provide measured marker displacements in three orthogonal directions. The marker was moved in ten steps in each direction, for each of seven step sizes (0.5, 1, 2, 3, 5, 10, and 20 microm), repeated five times. Spherical and diamond markers were tested. The system accuracy (i.e. percentage of maximum absolute error in range/measurement range), in the 20-200 microm ranges, was +/-1.17%, +/-1.67% and +/-1.31% for the diamond marker in x, y and z directions, while the system accuracy for the spherical marker was +/-1.81%, +/-2.37% and +/-1.39%. The system repeatability (i.e. maximum standard deviation in the measurement range) measured under the different days, light intensity and temperatures for five times, carried out step up and then step down measurements for the same step size, was +/-1.7, +/-2.3 and +/-1.9 microm for the diamond marker, and +/-2.6, +/-3.9 and +/-1.9 microm for the spherical marker in x, y and z directions, respectively. These results demonstrate that the system suffices accuracy for measuring tooth displacements and could potentially be useful in many other applications.

  4. Repeatability of central corneal thickness measurement with the Pentacam HR system

    Directory of Open Access Journals (Sweden)

    Ruiz Simonato Alonso

    2012-02-01

    Full Text Available PURPOSE: To assess the repeatability of central corneal thickness measurement at the geometrical center (Central Corneal Thickness - CCT given by the Pentacam High Resolution (HR Comprehensive Eye Scanner (Oculus, Wetzlar, Germany over time. METHODS: Prospective, single center, observational study. Two separate CCT measurements were taken by the Pentacam corneal tomography exam (CTm 3 to 12 months apart, and compared. RESULTS: One hundred and sixteen eyes (n=116 of 62 health patients were included in this study. Average CCT in first and last visits was 541.6±37 µm and 543.6±36.9 µm respectively. Mean difference between both measurements was 9.2±6.4 µm, and there was no statistically significant difference in CCT measurement between visits, with good correlation between them (P = 0.057, r² = 0,9209. CONCLUSION: Pentacam (HR CTm gives repeatable CCT measurements over time.

  5. Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

    Energy Technology Data Exchange (ETDEWEB)

    Dai, Shuyan; Sun, Cancan; Tan, Kemin; Ye, Sheng; Zhang, Rongguang

    2017-09-01

    Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystal structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.

  6. Graphic Methods for Interpreting Longitudinal Dyadic Patterns From Repeated-Measures Actor-Partner Interdependence Models

    DEFF Research Database (Denmark)

    Perry, Nicholas; Baucom, Katherine; Bourne, Stacia

    2017-01-01

    Researchers commonly use repeated-measures actor–partner interdependence models (RM-APIM) to understand how romantic partners change in relation to one another over time. However, traditional interpretations of the results of these models do not fully or correctly capture the dyadic temporal...

  7. Accuracy and repeatability of anthropometric facial measurements using cone beam computed tomography

    NARCIS (Netherlands)

    Fourie, Zacharias; Damstra, Janalt; Gerrits, Peter O.; Ren, Yijin

    2011-01-01

    Objective: The purpose of this study was to determine the accuracy and repeatability of linear anthropometric measurements on the soft tissue surface model generated from cone beam computed tomography scans. Materials and Methods: The study sample consisted of seven cadaver heads. The accuracy and r

  8. Cross-trimester repeated measures testing for Down's syndrome screening: an assessment.

    LENUS (Irish Health Repository)

    Wright, D

    2010-07-01

    To provide estimates and confidence intervals for the performance (detection and false-positive rates) of screening for Down\\'s syndrome using repeated measures of biochemical markers from first and second trimester maternal serum samples taken from the same woman.

  9. REPEATABILITY OF THE SUGAR ABSORPTION TEST, USING LACTULOSE AND MANNITOL, FOR MEASURING INTESTINAL PERMEABILITY FOR SUGARS

    NARCIS (Netherlands)

    VANELBURG, RM; UIL, JJ; KOKKE, FTM; MULDER, AM; VANDEBROEK, WGM; MULDER, CJJ; HEYMANS, HSA

    1995-01-01

    Differential sugar-absorption tests for measuring intestinal permeability for sugars have been studied in a variety of gastrointestinal diseases. Their use in general practice has been hampered by a lack of data on reference values and repeatability of the test and the laboratory assay. In this stud

  10. The Multilevel Approach to Repeated Measures for Complete and Incomplete Data

    NARCIS (Netherlands)

    Maas, CJM; Snijders, TAB

    2003-01-01

    Repeated measurements often are analyzed by multivariate analysis of variance (MANOVA). An alternative approach is provided by multilevel analysis, also called the hierarchical linear model (HLM), which makes use of random coefficient models. This paper is a tutorial which indicates that the HLM can

  11. Cognitive control mechanisms revealed by ERP and fMRI: evidence from repeated task-switching.

    Science.gov (United States)

    Swainson, R; Cunnington, R; Jackson, G M; Rorden, C; Peters, A M; Morris, P G; Jackson, S R

    2003-08-15

    We investigated the extent to which a common neural mechanism is involved in task set-switching and response withholding, factors that are frequently confounded in task-switching and go/no-go paradigms. Subjects' brain activity was measured using event-related electrical potentials (ERPs) and event-related functional MRI (fMRI) neuroimaging in separate studies using the same cognitive paradigm. Subjects made compatible left/right keypress responses to left/right arrow stimuli of 1000 msec duration; they switched every two trials between responding at stimulus onset (GO task-green arrows) and stimulus offset (WAIT task-red arrows). With-holding an immediate response (WAIT vs. GO) elicited an enhancement of the frontal N2 ERP and lateral PFC activation of the right hemisphere, both previously associated with the "no-go" response, but only on switch trials. Task-switching (switch vs. nonswitch) was associated with frontal N2 amplification and right hemisphere ventrolateral PFC activation, but only for the WAIT task. The anterior cingulate cortex (ACC) was the only brain region to be activated for both types of task switch, but this activation was located more rostrally for the WAIT than for the GO switch trials. We conclude that the frontal N2 ERP and lateral PFC activation are not markers for withholding an immediate response or switching tasks per se, but are associated with switching into a response-suppression mode. Different regions within the ACC may be involved in two processes integral to task-switching: processing response conflict (rostral ACC) and overcoming prior response suppression (caudal ACC).

  12. Tracking photon jumps with repeated quantum non-demolition parity measurements.

    Science.gov (United States)

    Sun, L; Petrenko, A; Leghtas, Z; Vlastakis, B; Kirchmair, G; Sliwa, K M; Narla, A; Hatridge, M; Shankar, S; Blumoff, J; Frunzio, L; Mirrahimi, M; Devoret, M H; Schoelkopf, R J

    2014-07-24

    Quantum error correction is required for a practical quantum computer because of the fragile nature of quantum information. In quantum error correction, information is redundantly stored in a large quantum state space and one or more observables must be monitored to reveal the occurrence of an error, without disturbing the information encoded in an unknown quantum state. Such observables, typically multi-quantum-bit parities, must correspond to a special symmetry property inherent in the encoding scheme. Measurements of these observables, or error syndromes, must also be performed in a quantum non-demolition way (projecting without further perturbing the state) and more quickly than errors occur. Previously, quantum non-demolition measurements of quantum jumps between states of well-defined energy have been performed in systems such as trapped ions, electrons, cavity quantum electrodynamics, nitrogen-vacancy centres and superconducting quantum bits. So far, however, no fast and repeated monitoring of an error syndrome has been achieved. Here we track the quantum jumps of a possible error syndrome, namely the photon number parity of a microwave cavity, by mapping this property onto an ancilla quantum bit, whose only role is to facilitate quantum state manipulation and measurement. This quantity is just the error syndrome required in a recently proposed scheme for a hardware-efficient protected quantum memory using Schrödinger cat states (quantum superpositions of different coherent states of light) in a harmonic oscillator. We demonstrate the projective nature of this measurement onto a region of state space with well-defined parity by observing the collapse of a coherent state onto even or odd cat states. The measurement is fast compared with the cavity lifetime, has a high single-shot fidelity and has a 99.8 per cent probability per single measurement of leaving the parity unchanged. In combination with the deterministic encoding of quantum information in cat

  13. Optimal selection of individuals for repeated covariate measurements in follow-up studies.

    Science.gov (United States)

    Reinikainen, Jaakko; Karvanen, Juha; Tolonen, Hanna

    2016-12-01

    Repeated covariate measurements bring important information on the time-varying risk factors in long epidemiological follow-up studies. However, due to budget limitations, it may be possible to carry out the repeated measurements only for a subset of the cohort. We study cost-efficient alternatives for the simple random sampling in the selection of the individuals to be remeasured. The proposed selection criteria are based on forms of the D-optimality. The selection methods are compared with the simulation studies and illustrated with the data from the East-West study carried out in Finland from 1959 to 1999. The results indicate that cost savings can be achieved if the selection is focused on the individuals with high expected risk of the event and, on the other hand, on those with extreme covariate values in the previous measurements. © The Author(s) 2014.

  14. Intraexaminer repeatability and agreement in stereoacuity measurements made in young adults

    Institute of Scientific and Technical Information of China (English)

    Beatriz; Antona; Ana; Barrio; Isabel; Sanchez; Enrique; Gonzalez; Guadalupe; Gonzalez

    2015-01-01

    AIM: To determine the repeatability and agreement of stereoacuity measurements made using some of the most widely used clinical tests: Frisby, TNO, Randot and Titmus.METHODS: Stereoacuity was measured in two different sessions separated by a time interval of at least 24 h but no longer than 1wk in 74 subjects of mean age 20.6y using the four methods. The study participants were divided into two groups: subjects with normal binocular vision and subjects with abnormal binocular vision.RESULTS: Best repeatability was shown by the Frisby and Titmus [coefficient of repeatability(COR): ±13 and±12s arc respectively] in the subjects with normal binocular vision though a clear ceiling effect was noted.In the subjects with abnormal binocular vision, best repeatability was shown by the Frisby(COR: ±69s arc)and Randot(COR: ±72s arc). In both groups, the TNO test showed poorest agreement with the other tests.CONCLUSION:Therepeatabilityofstereoacuitymeasures was low in subjects with poor binocular vision yet fairly good in subjects with normal binocular vision with the exception of the TNO test. The reduced agreement detected between the tests indicates they cannot be used interchangeably.

  15. Repeatability and reproducibility of optic nerve head perfusion measurements using optical coherence tomography angiography

    Science.gov (United States)

    Chen, Chieh-Li; Bojikian, Karine D.; Xin, Chen; Wen, Joanne C.; Gupta, Divakar; Zhang, Qinqin; Mudumbai, Raghu C.; Johnstone, Murray A.; Chen, Philip P.; Wang, Ruikang K.

    2016-06-01

    Optical coherence tomography angiography (OCTA) has increasingly become a clinically useful technique in ophthalmic imaging. We evaluate the repeatability and reproducibility of blood perfusion in the optic nerve head (ONH) measured using optical microangiography (OMAG)-based OCTA. Ten eyes from 10 healthy volunteers are recruited and scanned three times with a 68-kHz Cirrus HD-OCT 5000-based OMAG prototype system (Carl Zeiss Meditec Inc., Dublin, California) centered at the ONH involving two separate visits within six weeks. Vascular images are generated with OMAG processing by detecting the differences in OCT signals between consecutive B-scans acquired at the same retina location. ONH perfusion is quantified as flux, vessel area density, and normalized flux within the ONH for the prelaminar, lamina cribrosa, and the full ONH. Coefficient of variation (CV) and intraclass correlation coefficient (ICC) are used to evaluate intravisit and intervisit repeatability, and interobserver reproducibility. ONH perfusion measurements show high repeatability [CV≤3.7% (intravisit) and ≤5.2% (intervisit)] and interobserver reproducibility (ICC≤0.966) in all three layers by three metrics. OCTA provides a noninvasive method to visualize and quantify ONH perfusion in human eyes with excellent repeatability and reproducibility, which may add additional insight into ONH perfusion in clinical practice.

  16. Repeatability, variability and reference values of pulsed wave Doppler echocardiographic measurements in healthy Saanen goats

    Directory of Open Access Journals (Sweden)

    Leroux Aurélia A

    2012-10-01

    Full Text Available Abstract Background Pulsed wave (PW Doppler echocardiography has become a routine non invasive cardiac diagnostic tool in most species. However, evaluation of intracardiac blood flow requires reference values, which are poorly documented in goats. The aim of this study was to test the repeatability, the variability, and to establish the reference values of PW measurements in healthy adult Saanen goats. Using a standardised PW Doppler echocardiographic protocol, 10 healthy adult unsedated female Saanen goats were investigated three times at one day intervals by the same observer. Mitral, tricuspid, aortic and pulmonary flows were measured from a right parasternal view, and mitral and aortic flows were also measured from a left parasternal view. The difference between left and right side measurements and the intra-observer inter-day repeatability were tested and then the reference values of PW Doppler echocardiographic parameters in healthy adult female Saanen goats were established. Results As documented in other species, all caprine PW Doppler parameters demonstrated a poor inter-day repeatability and a moderate variability. Tricuspid and pulmonary flows were best evaluated on the right side whereas mitral and aortic flows were best obtained on the left side, and reference values are reported for healthy adult Saanen goats. Conclusions PW Doppler echocardiography allows the measurement of intracardiac blood flow indices in goats. The reference values establishment will help interpreting these indices of cardiac function in clinical cardiac cases and developing animal models for human cardiology research.

  17. Accounting for uncertainty in volumes of seabed change measured with repeat multibeam sonar surveys

    Science.gov (United States)

    Schimel, Alexandre C. G.; Ierodiaconou, Daniel; Hulands, Lachlan; Kennedy, David M.

    2015-12-01

    Seafloors of unconsolidated sediment are highly dynamic features; eroding or accumulating under the action of tides, waves and currents. Assessing which areas of the seafloor experienced change and measuring the corresponding volumes involved provide insights into these important active sedimentation processes. Computing the difference between Digital Elevation Models (DEMs) obtained from repeat Multibeam Echosounders (MBES) surveys has become a common technique to identify these areas, but the uncertainty in these datasets considerably affects the estimation of the volumes displaced. The two main techniques used to take into account uncertainty in volume estimations are the limitation of calculations to areas experiencing a change in depth beyond a chosen threshold, and the computation of volumetric confidence intervals. However, these techniques are still in their infancy and, as a result, are often crude, seldom used or poorly understood. In this article, we explored a number of possible methodological advances to address this issue, including: (1) using the uncertainty information provided by the MBES data processing algorithm CUBE, (2) adapting fluvial geomorphology techniques for volume calculations using spatially variable thresholds and (3) volumetric histograms. The nearshore seabed off Warrnambool harbour - located in the highly energetic southwest Victorian coast, Australia - was used as a test site. Four consecutive MBES surveys were carried out over a four-months period. The difference between consecutive DEMs revealed an area near the beach experiencing large sediment transfers - mostly erosion - and an area of reef experiencing increasing deposition from the advance of a nearby sediment sheet. The volumes of sediment displaced in these two areas were calculated using the techniques described above, both traditionally and using the suggested improvements. We compared the results and discussed the applicability of the new methodological improvements

  18. Using the Monte Carlo Simulation Methods in Gauge Repeatability and Reproducibility of Measurement System Analysis

    Directory of Open Access Journals (Sweden)

    Tsu-Ming Yeh

    2013-10-01

    Full Text Available Measurements are required to maintain the consistent quality of all finished and semi-finished products in a production line. Many firms in the automobile and general precision industries apply the TS 16949:2009 Technical Specifications and Measurement System Analysis (MSA manual to establish measurement systems. This work is undertaken to evaluate gauge repeatability and reproducibility (GR&R to verify the measuring ability and quality of the measurement frame, as well as to continuously improve and maintain the verification process. Nevertheless, the implementation of GR&R requires considerable time and manpower, and is likely to affect production adversely. In addition, the evaluation value for GR&R is always different owing to the sum of man-made and machine-made variations. Using a Monte Carlo simulation and the prediction of the repeatability and reproducibility of the measurement system analysis, this study aims to determine the distribution of %GR&R and the related number of distinct categories (ndc. This study uses two case studies of an automobile parts manufacturer and the combination of a Monte Carlo simulation, statistical bases, and the prediction of the repeatability and reproducibility of the measurement system analysis to determine the probability density function, the distribution of %GR&R, and the related number of distinct categories (ndc. The method used in this study could evaluate effectively the possible range of the GR&R of the measurement capability, in order to establish a prediction model for the evaluation of the measurement capacity of a measurement system.

  19. Validity and repeatability of three in-shoe pressure measurement systems.

    Science.gov (United States)

    Price, Carina; Parker, Daniel; Nester, Christopher

    2016-05-01

    In-shoe pressure measurement devices are used in research and clinic to quantify plantar foot pressures. Various devices are available, differing in size, sensor number and type; therefore accuracy and repeatability. Three devices (Medilogic, Tekscan and Pedar) were examined in a 2 day×3 trial design, quantifying insole response to regional and whole insole loading. The whole insole protocol applied an even pressure (50-600kPa) to the insole surface for 0-30s in the Novel TruBlue™ device. The regional protocol utilised cylinders with contact surfaces of 3.14 and 15.9cm(2) to apply pressures of 50 and 200kPa. The validity (% difference and Root Mean Square Error: RMSE) and repeatability (Intra-Class Correlation Coefficient: ICC) of the applied pressures (whole insole) and contact area (regional) were outcome variables. Validity of the Pedar system was highest (RMSE 2.6kPa; difference 3.9%), with the Medilogic (RMSE 27.0kPa; difference 13.4%) and Tekscan (RMSE 27.0kPa; difference 5.9%) systems displaying reduced validity. The average and peak pressures demonstrated high between-day repeatability for all three systems and each insole size (ICC≥0.859). The regional contact area % difference ranged from -97 to +249%, but the ICC demonstrated medium to high between-day repeatability (ICC≥0.797). Due to the varying responses of the systems, the choice of an appropriate pressure measurement device must be based on the loading characteristics and the outcome variables sought. Medilogic and Tekscan were most effective between 200 and 300kPa; Pedar performed well across all pressures. Contact area was less precise, but relatively repeatable for all systems.

  20. Predicting seed yield in perennial ryegrass using repeated canopy reflectance measurements and PLSR

    DEFF Research Database (Denmark)

    Gislum, René; Deleuran, Lise Christina; Boelt, Birte

    2009-01-01

    Repeated canopy reflectance measurements together with partial least-squares regression (PLSR) were used to predict seed yield in perennial ryegrass (Lolium perenne L.). The measurements were performed during the spring and summer growing seasons of 2001 to 2003 in three field experiments...... reflectance measurements was from approximately 600 cumulative growing degree-days (CGDD) to approximately 900 CGDD. This is the period just before and at heading of the seed crop. Furthermore, regression coefficients showed that information about N and water is important. The results support the development...

  1. Status of a UAV SAR Designed for Repeat Pass Interferometry for Deformation Measurements

    Science.gov (United States)

    Hensley, Scott; Wheeler, Kevin; Hoffman, Jim; Miller, Tim; Lou, Yunling; Muellerschoen, Ron; Zebker, Howard; Madsen, Soren; Rosen, Paul

    2004-01-01

    Under the NASA ESTO sponsored Instrument Incubator Program we have designed a lightweight, reconfigurable polarimetric L-band SAR designed for repeat pass deformation measurements of rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes. This radar will be installed on an unmanned airborne vehicle (UAV) or a lightweight, high-altitude, and long endurance platform such as the Proteus. After a study of suitable available platforms we selected the Proteus for initial development and testing of the system. We want to control the repeat track capability of the aircraft to be within a 10 m tube to support the repeat deformation capability. We conducted tests with the Proteus using real-time GPS with sub-meter accuracy to see if pilots could fly the aircraft within the desired tube. Our results show that pilots are unable to fly the aircraft with the desired accuracy and therefore an augmented autopilot will be required to meet these objectives. Based on the Proteus flying altitude of 13.7 km (45,000 ft), we are designing a fully polarimetric L-band radar with 80 MHz bandwidth and 16 km range swath. This radar will have an active electronic beam steering antenna to achieve Doppler centroid stability that is necessary for repeat-pass interferometry (RPI). This paper will present are design criteria, current design and expected science applications.

  2. Analysis of oligonucleotide array experiments with repeated measures using mixed models

    Directory of Open Access Journals (Sweden)

    Getchell Thomas V

    2004-12-01

    Full Text Available Abstract Background Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease or absence (Control of the disease, and brain regions including olfactory bulb (OB or cerebellum (CER. In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. Results In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH procedure of controlling false discovery rate (FDR at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the α-level (αnew = 0.0033 determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD procedure at the level of αnew to control the family-wise error rate (FWER for each gene examined. Conclusions A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

  3. Analysis of oligonucleotide array experiments with repeated measures using mixed models.

    Science.gov (United States)

    Li, Hao; Wood, Constance L; Getchell, Thomas V; Getchell, Marilyn L; Stromberg, Arnold J

    2004-12-30

    Two or more factor mixed factorial experiments are becoming increasingly common in microarray data analysis. In this case study, the two factors are presence (Patients with Alzheimer's disease) or absence (Control) of the disease, and brain regions including olfactory bulb (OB) or cerebellum (CER). In the design considered in this manuscript, OB and CER are repeated measurements from the same subject and, hence, are correlated. It is critical to identify sources of variability in the analysis of oligonucleotide array experiments with repeated measures and correlations among data points have to be considered. In addition, multiple testing problems are more complicated in experiments with multi-level treatments or treatment combinations. In this study we adopted a linear mixed model to analyze oligonucleotide array experiments with repeated measures. We first construct a generalized F test to select differentially expressed genes. The Benjamini and Hochberg (BH) procedure of controlling false discovery rate (FDR) at 5% was applied to the P values of the generalized F test. For those genes with significant generalized F test, we then categorize them based on whether the interaction terms were significant or not at the alpha-level (alphanew = 0.0033) determined by the FDR procedure. Since simple effects may be examined for the genes with significant interaction effect, we adopt the protected Fisher's least significant difference test (LSD) procedure at the level of alphanew to control the family-wise error rate (FWER) for each gene examined. A linear mixed model is appropriate for analysis of oligonucleotide array experiments with repeated measures. We constructed a generalized F test to select differentially expressed genes, and then applied a specific sequence of tests to identify factorial effects. This sequence of tests applied was designed to control for gene based FWER.

  4. The pugilistDominant Mutation of Drosophila melanogaster: A Simple-Sequence Repeat Disorder Reveals Localized Transport in the Eye.

    Directory of Open Access Journals (Sweden)

    Yikang S Rong

    Full Text Available The pugilist-Dominant mutation results from fusion of a portion of the gene encoding the tri-functional Methylene Tetrahydrofolate Dehydrogenase (E.C.1.5.1.5, E.C.3.5.4.9, E.C.6.3.4.3 to approximately one kb of a heterochromatic satellite repeat. Expression of this fusion gene results in an unusual ring pattern of pigmentation around the eye. We carried out experiments to determine the mechanism for this pattern. By using FLP-mediated DNA mobilization to place different pugD transgenes at pre-selected sites we found that variation in repeat length makes a strong contribution to variability of the pug phenotype. This variation is manifest primarily as differences in the thickness of the pigmented ring. We show that similar phenotypic variation can also be achieved by changing gene copy number. We found that the pugD pattern is not controlled by wingless, which is normally expressed in a similar ring pattern. Finally, we found that physical injury to a pugD eye can lead to pigment deposition in parts of the eye that would not have been pigmented in the absence of injury. Our results are consistent with a model in which a metabolite vital for pigment formation is imported from the periphery of the eye, and pugD limits the extent of its transport towards the center of the eye, thus revealing the existence of a hitherto unknown mechanism of localized transport in the eye.

  5. Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain.

    Science.gov (United States)

    Lamboy, Jorge A; Kim, Hajin; Dembinski, Holly; Ha, Taekjip; Komives, Elizabeth A

    2013-07-24

    Previous single-molecule fluorescence resonance energy transfer (smFRET) studies in which the second and sixth ankyrin repeats (ARs) of IκBα were labeled with FRET pairs showed slow fluctuations as if the IκBα AR domain was unfolding in its native state. To systematically probe where these slow dynamic fluctuations occur, we now present data from smFRET studies wherein FRET labels were placed at ARs 1 and 4 (mutant named AR 1-4), at ARs 2 and 5 (AR 2-5), and at ARs 3 and 6 (AR 3-6). The results presented here reveal that AR 6 most readily detaches/unfolds from the AR domain, undergoing substantial fluctuations at room temperature. AR 6 has fewer stabilizing consensus residues than the other IκBα ARs, probably contributing to the ease with which AR 6 "loses grip". AR 5 shows almost no fluctuations at room temperature, but a significant fraction of molecules shows fluctuations at 37 °C. Introduction of stabilizing mutations that are known to fold AR 6 dampen the fluctuations of AR 5, indicating that the AR 5 fluctuations are likely due to weakened inter-repeat stabilization from AR 6. AR 1 also fluctuates somewhat at room temperature, suggesting that fluctuations are a general behavior of ARs at ends of AR domains. Remarkably, AR 1 still fluctuates in the bound state, but mainly between 0.6 and 0.9 FRET efficiency, whereas in the free IκBα, the fluctuations extend to <0.5 FRET efficiency. Overall, our results provide a more complete picture of the energy landscape of the native state dynamics of an AR domain.

  6. A Network-Based Algorithm for Clustering Multivariate Repeated Measures Data

    Science.gov (United States)

    Koslovsky, Matthew; Arellano, John; Schaefer, Caroline; Feiveson, Alan; Young, Millennia; Lee, Stuart

    2017-01-01

    The National Aeronautics and Space Administration (NASA) Astronaut Corps is a unique occupational cohort for which vast amounts of measures data have been collected repeatedly in research or operational studies pre-, in-, and post-flight, as well as during multiple clinical care visits. In exploratory analyses aimed at generating hypotheses regarding physiological changes associated with spaceflight exposure, such as impaired vision, it is of interest to identify anomalies and trends across these expansive datasets. Multivariate clustering algorithms for repeated measures data may help parse the data to identify homogeneous groups of astronauts that have higher risks for a particular physiological change. However, available clustering methods may not be able to accommodate the complex data structures found in NASA data, since the methods often rely on strict model assumptions, require equally-spaced and balanced assessment times, cannot accommodate missing data or differing time scales across variables, and cannot process continuous and discrete data simultaneously. To fill this gap, we propose a network-based, multivariate clustering algorithm for repeated measures data that can be tailored to fit various research settings. Using simulated data, we demonstrate how our method can be used to identify patterns in complex data structures found in practice.

  7. High-Dimensional Multivariate Repeated Measures Analysis with Unequal Covariance Matrices

    Science.gov (United States)

    Harrar, Solomon W.; Kong, Xiaoli

    2015-01-01

    In this paper, test statistics for repeated measures design are introduced when the dimension is large. By large dimension is meant the number of repeated measures and the total sample size grow together but either one could be larger than the other. Asymptotic distribution of the statistics are derived for the equal as well as unequal covariance cases in the balanced as well as unbalanced cases. The asymptotic framework considered requires proportional growth of the sample sizes and the dimension of the repeated measures in the unequal covariance case. In the equal covariance case, one can grow at much faster rate than the other. The derivations of the asymptotic distributions mimic that of Central Limit Theorem with some important peculiarities addressed with sufficient rigor. Consistent and unbiased estimators of the asymptotic variances, which make efficient use of all the observations, are also derived. Simulation study provides favorable evidence for the accuracy of the asymptotic approximation under the null hypothesis. Power simulations have shown that the new methods have comparable power with a popular method known to work well in low-dimensional situation but the new methods have shown enormous advantage when the dimension is large. Data from Electroencephalograph (EEG) experiment is analyzed to illustrate the application of the results. PMID:26778861

  8. On the repeated measures designs and sample sizes for randomized controlled trials.

    Science.gov (United States)

    Tango, Toshiro

    2016-04-01

    For the analysis of longitudinal or repeated measures data, generalized linear mixed-effects models provide a flexible and powerful tool to deal with heterogeneity among subject response profiles. However, the typical statistical design adopted in usual randomized controlled trials is an analysis of covariance type analysis using a pre-defined pair of "pre-post" data, in which pre-(baseline) data are used as a covariate for adjustment together with other covariates. Then, the major design issue is to calculate the sample size or the number of subjects allocated to each treatment group. In this paper, we propose a new repeated measures design and sample size calculations combined with generalized linear mixed-effects models that depend not only on the number of subjects but on the number of repeated measures before and after randomization per subject used for the analysis. The main advantages of the proposed design combined with the generalized linear mixed-effects models are (1) it can easily handle missing data by applying the likelihood-based ignorable analyses under the missing at random assumption and (2) it may lead to a reduction in sample size, compared with the simple pre-post design. The proposed designs and the sample size calculations are illustrated with real data arising from randomized controlled trials.

  9. Fluorescence In Situ Hybridization (FISH-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris and Relatives

    Directory of Open Access Journals (Sweden)

    Aiko Iwata-Otsubo

    2016-04-01

    Full Text Available Fluorescence in situ hybridization (FISH-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.

  10. Repeatability and Comparison of Keratometry Values Measured with Potec PRK-6000 Autorefractometer, IOLMaster, and Pentacam

    Directory of Open Access Journals (Sweden)

    Adem Türk

    2014-05-01

    Full Text Available Objectives: To research the repeatability and intercompatibility of keratometry values measured with Potec PRK-6000 autorefractometer, IOL Master, and Pentacam. Materials and Methods: In this prospective study, consecutive measurements were performed in two different sessions with the mentioned three devices on 110 eyes of 55 subjects who had no additional ocular pathology except for refraction error. The consistency of flat and steep keratometry, average keratometry, and corneal astigmatism values obtained in both sessions was compared by using intraclass correlation coefficient (ICC. The measurement differences between the devices were statistically compared as well. Results: The mean age of the study subjects was 23.05±3.01 (18-30 years. ICC values of average keratometry measurements obtained in the sessions were 0.996 for Potec PRK-6000 autorefractometer, 0.997 for IOL Master, and 0.999 for Pentacam. There was high compatibility between the three devices in terms of average keratometry values in Bland-Altman analysis. However, there were statistically significant differences between the devices in terms of parameters other than corneal astigmatism. Conclusion: The repeatability of the three devices was found considerably high in keratometry measurements. However, it is not appropriate for these devices to be substituted for each other in keratometry measurements. (Turk J Ophthalmol 2014; 44: 179-83

  11. Repeatability and Reproducibility of Compression Strength Measurements Conducted According to ASTM E9

    Science.gov (United States)

    Luecke, William E.; Ma, Li; Graham, Stephen M.; Adler, Matthew A.

    2010-01-01

    Ten commercial laboratories participated in an interlaboratory study to establish the repeatability and reproducibility of compression strength tests conducted according to ASTM International Standard Test Method E9. The test employed a cylindrical aluminum AA2024-T351 test specimen. Participants measured elastic modulus and 0.2 % offset yield strength, YS(0.2 % offset), using an extensometer attached to the specimen. The repeatability and reproducibility of the yield strength measurement, expressed as coefficient of variations were cv(sub r)= 0.011 and cv(sub R)= 0.020 The reproducibility of the test across the laboratories was among the best that has been reported for uniaxial tests. The reported data indicated that using diametrically opposed extensometers, instead of a single extensometer doubled the precision of the test method. Laboratories that did not lubricate the ends of the specimen measured yield stresses and elastic moduli that were smaller than those measured in laboratories that lubricated the specimen ends. A finite element analysis of the test specimen deformation for frictionless and perfect friction could not explain the discrepancy, however. The modulus measured from stress-strain data were reanalyzed using a technique that finds the optimal fit range, and applies several quality checks to the data. The error in modulus measurements from stress-strain curves generally increased as the fit range decreased to less than 40 % of the stress range.

  12. The effect of repeated measurements and working memory on the most comfortable level in the ANL test

    DEFF Research Database (Denmark)

    Brännström, K Jonas; Olsen, Steen Østergaard; Holm, Lucas

    2014-01-01

    interleaved methodology during one session using a non-semantic version. Phonological (PWM) and visuospatial working memory (VSWM) was measured. STUDY SAMPLE: Thirty-two normal-hearing adults. RESULTS: Repeated measures ANOVA, intraclass correlations, and the coefficient of repeatability (CR) were used...

  13. Effect of repeated contact on adhesion measurements involving polydimethylsiloxane structural material

    Science.gov (United States)

    Kroner, E.; Maboudian, R.; Arzt, E.

    2009-09-01

    During the last few years several research groups have focused on the fabrication of artificial gecko inspired adhesives. For mimicking these structures, different polymers are used as structure material, such as polydimethylsiloxanes (PDMS), polyurethanes (PU), and polypropylene (PP). While these polymers can be structured easily and used for artificial adhesion systems, the effects of repeated adhesion testing have never been investigated closely. In this paper we report on the effect of repeated adhesion measurements on the commercially available poly(dimethylsiloxane) polymer kit Sylgard 184 (Dow Corning). We show that the adhesion force decreases as a function of contact cycles. The rate of change and the final value of adhesion are found to depend on the details of the PDMS synthesis and structuring.

  14. Effect of repeated contact on adhesion measurements involving polydimethylsiloxane structural material

    Energy Technology Data Exchange (ETDEWEB)

    Kroner, E; Arzt, E [INM-Leibniz Institute for New Materials, Campus D2 2, 66125 Saarbruecken (Germany); Maboudian, R, E-mail: elmar.kroner@inm-gmbh.de [Department of Chem. Eng., 201 Gilman Hall, University of California, Berkeley, CA 94720-1462 (United States)

    2009-09-15

    During the last few years several research groups have focused on the fabrication of artificial gecko inspired adhesives. For mimicking these structures, different polymers are used as structure material, such as polydimethylsiloxanes (PDMS), polyurethanes (PU), and polypropylene (PP). While these polymers can be structured easily and used for artificial adhesion systems, the effects of repeated adhesion testing have never been investigated closely. In this paper we report on the effect of repeated adhesion measurements on the commercially available poly(dimethylsiloxane) polymer kit Sylgard 184 (Dow Corning). We show that the adhesion force decreases as a function of contact cycles. The rate of change and the final value of adhesion are found to depend on the details of the PDMS synthesis and structuring.

  15. Repeated Geophysical Surface Measurements to Estimate the Dynamics of Underground Coalfires

    Science.gov (United States)

    Wuttke, M. W.; Kessels, W.; Han, J.; Halisch, M.; Rüter, H.; Lindner, H.

    2009-04-01

    in a range between -130 and 176 nT. The maxima are most likely caused by the conversion of pyrite and markasit into maghemite, hematite and magnetite. Therefore the identified patches with high magnetic anomalies should have a direct connection to the burning coal in firezone 18. The firezone in Wuda has been visited now for five, that in Queergou for two times. All the discussed geophysical measurements together allow an integrated interpretation. Each result can be related to the combustion process with a particular likelihood for the vertical projection to the combustion centre. Probability calculations with chosen weight factors for each observation method are discussed. A so called fireindex deduced from the repeated measurements reveals the dynamics of the coal fire.

  16. Measuring environmental change in forest ecosystems by repeated soil sampling: a North American perspective

    Science.gov (United States)

    Lawrence, Gregory B.; Fernandez, Ivan J.; Richter, Daniel D.; Ross, Donald S.; Hazlett, Paul W.; Bailey, Scott W.; Oiumet, Rock; Warby, Richard A.F.; Johnson, Arthur H.; Lin, Henry; Kaste, James M.; Lapenis, Andrew G.; Sullivan, Timothy J.

    2013-01-01

    Environmental change is monitored in North America through repeated measurements of weather, stream and river flow, air and water quality, and most recently, soil properties. Some skepticism remains, however, about whether repeated soil sampling can effectively distinguish between temporal and spatial variability, and efforts to document soil change in forest ecosystems through repeated measurements are largely nascent and uncoordinated. In eastern North America, repeated soil sampling has begun to provide valuable information on environmental problems such as air pollution. This review synthesizes the current state of the science to further the development and use of soil resampling as an integral method for recording and understanding environmental change in forested settings. The origins of soil resampling reach back to the 19th century in England and Russia. The concepts and methodologies involved in forest soil resampling are reviewed and evaluated through a discussion of how temporal and spatial variability can be addressed with a variety of sampling approaches. Key resampling studies demonstrate the type of results that can be obtained through differing approaches. Ongoing, large-scale issues such as recovery from acidification, long-term N deposition, C sequestration, effects of climate change, impacts from invasive species, and the increasing intensification of soil management all warrant the use of soil resampling as an essential tool for environmental monitoring and assessment. Furthermore, with better awareness of the value of soil resampling, studies can be designed with a long-term perspective so that information can be efficiently obtained well into the future to address problems that have not yet surfaced.

  17. Validity and repeatability of a depth camera-based surface imaging system for thigh volume measurement.

    Science.gov (United States)

    Bullas, Alice M; Choppin, Simon; Heller, Ben; Wheat, Jon

    2016-10-01

    Complex anthropometrics such as area and volume, can identify changes in body size and shape that are not detectable with traditional anthropometrics of lengths, breadths, skinfolds and girths. However, taking these complex with manual techniques (tape measurement and water displacement) is often unsuitable. Three-dimensional (3D) surface imaging systems are quick and accurate alternatives to manual techniques but their use is restricted by cost, complexity and limited access. We have developed a novel low-cost, accessible and portable 3D surface imaging system based on consumer depth cameras. The aim of this study was to determine the validity and repeatability of the system in the measurement of thigh volume. The thigh volumes of 36 participants were measured with the depth camera system and a high precision commercially available 3D surface imaging system (3dMD). The depth camera system used within this study is highly repeatable (technical error of measurement (TEM) of <1.0% intra-calibration and ~2.0% inter-calibration) but systematically overestimates (~6%) thigh volume when compared to the 3dMD system. This suggests poor agreement yet a close relationship, which once corrected can yield a usable thigh volume measurement.

  18. Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant.

    Science.gov (United States)

    Yuchi, Zhiguang; Yuen, Siobhan M Wong King; Lau, Kelvin; Underhill, Ainsley Q; Cornea, Razvan L; Fessenden, James D; Van Petegem, Filip

    2015-08-06

    Ryanodine receptors (RyRs) form calcium release channels located in the membranes of the sarcoplasmic and endoplasmic reticulum. RyRs play a major role in excitation-contraction coupling and other Ca(2+)-dependent signalling events, and consist of several globular domains that together form a large assembly. Here we describe the crystal structures of the SPRY1 and tandem-repeat domains at 1.2-1.5 Å resolution, which reveal several structural elements not detected in recent cryo-EM reconstructions of RyRs. The cryo-EM studies disagree on the position of SPRY domains, which had been proposed based on homology modelling. Computational docking of the crystal structures, combined with FRET studies, show that the SPRY1 domain is located next to FK506-binding protein (FKBP). Molecular dynamics flexible fitting and mutagenesis experiments suggest a hydrophobic cluster within SPRY1 that is crucial for FKBP binding. A RyR1 disease mutation, N760D, appears to directly impact FKBP binding through interfering with SPRY1 folding.

  19. Accuracy and repeatability of an inertial measurement unit system for field-based occupational studies.

    Science.gov (United States)

    Schall, Mark C; Fethke, Nathan B; Chen, Howard; Oyama, Sakiko; Douphrate, David I

    2016-04-01

    The accuracy and repeatability of an inertial measurement unit (IMU) system for directly measuring trunk angular displacement and upper arm elevation were evaluated over eight hours (i) in comparison to a gold standard, optical motion capture (OMC) system in a laboratory setting, and (ii) during a field-based assessment of dairy parlour work. Sample-to-sample root mean square differences between the IMU and OMC system ranged from 4.1° to 6.6° for the trunk and 7.2°-12.1° for the upper arm depending on the processing method. Estimates of mean angular displacement and angular displacement variation (difference between the 90th and 10th percentiles of angular displacement) were observed to change IMU system may serve as an acceptable instrument for directly measuring trunk and upper arm postures in field-based occupational exposure assessment studies with long sampling durations. Practitioner Summary: Few studies have evaluated inertial measurement unit (IMU) systems in the field or over long sampling durations. Results of this study indicate that the IMU system evaluated has reasonably good accuracy and repeatability for use in a field setting over a long sampling duration.

  20. Complete gene sequence of spider attachment silk protein (PySp1) reveals novel linker regions and extreme repeat homogenization.

    Science.gov (United States)

    Chaw, Ro Crystal; Saski, Christopher A; Hayashi, Cheryl Y

    2017-02-01

    Spiders use a myriad of silk types for daily survival, and each silk type has a unique suite of task-specific mechanical properties. Of all spider silk types, pyriform silk is distinct because it is a combination of a dry protein fiber and wet glue. Pyriform silk fibers are coated with wet cement and extruded into "attachment discs" that adhere silks to each other and to substrates. The mechanical properties of spider silk types are linked to the primary and higher-level structures of spider silk proteins (spidroins). Spidroins are often enormous molecules (>250 kDa) and have a lengthy repetitive region that is flanked by relatively short (∼100 amino acids), non-repetitive amino- and carboxyl-terminal regions. The amino acid sequence motifs in the repetitive region vary greatly between spidroin type, while motif length and number underlie the remarkable mechanical properties of spider silk fibers. Existing knowledge of pyriform spidroins is fragmented, making it difficult to define links between the structure and function of pyriform spidroins. Here, we present the full-length sequence of the gene encoding pyriform spidroin 1 (PySp1) from the silver garden spider Argiope argentata. The predicted protein is similar to previously reported PySp1 sequences but the A. argentata PySp1 has a uniquely long and repetitive "linker", which bridges the amino-terminal and repetitive regions. Predictions of the hydrophobicity and secondary structure of A. argentata PySp1 identify regions important to protein self-assembly. Analysis of the full complement of A. argentata PySp1 repeats reveals extreme intragenic homogenization, and comparison of A. argentata PySp1 repeats with other PySp1 sequences identifies variability in two sub-repetitive expansion regions. Overall, the full-length A. argentata PySp1 sequence provides new evidence for understanding how pyriform spidroins contribute to the properties of pyriform silk fibers. Copyright © 2017 The Authors. Published by

  1. An L-band SAR for repeat pass deformation measurements on a UAV platform

    Science.gov (United States)

    Hensley, Scott; Lou, Yunling; Rosen, Paul; Wheeler, Kevin; Zebker, Howard; Madsen, Soren; Miller, Tim; Hoffman, Jim; Farra, Don

    2003-01-01

    We are proposing to develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for repeat-pass differential interferometric measurements of deformation for rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes that is to be flown on a unmanned aerial vehicle (UAV) or minimally piloted vehicle (MPV). Upon surveying the capabilities and availabilities of such aircraft, the Proteus aircraft and the ALTAIR UAV appear to meet our criteria in terms of payload capabilities, flying altitude, and endurance. To support the repeat pass deformation capability it is necessary to control flight track capability of the aircraft to be within a specified 10 m tube with a goal of 1 m. This requires real-time GPS control of the autopilot to achieve these objectives that has not been demonstrated on these aircraft. Based on the Proteus and ALTAIR's altitude of 13.7 km (45,000 ft), we are designing a fully polarimetric L-band radar with 80 MHz bandwidth and a 16 km range swath. The radar will have an active electronic beam steering antenna to achieve a Doppler centroid stability that is necessary for repeat-pass interferometry. This paper presents some of the trade studies for the platform, instrument and the expected science.

  2. Molecular phylogeny of the kelch-repeat superfamily reveals an expansion of BTB/kelch proteins in animals

    Directory of Open Access Journals (Sweden)

    Adams Josephine C

    2003-09-01

    Full Text Available Abstract Background The kelch motif is an ancient and evolutionarily-widespread sequence motif of 44–56 amino acids in length. It occurs as five to seven repeats that form a β-propeller tertiary structure. Over 28 kelch-repeat proteins have been sequenced and functionally characterised from diverse organisms spanning from viruses, plants and fungi to mammals and it is evident from expressed sequence tag, domain and genome databases that many additional hypothetical proteins contain kelch-repeats. In general, kelch-repeat β-propellers are involved in protein-protein interactions, however the modest sequence identity between kelch motifs, the diversity of domain architectures, and the partial information on this protein family in any single species, all present difficulties to developing a coherent view of the kelch-repeat domain and the kelch-repeat protein superfamily. To understand the complexity of this superfamily of proteins, we have analysed by bioinformatics the complement of kelch-repeat proteins encoded in the human genome and have made comparisons to the kelch-repeat proteins encoded in other sequenced genomes. Results We identified 71 kelch-repeat proteins encoded in the human genome, whereas 5 or 8 members were identified in yeasts and around 18 in C. elegans, D. melanogaster and A. gambiae. Multiple domain architectures were identified in each organism, including previously unrecognised forms. The vast majority of kelch-repeat domains are predicted to form six-bladed β-propellers. The most prevalent domain architecture in the metazoan animal genomes studied was the BTB/kelch domain organisation and we uncovered 3 subgroups of human BTB/kelch proteins. Sequence analysis of the kelch-repeat domains of the most robustly-related subgroups identified differences in β-propeller organisation that could provide direction for experimental study of protein-binding characteristics. Conclusion The kelch-repeat superfamily constitutes a

  3. Measurement of bedform migration rates on the Lower Missouri River in Missouri, USA using repeat measurements with a multibeam echosounder

    Science.gov (United States)

    Elliott, Caroline M.; Jacobson, Robert B.

    2016-01-01

    High-resolution repeat multibeam echosounder measurements on the Lower Missouri River near Boonville, Missouri, USA show bedform movement and sand storage patterns over daily to seasonal time scales and a range of discharges. Higher flows are frequently, but not always, associated with larger bedforms, higher bedform movement rates, and higher bedload transport rates. Measurements of the temporal and spatial variability in sand dune sizes, transport rates, and sand storage across the river channel have increased understanding of the dynamics of habitats utilized by benthic organisms over multiple life stages and daily to seasonal time scales.

  4. Specific Measurement of Tethered Running Kinetics and its Relationship to Repeated Sprint Ability

    Directory of Open Access Journals (Sweden)

    Sousa Filipe

    2015-12-01

    Full Text Available Repeated sprint ability has been widely studied by researchers, however, analysis of the relationship between most kinetic variables and the effect of fatigue is still an ongoing process. To search for the best biomechanical parameter to evaluate repeated sprint ability, several kinetic variables were measured in a tethered field running test and compared regarding their sensitivity to fatigue and correlation with time trials in a free running condition. Nine male sprint runners (best average times: 100 m = 10.45 ± 0.07 s; 200 m = 21.36 ± 0.17 s; 400 m = 47.35 ± 1.09 s completed two test sessions on a synthetic track. Each session consisted of six 35 m sprints interspersed by 10 s rest under tethered field running or free running conditions. Force, power, work, an impulse and a rate of force development were all directly measured using the sensors of a new tethered running apparatus, and a one-way ANOVA with Scheffé post-hoc test used to verify differences between sprints (p < 0.05. Pearson product-moment correlation measured the relationship between mechanical variables and free running performance. A total impulse, the rate of force development and maximum force did not show significant differences for most sprints. These three variables presented low to moderate correlations with free running performance (r between 0.01 and -0.35. Maximum and mean power presented the strongest correlations with free running performance (r = -0.71 and -0.76, respectively; p < 0.001, followed by mean force (r = -0.61; p < 0.001 and total work (r = -0.50; p < 0.001. It was concluded that under a severe work-to-rest ratio condition, power variables were better suited to evaluating repeated sprint ability than the other studied variables.

  5. Characterisation and measurement of signals generated by DVB-H 'GAP-filler' repeaters.

    Science.gov (United States)

    Baldini, M; Barellini, A; Bogi, L; Licitra, G; Silvi, A M; Zari, A

    2009-12-01

    DVB-H (Digital Video Broadcasting Handheld) is the standard developed by DVB Project and approved by ETSI with the aim of providing the reception of DVB signals even in mobility but also data transfers and multimedia services. The introduction and development of the DVB-H system is still ongoing. In this context, this work focuses on the temporal trend of electromagnetic impact of an urban DVB-H repeater (called 'gap-filler') for exposure assessment purposes; it also describes a method for its measurement by means of narrow band instrumental chains.

  6. Measuring the Activity of Leucine-Rich Repeat Kinase 2: A Kinase Involved in Parkinson's Disease

    Science.gov (United States)

    Lee, Byoung Dae; Li, Xiaojie; Dawson, Ted M.; Dawson, Valina L.

    2015-01-01

    Mutations in the LRRK2 (Leucine-Rich Repeat Kinase 2) gene are the most common cause of autosomal dominant Parkinson's disease. LRRK2 has multiple functional domains including a kinase domain. The kinase activity of LRRK2 is implicated in the pathogenesis of Parkinson's disease. Developing an assay to understand the mechanisms of LRRK2 kinase activity is important for the development of pharmacologic and therapeutic applications. Here, we describe how to measure in vitro LRRK2 kinase activity and its inhibition. PMID:21960214

  7. Iterative Weighted Semiparametric Least Squares Estimation in Repeated Measurement Partially Linear Regression Models

    Institute of Scientific and Technical Information of China (English)

    Ge-mai Chen; Jin-hong You

    2005-01-01

    Consider a repeated measurement partially linear regression model with an unknown vector pasemiparametric generalized least squares estimator (SGLSE) ofβ, we propose an iterative weighted semiparametric least squares estimator (IWSLSE) and show that it improves upon the SGLSE in terms of asymptotic covariance matrix. An adaptive procedure is given to determine the number of iterations. We also show that when the number of replicates is less than or equal to two, the IWSLSE can not improve upon the SGLSE.These results are generalizations of those in [2] to the case of semiparametric regressions.

  8. Measuring Starlight Deflection during the 2017 Eclipse: Repeating the Experiment that made Einstein Famous

    Science.gov (United States)

    Bruns, Donald

    2016-05-01

    In 1919, astronomers performed an experiment during a solar eclipse, attempting to measure the deflection of stars near the sun, in order to verify Einstein's theory of general relativity. The experiment was very difficult and the results were marginal, but the success made Albert Einstein famous around the world. Astronomers last repeated the experiment in 1973, achieving an error of 11%. In 2017, using amateur equipment and modern technology, I plan to repeat the experiment and achieve a 1% error. The best available star catalog will be used for star positions. Corrections for optical distortion and atmospheric refraction are better than 0.01 arcsec. During totality, I expect 7 or 8 measurable stars down to magnitude 9.5, based on analysis of previous eclipse measurements taken by amateurs. Reference images, taken near the sun during totality, will be used for precise calibration. Preliminary test runs performed during twilight in April 2016 and April 2017 can accurately simulate the sky conditions during totality, providing an accurate estimate of the final uncertainty.

  9. Repeatability and Accuracy of Exoplanet Eclipse Depths Measured with Post-Cryogenic Spitzer

    CERN Document Server

    Ingalls, James G; Carey, S J; Stauffer, John R; Lawrence, Patrick J; Grillmair, Carl J; Buzasi, Derek; Deming, Drake; Diamond-Lowe, Hannah; Evans, Thomas M; Morello, G; Stevenson, Kevin B; Wong, Ian; Capak, Peter; Glaccum, William; Laine, Seppo; Surace, Jason; Storrie-Lombardi, Lisa

    2016-01-01

    We examine the repeatability, reliability, and accuracy of differential exoplanet eclipse depth measurements made using the InfraRed Array Camera (IRAC) on the Spitzer Space Telescope during the post-cryogenic mission. We have re-analyzed an existing 4.5{\\mu}m dataset, consisting of 10 observations of the XO-3 b system during secondary eclipse, using 7 different techniques for removing correlated noise. We find that, on average, for a given technique the eclipse depth estimate is repeatable from epoch to epoch to within 150 parts per million (ppm). Most techniques derive eclipse depths that do not vary by more than a factor 2 of the photon noise limit. Nearly all methods accurately assess their own errors: for these methods the individual measurement uncertainties are comparable to the scatter in eclipse depths over the 10-epoch sample. To assess the accuracy of the techniques as well as clarify the difference between instrumental and other sources of measurement error, we have also analyzed a simulated datas...

  10. Repeatability and reproducibility of horizontal corneal diameter and anterior corneal power measurements using the Oculus Keratograph 4

    Directory of Open Access Journals (Sweden)

    Khathutshelo P. Mashige

    2016-03-01

    Full Text Available Purpose: To evaluate the repeatability and reproducibility of horizontal corneal diameter (HCD and anterior corneal power (ACP measurements obtained with the Oculus Keratograph 4 (OCULUS Optikgeräte GmbH.Methods: These parameters (HCD and ACP were prospectively measured in quick succession three times in each of the right eyes of 40 healthy subjects, aged 18–28 years, with normal vision (6/6 or better visual acuity in the first session by a single examiner. Measurements were then repeated in the second session scheduled 1 week later by the same examiner using the same instrument. Repeatability and reproducibility of HCD and ACP measurements was assessed based on the intra-session and intersession within-subject standard deviation (sw, repeatability (2.77sw, coefficient of variation (CoV and intra-class correlation coefficient (ICC.Results: Intra-session repeatability and intersession reproducibility of all measured parameters showed a repeatability (2.77sw of 0.35 mm or less for HCD and 0.35 D or less for ACP, a CoV of 0.30% or less and an ICC of more than 0.9.Conclusion: HCD and ACP measurements obtained using an Oculus Keratograph 4 show good repeatability and reproducibility in healthy eyes; therefore, these parameters can be used for longitudinal follow-up when measured with this device.

  11. Measuring the Dynamic Soil Response During Repeated Wheeling Using Seismic Methods

    DEFF Research Database (Denmark)

    Keller, Thomas; Carizzon, Marco; Berisso, Feto Esimo

    2013-01-01

    Our understanding of soil deformation processes, especially its dynamics, remains limited. This hampers accurate predictions of the impact of soil management practices such as agricultural field traffic on (physical) soil functions. The main objective of this study was to investigate whether...... seismic measurements could be used to assess the dynamic soil behavior during repeated loading. Moreover, we aimed at linking the velocity of P-waves, Vp, to traditionally measured soil properties associated with soil compaction, namely bulk density (ρb) and penetrometer resistance. A wheeling experiment......, and simulated the evolution of bulk density due to the wheeling using a soil compaction model. The dynamic soil response during loading–unloading–reloading cycles could be well captured with the seismic method. The measured Vp related to bulk density, and the compaction-induced increase in Vp correlated...

  12. Genetic variation in Rhodomyrtus tomentosa (Kemunting) populations from Malaysia as revealed by inter-simple sequence repeat markers.

    Science.gov (United States)

    Hue, T S; Abdullah, T L; Abdullah, N A P; Sinniah, U R

    2015-12-14

    Kemunting (Rhodomyrtus tomentosa) from the Myrtaceae family, is native to Malaysia. It is widely used in traditional medicine to treat various illnesses and possesses significant antibacterial properties. In addition, it has great potential as ornamental in landscape design. Genetic variability studies are important for the rational management and conservation of genetic material. In the present study, inter-simple sequence repeat markers were used to assess the genetic diversity of 18 R. tomentosa populations collected from ten states of Peninsular Malaysia. The 11 primers selected generated 173 bands that ranged in size from 1.6 kb to 130 bp, which corresponded to an average of 15.73 bands per primer. Of these bands, 97.69% (169 in total) were polymorphic. High genetic diversity was documented at the species level (H(T) = 0.2705; I = 0.3973; PPB = 97.69%) but there was a low diversity at population level (H(S) = 0.0073; I = 0 .1085; PPB = 20.14%). The high level of genetic differentiation revealed by G(ST) (73%) and analysis of molecular variance (63%), together with the limited gene flow among population (N(m) = 0.1851), suggests that the populations examined are isolated. Results from an unweighted pair group method with arithmetic mean dendrogram and principal coordinate analysis clearly grouped the populations into two geographic groups. This clear grouping can also be demonstrated by the significant Mantel test (r = 0.581, P = 0.001). We recommend that all the R. tomentosa populations be preserved in conservation program.

  13. A comparative proteomic analysis of the simple amino acid repeat distributions in Plasmodia reveals lineage specific amino acid selection.

    Directory of Open Access Journals (Sweden)

    Andrew R Dalby

    Full Text Available BACKGROUND: Microsatellites have been used extensively in the field of comparative genomics. By studying microsatellites in coding regions we have a simple model of how genotypic changes undergo selection as they are directly expressed in the phenotype as altered proteins. The simplest of these tandem repeats in coding regions are the tri-nucleotide repeats which produce a repeat of a single amino acid when translated into proteins. Tri-nucleotide repeats are often disease associated, and are also known to be unstable to both expansion and contraction. This makes them sensitive markers for studying proteome evolution, in closely related species. RESULTS: The evolutionary history of the family of malarial causing parasites Plasmodia is complex because of the life-cycle of the organism, where it interacts with a number of different hosts and goes through a series of tissue specific stages. This study shows that the divergence between the primate and rodent malarial parasites has resulted in a lineage specific change in the simple amino acid repeat distribution that is correlated to A-T content. The paper also shows that this altered use of amino acids in SAARs is consistent with the repeat distributions being under selective pressure. CONCLUSIONS: The study shows that simple amino acid repeat distributions can be used to group related species and to examine their phylogenetic relationships. This study also shows that an outgroup species with a similar A-T content can be distinguished based only on the amino acid usage in repeats, and suggest that this might be a useful feature for proteome clustering. The lineage specific use of amino acids in repeat regions suggests that comparative studies of SAAR distributions between proteomes gives an insight into the mechanisms of expansion and the selective pressures acting on the organism.

  14. Information Contents of a Signal at Repeated Positioning Measurements of the Coordinate Measuring Machine (CMM by Laser Interferometer

    Directory of Open Access Journals (Sweden)

    Stejskal Tomáš

    2016-10-01

    Full Text Available The input of this paper lies in displaying possibilities how to determine the condition of a coordinate measuring machine (CMM based on a large number of repeated measurements. The number of repeated measurements exceeds common requirements for determining positioning accuracy. The total offset in the accuracy of spatial positioning consists of partial inaccuracies of individual axes. 6 basic errors may be defined at each axis. In a triaxial set, that translates into 18 errors, to which an offset from the perpendicularity between the axial pairs must be added. Therefore, the combined number of errors in a single position is 21. These errors are systemic and stem from the machine’s geometry. In addition, there are accidental errors to account for as well. Accidental errors can be attributed to vibrations, mass inertness, passive resistance, and in part to fluctuations in temperature. A peculiar set of systemic errors are time-varying errors. The nature of those errors may be reversible, for instance if they result from influence of temperature or elastic deformation. They can be also irreversible, for example as a result of wear and tear or line clogging, due to loosened connection or permanent deformation of a part post collision. A demonstration of thermal equalizing of the machine’s parts may also be observed in case of failure to adhere to a sufficient time interval from the moment the air-conditioning is turned on. Repeated measurements done on a selected axis with linear interferometer can provide complex information on the CMM condition and also on the machine’s interaction with the given technical environment.

  15. Specific Measurement of Tethered Running Kinetics and its Relationship to Repeated Sprint Ability.

    Science.gov (United States)

    Sousa, Filipe; Dos Reis, Ivan; Ribeiro, Luiz; Martins, Luiz; Gobatto, Claudio

    2015-12-22

    Repeated sprint ability has been widely studied by researchers, however, analysis of the relationship between most kinetic variables and the effect of fatigue is still an ongoing process. To search for the best biomechanical parameter to evaluate repeated sprint ability, several kinetic variables were measured in a tethered field running test and compared regarding their sensitivity to fatigue and correlation with time trials in a free running condition. Nine male sprint runners (best average times: 100 m = 10.45 ± 0.07 s; 200 m = 21.36 ± 0.17 s; 400 m = 47.35 ± 1.09 s) completed two test sessions on a synthetic track. Each session consisted of six 35 m sprints interspersed by 10 s rest under tethered field running or free running conditions. Force, power, work, an impulse and a rate of force development were all directly measured using the sensors of a new tethered running apparatus, and a one-way ANOVA with Scheffé post-hoc test used to verify differences between sprints (p sprints. These three variables presented low to moderate correlations with free running performance (r between 0.01 and -0.35). Maximum and mean power presented the strongest correlations with free running performance (r = -0.71 and -0.76, respectively; p sprint ability than the other studied variables.

  16. On the Analysis of a Repeated Measure Design in Genome-Wide Association Analysis

    Directory of Open Access Journals (Sweden)

    Young Lee

    2014-11-01

    Full Text Available Longitudinal data enables detecting the effect of aging/time, and as a repeated measures design is statistically more efficient compared to cross-sectional data if the correlations between repeated measurements are not large. In particular, when genotyping cost is more expensive than phenotyping cost, the collection of longitudinal data can be an efficient strategy for genetic association analysis. However, in spite of these advantages, genome-wide association studies (GWAS with longitudinal data have rarely been analyzed taking this into account. In this report, we calculate the required sample size to achieve 80% power at the genome-wide significance level for both longitudinal and cross-sectional data, and compare their statistical efficiency. Furthermore, we analyzed the GWAS of eight phenotypes with three observations on each individual in the Korean Association Resource (KARE. A linear mixed model allowing for the correlations between observations for each individual was applied to analyze the longitudinal data, and linear regression was used to analyze the first observation on each individual as cross-sectional data. We found 12 novel genome-wide significant disease susceptibility loci that were then confirmed in the Health Examination cohort, as well as some significant interactions between age/sex and SNPs.

  17. Multiple-objective response-adaptive repeated measurement designs in clinical trials for binary responses.

    Science.gov (United States)

    Liang, Yuanyuan; Li, Yin; Wang, Jing; Carriere, Keumhee C

    2014-02-20

    A multiple-objective allocation strategy was recently proposed for constructing response-adaptive repeated measurement designs for continuous responses. We extend the allocation strategy to constructing response-adaptive repeated measurement designs for binary responses. The approach with binary responses is quite different from the continuous case, as the information matrix is a function of responses, and it involves nonlinear modeling. To deal with these problems, we first build the design on the basis of success probabilities. Then we illustrate how various models can accommodate carryover effects on the basis of logits of response profiles as well as any correlation structure. Through computer simulations, we find that the allocation strategy developed for continuous responses also works well for binary responses. As expected, design efficiency in terms of mean squared error drops sharply, as more emphasis is placed on increasing treatment benefit than estimation precision. However, we find that it can successfully allocate more patients to better treatment sequences without sacrificing much estimation precision.

  18. Role of Repeat Muscle Compartment Pressure Measurements in Chronic Exertional Compartment Syndrome of the Lower Leg

    Science.gov (United States)

    van Zantvoort, Aniek P. M.; de Bruijn, Johan A.; Winkes, Michiel B.; Hoogeveen, Adwin R.; Teijink, Joep A. W.; Scheltinga, Marc R.

    2017-01-01

    Background: The diagnostic gold standard for diagnosing chronic exertional compartment syndrome (CECS) is a dynamic intracompartmental pressure (ICP) measurement of the muscle. The potential role of a repeat ICP (re-ICP) measurement in patients with persistent lower leg symptoms after surgical decompression or with ongoing symptoms after an earlier normal ICP is unknown. Purpose: To study whether re-ICP measurements in patients with persistent CECS-like symptoms of the lower leg may contribute to the diagnosis of CECS after both surgical decompression and a previously normal ICP measurement. Study Design: Case series; Level of evidence, 4. Methods: Charts of patients who underwent re-ICP measurement of lower leg compartments (anterior [ant], deep posterior [dp], and/or lateral [lat] compartments) between 2001 and 2013 were retrospectively studied. CECS was diagnosed on the basis of generally accepted cutoff pressures for newly onset CECS (Pedowitz criteria: ICP at rest ≥15 mmHg, ≥30 mmHg after 1 minute, or ≥20 mmHg 5 minutes after a provocative test). Factors predicting recurrent CECS after surgery or after a previously normal ICP measurement were analyzed. Results: A total of 1714 ICP measurements were taken in 1513 patients with suspected CECS over a 13-year observation period. In all, 201 (12%) tests were re-ICP measurements for persistent lower leg symptoms. Based on the proposed ICP cutoff values, CECS recurrence was diagnosed in 16 of 62 previously operated compartments (recurrence rate, 26%; 53 patients [64% female]; median age, 24 years; age range, 15-78 years). Recurrence rates were not different among the 3 lower leg CECS compartments (ant-CECS, 17%; dp-CECS, 33%; lat-CECS, 30%; χ2 = 1.928, P = .381). Sex (χ2 = 0.058, P = .810), age (U = 378, z = 1.840, P = .066), bilaterality (χ2 = 0.019, P = .889), and prefasciotomy ICP did not predict recurrence. Re-ICP measurements evaluating 20 compartments with previously normal ICP measurements (15

  19. Role of Repeat Muscle Compartment Pressure Measurements in Chronic Exertional Compartment Syndrome of the Lower Leg.

    Science.gov (United States)

    van Zantvoort, Aniek P M; de Bruijn, Johan A; Winkes, Michiel B; Hoogeveen, Adwin R; Teijink, Joep A W; Scheltinga, Marc R

    2017-06-01

    The diagnostic gold standard for diagnosing chronic exertional compartment syndrome (CECS) is a dynamic intracompartmental pressure (ICP) measurement of the muscle. The potential role of a repeat ICP (re-ICP) measurement in patients with persistent lower leg symptoms after surgical decompression or with ongoing symptoms after an earlier normal ICP is unknown. To study whether re-ICP measurements in patients with persistent CECS-like symptoms of the lower leg may contribute to the diagnosis of CECS after both surgical decompression and a previously normal ICP measurement. Case series; Level of evidence, 4. Charts of patients who underwent re-ICP measurement of lower leg compartments (anterior [ant], deep posterior [dp], and/or lateral [lat] compartments) between 2001 and 2013 were retrospectively studied. CECS was diagnosed on the basis of generally accepted cutoff pressures for newly onset CECS (Pedowitz criteria: ICP at rest ≥15 mmHg, ≥30 mmHg after 1 minute, or ≥20 mmHg 5 minutes after a provocative test). Factors predicting recurrent CECS after surgery or after a previously normal ICP measurement were analyzed. A total of 1714 ICP measurements were taken in 1513 patients with suspected CECS over a 13-year observation period. In all, 201 (12%) tests were re-ICP measurements for persistent lower leg symptoms. Based on the proposed ICP cutoff values, CECS recurrence was diagnosed in 16 of 62 previously operated compartments (recurrence rate, 26%; 53 patients [64% female]; median age, 24 years; age range, 15-78 years). Recurrence rates were not different among the 3 lower leg CECS compartments (ant-CECS, 17%; dp-CECS, 33%; lat-CECS, 30%; χ(2) = 1.928, P = .381). Sex (χ(2) = 0.058, P = .810), age (U = 378, z = 1.840, P = .066), bilaterality (χ(2) = 0.019, P = .889), and prefasciotomy ICP did not predict recurrence. Re-ICP measurements evaluating 20 compartments with previously normal ICP measurements (15 patients [53% female]; mean age, 31 ± 10 years

  20. ±25ppm repeatable measurement of trapezoidal pulses with 5MHz bandwidth

    CERN Document Server

    AUTHOR|(SzGeCERN)712364; Arpaia, Pasquale; Cerqueira Bastos, Miguel; Martino, Michele

    2015-01-01

    High-quality measurements of pulses are nowadays widely used in fields such as radars, pulsed lasers, electromagnetic pulse generators, and particle accelerators. Whilst literature is mainly focused on fast systems for nanosecond regime with relaxed metrological requirements, in this paper, the high-performance measurement of slower pulses in microsecond regime is faced. In particular, the experimental proof demonstration for a 15 MS/s,_25 ppm repeatable acquisition system to characterize the flat-top of 3 ms rise-time trapezoidal pulses is given. The system exploits a 5MHz bandwidth circuit for analogue signal processing based on the concept of flat-top removal. The requirements, as well as the conceptual and physical designs are illustrated. Simulation results aimed at assessing the circuit performance are also presented. Finally, an experimental case study on the characterization of a pulsed power supply for the klystrons modulators of the Compact Linear Collider (CLIC) under study at CERN is reported. In ...

  1. Alcohol intake and colorectal cancer: a comparison of approaches for including repeated measures of alcohol consumption

    DEFF Research Database (Denmark)

    Thygesen, Lau Caspar; Wu, Kana; Grønbaek, Morten

    2008-01-01

    BACKGROUND: In numerous studies, alcohol intake has been found to be positively associated with colorectal cancer risk. However, the majority of studies included only one exposure measurement, which may bias the results if long-term intake is relevant.METHODS: We compared different approaches...... for including repeated measures of alcohol intake among 47,432 US men enrolled in the Health Professionals Follow-up Study. Questionnaires including questions on alcohol intake had been completed in 1986, 1990, 1994, and 1998. The outcome was incident colorectal cancer during follow-up from 1986 to 2002.RESULTS......: During follow-up, 868 members of the cohort experienced colorectal cancer. Baseline, updated, and cumulative average alcohol intakes were positively associated with colorectal cancer, with only minor differences among the approaches. These results support moderately increased risk for intake >30 g...

  2. Impact of repeated measures and sample selection on genome-wide association studies of fasting glucose

    Science.gov (United States)

    Rasmussen-Torvik, Laura J.; Alonso, Alvaro; Li, Man; Kao, Wen; Köttgen, Anna; Yan, Yuer; Couper, David; Boerwinkle, Eric; Bielinski, Suzette J.; Pankow, James S.

    2010-01-01

    Although GWAS have been performed in longitudinal studies, most used only a single trait measure. GWAS of fasting glucose have generally included only normoglycemic individuals. We examined the impact of both repeated measures and sample selection on GWAS in ARIC, a study which obtained four longitudinal measures of fasting glucose and included both individuals with and without prevalent diabetes. The sample included Caucasians and the Affymetrix 6.0 chip was used for genotyping. Sample sizes for GWAS analyses ranged from 8372 (first study visit) to 5782 (average fasting glucose). Candidate SNP analyses with SNPs identified through fasting glucose or diabetes GWAS were conducted in 9133 individuals, including 761 with prevalent diabetes. For a constant sample size, smaller p-values were obtained for the average measure of fasting glucose compared to values at any single visit, and two additional significant GWAS signals were detected. For four candidate SNPs (rs780094, rs10830963, rs7903146, and rs4607517), the strength of association between genotype and glucose was significantly (p-interaction fasting glucose candidate SNPs (rs780094, rs10830963, rs560887, rs4607517, rs13266634) the association with measured fasting glucose was more significant in the smaller sample without prevalent diabetes than in the larger combined sample of those with and without diabetes. This analysis demonstrates the potential utility of averaging trait values in GWAS studies and explores the advantage of using only individuals without prevalent diabetes in GWAS of fasting glucose. PMID:20839289

  3. Estimation of the concordance correlation coefficient for repeated measures using SAS and R.

    Science.gov (United States)

    Carrasco, Josep L; Phillips, Brenda R; Puig-Martinez, Josep; King, Tonya S; Chinchilli, Vernon M

    2013-03-01

    The concordance correlation coefficient is one of the most common approaches used to assess agreement among different observers or instruments when the outcome of interest is a continuous variable. A SAS macro and R package are provided here to estimate the concordance correlation coefficient (CCC) where the design of the data involves repeated measurements by subject and observer. The CCC is estimated using U-statistics (UST) and variance components (VC) approaches. Confidence intervals and standard errors are reported along with the point estimate of the CCC. In the case of the VC approach, the linear mixed model output and variance components estimates are also provided. The performance of each function is shown by means of some examples with real data sets.

  4. Graphic Methods for Interpreting Longitudinal Dyadic Patterns From Repeated-Measures Actor-Partner Interdependence Models

    DEFF Research Database (Denmark)

    Perry, Nicholas; Baucom, Katherine; Bourne, Stacia

    2017-01-01

    Researchers commonly use repeated-measures actor–partner interdependence models (RM-APIM) to understand how romantic partners change in relation to one another over time. However, traditional interpretations of the results of these models do not fully or correctly capture the dyadic temporal...... patterns estimated in RM-APIM. Interpretation of results from these models largely focuses on the meaning of single-parameter estimates in isolation from all the others. However, considering individual coefficients separately impedes the understanding of how these associations combine to produce...... to improve the understanding and presentation of dyadic patterns of association described by standard RM-APIMs. The current article briefly reviews the conceptual foundations of RM-APIMs, demonstrates how change-as-outcome RM-APIMs and VFDs can aid interpretation of standard RM-APIMs, and provides a tutorial...

  5. Inmate responses to prison-based drug treatment: a repeated measures analysis.

    Science.gov (United States)

    Welsh, Wayne N

    2010-06-01

    Using a sample of 347 prison inmates and general linear modeling (GLM) repeated measures analyses, this paper examined during-treatment responses (e.g., changes in psychological and social functioning) to prison-based TC drug treatment. These effects have rarely been examined in previous studies, and never with a fully multivariate model accounting for within-subjects effects (changes over time), between-subjects effects (e.g., levels of risk and motivation), and within/between-subjects interactions (timexriskxmotivation). The results provide evidence of positive inmate change in response to prison TC treatment, but the patterns of results varied depending upon: (a) specific indicators of psychological and social functioning, motivation, and treatment process; (b) the time periods examined (1, 6, and 12 months during treatment); and (c) baseline levels of risk and motivation. Significant interactions between time and type of inmate suggest important new directions for research, theory, and practice in offender-based substance abuse treatment.

  6. Bayesian latent variable models for hierarchical clustered count outcomes with repeated measures in microbiome studies.

    Science.gov (United States)

    Xu, Lizhen; Paterson, Andrew D; Xu, Wei

    2017-04-01

    Motivated by the multivariate nature of microbiome data with hierarchical taxonomic clusters, counts that are often skewed and zero inflated, and repeated measures, we propose a Bayesian latent variable methodology to jointly model multiple operational taxonomic units within a single taxonomic cluster. This novel method can incorporate both negative binomial and zero-inflated negative binomial responses, and can account for serial and familial correlations. We develop a Markov chain Monte Carlo algorithm that is built on a data augmentation scheme using Pólya-Gamma random variables. Hierarchical centering and parameter expansion techniques are also used to improve the convergence of the Markov chain. We evaluate the performance of our proposed method through extensive simulations. We also apply our method to a human microbiome study.

  7. Causal inference in longitudinal comparative effectiveness studies with repeated measures of a continuous intermediate variable.

    Science.gov (United States)

    Wang, Chen-Pin; Jo, Booil; Brown, C Hendricks

    2014-09-10

    We propose a principal stratification approach to assess causal effects in nonrandomized longitudinal comparative effectiveness studies with a binary endpoint outcome and repeated measures of a continuous intermediate variable. Our method is an extension of the principal stratification approach originally proposed for the longitudinal randomized study "Prevention of Suicide in Primary Care Elderly: Collaborative Trial" to assess the treatment effect on the continuous Hamilton depression score adjusting for the heterogeneity of repeatedly measured binary compliance status. Our motivation for this work comes from a comparison of the effect of two glucose-lowering medications on a clinical cohort of patients with type 2 diabetes. Here, we consider a causal inference problem assessing how well the two medications work relative to one another on two binary endpoint outcomes: cardiovascular disease-related hospitalization and all-cause mortality. Clinically, these glucose-lowering medications can have differential effects on the intermediate outcome, glucose level over time. Ultimately, we want to compare medication effects on the endpoint outcomes among individuals in the same glucose trajectory stratum while accounting for the heterogeneity in baseline covariates (i.e., to obtain 'principal effects' on the endpoint outcomes). The proposed method involves a three-step model estimation procedure. Step 1 identifies principal strata associated with the intermediate variable using hybrid growth mixture modeling analyses. Step 2 obtains the stratum membership using the pseudoclass technique and derives propensity scores for treatment assignment. Step 3 obtains the stratum-specific treatment effect on the endpoint outcome weighted by inverse propensity probabilities derived from Step 2.

  8. Microcomputer-based tests for repeated-measures: Metric properties and predictive validities

    Science.gov (United States)

    Kennedy, Robert S.; Baltzley, Dennis R.; Dunlap, William P.; Wilkes, Robert L.; Kuntz, Lois-Ann

    1989-01-01

    A menu of psychomotor and mental acuity tests were refined. Field applications of such a battery are, for example, a study of the effects of toxic agents or exotic environments on performance readiness, or the determination of fitness for duty. The key requirement of these tasks is that they be suitable for repeated-measures applications, and so questions of stability and reliability are a continuing, central focus of this work. After the initial (practice) session, seven replications of 14 microcomputer-based performance tests (32 measures) were completed by 37 subjects. Each test in the battery had previously been shown to stabilize in less than five 90-second administrations and to possess retest reliabilities greater than r = 0.707 for three minutes of testing. However, all the tests had never been administered together as a battery and they had never been self-administered. In order to provide predictive validity for intelligence measurement, the Wechsler Adult Intelligence Scale-Revised and the Wonderlic Personnel Test were obtained on the same subjects.

  9. Diversity and Plasticity of the Intracellular Plant Pathogen and Insect Symbiont “Candidatus Liberibacter asiaticus” as Revealed by Hypervariable Prophage Genes with Intragenic Tandem Repeats ▿ †

    Science.gov (United States)

    Zhou, Lijuan; Powell, Charles A.; Hoffman, Michele T.; Li, Wenbin; Fan, Guocheng; Liu, Bo; Lin, Hong; Duan, Yongping

    2011-01-01

    “Candidatus Liberibacter asiaticus” is a psyllid-transmitted, phloem-limited alphaproteobacterium and the most prevalent species of “Ca. Liberibacter” associated with a devastating worldwide citrus disease known as huanglongbing (HLB). Two related and hypervariable genes (hyvI and hyvII) were identified in the prophage regions of the Psy62 “Ca. Liberibacter asiaticus” genome. Sequence analyses of the hyvI and hyvII genes in 35 “Ca. Liberibacter asiaticus” DNA isolates collected globally revealed that the hyvI gene contains up to 12 nearly identical tandem repeats (NITRs, 132 bp) and 4 partial repeats, while hyvII contains up to 2 NITRs and 4 partial repeats and shares homology with hyvI. Frequent deletions or insertions of these repeats within the hyvI and hyvII genes were observed, none of which disrupted the open reading frames. Sequence conservation within the individual repeats but an extensive variation in repeat numbers, rearrangement, and the sequences flanking the repeat region indicate the diversity and plasticity of “Ca. Liberibacter asiaticus” bacterial populations in the world. These differences were found not only in samples of distinct geographical origins but also in samples from a single origin and even from a single “Ca. Liberibacter asiaticus”-infected sample. This is the first evidence of different “Ca. Liberibacter asiaticus” populations coexisting in a single HLB-affected sample. The Florida “Ca. Liberibacter asiaticus” isolates contain both hyvI and hyvII, while all other global “Ca. Liberibacter asiaticus” isolates contain either one or the other. Interclade assignments of the putative HyvI and HyvII proteins from Florida isolates with other global isolates in phylogenetic trees imply multiple “Ca. Liberibacter asiaticus” populations in the world and a multisource introduction of the “Ca. Liberibacter asiaticus” bacterium into Florida. PMID:21784907

  10. Characterization of the peripheral blood transcriptome in a repeated measures design using a panel of healthy individuals

    DEFF Research Database (Denmark)

    De Boever, Patrick; Wens, Britt; Forcheh, Anyiawung Chiara

    2014-01-01

    A repeated measures microarray design with 22 healthy, non-smoking volunteers (aging 32. ±. 5. years) was set up to study transcriptome profiles in whole blood samples. The results indicate that repeatable data can be obtained with high within-subject correlation. Probes that could discriminate....... Our study suggests that the blood transcriptome of healthy individuals is reproducible over a time period of several months. © 2013 Elsevier Inc....

  11. Status of a UAVSAR designed for repeat pass interferometry for deformation measurements

    Science.gov (United States)

    Hensley, Scott; Wheeler, Kevin; Sadowy, Greg; Miller, Tim; Shaffer, Scott; Muellerschoen, Ron; Jones, Cathleen; Zebker, Howard; Madsen, Soren; Paul, Rose

    2005-01-01

    NASA's Jet Propulsion Laboratory is currently implementing a reconfigurable polarimetric L-band synthetic aperture radar (SAR), specifically designed to acquire airborne repeat track interferometric (RTI) SAR data, also known as differential interferometric measurements. Differential interferometry can provide key deformation measurements, important for the scientific studies of Earthquakes and volcanoes. Using precision real-time GPS and a sensor controlled flight management system, the system will be able to fly predefined paths with great precision. The expected performance of the flight control system will constrain the flight path to be within a 10 m diameter tube about the desired flight track. The radar wilI be designed to operate on a UAV (Unpiloted Aria1 Vehicle) but will initially be demonstrated on a minimally piloted vehicle (MPV), such as the Proteus buitt by Scaled Composites or on a NASA Gulfstream III. The radar design is a fully polarimetric with an 80 MHz bandwidth (2 m range resolution) and 16 km range swath. The antenna is an electronically steered along track to assure that the actual antenna pointing can be controlled independent of the wind direction and speed. Other features supported by the antenna include an elevation monopulse option and a pulse-to-pulse resteering capability that will enable some novel modes of operation. The system will nominally operate at 45,000 ft (13800 m). The program began out as an Instrument Incubator Project (IIP) funded by NASA Earth Science and Technology Office (ESTO).

  12. Repeated measures of serum glucose and insulin in relation to postmenopausal breast cancer.

    Science.gov (United States)

    Kabat, Geoffrey C; Kim, Mimi; Caan, Bette J; Chlebowski, Rowan T; Gunter, Marc J; Ho, Gloria Y F; Rodriguez, Beatriz L; Shikany, James M; Strickler, Howard D; Vitolins, Mara Z; Rohan, Thomas E

    2009-12-01

    Experimental and epidemiological evidence suggests that circulating glucose and insulin may play a role in breast carcinogenesis. However, few cohort studies have examined breast cancer risk in association with glucose and insulin levels, and studies to date have had only baseline measurements of exposure. We conducted a longitudinal study of postmenopausal breast cancer risk using the 6% random sample of women in the Women's Health Initiative clinical trials whose fasting blood samples, provided at baseline and at years 1, 3 and 6, were analyzed for glucose and insulin. In addition, a 1% sample of women in the observational study, who had glucose and insulin measured in fasting blood samples drawn at baseline and in year 3, were included in the analysis. We used Cox proportional hazards models to estimate hazard ratios and 95% confidence intervals for the association of baseline and follow-up measurements of serum glucose and insulin with breast cancer risk. All statistical tests were 2-sided. Among 5,450 women with baseline serum glucose and insulin values, 190 incident cases of breast cancer were ascertained over a median of 8.0 years of follow-up. The highest tertile of baseline insulin, relative to the lowest, was associated with a 2-fold increase in risk in the total population (multivariable hazard ratio 2.22, 95% confidence interval 1.39-3.53) and with a 3-fold increase in risk in women who were not enrolled in the intervention arm of any clinical trial (multivariable hazard ratio 3.15, 95% confidence interval 1.61-6.17). Glucose levels showed no association with risk. Analysis of the repeated measurements supported the results of the baseline analysis. These data suggest that elevated serum insulin levels may be a risk factor for postmenopausal breast cancer.

  13. Repeated Blood Pressure Measurements in Childhood in Prediction of Hypertension in Adulthood.

    Science.gov (United States)

    Oikonen, Mervi; Nuotio, Joel; Magnussen, Costan G; Viikari, Jorma S A; Taittonen, Leena; Laitinen, Tomi; Hutri-Kähönen, Nina; Jokinen, Eero; Jula, Antti; Cheung, Michael; Sabin, Matthew A; Daniels, Stephen R; Raitakari, Olli T; Juonala, Markus

    2016-01-01

    Hypertension may be predicted from childhood risk factors. Repeated observations of abnormal blood pressure in childhood may enhance prediction of hypertension and subclinical atherosclerosis in adulthood compared with a single observation. Participants (1927, 54% women) from the Cardiovascular Risk in Young Finns Study had systolic and diastolic blood pressure measurements performed when aged 3 to 24 years. Childhood/youth abnormal blood pressure was defined as above 90th or 95th percentile. After a 21- to 31-year follow-up, at the age of 30 to 45 years, hypertension (>140/90 mm Hg or antihypertensive medication) prevalence was found to be 19%. Carotid intima-media thickness was examined, and high-risk intima-media was defined as intima-media thickness >90th percentile or carotid plaques. Prediction of adulthood hypertension and high-risk intima-media was compared between one observation of abnormal blood pressure in childhood/youth and multiple observations by improved Pearson correlation coefficients and area under the receiver operating curve. When compared with a single measurement, 2 childhood/youth observations improved the correlation for adult systolic (r=0.44 versus 0.35, Ppressure. In addition, 2 abnormal childhood/youth blood pressure observations increased the prediction of hypertension in adulthood (0.63 for 2 versus 0.60 for 1 observation, P=0.003). When compared with 2 measurements, third observation did not provide any significant improvement for correlation or prediction (P always >0.05). A higher number of childhood/youth observations of abnormal blood pressure did not enhance prediction of adult high-risk intima-media thickness. Compared with a single measurement, the prediction of adult hypertension was enhanced by 2 observations of abnormal blood pressure in childhood/youth. © 2015 American Heart Association, Inc.

  14. Corneal Topographic and Aberrometric Measurements Obtained with a Multidiagnostic Device in Healthy Eyes: Intrasession Repeatability

    Directory of Open Access Journals (Sweden)

    David P. Piñero

    2017-01-01

    Full Text Available Purpose. To evaluate the intrasession repeatability of corneal curvature, eccentricity, and aberrometric measurements obtained with a multidiagnostic device in healthy eyes. Methods. This study enrolled 107 eyes of 107 patients ranging in age from 23 to 65 years. All of them underwent a complete anterior segment examination with the VX120 system (Visionix-Luneau Technologies, Chartres, France. Three consecutive measurements were obtained. The within-subject standard deviation (Sw, intrasubject precision (1.96×Sw, and intraclass correlation coefficient (ICC were calculated. Results. All Sw for corneal power measurements were below 0.26 D, with ICC above 0.982. The Sw for corneal astigmatism at different areas (3, 5, and 7 mm was below 0.21 D, with ICC above 0.913. Concerning the axis of astigmatism, its Sw was below 11.27°, with ICC above 0.975. The Sw and ICC for corneal eccentricity were 0.067 and 0.957, respectively. The Sw and ICC for high-order aberration root mean square (RMS were 0.048 µm and 0.901, respectively. For 3rd- and 4th-order aberrometric parameters, all Sw were below 0.037 µm and all ICC were higher than 0.84, except for quadrafoil RMS (ICC: 0.689. Conclusions. The multidiagnostic device evaluated is able to provide consistent measurements of corneal power, eccentricity, and third- and fourth-order aberrations in healthy eyes.

  15. Measurement of repeat effects in Chicago’s criminal social network

    Directory of Open Access Journals (Sweden)

    Paul Kump

    2016-07-01

    Full Text Available The “near-repeat” effect is a well-known criminological phenomenon in which the occurrence of a crime incident gives rise to a temporary elevation of crime risk within close physical proximity to an initial incident. Adopting a social network perspective, we instead define a near repeat in terms of geodesic distance within a criminal social network, rather than spatial distance. Specifically, we report a statistical analysis of repeat effects in arrest data for Chicago during the years 2003–2012. We divide the arrest data into two sets (violent crimes and other crimes and, for each set, we compare the distributions of time intervals between repeat incidents to theoretical distributions in which repeat incidents occur only by chance. We first consider the case of the same arrestee participating in repeat incidents (“exact repeats” and then extend the analysis to evaluate repeat risks of those arrestees near one another in the social network. We observe repeat effects that diminish as a function of geodesic distance and time interval, and we estimate typical time scales for repeat crimes in Chicago.

  16. Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements

    OpenAIRE

    2015-01-01

    The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma arthritidis MAV-1. Comparative analysis with the genome of M. hominis PG21T reveals distinctive arrangements of repeat-containing surface proteins.

  17. Analysis of the Complete Mycoplasma hominis LBD-4 Genome Sequence Reveals Strain-Variable Prophage Insertion and Distinctive Repeat-Containing Surface Protein Arrangements.

    Science.gov (United States)

    Calcutt, Michael J; Foecking, Mark F

    2015-02-26

    The complete genome sequence of Mycoplasma hominis LBD-4 has been determined and the gene content ascribed. The 715,165-bp chromosome contains 620 genes, including 14 carried by a strain-variable prophage genome related to Mycoplasma fermentans MFV-1 and Mycoplasma arthritidis MAV-1. Comparative analysis with the genome of M. hominis PG21(T) reveals distinctive arrangements of repeat-containing surface proteins.

  18. Constructing Measure by Repeated Infinite Subdivision%通过反复无限细分定义测度

    Institute of Scientific and Technical Information of China (English)

    严质彬

    2005-01-01

    This paper generalizes the method of constructing measure by repeated finite subdivision in fTactal geometry to that by infinite subdivision. Two conditions for the existing method are removed. A measure on the interval [0, 1] is constructed using this generalized method.

  19. Cardiometabolic treatment decisions in patients with type 2 diabetes : the role of repeated measurements and medication burden

    NARCIS (Netherlands)

    Voorham, J.; Haaijer-Ruskamp, F. M.; Wolffenbuttel, B. H. R.; Stolk, R. P.; Denig, P.

    2010-01-01

    Purpose Clinical guidelines for cardiometabolic risk management indicate a simple threshold-based strategy for treatment, but physicians and their patients may be reluctant to modify drug treatment after a single elevated measurement. We determined how repeated measurements of blood pressure, choles

  20. Cardiometabolic treatment decisions in patients with type 2 diabetes : the role of repeated measurements and medication burden

    NARCIS (Netherlands)

    Voorham, J.; Haaijer-Ruskamp, F. M.; Wolffenbuttel, B. H. R.; Stolk, R. P.; Denig, P.

    2010-01-01

    Purpose Clinical guidelines for cardiometabolic risk management indicate a simple threshold-based strategy for treatment, but physicians and their patients may be reluctant to modify drug treatment after a single elevated measurement. We determined how repeated measurements of blood pressure,

  1. Dynamic Feedbacks Between Flow, Erosion and Evolving River Bank Roughness Revealed Through Repeat High-Resolution Topographic Surveys

    Science.gov (United States)

    Leyland, J.; Darby, S. E.; Rinaldi, M.; Teruggi, L. B.; Ostuni, D.

    2012-12-01

    Bank erosion is a key process in fluvial dynamics, with significant fractions of the total sediment load being sourced from river banks. Studies have shown that hydraulic erosion of the bank toe is a driving factor of long term rates of bank retreat. Fluvial bank erosion rates are often quantified using an excess shear stress model where the erosion rate is a function of the boundary shear stress applied by the flow above a critical threshold. Research has shown that the form roughness induced by natural topographic bank features such as slumps, spurs and embayments, is a major component of the spatially-averaged total shear stress. The skin friction component of this shear stress is typically an order of magnitude less than the total, meaning that the form roughness provides an important control on bank erosion rates. However, measuring the relative components of the total shear stress for a natural system is not straightforward. In this research we apply the method of Kean and Smith [2006, J. Geophys. Res., 111(4), F04009, doi:10.1029/2006JF000467] to partition the form and skin drag components of river bank roughness for an eroding bank of the Cecina River in central Italy. This method approximates the form drag component of the roughness along a longitudinal bank profile as a series of user defined Gaussian curves, with the skin friction component estimated through analysis of the deviations of the data from the fitted curves. For our site, a temporal sequence (2003 - 2011) of high-resolution topographic surveys has been collected through a combination of photogrammetry and Terrestrial Laser Scanning. For each survey five vertically equidistant profiles are extracted and analysed alongside DEMs of difference and associated flow data modelled using the distributed hydrological model MOBIDIC. The data are used to explore the dynamic feedbacks that exist between river discharge, bank erosion processes and bank form roughness, revealing insights into the self

  2. Assessing variability and comparing short-term biomarkers of styrene exposure using a repeated measurements approach.

    Science.gov (United States)

    Fustinoni, S; Manini, P; Campo, L; De Palma, G; Andreoli, R; Mutti, A; Bertazzi, P A; Rappaport, S M

    2010-01-15

    The aim of this work is to compare several short-term biomarkers of styrene exposure, namely urinary styrene (StyU), mercapturic acids (M1+M2), mandelic acid (MA), phenylglyoxylic acid (PGA), phenylglycine (PHG), and 4-vinylphenol conjugates (VP), for use as biomarkers of exposure in epidemiologic studies. A repeated measurements protocol (typically 4 measurements per worker over 6 weeks) was applied to measure airborne styrene (StyA) and urinary biomarkers in 10 varnish and 8 fiberglass reinforced plastic workers. Estimated geometric mean personal exposures to StyA were 2.96mg/m(3) in varnish workers and 15.7mg/m(3) in plastic workers. The corresponding levels of StyU, M1+M2, MA, PGA, MA+PGA, PHG and VP were 5.13microg/L, 0.111, 38.2, 22.7, 62.6, 0.978, and 3.97mg/g creatinine in varnish workers and 8.38microg/L, 0.303, 146, 83.4, 232, 2.85 and 3.97mg/g creatinine in plastic workers. Within-worker (sigma(wY)(2)) and between-worker (sigma(bY)(2)) variance components were estimated from the log-transformed data as were the corresponding fold ranges containing 95% of the respective lognormal distributions of daily levels ((w)R(0.95)) and subject-specific mean levels ((b)R(0.95)). Estimates of (w)R(0.95) (range: 4-26) were generally smaller than those of (b)R(0.95) (range: 5-790) for both environmental and biological markers; this indicates that exposures varied much more between workers than within workers in these groups. Since attenuation bias in an estimated exposure-response relationship increases with the variance ratio lambda=sigma(wY)(2)/sigma(bY)(2), we estimated values of lambda for all exposure measures in our study. Values of lambda were typically much less than one (median=0.220) and ranged from 0.089 for M1+M2 in plastic workers to 1.38 for PHG in varnish workers. Since values of lambda were 0.147 and 0.271 for StyA in varnish workers and plastic workers, respectively, compared to 0.178 and 0.210 for MA in the same groups, our results suggest that either

  3. Analyzing repeated measures semi-continuous data, with application to an alcohol dependence study.

    Science.gov (United States)

    Liu, Lei; Strawderman, Robert L; Johnson, Bankole A; O'Quigley, John M

    2016-02-01

    Two-part random effects models (Olsen and Schafer,(1) Tooze et al.(2)) have been applied to repeated measures of semi-continuous data, characterized by a mixture of a substantial proportion of zero values and a skewed distribution of positive values. In the original formulation of this model, the natural logarithm of the positive values is assumed to follow a normal distribution with a constant variance parameter. In this article, we review and consider three extensions of this model, allowing the positive values to follow (a) a generalized gamma distribution, (b) a log-skew-normal distribution, and (c) a normal distribution after the Box-Cox transformation. We allow for the possibility of heteroscedasticity. Maximum likelihood estimation is shown to be conveniently implemented in SAS Proc NLMIXED. The performance of the methods is compared through applications to daily drinking records in a secondary data analysis from a randomized controlled trial of topiramate for alcohol dependence treatment. We find that all three models provide a significantly better fit than the log-normal model, and there exists strong evidence for heteroscedasticity. We also compare the three models by the likelihood ratio tests for non-nested hypotheses (Vuong(3)). The results suggest that the generalized gamma distribution provides the best fit, though no statistically significant differences are found in pairwise model comparisons.

  4. Preliminary evaluation of a micro-based repeated measures testing system

    Science.gov (United States)

    Kennedy, Robert S.; Wilkes, Robert L.; Lane, Norman E.

    1985-01-01

    A need exists for an automated performance test system to study the effects of various treatments which are of interest to the aerospace medical community, i.e., the effects of drugs and environmental stress. The ethics and pragmatics of such assessment demand that repeated measures in small groups of subjects be the customary research paradigm. Test stability, reliability-efficiency and factor structure take on extreme significance; in a program of study by the U.S. Navy, 80 percent of 150 tests failed to meet minimum metric requirements. The best is being programmed on a portable microprocessor and administered along with tests in their original formats in order to examine their metric properties in the computerized mode. Twenty subjects have been tested over four replications on a 6.0 minute computerized battery (six tests) and which compared with five paper and pencil marker tests. All tests achieved stability within the four test sessions, reliability-efficiencies were high (r greater than .707 for three minutes testing), and the computerized tests were largely comparable to the paper and pencil version from which they were derived. This computerized performance test system is portable, inexpensive and rugged.

  5. A repeated measures experiment of green exercise to improve self-esteem in UK school children.

    Directory of Open Access Journals (Sweden)

    Katharine Reed

    Full Text Available Exercising in natural, green environments creates greater improvements in adult's self-esteem than exercise undertaken in urban or indoor settings. No comparable data are available for children. The aim of this study was to determine whether so called 'green exercise' affected changes in self-esteem; enjoyment and perceived exertion in children differently to urban exercise. We assessed cardiorespiratory fitness (20 m shuttle-run and self-reported physical activity (PAQ-A in 11 and 12 year olds (n = 75. Each pupil completed two 1.5 mile timed runs, one in an urban and another in a rural environment. Trials were completed one week apart during scheduled physical education lessons allocated using a repeated measures design. Self-esteem was measured before and after each trial, ratings of perceived exertion (RPE and enjoyment were assessed after completing each trial. We found a significant main effect (F (1,74, = 12.2, p<0.001, for the increase in self-esteem following exercise but there was no condition by exercise interaction (F (1,74, = 0.13, p = 0.72. There were no significant differences in perceived exertion or enjoyment between conditions. There was a negative correlation (r = -0.26, p = 0.04 between habitual physical activity and RPE during the control condition, which was not evident in the green exercise condition (r = -0.07, p = 0.55. Contrary to previous studies in adults, green exercise did not produce significantly greater increases in self-esteem than the urban exercise condition. Green exercise was enjoyed more equally by children with differing levels of habitual physical activity and has the potential to engage less active children in exercise.

  6. Repeatability and reproducibility of anterior chamber volume measurements using 3-dimensional corneal and anterior segment optical coherence tomography.

    Science.gov (United States)

    Fukuda, Shinichi; Kawana, Keisuke; Yasuno, Yoshiaki; Oshika, Tetsuro

    2011-03-01

    To evaluate the repeatability and reproducibility of anterior chamber volume (ACV) measurements using swept-source 3-dimensional corneal and anterior segment optical coherence tomography (CAS-OCT) and dual Scheimpflug imaging. Department of Ophthalmology, Institute of Clinical Medicine, University of Tsukuba, Ibaraki, Japan. Nonrandomized clinical trial. Measurements were taken in normal eyes (subject group) and in eyes with primary angle closure (PAC) (patient group). In the subject group, the entire ACV and the central 8.0 mm diameter ACV were measured using CAS-OCT and dual Scheimpflug imaging. In the patient group, the entire ACV and 8.0 mm ACV were measured using CAS-OCT. The coefficient of variation and intraclass correlation coefficient (ICC) were calculated to evaluate repeatability and reproducibility, and the correlation between the 2 devices was assessed. In the subject group, the mean 8.0 mm ACV was 110.14 mm(3) ± 12.57 (SD) using CAS-OCT and 114.51 ± 14.69 mm(3) using Scheimpflug imaging; there was a significant linear correlation (r = 0.878, P ACV on CAS-OCT was 165.15 ± 29.29 mm(3). The ICCs of the 8.0 mm and entire ACV measurements were greater than 0.94. The coefficients of repeatability and reproducibility of the 8.0 mm ACV and entire ACV measurements were less than 5%. In the patient group, the 8.0 mm and entire ACV measurements showed good reproducibility and repeatability. The CAS-OCT method allowed noninvasive measurement of the entire ACV with sufficient repeatability and reproducibility. The 8.0 mm ACV measurements with CAS-OCT and Scheimpflug imaging were comparable. Copyright © 2011 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  7. Crystal Structure of DNA-PKcs Reveals a Large Open-Ring Cradle Comprised of HEAT Repeats

    Science.gov (United States)

    Sibanda, Bancinyane L.; Chirgadze, Dimitri Y.; Blundell, Tom L.

    2009-01-01

    Broken chromosomes arising from DNA double strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation1, 2, 3. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holo-enzyme that comprises DNA-dependent protein kinase catalytic subunit (DNA-PKcs)4, 5 and the heterodimer Ku70/Ku80, plays a major role in non-homologous end joining (NHEJ), the main pathway in mammals used to repair double strand breaks6, 7, 8. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4128 amino acids and belonging to the phosphotidyl inositol 3-kinase (PI3-K)- related protein family9. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest10, 11. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA12. Here we present the crystal structure of human DNA-PKcs at 6.6Å resolution, in which the overall fold is for the first time clearly visible. The many α-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The C-terminal kinase domain is located on top of this structure and a small HEAT repeat domain that likely binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair. PMID:20023628

  8. Characterization of fetal growth by repeated ultrasound measurements in the wild guinea pig (Cavia aperea).

    Science.gov (United States)

    Schumann, K; Guenther, A; Göritz, F; Jewgenow, K

    2014-08-01

    Fetal growth during pregnancy has previously been studied in the domesticated guinea pig (Cavia aperea f. porcellus) after dissecting pregnant females, but there are no studies describing the fetal growth in their wild progenitor, the wild guinea pig (C aperea). In this study, 50 pregnancies of wild guinea pig sows were investigated using modern ultrasound technique. The two most common fetal growth parameters (biparietal diameter [BPD] and crown-rump-length [CRL]) and uterine position were measured. Data revealed similar fetal growth patterns in the wild guinea pig and domesticated guinea pig in the investigated gestation period, although they differ in reproductive milestones such as gestation length (average duration of pregnancy 68 days), average birth weight, and litter mass. In this study, pregnancy lasted on average 60.2 days with a variance of less than a day (0.96 days). The measured fetal growth parameters are strongly correlated with each (R = 0.91; P guinea pig.

  9. Precision (Repeatability and Reproducibility and Agreement of Corneal Power Measurements Obtained by Topcon KR-1W and iTrace.

    Directory of Open Access Journals (Sweden)

    Yanjun Hua

    Full Text Available To evaluate the repeatability and reproducibility of corneal power measurements obtained by Topcon KR-1W and iTrace, and assess the agreement with measurements obtained by Allegro Topolyzer and IOLMaster.The right eyes of 100 normal subjects were prospectively scanned 3 times using all the 4 devices. Another observer performed additional 3 consecutive scans using the Topcon KR-1W and iTrace in the same session. About one week later, the first observer repeated the measurements using the Topcon KR-1W and iTrace. The steep keratometry (Ks, flat keratometry (Kf, mean keratometry (Km, J0 and J45 were analyzed. Repeatability and reproducibility of measurements were evaluated by the within-subject standard deviation (Sw, coefficient of variation (CoV, test-retest repeatability (2.77Sw, and intraclass correlation coefficient (ICC. Agreements between devices were assessed using Bland-Altman analysis and 95% limits of agreement (LoA.Intraobserver repeatability and interobserver and intersession reproducibility of the Ks, Kf and Km showed a CoV of no more than 0.5%, a 2.77Sw of 0.70 D or less, and an ICC of no less than 0.99. However, J0 and J45 showed poor intraobserver repeatability and interobserver and intersession reproducibility (all ICCs not greater than 0.446. Statistically significant differences existed between Topcon KR-1W and IOLMaster, Topcon KR-1W and iTrace, Topcon KR-1W and Topolyzer, iTrace and Topolyzer, iTrace and IOLMaster for Ks, Kf and Km measurements (all P < 0.05. The mean differences between Topcon KR-1W, iTrace, and the other 2 devices were small. The 95% LoA were approximately 1.0 D to 1.5 D for all measurements.The Ks, Kf and Km obtained by Topcon KR-1W and iTrace showed excellent intraobserver repeatability and interobserver and intersession reproducibility in normal eyes. The agreement between Topcon KR-1W and Topolyzer, Topcon KR-1W and IOLMaster, iTrace and Topolyzer, iTrace and IOLMaster, Topcon KR-1W and iTrace were not

  10. Separating climate-induced mass transfers and instrumental effects from tectonic signal in repeated absolute gravity measurements

    Science.gov (United States)

    Van Camp, M.; Viron, O.; Avouac, J. P.

    2016-05-01

    We estimate the signature of the climate-induced mass transfers in repeated absolute gravity measurements based on satellite gravimetric measurements from the Gravity Recovery and Climate Experiment (GRACE) mission. We show results at the globe scale and compare them with repeated absolute gravity (AG) time behavior in three zones where AG surveys have been published: Northwestern Europe, Canada, and Tibet. For 10 yearly campaigns, the uncertainties affecting the determination of a linear gravity rate of change range 3-4 nm/s2/a in most cases, in the absence of instrumental artifacts. The results are consistent with what is observed for long-term repeated campaigns. We also discuss the possible artifact that can result from using short AG survey to determine the tectonic effects in a zone of high hydrological variability. We call into question the tectonic interpretation of several gravity changes reported from stations in Tibet, in particular the variation observed prior to the 2015 Gorkha earthquake.

  11. Transcriptome analysis reveals ginsenosides biosynthetic genes, microRNAs and simple sequence repeats in Panax ginseng C. A. Meyer

    Science.gov (United States)

    2013-01-01

    Background Panax ginseng C. A. Meyer is one of the most widely used medicinal plants. Complete genome information for this species remains unavailable due to its large genome size. At present, analysis of expressed sequence tags is still the most powerful tool for large-scale gene discovery. The global expressed sequence tags from P. ginseng tissues, especially those isolated from stems, leaves and flowers, are still limited, hindering in-depth study of P. ginseng. Results Two 454 pyrosequencing runs generated a total of 2,423,076 reads from P. ginseng roots, stems, leaves and flowers. The high-quality reads from each of the tissues were independently assembled into separate and shared contigs. In the separately assembled database, 45,849, 6,172, 4,041 and 3,273 unigenes were only found in the roots, stems, leaves and flowers database, respectively. In the jointly assembled database, 178,145 unigenes were observed, including 86,609 contigs and 91,536 singletons. Among the 178,145 unigenes, 105,522 were identified for the first time, of which 65.6% were identified in the stem, leaf or flower cDNA libraries of P. ginseng. After annotation, we discovered 223 unigenes involved in ginsenoside backbone biosynthesis. Additionally, a total of 326 potential cytochrome P450 and 129 potential UDP-glycosyltransferase sequences were predicted based on the annotation results, some of which may encode enzymes responsible for ginsenoside backbone modification. A BLAST search of the obtained high-quality reads identified 14 potential microRNAs in P. ginseng, which were estimated to target 100 protein-coding genes, including transcription factors, transporters and DNA binding proteins, among others. In addition, a total of 13,044 simple sequence repeats were identified from the 178,145 unigenes. Conclusions This study provides global expressed sequence tags for P. ginseng, which will contribute significantly to further genome-wide research and analyses in this species. The novel

  12. Heart failure re-admission: measuring the ever shortening gap between repeat heart failure hospitalizations.

    Directory of Open Access Journals (Sweden)

    Jeffrey A Bakal

    Full Text Available Many quality-of-care and risk prediction metrics rely on time to first rehospitalization even though heart failure (HF patients may undergo several repeat hospitalizations. The aim of this study is to compare repeat hospitalization models. Using a population-based cohort of 40,667 patients, we examined both HF and all cause re-hospitalizations using up to five years of follow-up. Two models were examined: the gap-time model which estimates the adjusted time between hospitalizations and a multistate model which considered patients to be in one of four states; community-dwelling, in hospital for HF, in hospital for any reason, or dead. The transition probabilities and times were then modeled using patient characteristics and number of repeat hospitalizations. We found that during the five years of follow-up roughly half of the patients returned for a subsequent hospitalization for each repeat hospitalization. Additionally, we noted that the unadjusted time between hospitalizations was reduced ∼40% between each successive hospitalization. After adjustment each additional hospitalization was associated with a 28 day (95% CI: 22-35 reduction in time spent out of hospital. A similar pattern was seen when considering the four state model. A large proportion of patients had multiple repeat hospitalizations. Extending the gap between hospitalizations should be an important goal of treatment evaluation.

  13. Benchmarking sample preparation/digestion protocols reveals tube-gel being a fast and repeatable method for quantitative proteomics.

    Science.gov (United States)

    Muller, Leslie; Fornecker, Luc; Van Dorsselaer, Alain; Cianférani, Sarah; Carapito, Christine

    2016-12-01

    Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD). A series of UPS1 standard mixtures (at 0.5, 1, 2.5, 5, 10, and 25 fmol) were spiked in a complex yeast lysate background. TG preparation allowed more yeast proteins to be identified than did the SG and LD approaches, with mean numbers of 1979, 1788, and 1323 proteins identified, respectively. Furthermore, the TG method proved equivalent to SG and superior to LD in terms of the repeatability of the subsequent experiments, with mean CV for yeast protein label-free quantifications of 7, 9, and 10%. Finally, known variant UPS1 proteins were successfully detected in the TG-prepared sample within a complex background with high sensitivity. All the data from this study are accessible on ProteomeXchange (PXD003841).

  14. Atomic model of human Rcd-1 reveals an armadillo-like-repeat protein with in vitro nucleic acid binding properties.

    Science.gov (United States)

    Garces, Robert G; Gillon, Wanda; Pai, Emil F

    2007-02-01

    Rcd-1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation-invoked differentiation in fission yeast, and its Saccharomyces cerevisiae homolog, CAF40, has been identified as part of the CCR4-NOT transcription complex, where it interacts with the NOT1 protein. Mammalian homologs are involved in various cellular differentiation processes including retinoic acid-induced differentiation and hematopoetic cell development. Here, we present the 2.2 A X-ray structure of the highly conserved region of human Rcd-1 and investigate possible functional abilities of this and the full-length protein. The monomer is made up of six armadillo repeats forming a solvent-accessible, positively-charged cleft 21-22 A wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer. Prompted by this finding, we established that Rcd-1 can bind to single- and double-stranded oligonucleotides in vitro with the affinity of G/C/T > A. Mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. Rcd-1's ability to bind to nucleic acids, in addition to the previously reported protein-protein interaction with NOT1, suggests a new feature in Rcd-1's role in regulation of overall cellular differentiation processes.

  15. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses.

    Science.gov (United States)

    Pride, David T; Salzman, Julia; Relman, David A

    2012-09-01

    Explorations of human microbiota have provided substantial insight into microbial community composition; however, little is known about interactions between various microbial components in human ecosystems. In response to the powerful impact of viral predation, bacteria have acquired potent defences, including an adaptive immune response based on the clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas system. To improve our understanding of the interactions between bacteria and their viruses in humans, we analysed 13 977 streptococcal CRISPR sequences and compared them with 2 588 172 virome reads in the saliva of four human subjects over 17 months. We found a diverse array of viruses and CRISPR spacers, many of which were specific to each subject and time point. There were numerous viral sequences matching CRISPR spacers; these matches were highly specific for salivary viruses. We determined that spacers and viruses coexist at the same time, which suggests that streptococcal CRISPR/Cas systems are under constant pressure from salivary viruses. CRISPRs in some subjects were just as likely to match viral sequences from other subjects as they were to match viruses from the same subject. Because interactions between bacteria and viruses help to determine the structure of bacterial communities, CRISPR-virus analyses are likely to provide insight into the forces shaping the human microbiome.

  16. New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards.

    Directory of Open Access Journals (Sweden)

    Maud Gits-Muselli

    Full Text Available Pneumocystis pneumonia is a severe opportunistic infection in immunocompromised patients caused by the unusual fungus Pneumocystis jirovecii. Transmission is airborne, with both immunocompromised and immunocompetent individuals acting as a reservoir for the fungus. Numerous reports of outbreaks in renal transplant units demonstrate the need for valid genotyping methods to detect transmission of a given genotype. Here, we developed a short tandem repeat (STR-based molecular typing method for P. jirovecii. We analyzed the P. jirovecii genome and selected six genomic STR markers located on different contigs of the genome. We then tested these markers in 106 P. jirovecii PCR-positive respiratory samples collected between October 2010 and November 2013 from 91 patients with various underlying medical conditions. Unique (one allele per marker and multiple (more than one allele per marker genotypes were observed in 34 (32% and 72 (68% samples, respectively. A genotype could be assigned to 55 samples (54 patients and 61 different genotypes were identified in total with a discriminatory power of 0.992. Analysis of the allelic distribution of the six markers and minimum spanning tree analysis of the 61 genotypes identified a specific genotype (Gt21 in our hospital, which may have been transmitted between 10 patients including six renal transplant recipients. Our STR-based molecular typing method is a quick, cheap and reliable approach to genotype Pneumocystis jirovecii in hospital settings and is sensitive enough to detect minor genotypes, thus enabling the study of the transmission and pathophysiology of Pneumocystis pneumonia.

  17. Female choice reveals terminal investment in male mealworm beetles, Tenebrio molitor, after a repeated activation of the immune system.

    Science.gov (United States)

    Krams, I; Daukšte, J; Kivleniece, I; Krama, T; Rantala, M J; Ramey, G; Šauša, L

    2011-01-01

    Increasing evidence suggests that secondary sexual traits reflect immunocompetence of males in many animal species. This study experimentally investigated whether a parasite-like immunological challenge via a nylon implant affects sexual attractiveness of males in Tenebrio molitor L. (Coleoptera: Tenebrionidae) Although a single immunological challenge significantly reduced sexual attractiveness and locomotor activity of males, it had no adverse effect on their survival. A second immune challenge of the same males increased their attractiveness. However, it was found that the repeated challenge significantly reduced locomotor activity of males and caused higher mortality. This result indicates terminal investment on sexual signaling, which is supposedly based on a trade-off between pheromone production and energy expenditures needed for such activities as recovery of immune system and locomotor activity. When the third implantation was carried out in the same group of males, melanization of nylon implants was found to be lower in more attractive than in less attractive males. This suggests that males that became sexually attractive after the second immune challenge did not invest in recovery of their immune system.

  18. Splashing Our Way to Playfulness! An Aquatic Playgroup for Young Children with Autism, A Repeated Measures Design

    Science.gov (United States)

    Fabrizi, Sarah E.

    2015-01-01

    This study investigated the effectiveness of an aquatic playgroup on the playfulness of children, ages 2 to 3 with autism spectrum disorder. Using a repeated measures design, we followed 10 children and their caregivers who participated in a 6-week aquatic playgroup in southwest Florida. Four dyads completed the entire 12-week study period. The…

  19. Splashing Our Way to Playfulness! An Aquatic Playgroup for Young Children with Autism, A Repeated Measures Design

    Science.gov (United States)

    Fabrizi, Sarah E.

    2015-01-01

    This study investigated the effectiveness of an aquatic playgroup on the playfulness of children, ages 2 to 3 with autism spectrum disorder. Using a repeated measures design, we followed 10 children and their caregivers who participated in a 6-week aquatic playgroup in southwest Florida. Four dyads completed the entire 12-week study period. The…

  20. A Correction for the Epsilon Approximate Test in Repeated Measures Designs with Two or More Independent Groups.

    Science.gov (United States)

    Lecoutre, Bruno

    1991-01-01

    The routine epsilon approximate test in repeated measures designs when the condition of circularity is unfulfilled uses an erroneous formula in the case of two or more groups. Because this may lead to underestimation of the deviation from circularity when the subject number is small, a correction is proposed. (Author/SLD)

  1. Repeatability of swept-source optical coherence tomography retinal and choroidal thickness measurements in neovascular age-related macular degeneration

    DEFF Research Database (Denmark)

    Hanumunthadu, Daren; Ilginis, Tomas; Restori, Marie

    2017-01-01

    BACKGROUND: The aim was to determine the intrasession repeatability of swept-source optical coherence tomography (SS-OCT)-derived retinal and choroidal thickness measurements in eyes with neovascular age-related macular degeneration (nAMD). METHODS: A prospective study consisting of patients with...

  2. GSTM1 and APE1 genotypes affect arsenic-induced oxidative stress: a repeated measures study

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    Quamruzzaman Quazi

    2007-12-01

    Full Text Available Abstract Background Chronic arsenic exposure is associated with an increased risk of skin, bladder and lung cancers. Generation of oxidative stress may contribute to arsenic carcinogenesis. Methods To investigate the association between arsenic exposure and oxidative stress, urinary 8-hydroxy-2'-deoxyguanosine (8-OHdG was evaluated in a cohort of 97 women recruited from an arsenic-endemic region of Bangladesh in 2003. Arsenic exposure was measured in urine, toenails, and drinking water. Drinking water and urine samples were collected on three consecutive days. Susceptibility to oxidative stress was evaluated by genotyping relevant polymorphisms in glutathione-s transferase mu (GSTM1, human 8-oxoguanine glycosylase (hOGG1 and apurinic/apyrimidinic endonuclease (APE1 genes using the Taqman method. Data were analyzed using random effects Tobit regression to account for repeated measures and 8-OHdG values below the detection limit. Results A consistent negative effect for APE1 was observed across water, toenail and urinary arsenic models. APE1 148 glu/glu + asp/glu genotype was associated with a decrease in logged 8-OHdG of 0.40 (95%CI -0.73, -0.07 compared to APE1 148 asp/asp. An association between total urinary arsenic and 8-OHdG was observed among women with the GSTM1 null genotype but not in women with GSTM1 positive. Among women with GSTM1 null, a comparison of the second, third, and fourth quartiles of total urinary arsenic to the first quartile resulted in a 0.84 increase (95% CI 0.27, 1.42, a 0.98 increase (95% CI 033, 1.66 and a 0.85 increase (95% CI 0.27, 1.44 in logged 8-OHdG, respectively. No effects between 8-OHdG and toenail arsenic or drinking water arsenic were observed. Conclusion These results suggest the APE1 variant genotype decreases repair of 8-OHdG and that arsenic exposure is associated with oxidative stress in women who lack a functional GSTM1 detoxification enzyme.

  3. Pilot study: Assessing repeatability of the EcoWalk platform resistive pressure sensors to measure plantar pressure during barefoot standing

    Science.gov (United States)

    Zequera, Martha; Perdomo, Oscar; Wilches, Carlos; Vizcaya, Pedro

    2013-06-01

    Plantar pressure provides useful information to assess the feet's condition. These systems have emerged as popular tools in clinical environment. These systems present errors and no compensation information is presented by the manufacturer, leading to uncertainty in the measurements. Ten healthy subjects, 5 females and 5 males, were recruited. Lateral load distribution, antero-posterior load distribution, average pressure, contact area, and force were recorded. The aims of this study were to assess repeatability of the EcoWalk system and identify the range of pressure values observed in the normal foot. The coefficient of repeatability was less than 4% for all parameters considered.

  4. Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs)

    Science.gov (United States)

    Shumayla; Sharma, Shailesh; Kumar, Rohit; Mendu, Venugopal; Singh, Kashmir; Upadhyay, Santosh K.

    2016-01-01

    The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

  5. Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs).

    Science.gov (United States)

    Shumayla; Sharma, Shailesh; Kumar, Rohit; Mendu, Venugopal; Singh, Kashmir; Upadhyay, Santosh K

    2016-01-01

    The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

  6. Genomic dissection and expression profiling revealed functional divergence in Triticum aestivum leucine rich repeat receptor like kinases (TaLRRKs

    Directory of Open Access Journals (Sweden)

    Shumayla .

    2016-09-01

    Full Text Available The leucine rich repeat receptor like kinases (LRRK constitute the largest subfamily of receptor like kinases (RLK, which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat, which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought and salt stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat.

  7. Drought sensitivity of Amazonian carbon balance revealed by atmospheric measurements.

    Science.gov (United States)

    Gatti, L V; Gloor, M; Miller, J B; Doughty, C E; Malhi, Y; Domingues, L G; Basso, L S; Martinewski, A; Correia, C S C; Borges, V F; Freitas, S; Braz, R; Anderson, L O; Rocha, H; Grace, J; Phillips, O L; Lloyd, J

    2014-02-06

    Feedbacks between land carbon pools and climate provide one of the largest sources of uncertainty in our predictions of global climate. Estimates of the sensitivity of the terrestrial carbon budget to climate anomalies in the tropics and the identification of the mechanisms responsible for feedback effects remain uncertain. The Amazon basin stores a vast amount of carbon, and has experienced increasingly higher temperatures and more frequent floods and droughts over the past two decades. Here we report seasonal and annual carbon balances across the Amazon basin, based on carbon dioxide and carbon monoxide measurements for the anomalously dry and wet years 2010 and 2011, respectively. We find that the Amazon basin lost 0.48 ± 0.18 petagrams of carbon per year (Pg C yr(-1)) during the dry year but was carbon neutral (0.06 ± 0.1 Pg C yr(-1)) during the wet year. Taking into account carbon losses from fire by using carbon monoxide measurements, we derived the basin net biome exchange (that is, the carbon flux between the non-burned forest and the atmosphere) revealing that during the dry year, vegetation was carbon neutral. During the wet year, vegetation was a net carbon sink of 0.25 ± 0.14 Pg C yr(-1), which is roughly consistent with the mean long-term intact-forest biomass sink of 0.39 ± 0.10 Pg C yr(-1) previously estimated from forest censuses. Observations from Amazonian forest plots suggest the suppression of photosynthesis during drought as the primary cause for the 2010 sink neutralization. Overall, our results suggest that moisture has an important role in determining the Amazonian carbon balance. If the recent trend of increasing precipitation extremes persists, the Amazon may become an increasing carbon source as a result of both emissions from fires and the suppression of net biome exchange by drought.

  8. Reliability of near-infrared spectroscopy for measuring biceps brachii oxygenation during sustained and repeated isometric contractions

    Science.gov (United States)

    Muthalib, Makii; Millet, Guillaume Y.; Quaresima, Valentina; Nosaka, Kazunori

    2010-01-01

    We examine the test-retest reliability of biceps brachii tissue oxygenation index (TOI) parameters measured by near-infrared spectroscopy during a 10-s sustained and a 30-repeated (1-s contraction, 1-s relaxation) isometric contraction task at 30% of maximal voluntary contraction (30% MVC) and maximal (100% MVC) intensities. Eight healthy men (23 to 33 yr) were tested on three sessions separated by 3 h and 24 h, and the within-subject reliability of torque and each TOI parameter were determined by Bland-Altman+/-2 SD limits of agreement plots and coefficient of variation (CV). No significant (P>0.05) differences between the three sessions were found for mean values of torque and TOI parameters during the sustained and repeated tasks at both contraction intensities. All TOI parameters were within+/-2 SD limits of agreement. The CVs for torque integral were similar between the sustained and repeated task at both intensities (4 to 7%) however, the CVs for TOI parameters during the sustained and repeated task were lower for 100% MVC (7 to 11%) than for 30% MVC (22 to 36%). It is concluded that the reliability of the biceps brachii NIRS parameters during both sustained and repeated isometric contraction tasks is acceptable.

  9. Comparison of Central Corneal Thickness Measurements by Ultrasonic Pachymetry and Orbscan II Corneal Topography and Evaluation of Ultrasonic Pachymetry Repeatability

    Directory of Open Access Journals (Sweden)

    Semra Tiryaki Demir

    2014-08-01

    Full Text Available Objectives: Comparison of central corneal thickness (CCT measurements by ultrasonic pachymetry and Orbscan II corneal topography and evaluation of ultrasonic pachymetry repeatability for same observer. Materials and Methods: The study included 132, 82, and 80 eyes of 66 patients with primary open-angle glaucoma (POAG, 41 patients with ocular hypertension (OHT, and 40 controls, respectively. All subjects were subjected to routine ophthalmic examination. Orbscan II (Bausch&Lomb corneal topography and ultrasonic pachymetry (Nidek Ultrasonic Pachymetry UP-1000 were used for measurement of CCT. ANOVA (Turkey test was used for variable distribution, paired sample t-test was used for repeated measurements, and the analyses were done by SPSS 20.0. Results: Mean CCT was 558.9±37.2 µm by ultrasonic pachymetry and 553.4±37 µm by corneal topography. There was a significant difference between the two measurements (p0.05. CCT was 555±39.2 µm, 564.3±28.4 µm, and 559.7±41.5 µm by ultrasonic pachymetry in POAG, OHT, and control subjects, respectively; CCT was 550.3±38.3 µm, 558.5±28 µm, and 553.2±42.5 µm by Orbscan II corneal topography in POAG, OHT, and control subjects, respectively. There was a significant linear correlation between Orbscan II corneal topography and ultrasonic pachymetry in CCT measurements (r=0.975, p<0.0001. Repeatability of ultrasonic pachymetry for same observer was (ICC value 0.990. Conclusion: There is a significant correlation between Orbscan II corneal topography and ultrasonic pachymetry in CCT measurements. These two methods of measurements should not be substituted for each other, since ultrasonic pachymetry measures CCT greater than Orbscan II corneal topography. Repeatability of ultrasonic pachymetry for same observer is very high. (Turk J Ophthalmol 2014; 44: 263-7

  10. Analyzing repeated data collected by mobile phones and frequent text messages. An example of Low back pain measured weekly for 18 weeks

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    Axén Iben

    2012-07-01

    within the studied population? A visual approach and hierarchical cluster analyses revealed different subgroups using subsets of the model data. Conclusions We have illustrated several ways of analysing repeated measures with both traditional analytic approaches using standard statistical packages, as well as recently developed statistical methods that will utilize all the vital features inherent in the data.

  11. An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length.

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    Hua Wong

    Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.

  12. Repeatability of Volume and Regional Body Composition Measurements of the Lower Limb Using Dual-energy X-ray Absorptiometry

    DEFF Research Database (Denmark)

    Gjorup, Caroline A; Zerahn, Bo; Juul, Sarah

    2016-01-01

    Lower limb lymphedema is a dynamic condition in which tissue composition and volume measurements are affected. Various definitions of lower limb lymphedema exist but volume differences between the limbs are widely used. It is therefore necessary to have a readily available noninvasive measurement...... of agreement on the Bland-Altman plots. These results confirm DXA to be a highly repeatable method for volume and tissue composition measurements of the lower limb. In a population at risk of lymphedema, DXA offers a clinically readily available noninvasive method allowing multiple measurements of volume...... and tissue composition on a routine basis, important for diagnosing, monitoring, managing, and researching lymphedema....

  13. Power analysis for multivariate and repeated measurements designs via SPSS: correction and extension of D'Amico, Neilands, and Zambarano (2001).

    Science.gov (United States)

    Osborne, Jason W

    2006-05-01

    D'Amico, Neilands, and Zambarano (2001) published SPSS syntax to perform power analyses for three complex procedures: ANCOVA, MANOVA, and repeated measures ANOVA. Unfortunately, the published SPSS syntax for performing the repeated measures analysis needed some minor revision in order to perform the analysis correctly. This article presents the corrected syntax that will successfully perform the repeated measures analysis and provides some guidance on modifying the syntax to customize the analysis.

  14. Repeatability and reproducibility of measurements of the suburethral tape location obtained in pelvic floor ultrasound performed with a transvaginal probe

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    Maria Magdalena Dresler

    2017-06-01

    Full Text Available Introduction: Implants used to treat patients with urogynecological conditions are well visible in US examination. The position of the suburethral tape (sling is determined in relation to the urethra or the pubic symphysis. Aim of the study: The study was aimed at assessing the accuracy of measurements determining suburethral tape location obtained in pelvic US examination performed with a transvaginal probe. Material and methods: The analysis covered the results of sonographic measurements obtained according to a standardized technique in women referred for urogynecological diagnostics. Data from a total of 68 patients were used to analyse the repeatability and reproducibility of results obtained on the same day. Results: The intraclass correlation coefficient for the repeatability and reproducibility of the sonographic measurements of suburethral tape location obtained with a transvaginal probe ranged from 0.6665 to 0.9911. The analysis of the measurements confirmed their consistency to be excellent or good. Conclusions: Excellent and good repeatability and reproducibility of the measurements of the suburethral tape location obtained in a pelvic ultrasound performed with a transvaginal probe confirm the test’s validity and usefulness for clinical and academic purposes.

  15. Genetic diversity of Pinus nigra Arn. populations in Southern Spain and Northern Morocco revealed by inter-simple sequence repeat profiles.

    Science.gov (United States)

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E; Tiscar, Pedro A; Viñegla, Benjamin; Linares, Juan C; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei's genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei's genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups-Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco-while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

  16. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

    Science.gov (United States)

    Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

  17. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

    Science.gov (United States)

    Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

  18. Individual Variability and Test-Retest Reliability Revealed by Ten Repeated Resting-State Brain Scans over One Month.

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    Bing Chen

    Full Text Available Individual differences in mind and behavior are believed to reflect the functional variability of the human brain. Due to the lack of a large-scale longitudinal dataset, the full landscape of variability within and between individual functional connectomes is largely unknown. We collected 300 resting-state functional magnetic resonance imaging (rfMRI datasets from 30 healthy participants who were scanned every three days for one month. With these data, both intra- and inter-individual variability of six common rfMRI metrics, as well as their test-retest reliability, were estimated across multiple spatial scales. Global metrics were more dynamic than local regional metrics. Cognitive components involving working memory, inhibition, attention, language and related neural networks exhibited high intra-individual variability. In contrast, inter-individual variability demonstrated a more complex picture across the multiple scales of metrics. Limbic, default, frontoparietal and visual networks and their related cognitive components were more differentiable than somatomotor and attention networks across the participants. Analyzing both intra- and inter-individual variability revealed a set of high-resolution maps on test-retest reliability of the multi-scale connectomic metrics. These findings represent the first collection of individual differences in multi-scale and multi-metric characterization of the human functional connectomes in-vivo, serving as normal references for the field to guide the use of common functional metrics in rfMRI-based applications.

  19. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

    Directory of Open Access Journals (Sweden)

    Alejandro Arteaga

    Full Text Available Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

  20. Repeatability of swept-source optical coherence tomography retinal and choroidal thickness measurements in neovascular age-related macular degeneration.

    Science.gov (United States)

    Hanumunthadu, Daren; Ilginis, Tomas; Restori, Marie; Sagoo, Mandeep S; Tufail, Adnan; Balaggan, Kamaljit S; Patel, Praveen J

    2017-05-01

    The aim was to determine the intrasession repeatability of swept-source optical coherence tomography (SS-OCT)-derived retinal and choroidal thickness measurements in eyes with neovascular age-related macular degeneration (nAMD). A prospective study consisting of patients with active nAMD enrolled in the Distance of Choroid Study at Moorfields Eye Hospital, London. Patients underwent three 12×9 mm macular raster scans using the deep range imaging (DRI) OCT-1 SS-OCT (Topcon) device in a single imaging session. Retinal and choroidal thicknesses were calculated for the ETDRS macular subfields. Repeatability was calculated according to methods described by Bland and Altman. 39 eyes of 39 patients with nAMD were included with a mean (±SD) age of 73.9 (±7.2) years. The mean (±SD) retinal thickness of the central macular subfield was 225.7 μm (±12.4 μm). The repeatability this subfield, expressed as a percentage of the mean central macular subfield thickness, was 23.2%. The percentage repeatability of the other macular subfields ranged from 13.2% to 28.7%. The intrasession coefficient of repeatability of choroidal thickness of the central macular subfield was 57.2 μm with a mean choroidal thickness (±SD) of 181 μm (±15.8 μm). This study suggests that a change >23.2% of retinal thickness and 57.2 μm choroidal thickness in the central macular subfield is required to distinguish true clinical change from measurement variability when using the DRI OCT-1 device to manage patients with nAMD. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  1. Comparison of Central Corneal Thickness Measurements by Ultrasonic Pachymetry and Orbscan II Corneal Topography and Evaluation of Ultrasonic Pachymetry Repeatability

    OpenAIRE

    Semra Tiryaki Demir; Mahmut Odabaşı; Mehmet Ersin Oba; Ayşe Burcu Dirim; Efe Can; Orhan Kara

    2014-01-01

    Objectives: Comparison of central corneal thickness (CCT) measurements by ultrasonic pachymetry and Orbscan II corneal topography and evaluation of ultrasonic pachymetry repeatability for same observer. Materials and Methods: The study included 132, 82, and 80 eyes of 66 patients with primary open-angle glaucoma (POAG), 41 patients with ocular hypertension (OHT), and 40 controls, respectively. All subjects were subjected to routine ophthalmic examination. Orbscan II (Bausch&Lomb) ...

  2. Comparison of Repeated Measurement Design and Mixed Models in Evaluation of the Entonox Effect on Labor Pain

    Directory of Open Access Journals (Sweden)

    Nasim Karimi

    2017-01-01

    Full Text Available Background & objectives: In many medical studies, the response variable is measured repeatedly over time to evaluate the treatment effect that is known as longitudinal study. The analysis method for this type of data is repeated measures ANOVA that uses only one correlation structure and the results are not valid with inappropriate correlation structure. To avoid this problem, a convenient alternative is mixed models. So, the aim of this study was to compare of mixed and repeated measurement models for examination of the Entonox effect on the labor pain. Methods: This experimental study was designed to compare the effect of Entonox and oxygen inhalation on pain relief between two groups. Data were analyzed using repeated measurement and mixed models with different correlation structures. Selection and comparison of proper correlation structures performed using Akaike information criterion, Bayesian information criterion and restricted log-likelihood. Data were analyzed using SPSS-22. Results: Results of our study showed that all variables containing analgesia methods, labor duration of the first and second stages, and time were significant in these tests. In mixed model, heterogeneous first-order autoregressive, first-order autoregressive, heterogeneous Toeplitz and unstructured correlation structures were recognized as the best structures. Also, all variables were significant in these structures. Unstructured variance covariance matrix was recognized as the worst structure and labor duration of the first and second stages was not significant in this structure. Conclusions: This study showed that the Entonox inhalation has a significant effect on pain relief in primiparous and it is confirmed by all of the models.

  3. Incomplete quality of life data in lung transplant research: comparing cross sectional, repeated measures ANOVA, and multi-level analysis

    Directory of Open Access Journals (Sweden)

    van der Bij Wim

    2005-09-01

    Full Text Available Abstract Background In longitudinal studies on Health Related Quality of Life (HRQL it frequently occurs that patients have one or more missing forms, which may cause bias, and reduce the sample size. Aims of the present study were to address the problem of missing data in the field of lung transplantation (LgTX and HRQL, to compare results obtained with different methods of analysis, and to show the value of each type of statistical method used to summarize data. Methods Results from cross-sectional analysis, repeated measures on complete cases (ANOVA, and a multi-level analysis were compared. The scores on the dimension 'energy' of the Nottingham Health Profile (NHP after transplantation were used to illustrate the differences between methods. Results Compared to repeated measures ANOVA, the cross-sectional and multi-level analysis included more patients, and allowed for a longer period of follow-up. In contrast to the cross sectional analyses, in the complete case analysis, and the multi-level analysis, the correlation between different time points was taken into account. Patterns over time of the three methods were comparable. In general, results from repeated measures ANOVA showed the most favorable energy scores, and results from the multi-level analysis the least favorable. Due to the separate subgroups per time point in the cross-sectional analysis, and the relatively small number of patients in the repeated measures ANOVA, inclusion of predictors was only possible in the multi-level analysis. Conclusion Results obtained with the various methods of analysis differed, indicating some reduction of bias took place. Multi-level analysis is a useful approach to study changes over time in a data set where missing data, to reduce bias, make efficient use of available data, and to include predictors, in studies concerning the effects of LgTX on HRQL.

  4. Repeated Microsphere Delivery for Serial Measurement of Regional Blood Perfusion in the Chronically Instrumented, Conscious Canine

    Science.gov (United States)

    Bartoli, Carlo R.; Okabe, Kazunori; Akiyama, Ichiro; Coull, Brent; Godleski, John J.

    2008-01-01

    INTRODUCTION For chronic, repeated hemodynamic studies in conscious dogs, we designed and tested a chronically instrumented canine, microsphere delivery model. The goals of this study were to investigate the accuracy of repeated estimations of blood perfusion using fluorescent-labeled microspheres and to develop and validate a chronic preparation that permits consecutive estimations in the same conscious animal over an extended protocol. METHODS Via thoracotomy, 9 dogs were instrumented with left atrial appendage and aortic vascular access catheters connected to subcutaneous vascular access ports (VAPs). Four animals received 7 serial injections of 1.6 million 15μm microspheres (total: 11.2 million), and five animals received 8 serial injections of 2.25 million microspheres (total: 18 million) over the course of 11 or 18 weeks. RESULTS All catheters have remained bidirectionally patent during protocol for 14.9±0.8 (Mean±SEM) weeks. Sphere accumulation did not significantly alter global myocardial (p=0.69, p=0.25), renal (p=0.92, p=0.12), hepatic (p=0.84, p=0.32), or splenic (p=0.33, p=0.70) blood perfusion in either set of animals. CONCLUSIONS Catheters remained bidirectionally patent for months, did not interfere with the hemodynamic responses of the preparation, and allowed repeat percutaneous injection of microspheres and withdrawal of reference arterial blood from within conscious canines. Eight serial injections totaling 18 million microspheres over 18 weeks did not alter regional myocardial, hepatic, renal, or splenic blood flow. This dependable, chronic, percutaneous arterial access preparation provides a means for examining acute and long-term effects of pathophysiological, pharmaceutical, and environmental influences on regional arterial blood perfusion in conscious, large animals. PMID:17632127

  5. Measuring Aseismic Slip through Characteristically Repeating Earthquakes at the Mendocino Triple Junction, Northern California

    Science.gov (United States)

    Materna, K.; Taira, T.; Burgmann, R.

    2016-12-01

    The Mendocino Triple Junction (MTJ), at the transition point between the San Andreas fault system, the Mendocino Transform Fault, and the Cascadia Subduction Zone, undergoes rapid tectonic deformation and produces more large (M>6.0) earthquakes than any region in California. Most of the active faults of the triple junction are located offshore, making it difficult to characterize both seismic slip and aseismic creep. In this work, we study aseismic creep rates near the MTJ using characteristically repeating earthquakes (CREs) as indicators of creep rate. CREs are generally interpreted as repeated failures of the same seismic patch within an otherwise creeping fault zone; as a consequence, the magnitude and recurrence time of the CREs can be used to determine a fault's creep rate through empirically calibrated scaling relations. Using seismic data from 2010-2016, we identify CREs as recorded by an array of eight 100-Hz PBO borehole seismometers deployed in the Cape Mendocino area. For each event pair with epicenters less than 30 km apart, we compute the cross-spectral coherence of 20 seconds of data starting one second before the P-wave arrival. We then select pairs with high coherence in an appropriate frequency band, which is determined uniquely for each event pair based on event magnitude, station distance, and signal-to-noise ratio. The most similar events (with median coherence above 0.95 at two or more stations) are selected as CREs and then grouped into CRE families, and each family is used to infer a local creep rate. On the Mendocino Transform Fault, we find relatively high creep rates of >5 cm/year that increase closer to the Gorda Ridge. Closer to shore and to the MTJ itself, we find many families of repeaters on and off the transform fault with highly variable creep rates, indicative of the complex deformation that takes place there.

  6. Quantification of age-dependent somatic CAG repeat instability in Hdh CAG knock-in mice reveals different expansion dynamics in striatum and liver.

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    Jong-Min Lee

    Full Text Available BACKGROUND: Age at onset of Huntington's disease (HD is largely determined by the CAG trinucleotide repeat length in the HTT gene. Importantly, the CAG repeat undergoes tissue-specific somatic instability, prevalent in brain regions that are disease targets, suggesting a potential role for somatic CAG repeat instability in modifying HD pathogenesis. Thus, understanding underlying mechanisms of somatic CAG repeat instability may lead to discoveries of novel therapeutics for HD. Investigation of the dynamics of the CAG repeat size changes over time may provide insights into the mechanisms underlying CAG repeat instability. METHODOLOGY/PRINCIPAL FINDINGS: To understand how the HTT CAG repeat length changes over time, we quantified somatic instability of the CAG repeat in Huntington's disease CAG knock-in mice from 2-16 months of age in liver, striatum, spleen and tail. The HTT CAG repeat in spleen and tail was very stable, but that in liver and striatum expanded over time at an average rate of one CAG per month. Interestingly, the patterns of repeat instability were different between liver and striatum. Unstable CAG repeats in liver repeatedly gained similar sizes of additional CAG repeats (approximately two CAGs per month, maintaining a distinct population of unstable repeats. In contrast, unstable CAG repeats in striatum gained additional repeats with different sizes resulting in broadly distributed unstable CAG repeats. Expanded CAG repeats in the liver were highly enriched in polyploid hepatocytes, suggesting that the pattern of liver instability may reflect the restriction of the unstable repeats to a unique cell type. CONCLUSIONS/SIGNIFICANCE: Our results are consistent with repeat expansion occurring as a consequence of recurrent small repeat insertions that differ in different tissues. Investigation of the specific mechanisms that underlie liver and striatal instability will contribute to our understanding of the relationship between

  7. Persistent repeated measurements by magnetic resonance spectroscopy demonstrate minimal hepatic encephalopathy: a case report.

    Science.gov (United States)

    Scheau, C; Popa, G A; Ghergus, A E; Preda, E M; Capsa, R A; Lupescu, I G

    2013-09-15

    Minimal Hepatic Encephalopathy (MHE), previously referred to as infraclinical or subclinical is a precursor in the development of clinical hepatic encephalopathy (HE). The demonstration of MHE is done through neuropsychological testing in the absence of clinical evidence of HE, patients showing only a mild cognitive impairment. Neuropsychological tests employed consist of Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and portosystemic encephalopathy (PSE) test score. Unfortunately, there are numerous occasions when the tests prove irrelevant: in the situation of inexperienced investigators, the patient's poor education, vision problems or concurring central nervous system disease, all of which may delay or deviate from the correct diagnosis.

  8. More on Measuring the Overall Revealed Comparative Advantage

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    Veselin Hadzhiev

    2014-11-01

    Full Text Available The overall revealed comparative advantages approach aims to summarize the divergent expression of comparative advantages by commodity groups and countries. It represents an alternative to the traditional approach of Bella Balassa, Thomas Vollrath and others. The innovativeness of the overall revealed comparative advantages approach preconditions a certain prudence with regard to its use and interpretation. It is necessary to explore the potential of the approach in different conditions and different circumstances. It was found that the approach of overall revealed comparative advantages is resistant to the Euclidean distances and commodity classifications used for metrification. It has the potential to synthesize uniformly divergent changes in specialization by country and commodity groups and is a useful tool for the analysis of comparative advantages.

  9. Accuracy and repeatability of direct ciliary sulcus diameter measurements by full-scale 50-megahertz ultrasound biomicroscopy

    Institute of Scientific and Technical Information of China (English)

    LI De-jiao; WANG Ning-li; CHEN Shu; LI Shu-ning; MU Da-peng; WANG Tao

    2009-01-01

    Background Phakic intraocular lens (pIOL) implantation has been a popular means for the treatment of high ametropia. Measurements of ciliary sulcus diameter is important for pIOL size determining. But till now, no perfect system can directly measure it. The present study was to evaluate the accuracy, repeatability and reproducibility of direct sulcus diameter measurements obtained by a full-scale 50-megahertz (MHz) ultrasound biomicroscopy (UBM).Methods A fresh cadaver human eye with a scale marker inserted through the posterior chamber plane from 3 o'clock to 9 o'clock meridian and 30 randomly selected eyes from 30 normal subjects were scanned by full-scale 50-MHz UBM in horizontal meridional scan plane. The distance between the scales and the whole length of the marker inside the cadaver eye were measured by the same observer using the "built-in" measurement tools and the indicating error of instrument was calculated. Reproducibility of the measurement was evaluated in 30 eyes by 2 operators using Blander and Altman plot test. Repeatability was evaluated from 10 successive eyes randomly selected from the 30 eyes by one operator.Results On a scale of 1 mm, the greatest indicating error was 40 μm; the mean largest indicating error of 1 mm scale from the 10 images was (26±14) μm; on a scale of 11 mm, the greatest indicating error was 70 μo; the error rate was 0.64%. The mean length of the needle inside the eye of the 10 images was 11.05 mm, with the mean indicating error of 47 μm, the average error rate was 0.43%. For ciliary sulcus diameter measurements in vivo, the coefficient of variation was 0.38%; the coefficients of repeatability for intra-observer and inter-observer measurements were 1.99% and 2.55%, respectively. The limits of agreement for intra-observer and inter-observer measurement were-0.41 mm to 0.48 mm and -0.59 mm to 0.58 ram, respectively.Conclusion The full-scale 50-MHz UBM can be a high accuracy and good repeatability means for direct

  10. Structural Insights Reveal the Dynamics of the Repeating r(CAG) Transcript Found in Huntington's Disease (HD) and Spinocerebellar Ataxias (SCAs).

    Science.gov (United States)

    Tawani, Arpita; Kumar, Amit

    2015-01-01

    In humans, neurodegenerative disorders such as Huntington's disease (HD) and many spinocerebellar ataxias (SCAs) have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein) to expanded r(CAG) repeats. Moreover, mutant huntingtin protein translated from expanded r(CAG) also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(CAG) motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD) simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different syn and anti conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(CAG) motif.

  11. The crystal structure of HIV CRF07 B′/C gp41 reveals a hyper-mutant site in the middle of HR2 heptad repeat

    Energy Technology Data Exchange (ETDEWEB)

    Du, Jiansen; Xue, Hailing; Ma, Jing; Liu, Fang [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China); Zhou, Jianhua [Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001 (China); Shao, Yiming [State Key Laboratory for Infectious Disease Prevention and Control, and National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206 (China); Qiao, Wentao, E-mail: wentaoqiao@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China); Liu, Xinqi, E-mail: liu2008@nankai.edu.cn [State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071 (China)

    2013-11-15

    HIV CRF07 B′/C is a strain circulating mainly in northwest region of China. The gp41 region of CRF07 is derived from a clade C virus. In order to compare the difference of CRF07 gp41 with that of typical clade B virus, we solved the crystal structure of the core region of CRF07 gp41. Compared with clade B gp41, CRF07 gp41 evolved more basic and hydrophilic residues on its helix bundle surface. Based on sequence alignment, a hyper-mutant cluster located in the middle of HR2 heptads repeat was identified. The mutational study of these residues revealed that this site is important in HIV mediated cell–cell fusion and plays critical roles in conformational changes during viral invasion. - Highlights: • We solved the crystal structure of HIV CRF07 gp41 core region. • A hyper-mutant cluster in the middle of HR2 heptads repeat was identified. • The hyper-mutant site is important in HIV-cell fusion. • The model will help to understand the HIV fusion process.

  12. Structural Insights Reveal the Dynamics of the Repeating r(CAG Transcript Found in Huntington's Disease (HD and Spinocerebellar Ataxias (SCAs.

    Directory of Open Access Journals (Sweden)

    Arpita Tawani

    Full Text Available In humans, neurodegenerative disorders such as Huntington's disease (HD and many spinocerebellar ataxias (SCAs have been found to be associated with CAG trinucleotide repeat expansion. An important RNA-mediated mechanism that causes these diseases involves the binding of the splicing regulator protein MBNL1 (Muscleblind-like 1 protein to expanded r(CAG repeats. Moreover, mutant huntingtin protein translated from expanded r(CAG also yields toxic effects. To discern the role of mutant RNA in these diseases, it is essential to gather information about its structure. Detailed insight into the different structures and conformations adopted by these mutant transcripts is vital for developing therapeutics targeting them. Here, we report the crystal structure of an RNA model with a r(CAG motif, which is complemented by an NMR-based solution structure obtained from restrained Molecular Dynamics (rMD simulation studies. Crystal structure data of the RNA model resolved at 2.3 Å reveals non-canonical pairing of adenine in 5´-CAG/3´-GAC motif samples in different syn and anti conformations. The overall RNA structure has helical parameters intermediate to the A- and B-forms of nucleic acids due to the global widening of major grooves and base-pair preferences near internal AA loops. The comprehension of structural behaviour by studying the spectral features and the dynamics also supports the flexible nature of the r(CAG motif.

  13. Measurement repeatability of tibial tuberosity-trochlear groove offset distance in red fox (Vulpes vulpes) cadavers

    DEFF Research Database (Denmark)

    Miles, James Edward; Jensen, Bente Rona; Kirpensteijn, Jolle

    2013-01-01

    Objective-To describe CT image reconstruction criteria for measurement of the tibial tuberosity-trochlear groove (TT-TG) offset distance, evaluate intra- and inter-reconstruction repeatability, and identify key sources of error in the measurement technique, as determined in vulpine hind limbs. An...... and applied criteria. The TT-TG offset distance has potential as an objective assessment of alignment of the distal portion of the quadriceps mechanism; its use as an aid in case selection for corrective femoral osteotomy among dogs with medial patellar luxation warrants investigation....

  14. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    Directory of Open Access Journals (Sweden)

    Oussama Ahrazem

    2012-05-01

    Full Text Available Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

  15. Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.

    Directory of Open Access Journals (Sweden)

    Augix Guohua Xu

    Full Text Available Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20-28% of non-ribosomal transcripts correspond to annotated exons and 20-23% to introns. By contrast, transcripts originating within intronic and intergenic repetitive sequences constitute 40-48% of the total brain transcriptome. Notably, some repeat families show elevated transcription. In non-repetitive intergenic regions, we identify and characterize 1,093 distinct regions highly expressed in the human brain. These regions are conserved at the RNA expression level across primates studied and at the DNA sequence level across mammals. A large proportion of these transcripts (20% represents 3'UTR extensions of known genes and may play roles in alternative microRNA-directed regulation. Finally, we show that while transcriptome divergence between species increases with evolutionary time, intergenic transcripts show more expression differences among species and exons show less. Our results show that many yet uncharacterized evolutionary conserved transcripts exist in the human brain. Some of these transcripts may play roles in transcriptional regulation and contribute to evolution of human-specific phenotypic traits.

  16. A Description of Quasar Variability Measured Using Repeated SDSS and POSS Imaging

    CERN Document Server

    MacLeod, Chelsea L; Sesar, Branimir; de Vries, Wim; Kochanek, Christopher S; Kelly, Brandon C; Becker, Andrew C; Lupton, Robert H; Hall, Patrick B; Richards, Gordon T; Anderson, Scott F; Schneider, Donald P

    2011-01-01

    We provide a quantitative description and statistical interpretation of the optical continuum variability of quasars. The Sloan Digital Sky Survey (SDSS) has obtained repeated imaging in five UV-to-IR photometric bands for 34,727 spectroscopically confirmed quasars. About 10,000 quasars have an average of 60 observations in each band obtained over a decade along stripe 82 (S82), whereas the remaining ~25,000 have 2-3 observations due to scan overlaps. The observed time lags span the range from a day to almost 10 years, and constrain quasar variability at rest-frame time lags of up to 4 years, and at rest-frame wavelengths from 1000A to 6000A. We publicly release a user-friendly catalog of quasars from the SDSS Data Release 7 that have been observed at least twice in SDSS or once in both SDSS and the Palomar Observatory Sky Survey, and we use it to analyze the ensemble properties of quasar variability. Based on a damped random walk (DRW) model defined by a characteristic time scale and an asymptotic variabilit...

  17. Genetic variability and geographic differentiation in Thymus daenensis subsp. daenensis, an endangered medicinal plant, as revealed by inter simple sequence repeat (ISSR) markers.

    Science.gov (United States)

    Rahimmalek, Mehdi; Bahreininejad, Babak; Khorrami, Mojtaba; Tabatabaei, Badraldin Ebrahim Sayed

    2009-12-01

    Thymus daenensis is an aromatic medicinal plant endemic to Iran. We used inter simple sequence repeat (ISSR) markers to detect genetic polymorphism in this herb using 17 T. daenensis accessions collected from different geographic regions in Iran. The 15 primers chosen for analysis revealed 256 bands, of which 228 (88.9%) were polymorphic. Jaccard's similarity indices based on ISSR profiles were subjected to UPGMA cluster analysis. The generated dendrogram revealed two major groups. The Tc group included the accessions collected from the center of the Zagros Mountains, and the Te group was collected from the extremes of the Zagros range. A principal coordinate analysis confirmed the results of clustering. The results showed that the divergence of accessions based on the Zagros Mountains is more logical in comparison with classification on the basis of provincial borders. Gene diversity and expected heterozygosity were greater in the Tc group than in the Te group, suggesting that the germplasm collected from the center of the Zagros Mountains is more variable.

  18. Estimation of spatial patterns of urban air pollution over a 4-week period from repeated 5-min measurements

    Science.gov (United States)

    Gillespie, Jonathan; Masey, Nicola; Heal, Mathew R.; Hamilton, Scott; Beverland, Iain J.

    2017-02-01

    Determination of intra-urban spatial variations in air pollutant concentrations for exposure assessment requires substantial time and monitoring equipment. The objective of this study was to establish if short-duration measurements of air pollutants can be used to estimate longer-term pollutant concentrations. We compared 5-min measurements of black carbon (BC) and particle number (PN) concentrations made once per week on 5 occasions, with 4 consecutive 1-week average nitrogen dioxide (NO2) concentrations at 18 locations at a range of distances from busy roads in Glasgow, UK. 5-min BC and PN measurements (averaged over the two 5-min periods at the start and end of a week) explained 40-80%, and 7-64% respectively, of spatial variation in the intervening 1-week NO2 concentrations for individual weeks. Adjustment for variations in background concentrations increased the percentage of explained variation in the bivariate relationship between the full set of NO2 and BC measurements over the 4-week period from 28% to 50% prior to averaging of repeat measurements. The averages of five 5-min BC and PN measurements made over 5 weeks explained 75% and 33% respectively of the variation in average 1-week NO2 concentrations over the same period. The relatively high explained variation observed between BC and NO2 measured on different time scales suggests that, with appropriate steps to correct or average out temporal variations, repeated short-term measurements can be used to provide useful information on longer-term spatial patterns for these traffic-related pollutants.

  19. Variation in repeated mouth-opening measurements in head and neck cancer patients with and without trismus.

    Science.gov (United States)

    Jager-Wittenaar, H; Dijkstra, P U; Vissink, A; van Oort, R P; Roodenburg, J L N

    2009-01-01

    Trismus after head and neck cancer treatment may severely limit mandibular functioning. Interventions aimed at reducing trismus can only be evaluated when the amount of variation associated with these measurements is known. The aim of this study was to analyse the variation in mouth-opening measurements in patients treated for head and neck cancer, with and without trismus. Maximal mouth opening was measured in 120 patients in two sessions of three repeated measurements by one observer. To analyse the influence of interobserver variation on mouth-opening measurements a subgroup of 30 patients was measured by a second observer. The standard deviation of the six measurements per patient was used as the variation in measurements of maximal mouth opening. No significant difference was found in maximal mouth opening in patients with (n=33) or without (n=87) trismus. The interobserver intraclass correlation coefficient (ICC) was 0.98. Intraobserver ICC and intersession ICC reliabilities both were 0.99. The variation in the mean values of the three measurements was only slightly smaller than the variation of the single measurements. Variation in maximal mouth opening in patients with trismus does not differ from variation in maximal mouth opening in patients without trismus. Interobserver variation is limited.

  20. Nanoviscosity Measurements Revealing Domain Formation in Biomimetic Membranes.

    Science.gov (United States)

    Hasan, Imad Younus; Mechler, Adam

    2017-02-07

    Partitioning of lipid molecules in biomimetic membranes is a model system for the study of naturally occurring domains, such as rafts, in biological membranes. The existence of nanometer scale membrane domains in binary lipid mixtures has been shown with microscopy methods; however, the nature of these domains has not been established unequivocally. A common notion is to ascribe domain separation to thermodynamic phase equilibria. However, characterizing thermodynamic phases of single bilayer membranes has not been possible due to their extreme dimensions: the size of the domains falls to the order of tens to hundreds of nanometers whereas the membrane thickness is only a few nanometers. Here, we present direct measurements of phase transitions in single bilayers of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) phospholipid mixtures using quartz crystal microbalance-based nanoviscosity measurements. Coexisting thermodynamic phases have been successfully identified, and a phase diagram was constructed for the single bilayer binary lipid system. It was demonstrated that domain separation only takes place in planar membranes, and thus, it is absent in liposomes and not detectable in calorimetric measurements on liposome suspensions. On the basis of energetic analysis, the main transition was identified as the breaking of van der Waals interactions between the acyl chains.

  1. The use of a measure of acute irritation to predict the outcome of repeated usage of hand soap products.

    Science.gov (United States)

    Williams, C; Wilkinson, M; McShane, P; Pennington, D; Fernandez, C; Pierce, S

    2011-06-01

    Healthcare-associated infection is an important worldwide problem that could be reduced by better hand hygiene practice. However, an increasing number of healthcare workers are experiencing irritant contact dermatitis of the hands as a result of repeated hand washing. This may lead to a reduced level of compliance with regard to hand hygiene. To assess whether a measure of acute irritation by hand soaps could predict the effects of repeated usage over a 2-week period. In a double-blind, randomized comparison study, the comparative irritation potential of four different hand soaps was assessed over a 24-h treatment period. The effect of repeated hand washing with the hand soap products over a 2-week period in healthy adult volunteers on skin barrier function was then determined by assessment of transepidermal water loss (TEWL), epidermal hydration and a visual assessment using the Hand Eczema Severity Index (HECSI) at days 0, 7 and 14. A total of 121 subjects from the 123 recruited completed phase 1 of the study. All four products were seen to be significantly different from each other in terms of the irritant reaction observed and all products resulted in a significantly higher irritation compared with the no-treatment control. Seventy-nine of the initial 121 subjects were then enrolled into the repeated usage study. A statistically significant worsening of the clinical condition of the skin as measured by HECSI was seen from baseline to day 14 in those subjects repeatedly washing their hands with two of the four soap products (products C and D) with P-values of 0·02 and 0·01, respectively. Subclinical assessment of the skin barrier function by measuring epidermal hydration was significantly increased from baseline to day 7 after repeated hand washing with products A, B and D but overall no significant change was seen in all four products tested by day 14. A statistically significant increase in TEWL at day 14 was seen for product A (P = 0·02) indicating a

  2. Rosa26-GFP direct repeat (RaDR-GFP mice reveal tissue- and age-dependence of homologous recombination in mammals in vivo.

    Directory of Open Access Journals (Sweden)

    Michelle R Sukup-Jackson

    2014-06-01

    Full Text Available Homologous recombination (HR is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.

  3. A DESCRIPTION OF QUASAR VARIABILITY MEASURED USING REPEATED SDSS AND POSS IMAGING

    Energy Technology Data Exchange (ETDEWEB)

    MacLeod, Chelsea L.; Ivezic, Zeljko; Becker, Andrew C.; Anderson, Scott F. [Department of Astronomy, University of Washington, Box 351580, Seattle, WA 98195 (United States); Sesar, Branimir [Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); De Vries, Wim [Department of Physics, University of California, One Shields Ave, Davis, CA 95616 (United States); Kochanek, Christopher S. [Department of Astronomy, Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Kelly, Brandon C. [Department of Physics, University of California, Santa Barbara, CA 93106 (United States); Lupton, Robert H. [Department of Astrophysical Sciences, Princeton University, Princeton, New Jersey 08544 (United States); Hall, Patrick B. [Department of Physics and Astronomy, York University, Toronto, ON M3J 1P3 (Canada); Richards, Gordon T. [Department of Physics, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Schneider, Donald P. [Department of Astronomy and Astrophysics, Pennsylvania State University, 525 Davey Laboratory, University Park, PA 16802 (United States)

    2012-07-10

    We provide a quantitative description and statistical interpretation of the optical continuum variability of quasars. The Sloan Digital Sky Survey (SDSS) has obtained repeated imaging in five UV-to-IR photometric bands for 33,881 spectroscopically confirmed quasars. About 10,000 quasars have an average of 60 observations in each band obtained over a decade along Stripe 82 (S82), whereas the remaining {approx}25,000 have 2-3 observations due to scan overlaps. The observed time lags span the range from a day to almost 10 years, and constrain quasar variability at rest-frame time lags of up to 4 years, and at rest-frame wavelengths from 1000 A to 6000 A. We publicly release a user-friendly catalog of quasars from the SDSS Data Release 7 that have been observed at least twice in SDSS or once in both SDSS and the Palomar Observatory Sky Survey, and we use it to analyze the ensemble properties of quasar variability. Based on a damped random walk (DRW) model defined by a characteristic timescale and an asymptotic variability amplitude that scale with the luminosity, black hole mass, and rest wavelength for individual quasars calibrated in S82, we can fully explain the ensemble variability statistics of the non-S82 quasars such as the exponential distribution of large magnitude changes. All available data are consistent with the DRW model as a viable description of the optical continuum variability of quasars on timescales of {approx}5-2000 days in the rest frame. We use these models to predict the incidence of quasar contamination in transient surveys such as those from the Palomar Transient Factory and Large Synoptic Survey Telescope.

  4. Partial radiogenic heat model for Earth revealed by geoneutrino measurements

    Science.gov (United States)

    Kamland Collaboration; Gando, A.; Gando, Y.; Ichimura, K.; Ikeda, H.; Inoue, K.; Kibe, Y.; Kishimoto, Y.; Koga, M.; Minekawa, Y.; Mitsui, T.; Morikawa, T.; Nagai, N.; Nakajima, K.; Nakamura, K.; Narita, K.; Shimizu, I.; Shimizu, Y.; Shirai, J.; Suekane, F.; Suzuki, A.; Takahashi, H.; Takahashi, N.; Takemoto, Y.; Tamae, K.; Watanabe, H.; Xu, B. D.; Yabumoto, H.; Yoshida, H.; Yoshida, S.; Enomoto, S.; Kozlov, A.; Murayama, H.; Grant, C.; Keefer, G.; Piepke, A.; Banks, T. I.; Bloxham, T.; Detwiler, J. A.; Freedman, S. J.; Fujikawa, B. K.; Han, K.; Kadel, R.; O'Donnell, T.; Steiner, H. M.; Dwyer, D. A.; McKeown, R. D.; Zhang, C.; Berger, B. E.; Lane, C. E.; Maricic, J.; Miletic, T.; Batygov, M.; Learned, J. G.; Matsuno, S.; Sakai, M.; Horton-Smith, G. A.; Downum, K. E.; Gratta, G.; Tolich, K.; Efremenko, Y.; Perevozchikov, O.; Karwowski, H. J.; Markoff, D. M.; Tornow, W.; Heeger, K. M.; Decowski, M. P.

    2011-09-01

    The Earth has cooled since its formation, yet the decay of radiogenic isotopes, and in particular uranium, thorium and potassium, in the planet's interior provides a continuing heat source. The current total heat flux from the Earth to space is 44.2+/-1.0TW, but the relative contributions from residual primordial heat and radiogenic decay remain uncertain. However, radiogenic decay can be estimated from the flux of geoneutrinos, electrically neutral particles that are emitted during radioactive decay and can pass through the Earth virtually unaffected. Here we combine precise measurements of the geoneutrino flux from the Kamioka Liquid-Scintillator Antineutrino Detector, Japan, with existing measurements from the Borexino detector, Italy. We find that decay of uranium-238 and thorium-232 together contribute TW to Earth's heat flux. The neutrinos emitted from the decay of potassium-40 are below the limits of detection in our experiments, but are known to contribute 4TW. Taken together, our observations indicate that heat from radioactive decay contributes about half of Earth's total heat flux. We therefore conclude that Earth's primordial heat supply has not yet been exhausted.

  5. Repeatability of Cone Spacing Measures in Eyes With Inherited Retinal Degenerations

    National Research Council Canada - National Science Library

    Zayit-Soudry, Shiri; Sippl-Swezey, Nicolas; Porco, Travis C; Lynch, Stephanie K; Syed, Reema; Ratnam, Kavitha; Menghini, Moreno; Roorda, Austin J; Duncan, Jacque L

    2015-01-01

    ...)-derived cone spacing measures in eyes with inherited retinal degenerations (IRD) and in normal eyes. Twenty IRD patients and 10 visually normal subjects underwent AOSLO imaging at two visits separated by no more than 1 month...

  6. Repeatability of Choroidal Thickness Measurements on Enhanced Depth Imaging Optical Coherence Tomography Using Different Posterior Boundaries.

    Science.gov (United States)

    Vuong, Vivian S; Moisseiev, Elad; Cunefare, David; Farsiu, Sina; Moshiri, Ala; Yiu, Glenn

    2016-09-01

    To assess the reliability of manual choroidal thickness measurements by comparing different posterior boundary definitions of the choroidal-scleral junction on enhanced depth imaging optical coherence tomography (EDI-OCT). Reliability analysis. Two graders marked the choroidal-scleral junction with segmentation software using different posterior boundaries: (1) the outer border of the choroidal vessel lumen, (2) the outer border of the choroid stroma, and (3) the inner border of the sclera, to measure the vascular choroidal thickness (VCT), stromal choroidal thickness (SCT), and total choroidal thickness (TCT), respectively. Measurements were taken at 0.5-mm intervals from 1.5 mm nasal to 1.5 mm temporal to the fovea, and averaged continuously across the central 3 mm of the macula. Intraclass correlation coefficient (ICC) and coefficient of reliability (CR) were compared to assess intergrader and intragrader reliability. Choroidal thickness measurements varied significantly with different posterior boundaries (P choroidal-scleral junction visibility was Choroidal thickness measurements are more reproducible when measured to the border of the choroid stroma (SCT) than the vascular lumen (VCT) or sclera (TCT). Copyright © 2016 Elsevier Inc. All rights reserved.

  7. The Repeatability Assessment of Three-Dimensional Capsule-Intraocular Lens Complex Measurements by Means of High-Speed Swept-Source Optical Coherence Tomography

    Science.gov (United States)

    Chang, Pingjun; Li, Jin; Savini, Giacomo; Huang, Jinhai; Huang, Shenghai; Zhao, Yinying; Liao, Na; Lin, Lei; Yu, Xiaoyu; Zhao, Yun-e

    2015-01-01

    Purpose To rebuild the three-dimensional (3-D) model of the anterior segment by high-speed swept-source optical coherence tomography (SSOCT) and evaluate the repeatability of measurement for the parameters of capsule-intraocular lens (C-IOL) complex. Methods Twenty-two pseudophakic eyes from 22 patients were enrolled. Three continuous SSOCT measurements were performed in all eyes and the tomograms obtained were used for 3-D reconstruction. The output data were used to evaluate the measurement repeatability. The parameters included postoperative aqueous depth (PAD), the area and diameter of the anterior capsule opening (Area and D), IOL tilt (IOL-T), horizontal, vertical, and space decentration of the IOL, anterior capsule opening, and IOL-anterior capsule opening. Results PAD, IOL-T, Area, D, and all decentration measurements showed high repeatability. Repeated measure analysis showed there was no statistically significant difference among the three continuous measurements (all P > .05). Pearson correlation analysis showed high correlation between each pair of them (all r >0.90, P<0.001). ICCs were all more than 0.9 for all parameters. The 95% LoAs of all parameters were narrow for comparison of three measurements, which showed high repeatability for three measurements. Conclusion SSOCT is available to be a new method for the 3-D measurement of C-IOL complex after cataract surgery. This method presented high repeatability in measuring the parameters of the C-IOL complex. PMID:26600254

  8. Repeatability of measurements: Non-Hermitian observables and quantum Coriolis force

    Science.gov (United States)

    Gardas, Bartłomiej; Deffner, Sebastian; Saxena, Avadh

    2016-08-01

    A noncommuting measurement transfers, via the apparatus, information encoded in a system's state to the external "observer." Classical measurements determine properties of physical objects. In the quantum realm, the very same notion restricts the recording process to orthogonal states as only those are distinguishable by measurements. Therefore, even a possibility to describe physical reality by means of non-Hermitian operators should volens nolens be excluded as their eigenstates are not orthogonal. Here, we show that non-Hermitian operators with real spectra can be treated within the standard framework of quantum mechanics. Furthermore, we propose a quantum canonical transformation that maps Hermitian systems onto non-Hermitian ones. Similar to classical inertial forces this map is accompanied by an energetic cost, pinning the system on the unitary path.

  9. Mediation of the Relationship between Maternal Phthalate Exposure and Preterm Birth by Oxidative Stress with Repeated Measurements across Pregnancy.

    Science.gov (United States)

    Ferguson, Kelly K; Chen, Yin-Hsiu; VanderWeele, Tyler J; McElrath, Thomas F; Meeker, John D; Mukherjee, Bhramar

    2017-03-01

    Mediation analysis is useful for understanding mechanisms and has been used minimally in the study of the environment and disease. We examined mediation of the association between phthalate exposure during pregnancy and preterm birth by oxidative stress. This nested case-control study of preterm birth (n = 130 cases, 352 controls) included women who delivered in Boston, Massachusestts, from 2006 through 2008. Phthalate metabolites and 8-isoprostane, an oxidative stress biomarker, were measured in urine from three visits in pregnancy. We applied four counterfactual mediation methods: method 1, utilizing exposure and mediator averages; method 2, using averages but allowing for an exposure-mediator interaction; method 3, incorporating longitudinal measurements of the exposure and mediator; and method 4, using longitudinal measurements and allowing for an exposure-mediator interaction. We observed mediation of the associations between phthalate metabolites and all preterm birth by 8-isoprostane, with the greatest estimated proportion mediated observed for spontaneous preterm births specifically. Fully utilizing repeated measures of the exposure and mediator improved precision of indirect (i.e., mediated) effect estimates, and including an exposure-mediator interaction increased the estimated proportion mediated. For example, for mono(2-ethyl-carboxy-propyl) phthalate (MECPP), a metabolite of di(2-ethylhexyl) phthalate (DEHP), the percent of the total effect mediated by 8-isoprostane increased from 47% to 60% with inclusion of an exposure-mediator interaction term, in reference to a total adjusted odds ratio of 1.67 or 1.48, respectively. This demonstrates mediation of the phthalate-preterm birth relationship by oxidative stress, and the utility of complex regression models in capturing mediated associations when repeated measures of exposure and mediator are available and an exposure-mediator interaction may exist. Citation: Ferguson KK, Chen YH, VanderWeele TJ, Mc

  10. Reliability and Repeatability of Cone Density Measurements in Patients with Congenital Achromatopsia.

    Science.gov (United States)

    Abozaid, Mortada A; Langlo, Christopher S; Dubis, Adam M; Michaelides, Michel; Tarima, Sergey; Carroll, Joseph

    2016-01-01

    Adaptive optics scanning light ophthalmoscopy (AOSLO) allows non-invasive assessment of the cone photoreceptor mosaic. Confocal AOSLO imaging of patients with achromatopsia (ACHM) reveals an altered reflectivity of the remaining cone structure, making identification of the cells more challenging than in normal retinas. Recently, a "split-detector" AOSLO imaging method was shown to enable direct visualization of cone inner segments in patients with ACHM. Several studies have demonstrated gene replacement therapy effective in restoring cone function in animal models of ACHM and human trials have on the horizon, making the ability to reliably assess cone structure increasingly important. Here we sought to examine whether absolute estimates of cone density obtained from split-detector and confocal AOSLO images differed from one another and whether the inter- and intra-observer reliability is significantly different between these modes. These findings provide an important foundation for evaluating the role of these images as tools to assess the efficacy of future gene therapy trials.

  11. An L-band SAR for repeat pass deformation measurements on a UAV platform

    Science.gov (United States)

    Wheeler, Kevin; Hensley, Scott; Lou, Yunling

    2004-01-01

    We are proposing to develop a miniaturized polarimetric L-band synthetic aperture radar (SAR) for repeatpass differential interferometric measurements of deformation for rapidly deforming surfaces of geophysical interest such as volcanoes or earthquakes that is to be flown on a unmanned aerial vehicle (UAV or minimally piloted vehicle (MPV).

  12. Repeated measurements of P retention in ponies fed rations with various Ca:P ratios

    NARCIS (Netherlands)

    van Doorn, D A; Schaafstra, F J W C; Wouterse, H; Everts, H; Estepa, J C; Aguilera-Tejero, E; Beynen, A C

    2014-01-01

    This study addresses the question of whether feeding rations rich in P for a period of up to 42 d induces a positive P balance in adult ponies. Biochemical bone markers and parathyroid hormone (PTH; intact as well as whole PTH) were measured to obtain clues as to the effect of P loading on bone meta

  13. Neural measures reveal a fixed item limit in subitizing.

    Science.gov (United States)

    Ester, Edward F; Drew, Trafton; Klee, Daniel; Vogel, Edward K; Awh, Edward

    2012-05-23

    For centuries, it has been known that humans can rapidly and accurately enumerate small sets of items, a process referred to as subitizing. However, there is still active debate regarding the mechanisms that mediate this ability. For example, some have argued that subitizing reflects the operation of a fixed-capacity individuation mechanism that enables concurrent access to a small number of items. However, others have argued that subitizing reflects the operation of a continuous numerical estimation mechanism whose precision varies with numerosity in a manner consistent with Weber's law. Critically, quantitative models based on either of these predictions can provide a reasonable description of subitizing performance, making it difficult to discriminate between these alternatives solely on the basis of subjects' behavioral performance. Here, we attempted to discriminate between fixed-capacity and continuous estimation models of subitizing using neural measures. In two experiments, we recorded EEGs while subjects performed a demanding subitizing task and examined set-size-dependent changes in a neurophysiological marker of visual selection (the N2pc event-related potential component) evoked by an array of to-be-enumerated items. In both experiments, N2pc amplitudes increased monotonically within the subitizing range before reaching an asymptotic limit at approximately three items. Moreover, inter-participant differences in the location of this asymptote were strongly predictive of behavioral estimates of subitizing span derived from a fixed-capacity model. Thus, neural activity linked with subitizing ability shows evidence of an early and discrete limit in the number of items that can be concurrently apprehended, supporting a fixed-capacity model of this process.

  14. Repeated measures of urinary oxidative stress biomarkers during pregnancy and preterm birth.

    Science.gov (United States)

    Ferguson, Kelly K; McElrath, Thomas F; Chen, Yin-Hsiu; Loch-Caruso, Rita; Mukherjee, Bhramar; Meeker, John D

    2015-02-01

    The purpose of this study was to investigate oxidative stress as a mechanism of preterm birth in human subjects; we examined associations between urinary biomarkers of oxidative stress that were measured at multiple time points during pregnancy and preterm birth. This nested case-control study included 130 mothers who delivered preterm and 352 mothers who delivered term who were originally recruited as part of an ongoing prospective birth cohort at Brigham and Women's Hospital. Two biomarkers that included 8-hydroxydeoxyguanosine (8-OHdG) and 8-isoprostane were measured in urine samples that were collected at up to 4 time points (median 10, 18, 26, and 35 weeks) during gestation. Urinary concentrations of 8-isoprostane and 8-OHdG decreased and increased, respectively, as pregnancy progressed. Average levels of 8-isoprostane across pregnancy were associated with increased odds of spontaneous preterm birth (adjusted odds ratio, 6.25; 95% confidence interval, 2.86-13.7), and associations were strongest with levels measured later in pregnancy. Average levels of 8-OHdG were protective against overall preterm birth (adjusted odds ratio, 0.19; 95% confidence interval, 0.10-0.34), and there were no apparent differences in the protective effect in cases of spontaneous preterm birth compared with cases of placental origin. Odds ratios for overall preterm birth were more protective in association with urinary 8-OHdG concentrations that were measured early in pregnancy. Maternal oxidative stress may be an important contributor to preterm birth, regardless of subtype and timing of exposure during pregnancy. The 2 biomarkers that were measured in the present study had opposite associations with preterm birth; an improved understanding of what each represents may help to identify more precisely important mechanisms in the pathway to preterm birth. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Extended fluctuation theorems for repeated measurements and feedback within Hamiltonian framework

    Energy Technology Data Exchange (ETDEWEB)

    Lahiri, Sourabh, E-mail: sourabhlahiri@gmail.com [Laboratoire de Physico-Chimie Théorique, ESPCI, 10 rue Vauquelin, F-75231 Paris (France); Jayannavar, A.M. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India)

    2016-04-29

    We derive the extended fluctuation theorems in presence of multiple measurements and feedback, when the system is governed by Hamiltonian dynamics. We use only the forward phase space trajectories in the derivation. However, to obtain an expression for the efficacy parameter, we must necessarily use the notion of reverse trajectory. Our results show that the correction term appearing in the exponent of the extended fluctuation theorems is non-unique, whereas the physical meaning of the efficacy parameter is unique. - Highlights: • Extended Fluctuation Theorems under multiple measurements and feedback have been derived using Hamiltonian dynamics. • We prove the theorems without using the notion of reverse trajectory. • We show that the correction terms are not unique. • The efficacy parameter is shown to have a unique physical meaning.

  16. Composite tube and plate manufacturing repeatability as determined by precision measurements of thermal strain

    Science.gov (United States)

    Riddle, Lenn A.; Tucker, James R.; Bluth, A. Marcel

    2013-09-01

    Composite materials often carry the reputation of demonstrating high variability in critical material properties. The JWST telescope metering structure is fabricated of several thousand separate composite piece parts. The stringent dimensional stability requirements on the metering structure require the critical thermal strain response of every composite piece be verified either at the billet or piece part level. JWST is a unique composite space structure in that it has required the manufacturing of several hundred composite billets that cover many lots of prepreg and many years of fabrication. The flight billet thermal expansion acceptance criteria limits the coefficient of thermal expansion (CTE) to a tolerance ranging between +/-0.014 ppm/K to +/-0.04 ppm/K around a prescribed nominal when measured from 293 K down to 40 K. The different tolerance values represent different material forms including flat plates and different tube cross-section dimensions. A precision measurement facility was developed that could measure at the required accuracy and at a pace that supported the composite part fabrication rate. The test method and facility is discussed and the results of a statistical process analysis of the flight composite billets are surveyed.

  17. Are exhaled nitric oxide measurements using the portable NIOX MINO repeatable?

    Directory of Open Access Journals (Sweden)

    Raza Abid

    2010-04-01

    Full Text Available Abstract Background Exhaled nitric oxide is a non-invasive marker of airway inflammation and a portable analyser, the NIOX MINO (Aerocrine AB, Solna, Sweden, is now available. This study aimed to assess the reproducibility of the NIOX MINO measurements across age, sex and lung function for both absolute and categorical exhaled nitric oxide values in two distinct groups of children and teenagers. Methods Paired exhaled nitric oxide readings were obtained from 494 teenagers, aged 16-18 years, enrolled in an unselected birth cohort and 65 young people, aged 6-17 years, with asthma enrolled in an interventional asthma management study. Results The birth cohort participants showed a high degree of variability between first and second exhaled nitric oxide readings (mean intra-participant difference 1.37 ppb, 95% limits of agreement -7.61 to 10.34 ppb, although there was very close agreement when values were categorised as low, normal, intermediate or high (kappa = 0.907, p Conclusions The reproducibility of exhaled nitric oxide is poor for absolute values but acceptable when values are categorised as low, normal, intermediate or high in children and teenagers. One measurement is therefore sufficient when using categorical exhaled nitric oxide values to direct asthma management but a mean of at least two measurements is required for absolute values.

  18. Reliability of plasma lipopolysaccharide-binding protein (LBP) from repeated measures in healthy adults.

    Science.gov (United States)

    Citronberg, Jessica S; Wilkens, Lynne R; Lim, Unhee; Hullar, Meredith A J; White, Emily; Newcomb, Polly A; Le Marchand, Loïc; Lampe, Johanna W

    2016-09-01

    Plasma lipopolysaccharide-binding protein (LBP), a measure of internal exposure to bacterial lipopolysaccharide, has been associated with several chronic conditions and may be a marker of chronic inflammation; however, no studies have examined the reliability of this biomarker in a healthy population. We examined the temporal reliability of LBP measured in archived samples from participants in two studies. In Study one, 60 healthy participants had blood drawn at two time points: baseline and follow-up (either three, six, or nine months). In Study two, 24 individuals had blood drawn three to four times over a seven-month period. We measured LBP in archived plasma by ELISA. Test-retest reliability was estimated by calculating the intraclass correlation coefficient (ICC). Plasma LBP concentrations showed moderate reliability in Study one (ICC 0.60, 95 % CI 0.43-0.75) and Study two (ICC 0.46, 95 % CI 0.26-0.69). Restricting the follow-up period improved reliability. In Study one, the reliability of LBP over a three-month period was 0.68 (95 % CI: 0.41-0.87). In Study two, the ICC of samples taken ≤seven days apart was 0.61 (95 % CI 0.29-0.86). Plasma LBP concentrations demonstrated moderate test-retest reliability in healthy individuals with reliability improving over a shorter follow-up period.

  19. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  20. Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis.

    Science.gov (United States)

    Yang, Li; Wu, Gang; Poethig, R Scott

    2012-01-03

    Plant microRNAs (miRNAs) typically mediate RNA cleavage, but examples of miRNA-mediated translational repression have also been reported. However, the functional significance of this latter process is unknown. We identified SUO in a screen for Arabidopsis mutations that increase the accumulation of the miR156-regulated gene SPL3. suo has a loss-of-function phenotype characteristic of plants with reduced Argonaute (AGO)1 activity. An analysis of RNA and protein levels in suo mutants demonstrated that this phenotype is a consequence of a defect in miRNA-mediated translational repression; the effect of suo on vegetative phase change is attributable to a reduction in miR156/miR157 activity. SUO encodes a large protein with N-terminal bromo-adjacent homology (BAH) and transcription elongation factor S-II (TFS2N) domains and two C-terminal GW (glycine and tryptophan) repeats. SUO is present in the nucleus, and colocalizes with the processing-body component DCP1 in the cytoplasm. Our results reveal that SOU is a component of the miRNA pathway in Arabidopsis and demonstrate that translational repression is a functionally important aspect of miRNA activity in plants.

  1. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    Science.gov (United States)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  2. Global sensitivity analysis for repeated measures studies with informative drop-out: A semi-parametric approach.

    Science.gov (United States)

    Scharfstein, Daniel; McDermott, Aidan; Díaz, Iván; Carone, Marco; Lunardon, Nicola; Turkoz, Ibrahim

    2017-05-23

    In practice, both testable and untestable assumptions are generally required to draw inference about the mean outcome measured at the final scheduled visit in a repeated measures study with drop-out. Scharfstein et al. (2014) proposed a sensitivity analysis methodology to determine the robustness of conclusions within a class of untestable assumptions. In their approach, the untestable and testable assumptions were guaranteed to be compatible; their testable assumptions were based on a fully parametric model for the distribution of the observable data. While convenient, these parametric assumptions have proven especially restrictive in empirical research. Here, we relax their distributional assumptions and provide a more flexible, semi-parametric approach. We illustrate our proposal in the context of a randomized trial for evaluating a treatment of schizoaffective disorder. © 2017, The International Biometric Society.

  3. A fly model for the CCUG-repeat expansion of myotonic dystrophy type 2 reveals a novel interaction with MBNL1.

    Science.gov (United States)

    Yu, Zhenming; Goodman, Lindsey D; Shieh, Shin-Yi; Min, Michelle; Teng, Xiuyin; Zhu, Yongqing; Bonini, Nancy M

    2015-02-15

    Expanded non-coding RNA repeats of CUG and CCUG are the underlying genetic causes for myotonic dystrophy type 1 (DM1) and type 2 (DM2), respectively. A gain-of-function of these pathogenic repeat expansions is mediated at least in part by their abnormal interactions with RNA-binding proteins such as MBNL1 and resultant loss of activity of these proteins. To study pathogenic mechanisms of CCUG-repeat expansions in an animal model, we created a fly model of DM2 that expresses pure, uninterrupted CCUG-repeat expansions ranging from 16 to 720 repeats in length. We show that this fly model for DM2 recapitulates key features of human DM2 including RNA repeat-induced toxicity, ribonuclear foci formation and changes in alternative splicing. Interestingly, expression of two isoforms of MBNL1, MBNL135 and MBNL140, leads to cleavage and concurrent upregulation of the levels of the RNA-repeat transcripts, with MBNL140 having more significant effects than MBNL135. This property is shared with a fly CUG-repeat expansion model. Our results suggest a novel mechanism for interaction between the pathogenic RNA repeat expansions of myotonic dystrophy and MBNL1.

  4. Repeated serum creatinine measurement in primary care: Not all patients have chronic renal failure.

    Science.gov (United States)

    Gentille Lorente, Delicia; Gentille Lorente, Jorge; Salvadó Usach, Teresa

    2015-01-01

    To assess the prevalence of kidney failure in patients from a primary care centre in a basic healthcare district with laboratory availability allowing serum creatinine measurements. An observational descriptive cross-sectional study. A basic healthcare district serving 23,807 people aged ≥ 18 years. Prevalence of kidney failure among 17,240 patients having at least one laboratory measurement available was 8.5% (mean age 77.6 ± 12.05 years). In 33.2% of such patients an occult kidney failure was found (98.8% were women). Prevalence of chronic kidney failure among 10,011 patients having at least 2 laboratory measurements available (≥ 3 months apart) was 5.5% with mean age being 80.1 ± 10.0 years (most severely affected patients were those aged 75 to 84); 59.7% were men and 76.3% of cases were in stage 3. An occult kidney failure was found in 5.3% of patients with women being 86.2% of them (a glomerular filtration rate<60 ml/min was estimated for plasma creatinine levels of 0.9 mg/dl or higher). Comparison of present findings to those previously reported demonstrates the need for further studies on the prevalence of overall (chronic and acute) kidney failure in Spain in order to estimate the real scope of the disease. Primary care physicians play a critical role in disease detection, therapy, control and recording (in medical records). MDRD equation is useful and practical to estimate glomerular filtration rate. Copyright © 2015 The Authors. Published by Elsevier España, S.L.U. All rights reserved.

  5. Assessment of individual agreements with repeated measurements based on generalized confidence intervals.

    Science.gov (United States)

    Quiroz, Jorge; Burdick, Richard K

    2009-01-01

    Individual agreement between two measurement systems is determined using the total deviation index (TDI) or the coverage probability (CP) criteria as proposed by Lin (2000) and Lin et al. (2002). We used a variance component model as proposed by Choudhary (2007). Using the bootstrap approach, Choudhary (2007), and generalized confidence intervals, we construct bounds on TDI and CP. A simulation study was conducted to assess whether the bounds maintain the stated type I error probability of the test. We also present a computational example to demonstrate the statistical methods described in the paper.

  6. Prediction Accuracy in Multivariate Repeated-Measures Bayesian Forecasting Models with Examples Drawn from Research on Sleep and Circadian Rhythms

    Directory of Open Access Journals (Sweden)

    Clark Kogan

    2016-01-01

    Full Text Available In study designs with repeated measures for multiple subjects, population models capturing within- and between-subjects variances enable efficient individualized prediction of outcome measures (response variables by incorporating individuals response data through Bayesian forecasting. When measurement constraints preclude reasonable levels of prediction accuracy, additional (secondary response variables measured alongside the primary response may help to increase prediction accuracy. We investigate this for the case of substantial between-subjects correlation between primary and secondary response variables, assuming negligible within-subjects correlation. We show how to determine the accuracy of primary response predictions as a function of secondary response observations. Given measurement costs for primary and secondary variables, we determine the number of observations that produces, with minimal cost, a fixed average prediction accuracy for a model of subject means. We illustrate this with estimation of subject-specific sleep parameters using polysomnography and wrist actigraphy. We also consider prediction accuracy in an example time-dependent, linear model and derive equations for the optimal timing of measurements to achieve, on average, the best prediction accuracy. Finally, we examine an example involving a circadian rhythm model and show numerically that secondary variables can improve individualized predictions in this time-dependent nonlinear model as well.

  7. Prediction Accuracy in Multivariate Repeated-Measures Bayesian Forecasting Models with Examples Drawn from Research on Sleep and Circadian Rhythms.

    Science.gov (United States)

    Kogan, Clark; Kalachev, Leonid; Van Dongen, Hans P A

    2016-01-01

    In study designs with repeated measures for multiple subjects, population models capturing within- and between-subjects variances enable efficient individualized prediction of outcome measures (response variables) by incorporating individuals response data through Bayesian forecasting. When measurement constraints preclude reasonable levels of prediction accuracy, additional (secondary) response variables measured alongside the primary response may help to increase prediction accuracy. We investigate this for the case of substantial between-subjects correlation between primary and secondary response variables, assuming negligible within-subjects correlation. We show how to determine the accuracy of primary response predictions as a function of secondary response observations. Given measurement costs for primary and secondary variables, we determine the number of observations that produces, with minimal cost, a fixed average prediction accuracy for a model of subject means. We illustrate this with estimation of subject-specific sleep parameters using polysomnography and wrist actigraphy. We also consider prediction accuracy in an example time-dependent, linear model and derive equations for the optimal timing of measurements to achieve, on average, the best prediction accuracy. Finally, we examine an example involving a circadian rhythm model and show numerically that secondary variables can improve individualized predictions in this time-dependent nonlinear model as well.

  8. The clinical applicability of a daily summary of patients' self-reported postoperative pain-A repeated measure analysis.

    Science.gov (United States)

    Wikström, Lotta; Eriksson, Kerstin; Fridlund, Bengt; Nilsson, Mats; Årestedt, Kristofer; Broström, Anders

    2017-03-23

    (i) To determine whether a central tendency, median, based on patients' self-rated pain is a clinically applicable daily measure to show patients' postoperative pain on the first day after major surgery (ii) and to determine the number of self-ratings required for the calculation of this measure. Perioperative pain traits in medical records are difficult to overview. The clinical applicability of a daily documented summarising measure of patients' self-rated pain scores is little explored. A repeated measure design was carried out at three Swedish country hospitals. Associations between the measures were analysed with nonparametric statistical methods; systematic and individual group changes were analysed separately. Measure I: pain scores at rest and activity postoperative day 1; measure II: retrospective average pain from postoperative day 1. The sample consisted of 190 general surgery patients and 289 orthopaedic surgery patients with a mean age of 65; 56% were men. Forty-four percent had a pre-operative daily intake of analgesia, and 77% used postoperative opioids. A range of 4-9 pain scores seem to be eligible for the calculation of the daily measures of pain. Rank correlations for individual median scores, based on four ratings, vs. retrospective self-rated average pain, were moderate and strengthened with increased numbers of ratings. A systematic group change towards a higher level of reported retrospective pain was significant. The median values were clinically applicable daily measures. The risk of obtaining a higher value than was recalled by patients seemed to be low. Applicability increased with increased frequency of self-rated pain scores and with high-quality pain assessments. The documenting of daily median pain scores at rest and during activity could constitute the basis for obtaining patients' experiences by showing their pain severity trajectories. The measures could also be an important key to predicting postoperative health

  9. Understanding how adherence goals promote adherence behaviours: a repeated measure observational study with HIV seropositive patients

    Directory of Open Access Journals (Sweden)

    Jones Gareth

    2012-08-01

    Full Text Available Abstract Background The extent to which patients follow treatments as prescribed is pivotal to treatment success. An exceptionally high level (> 95% of HIV medication adherence is required to suppress viral replication and protect the immune system and a similarly high level (> 80% of adherence has also been suggested in order to benefit from prescribed exercise programmes. However, in clinical practice, adherence to both often falls below the desirable level. This project aims to investigate a wide range of psychological and personality factors that may lead to adherence/non-adherence to medical treatment and exercise programmes. Methods HIV positive patients who are referred to the physiotherapist-led 10-week exercise programme as part of the standard care are continuously recruited. Data on social cognitive variables (attitude, intention, subjective norms, self-efficacy, and outcome beliefs about the goal and specific behaviours, selected personality factors, perceived quality of life, physical activity, self-reported adherence and physical assessment are collected at baseline, at the end of the exercise programme and again 3 months later. The project incorporates objective measures of both exercise (attendance log and improvement in physical measures such as improved fitness level, weight loss, improved circumferential anthropometric measures and medication adherence (verified by non-invasive hair analysis. Discussion The novelty of this project comes from two key aspects, complemented with objective information on exercise and medication adherence. The project assesses beliefs about both the underlying goal such as following prescribed treatment; and about the specific behaviours such as undertaking the exercise or taking the medication, using both implicit and explicit assessments of patients’ beliefs and attitudes. We predict that i the way people think about the underlying goal of their treatments explains medication and exercise

  10. Repeated measures of inflammation and oxidative stress biomarkers in preeclamptic and normotensive pregnancies.

    Science.gov (United States)

    Ferguson, Kelly K; Meeker, John D; McElrath, Thomas F; Mukherjee, Bhramar; Cantonwine, David E

    2017-05-01

    Preeclampsia is a prevalent and enigmatic disease, in part characterized by poor remodeling of the spiral arteries. However, preeclampsia does not always clinically present when remodeling has failed to occur. Hypotheses surrounding the "second hit" that is necessary for the clinical presentation of the disease focus on maternal inflammation and oxidative stress. Yet, the studies to date that have investigated these factors have used cross-sectional study designs or small study populations. In the present study, we sought to explore longitudinal trajectories, beginning early in gestation, of a panel of inflammation and oxidative stress markers in women who went on to have preeclamptic or normotensive pregnancies. We examined 441 subjects from the ongoing LIFECODES prospective birth cohort, which included 50 mothers who experienced preeclampsia and 391 mothers with normotensive pregnancies. Participants provided urine and plasma samples at 4 time points during gestation (median, 10, 18, 26, and 35 weeks) that were analyzed for a panel of oxidative stress and inflammation markers. Oxidative stress biomarkers included 8-isoprostane and 8-hydroxydeoxyguanosine. Inflammation biomarkers included C-reactive protein, the cytokines interleukin-1β, -6, and -10, and tumor necrosis factor-α. We created Cox proportional hazard models to calculate hazard ratios based on time of preeclampsia diagnosis in association with biomarker concentrations at each of the 4 study visits. In adjusted models, hazard ratios of preeclampsia were significantly (Pinflammation biomarkers that were measured at visit 2 (median, 18 weeks; hazard ratios, 1.31-1.83, in association with an interquartile range increase in biomarker). Hazard ratios at this time point were the most elevated for C-reactive protein, for interleukin-1β, -6, and -10, and for the oxidative stress biomarker 8-isoprostane (hazard ratio, 1.68; 95% confidence interval, 1.14-2.48) compared to other time points. Hazard ratios for

  11. C-reactive Protein: Repeated Measurements will Improve Dialysis Patient Care.

    Science.gov (United States)

    Cobo, Gabriela; Qureshi, Abdul Rashid; Lindholm, Bengt; Stenvinkel, Peter

    2016-01-01

    Systemic inflammation is a common feature in the uremic phenotype and associates with poor outcomes. The awareness regarding the importance of inflammation assessment in chronic kidney disease (CKD) patients has risen in recent years, and despite the development of novel biomarkers, C-reactive protein (CRP) is still the most measured inflammatory parameter. Notwithstanding, the possible weak points of CRP determination, this biomarker has demonstrated being useful both for guidance in clinical practice and for risk estimation. In addition, regular determination of CRP among dialysis patients has been associated with better outcomes in different dialysis facilities. Because persistent inflammation may be a silent reflection of various pathophysiologic alterations in CKD, it is crucial that inflammatory markers are regularly monitored and therapeutic attempts be made to target this inflammation.

  12. Repeated heart rate measurement and cardiovascular outcomes in left ventricular systolic dysfunction.

    Science.gov (United States)

    Hamill, Victoria; Ford, Ian; Fox, Kim; Böhm, Michael; Borer, Jeffrey S; Ferrari, Roberto; Komajda, Michel; Steg, Philippe Gabriel; Tavazzi, Luigi; Tendera, Michal; Swedberg, Karl

    2015-10-01

    Elevated resting heart rate is associated with increased cardiovascular risk, particularly in patients with left ventricular systolic dysfunction. Heart rate is not monitored routinely in these patients. We hypothesized that routine monitoring of heart rate would increase its prognostic value in patients with left ventricular systolic dysfunction. We analyzed the relationship between heart rate measurements and a range of adverse cardiovascular outcomes, including hospitalization for worsening heart failure, in the pooled placebo-treated patients from the morBidity-mortality EvAlUaTion of the If inhibitor ivabradine in patients with coronary disease and left ventricULar dysfunction (BEAUTIFUL) trial and Systolic Heart failure treatment with the If inhibitor ivabradine (SHIFT) Trial, using standard and time-varying covariate Cox proportional hazards models. By adjusting for other prognostic factors, models were fitted for baseline heart rate alone or for time-updated heart rate (latest heart rate) alone or corrected for baseline heart rate or for immediate previous time-updated heart rate. Baseline heart rate was strongly associated with all outcomes apart from hospitalization for myocardial infarction. Time-updated heart rate increased the strengths of associations for all outcomes. Adjustment for baseline heart rate or immediate previous time-updated heart rate modestly reduced the prognostic importance of time-updated heart rate. For hospitalization for worsening heart failure, each 5 beats/min increase in baseline heart rate and time-updated heart rate was associated with a 15% (95% confidence interval, 12-18) and 22% (confidence interval, 19-40) increase in risk, respectively. Even after correction, the prognostic value of time-updated heart rate remained greater. In patients with left ventricular systolic dysfunction, time-updated heart rate is more strongly related with adverse cardiovascular outcomes than baseline heart rate. Heart rate should be measured to

  13. Psychological impact and recovery after involvement in a patient safety incident: a repeated measures analysis

    Science.gov (United States)

    Van Gerven, Eva; Bruyneel, Luk; Panella, Massimiliano; Euwema, Martin; Sermeus, Walter; Vanhaecht, Kris

    2016-01-01

    Objective To examine individual, situational and organisational aspects that influence psychological impact and recovery of a patient safety incident on physicians, nurses and midwives. Design Cross-sectional, retrospective surveys of physicians, midwives and nurses. Setting 33 Belgian hospitals. Participants 913 clinicians (186 physicians, 682 nurses, 45 midwives) involved in a patient safety incident. Main outcome measures The Impact of Event Scale was used to retrospectively measure psychological impact of the safety incident at the time of the event and compare it with psychological impact at the time of the survey. Results Individual, situational as well as organisational aspects influenced psychological impact and recovery of a patient safety incident. Psychological impact is higher when the degree of harm for the patient is more severe, when healthcare professionals feel responsible for the incident and among female healthcare professionals. Impact of degree of harm differed across clinicians. Psychological impact is lower among more optimistic professionals. Overall, impact decreased significantly over time. This effect was more pronounced for women and for those who feel responsible for the incident. The longer ago the incident took place, the stronger impact had decreased. Also, higher psychological impact is related with the use of a more active coping and planning coping strategy, and is unrelated to support seeking coping strategies. Rendered support and a support culture reduce psychological impact, whereas a blame culture increases psychological impact. No associations were found with job experience and resilience of the health professional, the presence of a second victim support team or guideline and working in a learning culture. Conclusions Healthcare organisations should anticipate on providing their staff appropriate and timely support structures that are tailored to the healthcare professional involved in the incident and to the specific

  14. Repeat-until-success quantum repeaters

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    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  15. A novel AX+/BX- paradigm to assess fear learning and safety-signal processing with repeated-measure designs.

    Science.gov (United States)

    Kazama, Andy M; Schauder, Kimberly B; McKinnon, Michael; Bachevalier, Jocelyne; Davis, Michael

    2013-04-15

    One of the core symptoms of anxiety disorders, such as post-traumatic stress disorder, is the failure to overcome feelings of danger despite being in a safe environment. This deficit likely stems from an inability to fully process safety signals, which are cues in the environment that enable healthy individuals to over-ride fear in aversive situations. Studies examining safety signal learning in rodents, humans, and non-human primates currently rely on between-groups designs. Because repeated-measure designs reduce the number of subjects required, and facilitate a broader range of safety signal studies, the current project sought to develop a repeated-measures safety-signal learning paradigm in non-human primates. Twelve healthy rhesus macaques of both sexes received three rounds of auditory fear-potentiated startle training and testing using an AX+/BX- design with all visual cues. Cue AX was paired with an aversive blast of air, whereas the same X cue in compound with another B cue (BX) signaled the absence of an air blast. Hence, cue B served as a safety signal. Once animals consistently discriminated between the aversive (AX+) and safe (BX-) cues, measured by greater startle amplitude in the presence of AX vs. BX, they were tested for conditioned inhibition by eliciting startle in the presence of a novel ambiguous combined cue (AB). Similar to previous AX+/BX- studies, healthy animals rapidly learned to discriminate between the AX+ and BX- cues as well as demonstrate conditioned inhibition in the presence of the combined AB cue (i.e. lower startle amplitude in the presence of AB vs. AX). Additionally, animals performed consistently across three rounds of testing using three new cues each time. The results validate this novel method that will serve as a useful tool for better understanding the mechanisms for the regulation of fear and anxiety. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Hepatic 18F-FDG Uptake Measurements on PET/MR: Impact of Volume of Interest Location on Repeatability

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    Liran Domachevsky

    2017-01-01

    Full Text Available Background. To investigate same day 18F-FDG (Fluorodeoxyglucose PET (Positron Emission Tomography/MR (Magnetic Resonance test-retest repeatability of Standardized Uptake Value measurements normalized for body weight (SUV and lean body mass (SUL in different locations in the liver. Methods. This prospective study was IRB approved with written informed consent obtained. 35 patients (20 women and 15 men, 61±11.2 years that performed a whole-body 18F-FDG PET/MR followed by liver-dedicated contrast-enhanced 18F-FDG PET/MR were included. SUV/L max, mean, and peak were measured inferior to, superior to, and at the right portal vein and in the left lobe of the liver. The coefficient of variation (CV and intraclass correlation coefficient (ICC were calculated and Bland-Altman plots were obtained. Results. The variability for SUV/L’s measurements was lowest inferior to the portal vein (<9.2% followed by measurements performed at the level of the portal vein (<14.6%. Conclusion. The area inferior to the portal vein is the most reliable location for hepatic 18F-FDG uptake measurements on PET/MR.

  17. Magnetic Resonance Spectroscopy in Patients with Insomnia: A Repeated Measurement Study.

    Science.gov (United States)

    Spiegelhalder, Kai; Regen, Wolfram; Nissen, Christoph; Feige, Bernd; Baglioni, Chiara; Riemann, Dieter; Hennig, Jürgen; Lange, Thomas

    2016-01-01

    Chronic insomnia is one of the most prevalent central nervous system disorders. It is characterized by increased arousal levels, however, the neurobiological causes and correlates of hyperarousal in insomnia remain to be further determined. In the current study, magnetic resonance spectroscopy was used in the morning and evening in a well-characterized sample of 20 primary insomnia patients (12 females; 8 males; 42.7 ± 13.4 years) and 20 healthy good sleepers (12 females; 8 males; 44.1 ± 10.6 years). The most important inhibitory and excitatory neurotransmitters of the central nervous system, γ-aminobutyric acid (GABA) and glutamate/glutamine (Glx), were assessed in the anterior cingulate cortex (ACC) and dorsolateral prefrontal cortex (DLPFC). The primary hypothesis, a diurnal effect on GABA levels in patients with insomnia, could not be confirmed. Moreover, the current results did not support previous findings of altered GABA levels in individuals with insomnia. Exploratory analyses, however, suggested that GABA levels in the ACC may be positively associated with habitual sleep duration, and, thus, reduced GABA levels may be a trait marker of objective sleep disturbances. Moreover, there was a significant GROUP x MEASUREMENT TIME interaction effect on Glx in the DLPFC with increasing Glx levels across the day in the patients but not in the control group. Therefore, Glx levels may reflect hyperarousal at bedtime in those with insomnia. Future confirmatory studies should include larger sample sizes to investigate brain metabolites in different subgroups of insomnia.

  18. Using high-dynamic-range digital repeat photography to measure plant phenology in a subarctic mire.

    Science.gov (United States)

    Garnello, A.; Dye, D. G.; Bogle, R.; Vogel, J.; Saleska, S. R.; Crill, P. M.

    2015-12-01

    A novel Visual Imaging System (VIS) was designed and deployed in a subarctic mire (68° 20' N, 19° 03'E) aimed at cataloging plant biological changes (phenology) and analyzing seasonal color shifts in relation to micrometeorological data along the summer growing season: June-November, 2015. The VIS is designed as a tower-based, solar-powered, automated phenology camera (Phenocam) that collects red, green, blue (RGB) and near-infrared (NIR) landscape images in High Dynamic Range (HDR) with fully programmable temporal resolution. HDR composite images are made through combining a series of rapid-capture photos with incremental increases of exposure times and a fixed focus, minimizing the spatial and visual data lost from shadows or from the over-saturation of light. This visual record of ecosystem phenology stages (Phenophases) is being used to (1) investigate vegetation-dependent spectral indices; (2) establish a cross-year comparison record of Phenophase seasonality; (3) investigate meteorological-dependent vegetation Phenophases; (4) provide ground-truthing measurements that enhance broader spatial-scale remote sensing analyses of subarctic wetlands.

  19. A Finite Mixture of Nonlinear Random Coefficient Models for Continuous Repeated Measures Data.

    Science.gov (United States)

    Kohli, Nidhi; Harring, Jeffrey R; Zopluoglu, Cengiz

    2016-09-01

    Nonlinear random coefficient models (NRCMs) for continuous longitudinal data are often used for examining individual behaviors that display nonlinear patterns of development (or growth) over time in measured variables. As an extension of this model, this study considers the finite mixture of NRCMs that combine features of NRCMs with the idea of finite mixture (or latent class) models. The efficacy of this model is that it allows the integration of intrinsically nonlinear functions where the data come from a mixture of two or more unobserved subpopulations, thus allowing the simultaneous investigation of intra-individual (within-person) variability, inter-individual (between-person) variability, and subpopulation heterogeneity. Effectiveness of this model to work under real data analytic conditions was examined by executing a Monte Carlo simulation study. The simulation study was carried out using an R routine specifically developed for the purpose of this study. The R routine used maximum likelihood with the expectation-maximization algorithm. The design of the study mimicked the output obtained from running a two-class mixture model on task completion data.

  20. Breath acidification in adolescent runners exposed to atmospheric pollution: A prospective, repeated measures observational study

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    Van Sickle David

    2008-03-01

    Full Text Available Abstract Background Vigorous outdoors exercise during an episode of air pollution might cause airway inflammation. The purpose of this study was to examine the effects of vigorous outdoor exercise during peak smog season on breath pH, a biomarker of airway inflammation, in adolescent athletes. Methods We measured breath pH both pre- and post-exercise on ten days during peak smog season in 16 high school athletes engaged in daily long-distance running in a downwind suburb of Atlanta. The association of post-exercise breath pH with ambient ozone and particulate matter concentrations was tested with linear regression. Results We collected 144 pre-exercise and 146 post-exercise breath samples from 16 runners (mean age 14.9 years, 56% male. Median pre-exercise breath pH was 7.58 (interquartile range: 6.90 to 7.86 and did not change significantly after exercise. We observed no significant association between ambient ozone or particulate matter and post-exercise breath pH. However both pre- and post-exercise breath pH were strikingly low in these athletes when compared to a control sample of 14 relatively sedentary healthy adults and to published values of breath pH in healthy subjects. Conclusion Although we did not observe an acute effect of air pollution exposure during exercise on breath pH, breath pH was surprisingly low in this sample of otherwise healthy long-distance runners. We speculate that repetitive vigorous exercise may induce airway acidification.

  1. Repeatability of corticospinal and spinal measures during lengthening and shortening contractions in the human tibialis anterior muscle.

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    Jamie Tallent

    Full Text Available UNLABELLED: Elements of the human central nervous system (CNS constantly oscillate. In addition, there are also methodological factors and changes in muscle mechanics during dynamic muscle contractions that threaten the stability and consistency of transcranial magnetic stimulation (TMS and perpherial nerve stimulation (PNS measures. PURPOSE: To determine the repeatability of TMS and PNS measures during lengthening and shortening muscle actions in the intact human tibialis anterior. METHODS: On three consecutive days, 20 males performed lengthening and shortening muscle actions at 15, 25, 50 and 80% of maximal voluntary contraction (MVC. The amplitude of the Motor Evoked Potentials (MEPs produced by TMS was measured at rest and during muscle contraction at 90° of ankle joint position. MEPs were normalised to Mmax determined with PNS. The corticospinal silent period was recorded at 80% MVC. Hoffman reflex (H-reflex at 10% isometric and 25% shortening and lengthening MVCs, and V-waves during MVCs were also evoked on each of the three days. RESULTS: With the exception of MEPs evoked at 80% shortening MVC, all TMS-derived measures showed good reliability (ICC = 0.81-0.94 from days 2 to 3. Confidence intervals (CI, 95% were lower between days 2 and 3 when compared to days 1 and 2. MEPs significantly increased at rest from days 1 to 2 (P = 0.016 and days 1 to 3 (P = 0.046. The H-reflex during dynamic muscle contraction was reliable across the three days (ICC = 0.76-0.84. V-waves (shortening, ICC = 0.77, lengthening ICC = 0.54 and the H-reflex at 10% isometric MVC (ICC = 0.66 was generally less reliable over the three days. CONCLUSION: Although it is well known that measures of the intact human CNS exhibit moment-to-moment fluctuations, careful experimental arrangements make it possible to obtain consistent and repeatable measurements of corticospinal and spinal excitability in the actively lengthening and shortening human

  2. Are There Linguistic Markers of Suicidal Writing That Can Predict the Course of Treatment? A Repeated Measures Longitudinal Analysis.

    Science.gov (United States)

    Brancu, Mira; Jobes, David; Wagner, Barry M; Greene, Jeffrey A; Fratto, Timothy A

    2016-07-02

    The purpose of this pilot study was to predict resolution of suicidal ideation and risk over the course of therapy among suicidal outpatients (N = 144) using a novel method for analyzing Self- verses Relationally oriented qualitative written responses to the Suicide Status Form (SSF). A content analysis software program was used to extract word counts and a repeated measures longitudinal design was implemented to assess improvement over time. Patients with primarily Relationally focused word counts were more likely to have a quicker suicide risk resolution than those with more Self-focused word counts (6-7 sessions versus 17-18 sessions). Implications of these data are discussed, including the potential for enhancing treatment outcomes using this method with individuals entering treatment.

  3. A Bayesian model for repeated measures zero-inflated count data with application to outpatient psychiatric service use

    Science.gov (United States)

    Neelon, Brian H.; O’Malley, A. James; Normand, Sharon-Lise T.

    2009-01-01

    In applications involving count data, it is common to encounter an excess number of zeros. In the study of outpatient service utilization, for example, the number of utilization days will take on integer values, with many subjects having no utilization (zero values). Mixed-distribution models, such as the zero-inflated Poisson (ZIP) and zero-inflated negative binomial (ZINB), are often used to fit such data. A more general class of mixture models, called hurdle models, can be used to model zero-deflation as well as zero-inflation. Several authors have proposed frequentist approaches to fitting zero-inflated models for repeated measures. We describe a practical Bayesian approach which incorporates prior information, has optimal small-sample properties, and allows for tractable inference. The approach can be easily implemented using standard Bayesian software. A study of psychiatric outpatient service use illustrates the methods. PMID:21339863

  4. Detection of quasi-periodic processes in repeated measurements: New approach for the fitting and clusterization of different data

    Science.gov (United States)

    Nigmatullin, R.; Rakhmatullin, R.

    2014-12-01

    Many experimentalists were accustomed to think that any independent measurement forms a non-correlated measurement that depends weakly from others. We are trying to reconsider this conventional point of view and prove that similar measurements form a strongly-correlated sequence of random functions with memory. In other words, successive measurements "remember" each other at least their nearest neighbors. This observation and justification on real data help to fit the wide set of data based on the Prony's function. The Prony's decomposition follows from the quasi-periodic (QP) properties of the measured functions and includes the Fourier transform as a partial case. New type of decomposition helps to obtain a specific amplitude-frequency response (AFR) of the measured (random) functions analyzed and each random function contains less number of the fitting parameters in comparison with its number of initial data points. Actually, the calculated AFR can be considered as the generalized Prony's spectrum (GPS), which will be extremely useful in cases where the simple model pretending on description of the measured data is absent but vital necessity of their quantitative description is remained. These possibilities open a new way for clusterization of the initial data and new information that is contained in these data gives a chance for their detailed analysis. The electron paramagnetic resonance (EPR) measurements realized for empty resonator (pure noise data) and resonator containing a sample (CeO2 in our case) confirmed the existence of the QP processes in reality. But we think that the detection of the QP processes is a common feature of many repeated measurements and this new property of successive measurements can attract an attention of many experimentalists. To formulate some general conditions that help to identify and then detect the presence of some QP process in the repeated experimental measurements. To find a functional equation and its solution that

  5. Association between proton magnetic resonance spectroscopy measurements and CAG repeat number in patients with spinocerebellar ataxias 2, 3, or 6.

    Directory of Open Access Journals (Sweden)

    Po-Shan Wang

    Full Text Available The aim of this study was to correlate magnetic resonance spectroscopy (MRS measurements, including that for the N-acetyl aspartate (NAA/creatine (Cr ratio in the vermis (denoted V-NAA, right cerebellar hemisphere (R-NAA, and left (L-NAA cerebellar hemisphere, with the clinical scale for the assessment and rating of ataxia (SARA score for patients with spinocerebellar ataxia (SCA types 2, 3, and 6. A total of 24 patients with SCA2, 48 with SCA3, and 16 with SCA6 were recruited; 12 patients with SCA2, 43 with SCA3, and 8 with SCA6 underwent detailed magnetic resonance neuroimaging. Forty-four healthy, age-matched individuals without history of neurologic disease served as control subjects. V-NAA and patient age were used to calculate the predicted age at which a patient with SCA2 or SCA3 would reach an onset V-NAA value. Results showed the following: the NAA/Cr ratio decreased with increasing age in patients with SCA but not in control subjects; the SARA score increased progressively with age and duration of illness; V-NAA showed a better correlation with SARA score than R-NAA in patients with SCA2 or SCA3; the ratio of age to V-NAA correlated well with CAG repeat number; the retrospectively predicted age of onset for SCA2 and SCA3 was consistent with patient-reported age of onset; R-NAA showed a better correlation with SARA score than V-NAA in patients with SCA6; V-NAA and R-NAA correlated with clinical severity (SARA score in patients with SCA. The correlation between CAG repeat number and age could be expressed as a simple linear function, which might explain previous observations claiming that the greater the CAG repeat number, the earlier the onset of illness and the faster the disease progression. These findings support the use of MRS values to predict age of disease onset and to retrospectively evaluate the actual age of disease onset in SCA.

  6. Association between proton magnetic resonance spectroscopy measurements and CAG repeat number in patients with spinocerebellar ataxias 2, 3, or 6.

    Science.gov (United States)

    Wang, Po-Shan; Chen, Hung-Chieh; Wu, Hsiu-Mei; Lirng, Jiing-Feng; Wu, Yu-Te; Soong, Bing-Wen

    2012-01-01

    The aim of this study was to correlate magnetic resonance spectroscopy (MRS) measurements, including that for the N-acetyl aspartate (NAA)/creatine (Cr) ratio in the vermis (denoted V-NAA), right cerebellar hemisphere (R-NAA), and left (L-NAA) cerebellar hemisphere, with the clinical scale for the assessment and rating of ataxia (SARA) score for patients with spinocerebellar ataxia (SCA) types 2, 3, and 6. A total of 24 patients with SCA2, 48 with SCA3, and 16 with SCA6 were recruited; 12 patients with SCA2, 43 with SCA3, and 8 with SCA6 underwent detailed magnetic resonance neuroimaging. Forty-four healthy, age-matched individuals without history of neurologic disease served as control subjects. V-NAA and patient age were used to calculate the predicted age at which a patient with SCA2 or SCA3 would reach an onset V-NAA value. Results showed the following: the NAA/Cr ratio decreased with increasing age in patients with SCA but not in control subjects; the SARA score increased progressively with age and duration of illness; V-NAA showed a better correlation with SARA score than R-NAA in patients with SCA2 or SCA3; the ratio of age to V-NAA correlated well with CAG repeat number; the retrospectively predicted age of onset for SCA2 and SCA3 was consistent with patient-reported age of onset; R-NAA showed a better correlation with SARA score than V-NAA in patients with SCA6; V-NAA and R-NAA correlated with clinical severity (SARA score) in patients with SCA. The correlation between CAG repeat number and age could be expressed as a simple linear function, which might explain previous observations claiming that the greater the CAG repeat number, the earlier the onset of illness and the faster the disease progression. These findings support the use of MRS values to predict age of disease onset and to retrospectively evaluate the actual age of disease onset in SCA.

  7. Diffusion-weighted magnetic resonance imaging for assessment of lung lesions: repeatability of the apparent diffusion coefficient measurement

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    Bernardin, L.; Douglas, N.H.M.; Collins, D.J.; Giles, S.L.; O' Flynn, E.A.M.; Orton, M.; DeSouza, N.M. [Institute of Cancer Research and Royal Marsden NHS Foundation Trust, CRUK and EPSRC Cancer Imaging Centre, Surrey (United Kingdom)

    2014-02-15

    To establish repeatability of apparent diffusion coefficients (ADCs) acquired from free-breathing diffusion-weighted magnetic resonance imaging (DW-MRI) in malignant lung lesions and investigate effects of lesion size, location and respiratory motion. Thirty-six malignant lung lesions (eight patients) were examined twice (1- to 5-h interval) using T1-weighted, T2-weighted and axial single-shot echo-planar DW-MRI (b = 100, 500, 800 s/mm{sup 2}) during free-breathing. Regions of interest around target lesions on computed b = 800 s/mm{sup 2} images by two independent observers yielded ADC values from maps (pixel-by-pixel fitting using all b values and a mono-exponential decay model). Intra- and inter-observer repeatability was assessed per lesion, per patient and by lesion size (> or <2 cm) or location. ADCs were similar between observers (mean ± SD, 1.15 ± 0.28 x 10{sup -3} mm{sup 2}/s, observer 1; 1.15 ± 0.29 x 10{sup -3} mm{sup 2}/s, observer 2). Intra-observer coefficients of variation of the mean [median] ADC per lesion and per patient were 11 % [11.4 %], 5.7 % [5.7 %] for observer 1 and 9.2 % [9.5 %], 3.9 % [4.7 %] for observer 2 respectively; inter-observer values were 8.9 % [9.3 %] (per lesion) and 3.0 % [3.7 %] (per patient). Inter-observer coefficient of variation (CoV) was greater for lesions <2 cm (n = 20) compared with >2 cm (n = 16) (10.8 % vs 6.5 % ADC{sub mean}, 11.3 % vs 6.7 % ADC{sub median}) and for mid (n = 14) vs apical (n = 9) or lower zone (n = 13) lesions (13.9 %, 2.7 %, 3.8 % respectively ADC{sub mean}; 14.2 %, 2.8 %, 4.7 % respectively ADC{sub median}). Free-breathing DW-MRI of whole lung achieves good intra- and inter-observer repeatability of ADC measurements in malignant lung tumours. (orig.)

  8. Accuracy and repeatability of quantitative fluoroscopy for the measurement of sagittal plane translation and finite centre of rotation in the lumbar spine.

    Science.gov (United States)

    Breen, Alexander; Breen, Alan

    2016-07-01

    Quantitative fluoroscopy (QF) was developed to measure intervertebral mechanics in vivo and has been found to have high repeatability and accuracy for the measurement of intervertebral rotations. However, sagittal plane translation and finite centre of rotation (FCR) are potential measures of stability but have not yet been fully validated for current QF. This study investigated the repeatability and accuracy of QF for measuring these variables. Repeatability was assessed from L2-S1 in 20 human volunteers. Accuracy was investigated using 10 consecutive measurements from each of two pairs of linked and instrumented dry human vertebrae as reference; one which tilted without translation and one which translated without tilt. The results found intra- and inter-observer repeatability for translation to be 1.1mm or less (SEM) with fair to substantial reliability (ICC 0.533-0.998). Intra-observer repeatability of FCR location for inter-vertebral rotations of 5° and above ranged from 1.5mm to 1.8mm (SEM) with moderate to substantial reliability (ICC 0.626-0.988). Inter-observer repeatability for FCR ranged from 1.2mm to 5.7mm, also with moderate to substantial reliability (ICC 0.621-0.878). Reliability was substantial (ICC>0.81) for 10/16 measures for translation and 5/8 for FCR location. Accuracy for translation was 0.1mm (fixed centre) and 2.2mm (moveable centre), with an FCR error of 0.3mm(x) and 0.4mm(y) (fixed centre). This technology was found to have a high level of accuracy and with a few exceptions, moderate to substantial repeatability for the measurement of translation and FCR from fluoroscopic motion sequences.

  9. The use of portable NIRS to measure muscle oxygenation and haemodynamics during a repeated sprint running test.

    Science.gov (United States)

    Jones, Ben; Hesford, Catherine M; Cooper, Chris E

    2013-01-01

    Portable near-infrared spectroscopy (NIRS) devices were originally developed for use in exercise and sports science by Britton Chance in the 1990s (the RunMan and microRunman series). However, only recently with the development of more robust, and wireless systems, has the routine use in elite sport become possible. As with the medical use of NIRS, finding applications of the technology that are relevant to practitioners is the key issue. One option is to use NIRS to track exercise training-induced adaptations in muscle. Portable NIRS devices enable monitoring during the normal 'field' routine uses to assess fitness, such as repeat sprint shuttle tests. Knowledge about the acute physiological responses to these specific tests has practical applications within team sport training prescription, where development of both central and peripheral determinants of high-intensity intermittent exercise needs to be considered. The purpose of this study was to observe NIRS-detected parameters during a repeat sprint test. We used the PortaMon, a two wavelength spatially resolved NIR spectrometer manufactured by Artinis Inc., to assess NIR changes in the gastrocnemius muscle of both the left and right leg during high-intensity running. Six university standard rugby players were assessed (age 20 ± 1.5 years; height 183 ± 1.0 cm; weight 89.4 ± 5.8 kg; body fat 12.2 ± 3.0 %); the subjects completed nine repeated shuttle runs, which incorporated forward, backward and change of direction movements. Individual sprint time, total time to complete test, blood lactate response (BL), heart rate values (HR) and haemoglobin variables (ΔHHb, ΔtHb, ΔHbO2 and ΔTSI%) were measured. Total time to complete the test was 260 ± 20 s, final blood lactate was 14.3 ± 2.8 mM, and maximal HR 182 ± 5 bpm. NIRS variables displayed no differences between right and left legs. During the test, the group-averaged data showed a clear decrease in HbO2 (max. decrease 11.41 ± 4.95 μM), increase in HHb

  10. How integrated are behavioral and endocrine stress response traits? A repeated measures approach to testing the stress-coping style model.

    Science.gov (United States)

    Boulton, Kay; Couto, Elsa; Grimmer, Andrew J; Earley, Ryan L; Canario, Adelino V M; Wilson, Alastair J; Walling, Craig A

    2015-02-01

    It is widely expected that physiological and behavioral stress responses will be integrated within divergent stress-coping styles (SCS) and that these may represent opposite ends of a continuously varying reactive-proactive axis. If such a model is valid, then stress response traits should be repeatable and physiological and behavioral responses should also change in an integrated manner along a major axis of among-individual variation. While there is some evidence of association between endocrine and behavioral stress response traits, few studies incorporate repeated observations of both. To test this model, we use a multivariate, repeated measures approach in a captive-bred population of Xiphophorus birchmanni. We quantify among-individual variation in behavioral stress response to an open field trial (OFT) with simulated predator attack (SPA) and measure waterborne steroid hormone levels (cortisol, 11-ketotestosterone) before and after exposure. Under the mild stress stimulus (OFT), (multivariate) behavioral variation among individuals was consistent with a strong axis of personality (shy-bold) or coping style (reactive-proactive) variation. However, behavioral responses to a moderate stressor (SPA) were less repeatable, and robust statistical support for repeatable endocrine state over the full sampling period was limited to 11-ketotestosterone. Although post hoc analysis suggested cortisol expression was repeatable over short time periods, qualitative relationships between behavior and glucocorticoid levels were counter to our a priori expectations. Thus, while our results clearly show among-individual differences in behavioral and endocrine traits associated with stress response, the correlation structure between these is not consistent with a simple proactive-reactive axis of integrated stress-coping style. Additionally, the low repeatability of cortisol suggests caution is warranted if single observations (or indeed repeat measures over short sampling

  11. Repeated-sprint cycling does not induce respiratory muscle fatigue in active adults: measurements from the powerbreathe® inspiratory muscle trainer.

    Science.gov (United States)

    Minahan, Clare; Sheehan, Beth; Doutreband, Rachel; Kirkwood, Tom; Reeves, Daniel; Cross, Troy

    2015-03-01

    This study examined respiratory muscle strength using the POWERbreathe® inspiratory muscle trainer (i.e., 'S-Index') before and after repeated-sprint cycling for comparison with maximal inspiratory pressure (MIP) values obtained during a Mueller maneuver. The S-Index was measured during six trials across two sessions using the POWERbreathe® and MIP was measured during three trials in a single session using a custom-made manometer in seven recreationally active adults. Global respiratory muscle strength was measured using both devices before and after the performance of sixteen, 6-s sprints on a cycle ergometer. Intraclass correlation coefficients for the POWERbreathe® S-index indicated excellent (p Repeated-sprint cycling had no effect on respiratory muscle strength as measured by the POWERbreathe® (p > 0.99) and during the Mueller maneuver (p > 0.99). The POWERbreathe® S-Index is a moderately reliable, but not equivalent, measure of MIP determined during a Mueller maneuver. Furthermore, repeated-sprint cycling does not induce globalized respiratory muscle fatigue in recreationally-active adults. Key pointsThe S-Index as measured by the POWERbreathe® is a reliable measure of respiratory muscle strengthThe S-Index does not accurately reflect maximal inspiratory pressure obtained from a Mueller maneuverRepeated-sprint cycling does not induce respiratory muscle fatigue as measured by the POWERbreathe® and the Manometer.

  12. Ambient particulate air pollution and circulating antioxidant enzymes: A repeated-measure study in healthy adults in Beijing, China.

    Science.gov (United States)

    Wu, Shaowei; Wang, Bin; Yang, Di; Wei, Hongying; Li, Hongyu; Pan, Lu; Huang, Jing; Wang, Xin; Qin, Yu; Zheng, Chanjuan; Shima, Masayuki; Deng, Furong; Guo, Xinbiao

    2016-01-01

    The association of systemic antioxidant activity with ambient air pollution has been unclear. A panel of 40 healthy college students underwent repeated blood collection for 12 occasions under three exposure scenarios before and after relocating from a suburban area to an urban area in Beijing, China in 2010-2011. We measured various air pollutants including fine particles (PM2.5) and determined circulating levels of antioxidant enzymes extracellular superoxide dismutase (EC-SOD) and glutathione peroxidase 1 (GPX1) in the laboratory. An interquartile range increase of 63.4 μg/m(3) at 3-d PM2.5 moving average was associated with a 6.3% (95% CI: 0.6, 12.4) increase in EC-SOD and a 5.5% (95% CI: 1.3, 9.8) increase in GPX1. Several PM2.5 chemical constituents, including negative ions (nitrate and chloride) and metals (e.g., iron and strontium), were consistently associated with increases in EC-SOD and GPX1. Our results support activation of circulating antioxidant enzymes following exposure to particulate air pollution. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. A method to construct a points system to predict cardiovascular disease considering repeated measures of risk factors

    Science.gov (United States)

    Carbayo-Herencia, Julio Antonio; Vigo, Maria Isabel; Gil-Guillén, Vicente Francisco

    2016-01-01

    Current predictive models for cardiovascular disease based on points systems use the baseline situation of the risk factors as independent variables. These models do not take into account the variability of the risk factors over time. Predictive models for other types of disease also exist that do consider the temporal variability of a single biological marker in addition to the baseline variables. However, due to their complexity these other models are not used in daily clinical practice. Bearing in mind the clinical relevance of these issues and that cardiovascular diseases are the leading cause of death worldwide we show the properties and viability of a new methodological alternative for constructing cardiovascular risk scores to make predictions of cardiovascular disease with repeated measures of the risk factors and retaining the simplicity of the points systems so often used in clinical practice (construction, statistical validation by simulation and explanation of potential utilization). We have also applied the system clinically upon a set of simulated data solely to help readers understand the procedure constructed. PMID:26893963

  14. Are diagnostic criteria for acute malnutrition affected by hydration status in hospitalized children? A repeated measures study

    Directory of Open Access Journals (Sweden)

    Fegan Gregory

    2011-09-01

    Full Text Available Abstract Introduction Dehydration and malnutrition commonly occur together among ill children in developing countries. Dehydration (change in total body water is known to alter weight. Although muscle tissue has high water content, it is not known whether mid-upper arm circumference (MUAC may be altered by changes in tissue hydration. We aimed to determine whether rehydration alters MUAC, MUAC Z score (MUACz, weight-for-length Z-score (WFLz and classification of nutritional status among hospitalised Kenyan children admitted with signs of dehydration. Study procedure We enrolled children aged from 3 months to 5 years admitted to a rural Kenyan district hospital with clinical signs compatible with dehydration, and without kwashiorkor. Anthropometric measurements were taken at admission and repeated after 48 hours of treatment, which included rehydration by WHO protocols. Changes in weight observed during this period were considered to be due to changes in hydration status. Results Among 325 children (median age 11 months the median weight gain (rehydration after 48 hours was 0.21 kg, (an increase of 2.9% of admission body weight. Each 1% change in weight was associated with a 0.40 mm (95% CI: 0.30 to 0.44 mm, p Conclusion MUAC is less affected by dehydration than WFLz and is therefore more suitable for nutritional assessment of ill children. However, both WFLz and MUAC misclassify SAM among dehydrated children. Nutritional status should be re-evaluated following rehydration, and management adjusted accordingly.

  15. Selecting a linear mixed model for longitudinal data: repeated measures analysis of variance, covariance pattern model, and growth curve approaches.

    Science.gov (United States)

    Liu, Siwei; Rovine, Michael J; Molenaar, Peter C M

    2012-03-01

    With increasing popularity, growth curve modeling is more and more often considered as the 1st choice for analyzing longitudinal data. Although the growth curve approach is often a good choice, other modeling strategies may more directly answer questions of interest. It is common to see researchers fit growth curve models without considering alterative modeling strategies. In this article we compare 3 approaches for analyzing longitudinal data: repeated measures analysis of variance, covariance pattern models, and growth curve models. As all are members of the general linear mixed model family, they represent somewhat different assumptions about the way individuals change. These assumptions result in different patterns of covariation among the residuals around the fixed effects. In this article, we first indicate the kinds of data that are appropriately modeled by each and use real data examples to demonstrate possible problems associated with the blanket selection of the growth curve model. We then present a simulation that indicates the utility of Akaike information criterion and Bayesian information criterion in the selection of a proper residual covariance structure. The results cast doubt on the popular practice of automatically using growth curve modeling for longitudinal data without comparing the fit of different models. Finally, we provide some practical advice for assessing mean changes in the presence of correlated data.

  16. Diabetic Foot Prevention: Repeatability of the Loran Platform Plantar Pressure and Load Distribution Measurements in Nondiabetic Subjects during Bipedal Standing—A Pilot Study

    Directory of Open Access Journals (Sweden)

    Martha Zequera

    2011-01-01

    Full Text Available This study was designed to assess the repeatability of the Loran Platform and evaluate the variability of plantar pressure and postural balance, during barefoot standing in nondiabetic subjects, for future diabetic foot clinical evaluation. Measurements were taken for eight nondiabetic subjects (4 females, 4 males, aged 47±7.2 years who had no musculoskeletal symptoms. Five variables were measured with the platform in the barefoot standing position. Ten measurements were taken using two different techniques for feet and posture positioning, during three sessions, once a week. For most measurements, no significant effect over time was found with Student's t-test (P<.000125. The ANOVA test of statistical significance confirmed that measurement differences between subjects showed higher variations than measurements taken from the same subject (P<.001. The measurements taken by the Loran Platform system were found to be repeatable.

  17. Repeated measurements of blood lactate concentration as a prognostic marker in horses with acute colitis evaluated with classification and regression trees (CART) and random forest analysis.

    Science.gov (United States)

    Petersen, M B; Tolver, A; Husted, L; Tølbøll, T H; Pihl, T H

    2016-07-01

    The objective of this study was to investigate the prognostic value of single and repeated measurements of blood l-lactate (Lac) and ionised calcium (iCa) concentrations, packed cell volume (PCV) and plasma total protein (TP) concentration in horses with acute colitis. A total of 66 adult horses admitted with acute colitis (2 mmol/L (sensitivity, 0.72; specificity, 0.8). In conclusion, blood lactate concentration measured at admission and repeated 6 h later aided the prognostic evaluation of horses with acute colitis in this population with a very high mortality rate. This should allow clinicians to give a more reliable prognosis for the horse.

  18. Cardiac output measurement in newborn infants using the ultrasonic cardiac output monitor: an assessment of agreement with conventional echocardiography, repeatability and new user experience.

    Science.gov (United States)

    Patel, Neil; Dodsworth, Melissa; Mills, John F

    2011-05-01

    To assess (1) agreement between the ultrasonic cardiac output monitor (USCOM) 1A device for measurement of cardiac output in newborn infants and conventional echocardiography (ECHO), (2) repeatability of USCOM measurements and (3) agreement between novice and expert users of the USCOM. A prospective observational study. The Neonatal Unit at the Royal Children's Hospital, Melbourne, Australia. 56 term and near-term infants, with no evidence of structural or functional cardiovascular disease, or haemodynamic shunts. Agreement between ECHO and USCOM was assessed by paired measurements of ventricular outputs by a single experienced user. Repeatability was assessed using five repeated measurements in 10 infants. Agreement between five novices and one expert user was assessed by paired USCOM measurements over 30 training measurements. Agreement between USCOM and ECHO for left ventricular output (LVO) was (bias, ±limits of agreement, mean % error): 14, ±108 ml/kg/min, 43%, and for right ventricular output (RVO): -59, ±160, ml/kg/min, 57%. Intra-observer repeatability was 6.7% for USCOM LVO and 3.6% for ECHO LVO. After five training measurements, the mean difference between USCOM measures of LVO by novice and expert users was less than 50 ml/kg/min, but with variability. Repeatability of USCOM measures is high in newborn infants. New users can be trained quickly, but with high inter-user variability. Agreement between USCOM and conventional ECHO is broad, and worse for RVO and LVO. Further studies are required to assess the ability of the device to detect clinically significant changes in infant cardiac output.

  19. Effects of CAG repeat length, HTT protein length and protein context on cerebral metabolism measured using magnetic resonance spectroscopy in transgenic mouse models of Huntington's disease.

    Science.gov (United States)

    Jenkins, Bruce G; Andreassen, Ole A; Dedeoglu, Alpaslan; Leavitt, Blair; Hayden, Michael; Borchelt, David; Ross, Christopher A; Ferrante, Robert J; Beal, M Flint

    2005-10-01

    Huntington's disease is a neurodegenerative illness caused by expansion of CAG repeats at the N-terminal end of the protein huntingtin. We examined longitudinal changes in brain metabolite levels using in vivo magnetic resonance spectroscopy in five different mouse models. There was a large (>50%) exponential decrease in N-acetyl aspartate (NAA) with time in both striatum and cortex in mice with 150 CAG repeats (R6/2 strain). There was a linear decrease restricted to striatum in N171-82Q mice with 82 CAG repeats. Both the exponential and linear decreases of NAA were paralleled in time by decreases in neuronal area measured histologically. Yeast artificial chromosome transgenic mice with 72 CAG repeats, but low expression levels, had less striatal NAA loss than the N171-82Q mice (15% vs. 43%). We evaluated the effect of gene context in mice with an approximate 146 CAG repeat on the hypoxanthine phosphoribosyltransferase gene (HPRT). HPRT mice developed an obese phenotype in contrast to weight loss in the R6/2 and N171-82Q mice. These mice showed a small striatal NAA loss (21%), and a possible increase in brain lipids detectable by magnetic resonance (MR) spectroscopy and decreased brain water T1. Our results indicate profound metabolic defects that are strongly affected by CAG repeat length, as well as gene expression levels and protein context.

  20. Post-seismic velocity changes along the 2008 M7.9 Wenchuan earthquake rupture zone revealed by S coda of repeating events

    Science.gov (United States)

    Li, Le; Niu, Fenglin; Chen, Qi-Fu; Su, Jinrong; He, Jiabin

    2017-02-01

    We investigated post-seismic velocity changes within the fault zone of the 2008 M7.9 Wenchuan earthquake using coda wave data of repeating small earthquakes. We employed template matching and grid search methods to identify well-defined repeating earthquakes in order to minimize artefacts induced by variations in source location. We identified a total of 12 isolated patches in the fault zone that ruptured more than twice in a 1 yr period after the M7.9 earthquake. We applied the coda wave interferometry technique to the waveform data of the 34 identified repeating earthquakes to estimate velocity changes between the first and subsequent events in each cluster. We found that major post-seismic velocity changes occurred in the southwestern part of the rupture area, where the main rupture was initiated and characterized by thrust motion, while the Beichuan area in the northeastern part of the rupture zone appears to experience very little post-seismic velocity changes.

  1. Detecting variable responses in time-series using repeated measures ANOVA: Application to physiologic challenges [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Paul M. Macey

    2016-07-01

    Full Text Available We present an approach to analyzing physiologic timetrends recorded during a stimulus by comparing means at each time point using repeated measures analysis of variance (RMANOVA. The approach allows temporal patterns to be examined without an a priori model of expected timing or pattern of response. The approach was originally applied to signals recorded from functional magnetic resonance imaging (fMRI volumes-of-interest (VOI during a physiologic challenge, but we have used the same technique to analyze continuous recordings of other physiological signals such as heart rate, breathing rate, and pulse oximetry. For fMRI, the method serves as a complement to whole-brain voxel-based analyses, and is useful for detecting complex responses within pre-determined brain regions, or as a post-hoc analysis of regions of interest identified by whole-brain assessments. We illustrate an implementation of the technique in the statistical software packages R and SAS. VOI timetrends are extracted from conventionally preprocessed fMRI images. A timetrend of average signal intensity across the VOI during the scanning period is calculated for each subject. The values are scaled relative to baseline periods, and time points are binned. In SAS, the procedure PROC MIXED implements the RMANOVA in a single step. In R, we present one option for implementing RMANOVA with the mixed model function “lme”. Model diagnostics, and predicted means and differences are best performed with additional libraries and commands in R; we present one example. The ensuing results allow determination of significant overall effects, and time-point specific within- and between-group responses relative to baseline. We illustrate the technique using fMRI data from two groups of subjects who underwent a respiratory challenge. RMANOVA allows insight into the timing of responses and response differences between groups, and so is suited to physiologic testing paradigms eliciting complex

  2. Gene expression profiling of R6/2 transgenic mice with different CAG repeat lengths reveals genes associated with disease onset and progression in Huntington's disease.

    Science.gov (United States)

    Tang, Bin; Seredenina, Tamara; Coppola, Giovanni; Kuhn, Alexandre; Geschwind, Daniel H; Luthi-Carter, Ruth; Thomas, Elizabeth A

    2011-06-01

    R6/2 transgenic mice with expanded CAG repeats (>300) have a surprisingly prolonged disease progression and longer lifespan than prototypical parent R6/2 mice (carrying 150 CAGs); however, the mechanism of this phenotype amelioration is unknown. We compared gene expression profiles in the striatum of R6/2 transgenic mice carrying ~300 CAG repeats (R6/2(Q300) transgenic mice) to those carrying ~150 CAG repeats (R6/2(Q150) transgenic mice) and littermate wildtype controls in order to identify genes that may play determinant roles in the time course of phenotypic expression in these mice. Of the top genes showing concordant expression changes in the striatum of both R6/2 lines, 85% were decreased in expression, while discordant expression changes were observed mostly for genes upregulated in R6/2(Q300) transgenic mice. Upregulated genes in the R6/2(Q300) mice were associated with the ubiquitin ligase complex, cell adhesion, protein folding, and establishment of protein localization. We qPCR-validated increases in expression of genes related to the latter category, including Lrsam1, Erp29, Nasp, Tap1, Rab9b, and Pfdn5 in R6/2(Q300) mice, changes that were not observed in R6/2 mice with shorter CAG repeats, even in late stages (i.e., 12 weeks of age). We further tested Lrsam1 and Erp29, the two genes showing the greatest upregulation in R6/2(Q300) transgenic mice, for potential neuroprotective effects in primary striatal cultures overexpressing a mutated human huntingtin (htt) fragment. Overexpression of Lrsam1 prevented the loss of NeuN-positive cell bodies in htt171-82Q cultures, concomitant with a reduction of nuclear htt aggregates. Erp29 showed no significant effects in this model. This is consistent with the distinct pattern of htt inclusion localization observed in R6/2(Q300) transgenic mice, in which smaller cytoplasmic inclusions represent the major form of insoluble htt in the cell, as opposed to large nuclear inclusions observed in R6/2(Q150) transgenic mice

  3. Revisiting the TALE repeat.

    Science.gov (United States)

    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.

  4. The Effects of Group Leader Learning Style on Student Knowledge Gain in a Leadership Camp Setting: A Repeated-Measures Experiment

    Science.gov (United States)

    Brown, Nicholas R.; Terry, Robert, Jr.

    2013-01-01

    Many state FFA associations conduct summer camps focusing on leadership and personal development for FFA members. Interestingly, little research has been conducted on the impact or outcomes of these common activities. The purpose of this split-plot factorial repeated-measures experiment was to assess the level of campers' learning of the…

  5. Power and sample size for the S:T repeated measures design combined with a linear mixed-effects model allowing for missing data.

    Science.gov (United States)

    Tango, Toshiro

    2017-02-13

    Tango (Biostatistics 2016) proposed a new repeated measures design called the S:T repeated measures design, combined with generalized linear mixed-effects models and sample size calculations for a test of the average treatment effect that depend not only on the number of subjects but on the number of repeated measures before and after randomization per subject used for analysis. The main advantages of the proposed design combined with the generalized linear mixed-effects models are (1) it can easily handle missing data by applying the likelihood-based ignorable analyses under the missing at random assumption and (2) it may lead to a reduction in sample size compared with the simple pre-post design. In this article, we present formulas for calculating power and sample sizes for a test of the average treatment effect allowing for missing data within the framework of the S:T repeated measures design with a continuous response variable combined with a linear mixed-effects model. Examples are provided to illustrate the use of these formulas.

  6. Predictors and Variability of Repeat Measurements of Urinary Phenols and Parabens in a Cohort of Shanghai Women and Men

    Science.gov (United States)

    Buckley, Jessie P.; Yang, Gong; Liao, Linda M.; Satagopan, Jaya; Calafat, Antonia M.; Matthews, Charles E.; Cai, Qiuyin; Ji, Bu-Tian; Cai, Hui; Wolff, Mary S.; Rothman, Nathaniel; Zheng, Wei; Xiang, Yong-Bing; Shu, Xiao-Ou; Gao, Yu-Tang; Chow, Wong-Ho

    2014-01-01

    , under certain circumstances, among women. Citation: Engel LS, Buckley JP, Yang G, Liao LM, Satagopan J, Calafat AM, Matthews CE, Cai Q, Ji BT, Cai H, Engel SM, Wolff MS, Rothman N, Zheng W, Xiang YB, Shu XO, Gao YT, Chow WH. 2014. Predictors and variability of repeat measurements of urinary phenols and parabens in a cohort of Shanghai women and men. Environ Health Perspect 122:733–740; http://dx.doi.org/10.1289/ehp.1306830 PMID:24659570

  7. A review of the reporting and handling of missing data in cohort studies with repeated assessment of exposure measures

    Directory of Open Access Journals (Sweden)

    Karahalios Amalia

    2012-07-01

    Full Text Available Abstract Background Retaining participants in cohort studies with multiple follow-up waves is difficult. Commonly, researchers are faced with the problem of missing data, which may introduce biased results as well as a loss of statistical power and precision. The STROBE guidelines von Elm et al. (Lancet, 370:1453-1457, 2007; Vandenbroucke et al. (PLoS Med, 4:e297, 2007 and the guidelines proposed by Sterne et al. (BMJ, 338:b2393, 2009 recommend that cohort studies report on the amount of missing data, the reasons for non-participation and non-response, and the method used to handle missing data in the analyses. We have conducted a review of publications from cohort studies in order to document the reporting of missing data for exposure measures and to describe the statistical methods used to account for the missing data. Methods A systematic search of English language papers published from January 2000 to December 2009 was carried out in PubMed. Prospective cohort studies with a sample size greater than 1,000 that analysed data using repeated measures of exposure were included. Results Among the 82 papers meeting the inclusion criteria, only 35 (43% reported the amount of missing data according to the suggested guidelines. Sixty-eight papers (83% described how they dealt with missing data in the analysis. Most of the papers excluded participants with missing data and performed a complete-case analysis (n = 54, 66%. Other papers used more sophisticated methods including multiple imputation (n = 5 or fully Bayesian modeling (n = 1. Methods known to produce biased results were also used, for example, Last Observation Carried Forward (n = 7, the missing indicator method (n = 1, and mean value substitution (n = 3. For the remaining 14 papers, the method used to handle missing data in the analysis was not stated. Conclusions This review highlights the inconsistent reporting of missing data in cohort studies and the continuing

  8. A review of the reporting and handling of missing data in cohort studies with repeated assessment of exposure measures.

    Science.gov (United States)

    Karahalios, Amalia; Baglietto, Laura; Carlin, John B; English, Dallas R; Simpson, Julie A

    2012-07-11

    Retaining participants in cohort studies with multiple follow-up waves is difficult. Commonly, researchers are faced with the problem of missing data, which may introduce biased results as well as a loss of statistical power and precision. The STROBE guidelines von Elm et al. (Lancet, 370:1453-1457, 2007); Vandenbroucke et al. (PLoS Med, 4:e297, 2007) and the guidelines proposed by Sterne et al. (BMJ, 338:b2393, 2009) recommend that cohort studies report on the amount of missing data, the reasons for non-participation and non-response, and the method used to handle missing data in the analyses. We have conducted a review of publications from cohort studies in order to document the reporting of missing data for exposure measures and to describe the statistical methods used to account for the missing data. A systematic search of English language papers published from January 2000 to December 2009 was carried out in PubMed. Prospective cohort studies with a sample size greater than 1,000 that analysed data using repeated measures of exposure were included. Among the 82 papers meeting the inclusion criteria, only 35 (43%) reported the amount of missing data according to the suggested guidelines. Sixty-eight papers (83%) described how they dealt with missing data in the analysis. Most of the papers excluded participants with missing data and performed a complete-case analysis (n=54, 66%). Other papers used more sophisticated methods including multiple imputation (n=5) or fully Bayesian modeling (n=1). Methods known to produce biased results were also used, for example, Last Observation Carried Forward (n=7), the missing indicator method (n=1), and mean value substitution (n=3). For the remaining 14 papers, the method used to handle missing data in the analysis was not stated. This review highlights the inconsistent reporting of missing data in cohort studies and the continuing use of inappropriate methods to handle missing data in the analysis. Epidemiological journals

  9. De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper.

    Directory of Open Access Journals (Sweden)

    Nisha Joy

    Full Text Available Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L., an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs. We used the array of transcripts generated, for the in silico prediction and detection of '43 pre-miRNA candidates bearing different types of SSR motifs'. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted 'pre-miRNA candidates bearing SSRs'. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted 'pre-miRNA candidates'. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of 'tandem repeats' in miRNAs.

  10. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles †

    OpenAIRE

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Juan C. Linares; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysi...

  11. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Juan C. Linares; Gómez-Gómez, Lourdes; Ahrazem, Oussama

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysi...

  12. Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles

    OpenAIRE

    Oussama Ahrazem; Benjamin Viñegla; Juan C. Linares; Lourdes Gómez-Gómez; David Candel-Perez; Tiscar, Pedro A.; Lucas-Borja, Manuel E.; Angela Rubio-Moraga

    2012-01-01

    Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina...

  13. Measuring revealed and emergent vulnerabilities of coastal communities to tsunami in Sri Lanka.

    Science.gov (United States)

    Birkmann, Jörn; Fernando, Nishara

    2008-03-01

    This paper presents the important findings of a study undertaken in two selected tsunami-affected coastal cities in Sri Lanka (Batticaloa and Galle) to measure the revealed and emergent vulnerability of coastal communities. International risk studies have failed to demonstrate the high vulnerability of coastal communities to tsunami in Sri Lanka. Therefore, indirect assessment tools to measure pre-event vulnerability have to be complemented by assessment tools that analyse revealed and emergent vulnerability in looking at the aftermath and impact patterns of a real scenario, as well as in examining the dynamics of disaster recovery in which different vulnerabilities can be identified. The paper first presents a conceptual framework for capturing vulnerability within a process-oriented approach linked to sustainable development. Next, it highlights selected indicators and methods to measure revealed and emergent vulnerability at the local level using the examples of Batticaloa and Galle. Finally, it discusses the usefulness and application of vulnerability indicators within the framework of reconstruction.

  14. Analyzing repeated data collected by mobile phones and frequent text messages. An example of Low back pain measured weekly for 18 weeks

    DEFF Research Database (Denmark)

    Axén, Iben; Bodin, Lennart; Kongsted, Alice

    2012-01-01

    ABSTRACT: BACKGROUND: Repeated data collection is desirable when monitoring fluctuating conditions. Mobile phones can be used to gather such data from large groups of respondents by sending and receiving frequently repeated short questions and answers as text messages. The analysis of repeated data...... for the clinical researcher in order for complex outcome measures to be interpreted in a clinically meaningful way. METHODS: A model data set was formed using data from two clinical studies, where patients with low back pain were followed with weekly text messages for 18 weeks. Different research questions...... questions with appropriate analytical methods 1: How many days with pain do patients experience? This question was answered with data summaries. 2: What is the proportion of participants "recovered" at a specific time point? This question was answered using logistic regression analysis. 3: What is the time...

  15. Analysis of the genome sequence of the pathogenic Muscovy duck parvovirus strain YY reveals a 14-nucleotide-pair deletion in the inverted terminal repeats.

    Science.gov (United States)

    Wang, Jianye; Huang, Yu; Zhou, Mingxu; Zhu, Guoqiang

    2016-09-01

    Genomic information about Muscovy duck parvovirus is still limited. In this study, the genome of the pathogenic MDPV strain YY was sequenced. The full-length genome of YY is 5075 nucleotides (nt) long, 57 nt shorter than that of strain FM. Sequence alignment indicates that the 5' and 3' inverted terminal repeats (ITR) of strain YY contain a 14-nucleotide-pair deletion in the stem of the palindromic hairpin structure in comparison to strain FM and FZ91-30. The deleted region contains one "E-box" site and one repeated motif with the sequence "TTCCGGT" or "ACCGGAA". Phylogenetic trees constructed based the protein coding genes concordantly showed that YY, together with nine other MDPV isolates from various places, clustered in a separate branch, distinct from the branch formed by goose parvovirus (GPV) strains. These results demonstrate that, despite the distinctive deletion, the YY strain still belongs to the classical MDPV group. Moreover, the deletion of ITR may contribute to the genome evolution of MDPV under immunization pressure.

  16. Intricate interactions between the bloom-forming cyanobacterium Microcystis aeruginosa and foreign genetic elements, revealed by diversified clustered regularly interspaced short palindromic repeat (CRISPR) signatures.

    Science.gov (United States)

    Kuno, Sotaro; Yoshida, Takashi; Kaneko, Takakazu; Sako, Yoshihiko

    2012-08-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) confer sequence-dependent, adaptive resistance in prokaryotes against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements. CRISPR loci are thus considered to provide records of past infections. To describe the host-parasite (i.e., cyanophages and plasmids) interactions involving the bloom-forming freshwater cyanobacterium Microcystis aeruginosa, we investigated CRISPR in four M. aeruginosa strains and in two previously sequenced genomes. The number of spacers in each locus was larger than the average among prokaryotes. All spacers were strain specific, except for a string of 11 spacers shared in two closely related strains, suggesting diversification of the loci. Using CRISPR repeat-based PCR, 24 CRISPR genotypes were identified in a natural cyanobacterial community. Among 995 unique spacers obtained, only 10 sequences showed similarity to M. aeruginosa phage Ma-LMM01. Of these, six spacers showed only silent or conservative nucleotide mutations compared to Ma-LMM01 sequences, suggesting a strategy by the cyanophage to avert CRISPR immunity dependent on nucleotide identity. These results imply that host-phage interactions can be divided into M. aeruginosa-cyanophage combinations rather than pandemics of population-wide infectious cyanophages. Spacer similarity also showed frequent exposure of M. aeruginosa to small cryptic plasmids that were observed only in a few strains. Thus, the diversification of CRISPR implies that M. aeruginosa has been challenged by diverse communities (almost entirely uncharacterized) of cyanophages and plasmids.

  17. Evaluation, including effects of storage and repeated freezing and thawing, of a method for measurement of urinary creatinine

    DEFF Research Database (Denmark)

    Garde, A H; Hansen, Åse Marie; Kristiansen, J

    2003-01-01

    The aims of this study were to elucidate to what extent storage and repeated freezing and thawing influenced the concentration of creatinine in urine samples and to evaluate the method for determination of creatinine in urine. The creatinine method was based on the well-known Jaffe's reaction and...

  18. Heart rate variability and DNA methylation levels are altered after short-term metal fume exposure among occupational welders: a repeated-measures panel study

    OpenAIRE

    2014-01-01

    Background: In occupational settings, boilermakers are exposed to high levels of metallic fine particulate matter (PM2.5) generated during the welding process. The effect of welding PM2.5 on heart rate variability (HRV) has been described, but the relationship between PM2.5, DNA methylation, and HRV is not known. Methods: In this repeated-measures panel study, we recorded resting HRV and measured DNA methylation levels in transposable elements Alu and long interspersed nuclear element-1 (LINE...

  19. Repeated measures dose-finding design with time-trend detection in the presence of correlated toxicity data.

    Science.gov (United States)

    Yin, Jun; Paoletti, Xavier; Sargent, Daniel J; Mandrekar, Sumithra J

    2017-08-01

    Phase I trials are designed to determine the safety, tolerability, and recommended phase 2 dose of therapeutic agents for subsequent testing. The dose-finding paradigm has thus traditionally focused on identifying the maximum tolerable dose of an agent or combination therapy under the assumption that there is a non-decreasing relationship between dose-toxicity and dose-efficacy. The dose is typically determined based on the probability of severe toxicity observed during the first treatment cycle. A novel endpoint, the total toxicity profile, was previously developed to account for the multiple toxicity types and grades experienced in the first cycle. More recently, this was extended to a repeated measures design based on the total toxicity profile to account for longitudinal toxicities over multiple treatment cycles in the absence of within-patient correlation. In this work, we propose to extend the design in the presence of within-patient correlation. Furthermore, we provide a framework to detect a toxicity time trend (toxicity increasing, decreasing, or stable) over multiple treatment cycles. We utilize a linear mixed model in the Bayesian framework, with the addition of Bayesian risk functions for decision-making in dose assignment. The performance of this design was evaluated using simulation studies and real data from a phase I trial. We demonstrated that using available toxicity data from all cycles of treatment improves the accuracy of maximum tolerated dose identification and allows for the detection of a time trend. The performance is consistent regardless of the strength of the within-patient correlation. In addition, the use of a quasi-continuous total toxicity profile score significantly increased the power to detect time trends compared to when binary data only were used. The increased interest in molecularly targeted agents and immunotherapies in oncology necessitates innovative phase I study designs. Our proposed framework provides a tool to tackle

  20. Young investigator challenge: Atypia of undetermined significance in thyroid FNA: Standardized terminology without standardized management--a closer look at repeat FNA and quality measures.

    Science.gov (United States)

    Brandler, Tamar C; Aziz, Mohamed S; Coutsouvelis, Constantinos; Rosen, Lisa; Rafael, Oana C; Souza, Fabiola; Jelloul, Fatima-Zahra; Klein, Melissa A

    2016-01-01

    The Bethesda system (TBS) for the reporting of thyroid cytopathology established the category of atypia of undetermined significance (AUS) with a 7% target rate and a 5% to 15% implied malignancy risk. Recent literature has reported a broad range of AUS rates, subsequent malignancy rates, and discrepant results from repeat fine-needle aspiration (FNA) versus surgical follow-up. Therefore, this study examined AUS data from the Hofstra North Shore-LIJ School of Medicine to determine the best clinical follow-up. Thyroid aspirates interpreted as AUS in 2012-2014 at the Hofstra North Shore-LIJ School of Medicine were collected. Repeat FNA and surgical follow-up data were tabulated to establish AUS, secondary AUS (diagnosed upon repeat FNA follow-up of a primary FNA AUS diagnosis), atypia of undetermined significance/malignancy (AUS:M) ratios (according to the TBS categories), and malignancy rates for AUS. The AUS rate was 8.5% (976/11,481), and there was follow-up data for 545 cases. The AUS:M ratio was 2.0. Repeat FNA was performed for 281 cases; 57 proceeded to surgical intervention. Repeat FNA reclassified 71.17% of the cases. The malignancy rates for AUS cases proceeding directly to surgery and for those receiving a surgical intervention after a repeat AUS diagnosis were 33.33% and 43.75%, respectively. Repeat FNA resulted in definitive diagnostic reclassification for 67.61% of primary AUS cases and reduced the number of patients triaged to surgery, with 56.58% of the cases recategorized as benign. Cases undergoing surgery after repeat AUS had a higher malignancy rate than those going straight to surgery, and this emphasizes the value of repeat FNA in selecting surgical candidates. In addition, this study highlights the utility of AUS rate monitoring as a quality measure that has contributed to the ability of the Hofstra North Shore-LIJ School of Medicine to adhere closely to TBS recommendations. © 2016 American Cancer Society.

  1. Negative differential mobility for negative carriers as revealed by space charge measurements on crosslinked polyethylene insulated model cables

    Science.gov (United States)

    Teyssedre, G.; Vu, T. T. N.; Laurent, C.

    2015-12-01

    Among features observed in polyethylene materials under relatively high field, space charge packets, consisting in a pulse of net charge that remains in the form of a pulse as it crosses the insulation, are repeatedly observed but without complete theory explaining their formation and propagation. Positive charge packets are more often reported, and the models based on negative differential mobility(NDM) for the transport of holes could account for some charge packets phenomenology. Conversely, NDM for electrons transport has never been reported so far. The present contribution reports space charge measurements by pulsed electroacoustic method on miniature cables that are model of HVDC cables. The measurements were realized at room temperature or with a temperature gradient of 10 °C through the insulation under DC fields on the order 30-60 kV/mm. Space charge results reveal systematic occurrence of a negative front of charges generated at the inner electrode that moves toward the outer electrode at the beginning of the polarization step. It is observed that the transit time of the front of negative charge increases, and therefore the mobility decreases, with the applied voltage. Further, the estimated mobility, in the range 10-14-10-13 m2 V-1 s-1 for the present results, increases when the temperature increases for the same condition of applied voltage. The features substantiate the hypothesis of negative differential mobility used for modelling space charge packets.

  2. Characterization of expressed Pgip genes in rice and wheat reveals similar extent of sequence variation to dicot PGIPs and identifies an active PGIP lacking an entire LRR repeat.

    Science.gov (United States)

    Janni, Michela; Di Giovanni, Michela; Roberti, Serena; Capodicasa, Cristina; D'Ovidio, Renato

    2006-11-01

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) proteins involved in plant defence. A number of PGIPs have been characterized from dicot species, whereas only a few data are available from monocots. Database searches and genome-specific cloning strategies allowed the identification of four rice (Oryza sativa L.) and two wheat (Triticum aestivum L.) Pgip genes. The rice Pgip genes (Ospgip1, Ospgip2, Ospgip3 and Ospgip4) are distributed over a 30 kbp region of the short arm of chromosome 5, whereas the wheat Pgip genes, Tapgip1 and Tapgip2, are localized on the short arm of chromosome 7B and 7D, respectively. Deduced amino acid sequences show the typical LRR modular organization and a conserved distribution of the eight cysteines at the N- and C-terminal regions. Sequence comparison suggests that monocot and dicot PGIPs form two separate clusters sharing about 40% identity and shows that this value is close to the extent of variability observed within each cluster. Gene-specific RT-PCR and biochemical analyses demonstrate that both Ospgips and Tapgips are expressed in the whole plant or in a tissue-specific manner, and that OsPGIP1, lacking an entire LRR repeat, is an active inhibitor of fungal polygalacturonases. This last finding can contribute to define the molecular features of PG-PGIP interactions and highlights that the genetic events that can generate variability at the Pgip locus are not only limited to substitutions or small insertions/deletions, as so far reported, but can also involve variation in the number of LRRs.

  3. The effects of repeated-sprint training on field-based fitness measures: a meta-analysis of controlled and non-controlled trials.

    Science.gov (United States)

    Taylor, Jonathan; Macpherson, Tom; Spears, Iain; Weston, Matthew

    2015-06-01

    Repeated-sprint training appears to be an efficient and practical means for the simultaneous development of different components of fitness relevant to team sports. Our objective was to systematically review the literature and meta-analyse the effect of repeated-sprint training on a selection of field-based measures of athletic performance, i.e. counter-movement jump, 10 m sprint, 20 m sprint, 30 m sprint, repeated-sprint ability and high-intensity intermittent running performance. The SPORTDiscus, PubMed, MEDLINE and Web of Science databases were searched for original research articles. Search terms included 'repeated-sprint training', 'sprint training', 'aerobic endurance', 'repeated-sprint ability', 'counter-movement jump' and 'sprint performance'. Inclusion criteria included intervention consisting of a series of ≤10 s sprints with ≤60 s recovery; trained participants; intervention duration of 2-12 weeks; field-based fitness measures; running- or cycling-based intervention; published up to, and including, February 2014. Our final dataset included six trials for counter-movement jump (two controlled trials), eight trials for 10 m sprint, four trials for 20 m sprint (three controlled trials), two trials for 30 m sprint, eight trials for repeated-sprint ability and three trials for high-intensity intermittent running performance. Analyses were conducted using comprehensive meta-analysis software. Uncertainty in the meta-analysed effect of repeated-sprint training was expressed as 95% confidence limits (CL), along with the probability that the true value of the effect was trivial, beneficial or harmful. Magnitude-based inferences were based on standardised thresholds for small, moderate and large changes of 0.2, 0.6 and 1.2 standard deviations, respectively. Repeated-sprint training had a likely small beneficial effect in non-controlled counter-movement jump trials (effect size 0.33; 95% CL ±0.30), with a possibly moderate beneficial effect in controlled

  4. Effects of repeatability measures on results of fMRI sICA: a study on simulated and real resting-state effects.

    Science.gov (United States)

    Remes, Jukka J; Starck, Tuomo; Nikkinen, Juha; Ollila, Esa; Beckmann, Christian F; Tervonen, Osmo; Kiviniemi, Vesa; Silven, Olli

    2011-05-15

    Spatial independent components analysis (sICA) has become a widely applied data-driven method for fMRI data, especially for resting-state studies. These sICA approaches are often based on iterative estimation algorithms and there are concerns about accuracy due to noise. Repeatability measures such as ICASSO, RAICAR and ARABICA have been introduced as remedies but information on their effects on estimates is limited. The contribution of this study was to provide more of such information and test if the repeatability analyses are necessary. We compared FastICA-based ordinary and repeatability approaches concerning mixing vector estimates. Comparisons included original FastICA, FSL4 Melodic FastICA and original and modified ICASSO. The effects of bootstrapping and convergence threshold were evaluated. The results show that there is only moderate improvement due to repeatability measures and only in the bootstrapping case. Bootstrapping attenuated power from time courses of resting-state network related ICs at frequencies higher than 0.1 Hz and made subsets of low frequency oscillations more emphasized IC-wise. The convergence threshold did not have a significant role concerning the accuracy of estimates. The performance results suggest that repeatability measures or strict converge criteria might not be needed in sICA analyses of fMRI data. Consequently, the results in existing sICA fMRI literature are probably valid in this sense. A decreased accuracy of original bootstrapping ICASSO was observed and corrected by using centrotype mixing estimates but the results warrant for thorough evaluations of data-driven methods in general. Also, given the fMRI-specific considerations, further development of sICA methods is strongly encouraged. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals.

    Science.gov (United States)

    Dievart, Anne; Perin, Christophe; Hirsch, Judith; Bettembourg, Mathilde; Lanau, Nadège; Artus, Florence; Bureau, Charlotte; Noel, Nicolas; Droc, Gaétan; Peyramard, Matthieu; Pereira, Serge; Courtois, Brigitte; Morel, Jean-Benoit; Guiderdoni, Emmanuel

    2016-01-01

    Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.

  6. Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers.

    Science.gov (United States)

    Jain, Shalu; Kumar, Ajay; Mamidi, Sujan; McPhee, Kevin

    2014-10-01

    Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars.

  7. ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought,flood,or salinity

    Institute of Scientific and Technical Information of China (English)

    Ch Surendhar REDDY; A.Prasad BABU; B.P.Mallikarjuna SWAMY; K.KALADHAR; N.SARLA

    2009-01-01

    Drought,flood,salinity,or a combination of these limits rice production.Several rice varieties are well known for their tolerance to specific abiotic stresses.We determined genetic relationship among 12 rice varieties including 9 tolerant to drought,flood,or salinity using inter-simple sequence repeat (ISSR) markers.Based on all markers,the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties.The salt-tolerant varieties were closest to two flood-tolerant varieties,and together they were distinct from the drought-tolerant varieties.(GA)8 YG was the most informative primer,showing the highest polymorphic information content (PIC) and resolving power (Rp).The drought-,flood-,and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties,when (GA)8 YG was used.Sabita was the only exception.The two aus varieties,Nagina22 and FR13A,were separated and grouped with the drought-and flood-tolerant varieties,respectively,but they were together in dendrograms based on other primers.The results show that ISSR markers associated with (GA)8 YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.

  8. Heterozygosities and genetic relationship of tea cultivars revealed by simple sequence repeat markers and implications for breeding and genetic mapping programs.

    Science.gov (United States)

    Tan, L Q; Zhang, C C; Qi, G N; Wang, L Y; Wei, K; Chen, S X; Zou, Y; Wu, L Y; Cheng, H

    2015-03-06

    Genetic maps are essential tools for quantitative trait locus analysis and marker-assisted selection breeding. In order to select parents that are highly heterozygous for genetic mapping, the heterozygosity (HS) of 24 tea cultivars (Camellia sinensis) was analyzed with 72 simple sequence repeat markers. In total, 359 alleles were obtained with an average of 4.99 per marker. The HS varied greatly from 37.5 to 71.0% with an average of 51.3%. On average, tea cultivars from Fujian Province showed a higher level of heterozygosity (59.8%) than those from Zhejiang (48.5%) and Yunnan (44.5%), and the 12 national tea cultivars were generally more heterozygous than the 12 provincial cultivars. Unweighted pair-group analysis using the arithmetic average grouping divided the 24 cultivars into 2 groups that are consistent with the morphological classification. All dual combinations of the 24 cultivars were studied to calculate the percentage of mappable markers when using pseudo-testcross mapping strategy, and results showed that this value also varied greatly from 51.4 to 90.3%. The genetic relationships and HS differences among different cultivars were discussed, and tea cultivars with high HS were recommended as cross parents for genetic mapping programs.

  9. Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-coupled Affinity Purification/Mass Spectrometry Analysis Revealed a Novel Role of Neurofibromin in mTOR Signaling.

    Science.gov (United States)

    Li, Xu; Gao, Min; Choi, Jong Min; Kim, Beom-Jun; Zhou, Mao-Tian; Chen, Zhen; Jain, Antrix N; Jung, Sung Yun; Yuan, Jingsong; Wang, Wenqi; Wang, Yi; Chen, Junjie

    2017-04-01

    Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    controlled to great precision, but in a Cubesat , there may be no attitude determination at all. Such a Cubesat might treat sun angle and tumbling rates as...could be sensitive to small differences in motor controller timing. In these cases, the analyst might choose to model the entire deployment path, with...knowledge of the material damage model or motor controller timing precision. On the other hand, if many repeated and environmentally representative

  11. Repeatability and Reproducibility of Retinal Neuronal and Axonal Measures on Spectral-Domain Optical Coherence Tomography in Patients with Cognitive Impairment

    Directory of Open Access Journals (Sweden)

    Edwin Hong-Teck Loh

    2017-08-01

    Full Text Available BackgroundWith increasing interest in determining if measurement of retinal neuronal structure with spectral-domain optical coherence tomography (SD-OCT is useful in accessing neurodegenerative process in cognitive decline and development of dementia, it is important to evaluate whether the SD-OCT measurements are repeatable and reproducible in these patients.MethodsThis is a retrospective cohort study. Patients with Alzheimer’s disease (AD or mild cognitive impairment (MCI with no change in global clinical dementia rating (CDR score at 1-year follow-up were eligible to be included. Ganglion cell-inner plexiform layer (GC-IPL and retinal nerve fiber layer (RNFL parameters were measured with SD-OCT at baseline, 6-month, and 1-year follow-up visits. At baseline, SD-OCT scans were repeated to access intra-visit repeatability of the SD-OCT measurement. SD-OCT measurement over three visits was used to access inter-visit reproducibility. We calculated intraclass correlation coefficients (ICC and coefficients of variation (CoVs.ResultsWe included 32 patients with stable AD and 29 patients with stable MCI in the final analysis. For GC-IPL measures, the average intra-visit ICC was 0.969 (range: 0.948–0.985, and CoV was 1.81% (range: 1.14–2.40; while the average inter-visit ICC was 0.968 (0.941–0.985, and CoV was 1.91% (range: 1.24–2.32. The average ICC and CoV of intra-visit RNFL measured were 0.965 (range: 0.937–0.986 and 2.32% (range: 1.34–2.90%, respectively. The average ICC and CoV of inter-visit RNFL measures were 0.927 (range: 0.845–0.961 and 3.83% (range: 2.71–5.25%, respectively.ConclusionBoth GC-IPL and RNFL measurements had good intra-visit repeatability and inter-visit reproducibility over 1 year in elderly patients with no decline in cognitive function, suggesting that SD-OCT is a reliable tool to assess neurodegenerative process over time.

  12. Repeatability and Reproducibility of Retinal Nerve Fiber Layer Parameters Measured by Scanning Laser Polarimetry with Enhanced Corneal Compensation in Normal and Glaucomatous Eyes

    Directory of Open Access Journals (Sweden)

    Mirian Ara

    2015-01-01

    Full Text Available Objective. To assess the intrasession repeatability and intersession reproducibility of peripapillary retinal nerve fiber layer (RNFL thickness parameters measured by scanning laser polarimetry (SLP with enhanced corneal compensation (ECC in healthy and glaucomatous eyes. Methods. One randomly selected eye of 82 healthy individuals and 60 glaucoma subjects was evaluated. Three scans were acquired during the first visit to evaluate intravisit repeatability. A different operator obtained two additional scans within 2 months after the first session to determine intervisit reproducibility. The intraclass correlation coefficient (ICC, coefficient of variation (COV, and test-retest variability (TRT were calculated for all SLP parameters in both groups. Results. ICCs ranged from 0.920 to 0.982 for intravisit measurements and from 0.910 to 0.978 for intervisit measurements. The temporal-superior-nasal-inferior-temporal (TSNIT average was the highest (0.967 and 0.946 in normal eyes, while nerve fiber indicator (NFI; 0.982 and inferior average (0.978 yielded the best ICC in glaucomatous eyes for intravisit and intervisit measurements, respectively. All COVs were under 10% in both groups, except NFI. TSNIT average had the lowest COV (2.43% in either type of measurement. Intervisit TRT ranged from 6.48 to 12.84. Conclusions. The reproducibility of peripapillary RNFL measurements obtained with SLP-ECC was excellent, indicating that SLP-ECC is sufficiently accurate for monitoring glaucoma progression.

  13. Repeatability and Reproducibility of Retinal Nerve Fiber Layer Parameters Measured by Scanning Laser Polarimetry with Enhanced Corneal Compensation in Normal and Glaucomatous Eyes.

    Science.gov (United States)

    Ara, Mirian; Ferreras, Antonio; Pajarin, Ana B; Calvo, Pilar; Figus, Michele; Frezzotti, Paolo

    2015-01-01

    To assess the intrasession repeatability and intersession reproducibility of peripapillary retinal nerve fiber layer (RNFL) thickness parameters measured by scanning laser polarimetry (SLP) with enhanced corneal compensation (ECC) in healthy and glaucomatous eyes. One randomly selected eye of 82 healthy individuals and 60 glaucoma subjects was evaluated. Three scans were acquired during the first visit to evaluate intravisit repeatability. A different operator obtained two additional scans within 2 months after the first session to determine intervisit reproducibility. The intraclass correlation coefficient (ICC), coefficient of variation (COV), and test-retest variability (TRT) were calculated for all SLP parameters in both groups. ICCs ranged from 0.920 to 0.982 for intravisit measurements and from 0.910 to 0.978 for intervisit measurements. The temporal-superior-nasal-inferior-temporal (TSNIT) average was the highest (0.967 and 0.946) in normal eyes, while nerve fiber indicator (NFI; 0.982) and inferior average (0.978) yielded the best ICC in glaucomatous eyes for intravisit and intervisit measurements, respectively. All COVs were under 10% in both groups, except NFI. TSNIT average had the lowest COV (2.43%) in either type of measurement. Intervisit TRT ranged from 6.48 to 12.84. The reproducibility of peripapillary RNFL measurements obtained with SLP-ECC was excellent, indicating that SLP-ECC is sufficiently accurate for monitoring glaucoma progression.

  14. Force measurements on natural membrane nanovesicles reveal a composition-independent, high Young's modulus

    Science.gov (United States)

    Calò, Annalisa; Reguera, David; Oncins, Gerard; Persuy, Marie-Annick; Sanz, Guenhaël; Lobasso, Simona; Corcelli, Angela; Pajot-Augy, Edith; Gomila, Gabriel

    2014-01-01

    Mechanical properties of nano-sized vesicles made up of natural membranes are crucial to the development of stable, biocompatible nanocontainers with enhanced functional, recognition and sensing capabilities. Here we measure and compare the mechanical properties of plasma and inner membrane nanovesicles ~80 nm in diameter obtained from disrupted yeast Saccharomyces cerevisiae cells. We provide evidence of a highly deformable behaviour for these vesicles, able to support repeated wall-to-wall compressions without irreversible deformations, accompanied by a noticeably high Young's modulus (~300 MPa) compared to that obtained for reconstituted artificial liposomes of similar size and approaching that of some virus particles. Surprisingly enough, the results are approximately similar for plasma and inner membrane nanovesicles, in spite of their different lipid compositions, especially on what concerns the ergosterol content. These results point towards an important structural role of membrane proteins in the mechanical response of natural membrane vesicles and open the perspective to their potential use as robust nanocontainers for bioapplications.Mechanical properties of nano-sized vesicles made up of natural membranes are crucial to the development of stable, biocompatible nanocontainers with enhanced functional, recognition and sensing capabilities. Here we measure and compare the mechanical properties of plasma and inner membrane nanovesicles ~80 nm in diameter obtained from disrupted yeast Saccharomyces cerevisiae cells. We provide evidence of a highly deformable behaviour for these vesicles, able to support repeated wall-to-wall compressions without irreversible deformations, accompanied by a noticeably high Young's modulus (~300 MPa) compared to that obtained for reconstituted artificial liposomes of similar size and approaching that of some virus particles. Surprisingly enough, the results are approximately similar for plasma and inner membrane nanovesicles, in

  15. Repeatability of Brain Volume Measurements Made with the Atlas-based Method from T1-weighted Images Acquired Using a 0.4 Tesla Low Field MR Scanner.

    Science.gov (United States)

    Goto, Masami; Suzuki, Makoto; Mizukami, Shinya; Abe, Osamu; Aoki, Shigeki; Miyati, Tosiaki; Fukuda, Michinari; Gomi, Tsutomu; Takeda, Tohoru

    2016-10-11

    An understanding of the repeatability of measured results is important for both the atlas-based and voxel-based morphometry (VBM) methods of magnetic resonance (MR) brain volumetry. However, many recent studies that have investigated the repeatability of brain volume measurements have been performed using static magnetic fields of 1-4 tesla, and no study has used a low-strength static magnetic field. The aim of this study was to investigate the repeatability of measured volumes using the atlas-based method and a low-strength static magnetic field (0.4 tesla). Ten healthy volunteers participated in this study. Using a 0.4 tesla magnetic resonance imaging (MRI) scanner and a quadrature head coil, three-dimensional T1-weighted images (3D-T1WIs) were obtained from each subject, twice on the same day. VBM8 software was used to construct segmented normalized images [gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) images]. The regions-of-interest (ROIs) of GM, WM, CSF, hippocampus (HC), orbital gyrus (OG), and cerebellum posterior lobe (CPL) were generated using WFU PickAtlas. The percentage change was defined as[100 × (measured volume with first segmented image - mean volume in each subject)/(mean volume in each subject)]The average percentage change was calculated as the percentage change in the 6 ROIs of the 10 subjects. The mean of the average percentage changes for each ROI was as follows: GM, 0.556%; WM, 0.324%; CSF, 0.573%; HC, 0.645%; OG, 1.74%; and CPL, 0.471%. The average percentage change was higher for the orbital gyrus than for the other ROIs. We consider that repeatability of the atlas-based method is similar between 0.4 and 1.5 tesla MR scanners. To our knowledge, this is the first report to show that the level of repeatability with a 0.4 tesla MR scanner is adequate for the estimation of brain volume change by the atlas-based method.

  16. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

    Energy Technology Data Exchange (ETDEWEB)

    Manning, Viola A.; Pandelova, Iovanna; Dhillon, Braham; Wilhelm, Larry J.; Goodwin, Stephen B.; Berlin, Aaron M.; Figueroa, Melania; Freitag, Michael; Hane, James K.; Henrissat, Bernard; Holman, Wade H.; Kodira, Chinnappa D.; Martin, Joel; Oliver, Richard P.; Robbertse, Barbara; Schackwitz, Wendy; Schwartz, David C.; Spatafora, Joseph W.; Turgeon, B. Gillian; Yandava, Chandri; Young, Sarah; Zhou, Shiguo; Zeng, Qiandong; Grigoriev, Igor V.; Ma, Li-Jun; Ciuffetti, Lynda M.

    2012-08-16

    Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.

  18. Negative differential mobility for negative carriers as revealed by space charge measurements on crosslinked polyethylene insulated model cables

    Energy Technology Data Exchange (ETDEWEB)

    Teyssedre, G., E-mail: gilbert.teyssedre@laplace.univ-tlse.fr; Laurent, C. [Université de Toulouse, UPS, INPT, LAPLACE (Laboratoire Plasma et Conversion d' Energie), 118 route de Narbonne, F-31062 Toulouse cedex 9 (France); CNRS, LAPLACE, F-31062 Toulouse (France); Vu, T. T. N. [Université de Toulouse, UPS, INPT, LAPLACE (Laboratoire Plasma et Conversion d' Energie), 118 route de Narbonne, F-31062 Toulouse cedex 9 (France); Electric Power University, 235 Hoang Quoc Viet, 10000 Hanoi (Viet Nam)

    2015-12-21

    Among features observed in polyethylene materials under relatively high field, space charge packets, consisting in a pulse of net charge that remains in the form of a pulse as it crosses the insulation, are repeatedly observed but without complete theory explaining their formation and propagation. Positive charge packets are more often reported, and the models based on negative differential mobility(NDM) for the transport of holes could account for some charge packets phenomenology. Conversely, NDM for electrons transport has never been reported so far. The present contribution reports space charge measurements by pulsed electroacoustic method on miniature cables that are model of HVDC cables. The measurements were realized at room temperature or with a temperature gradient of 10 °C through the insulation under DC fields on the order 30–60 kV/mm. Space charge results reveal systematic occurrence of a negative front of charges generated at the inner electrode that moves toward the outer electrode at the beginning of the polarization step. It is observed that the transit time of the front of negative charge increases, and therefore the mobility decreases, with the applied voltage. Further, the estimated mobility, in the range 10{sup −14}–10{sup −13} m{sup 2} V{sup −1} s{sup −1} for the present results, increases when the temperature increases for the same condition of applied voltage. The features substantiate the hypothesis of negative differential mobility used for modelling space charge packets.

  19. Fixed-flexion knee radiography using a new positioning device produced highly repeatable measurements of joint space width: ELSA-Brasil Musculoskeletal Study (ELSA-Brasil MSK).

    Science.gov (United States)

    Telles, Rosa Weiss; Costa-Silva, Luciana; Machado, Luciana A C; Reis, Rodrigo Citton Padilha Dos; Barreto, Sandhi Maria

    To describe the performance of a non-fluoroscopic fixed-flexion PA radiographic protocol with a new positioning device, developed for the assessment of knee osteoarthritis (OA) in Brazilian Longitudinal Study of Adult Health Musculoskeletal Study (ELSA-Brasil MSK). A test-retest design including 19 adults (38 knee images) was conducted. Feasibility of the radiographic protocol was assessed by image quality parameters and presence of radioanatomic alignment according to intermargin distance (IMD) values. Repeatability was assessed for IMD and joint space width (JSW) measured at three different locations. Approximately 90% of knee images presented excellent quality. Frequencies of nearly perfect radioanatomic alignment (IMD ≤1mm) ranged from 29% to 50%, and satisfactory alignment was found in up to 71% and 76% of the images (IMD ≤1.5mm and ≤1.7mm, respectively). Repeatability analyses yielded the following results: IMD [SD of mean difference=1.08; coefficient of variation (%CV)=54.68%; intraclass correlation coefficient (ICC) (95%CI)=0.59 (0.34-0.77)]; JSW [SD of mean difference=0.34-0.61; %CV=4.48%-9.80%; ICC (95%CI)=0.74 (0.55-0.85)-0.94 (0.87-0.97)]. Adequately reproducible measurements of IMD and JSW were found in 68% and 87% of the images, respectively. Despite the difficulty in achieving consistent radioanatomic alignment between subsequent radiographs in terms of IMD, the protocol produced highly repeatable JSW measurements when these were taken at midpoint and 10mm from the medial extremity of the medial tibial plateau. Therefore, measurements of JSW at these locations can be considered adequate for the assessment of knee OA in ELSA-Brasil MSK. Copyright © 2016. Published by Elsevier Editora Ltda.

  20. Chloroplast DNA phylogeography reveals repeated range expansion in a widespread aquatic herb Hippuris vulgaris in the Qinghai-Tibetan Plateau and adjacent areas.

    Directory of Open Access Journals (Sweden)

    Jin-Ming Chen

    Full Text Available BACKGROUND: The Qinghai-Tibetan Plateau (QTP is one of the most extensive habitats for alpine plants in the world. Climatic oscillations during the Quaternary ice age had a dramatic effect on species ranges on the QTP and the adjacent areas. However, how the distribution ranges of aquatic plant species shifted on the QTP in response to Quaternary climatic changes remains almost unknown. METHODOLOGY AND PRINCIPAL FINDINGS: We studied the phylogeography and demographic history of the widespread aquatic herb Hippuris vulgaris from the QTP and adjacent areas. Our sampling included 385 individuals from 47 natural populations of H. vulgaris. Using sequences from four chloroplast DNA (cpDNA non-coding regions, we distinguished eight different cpDNA haplotypes. From the cpDNA variation in H. vulgaris, we found a very high level of population differentiation (G ST = 0.819 but the phylogeographical structure remained obscure (N ST = 0.853>G ST = 0.819, P>0.05. Phylogenetic analyses revealed two main cpDNA haplotype lineages. The split between these two haplotype groups can be dated back to the mid-to-late Pleistocene (ca. 0.480 Myr. Mismatch distribution analyses showed that each of these had experienced a recent range expansion. These two expansions (ca. 0.12 and 0.17 Myr might have begun from the different refugees before the Last Glacial Maximum (LGM. CONCLUSIONS/SIGNIFICANCE: This study initiates a research on the phylogeography of aquatic herbs in the QTP and for the first time sheds light on the response of an alpine aquatic seed plant species in the QTP to Quaternary climate oscillations.

  1. Application of repeated passive source travel time tomography to reveal weak velocity changes related to the 2011 Tohoku-Oki Mw 9.0 earthquake

    Science.gov (United States)

    Koulakov, Ivan; Gladkov, Valery; El Khrepy, Sami; Al-Arifi, Nassir; Fathi, Ismail Husain

    2016-06-01

    Temporal changes of seismic velocities may provide important information on the processes that occur inside the Earth. However, using body wave data with passive sources faces the problem of an uneven distribution of rays, which may cause artifacts with stronger amplitudes than the actual velocity changes in the Earth. We propose an algorithm for the selection of similar data sets in different time periods that minimize the artifacts related to variable data distributions. In this study, we used the data of the Japan Meteorological Agency for several years before and after the Mw 9.0 Tohoku-Oki event that occurred on 11 March 2011. We performed careful testing using different synthetic models, showing that the selected data subsets allow detecting weak velocity changes with amplitudes above 0.2%. The analysis of the experimental data revealed important features associated with the stress and deformation distributions after the megathrust event. In the upper crust, we found a large zone along the coast with significant P velocity increase likely caused by compression of crustal rocks. This zone was cut by several elongated anomalies with local velocity decrease coinciding with the limits of the maximum slip area. These anomalies possibly mark the areas of major ruptures and deformations after the Tohoku-Oki earthquake. In the coupling zone at a depth of 40 km, we observe a velocity decrease in the area of the Mw 7.7 aftershock representing strong fracturing in the focal zone. Beneath the volcanic arc, we observe significant (up to 0.5%) decrease of P velocity but less prominent S velocity changes.

  2. Repeated-Sprint Cycling Does Not Induce Respiratory Muscle Fatigue in Active Adults: Measurements from The Powerbreathe® Inspiratory Muscle Trainer

    Directory of Open Access Journals (Sweden)

    Clare Minahan, Beth Sheehan, Rachel Doutreband, Tom Kirkwood, Daniel Reeves, Troy Cross

    2015-03-01

    Full Text Available This study examined respiratory muscle strength using the POWERbreathe® inspiratory muscle trainer (i.e., ‘S-Index’ before and after repeated-sprint cycling for comparison with maximal inspiratory pressure (MIP values obtained during a Mueller maneuver. The S-Index was measured during six trials across two sessions using the POWERbreathe® and MIP was measured during three trials in a single session using a custom-made manometer in seven recreationally active adults. Global respiratory muscle strength was measured using both devices before and after the performance of sixteen, 6-s sprints on a cycle ergometer. Intraclass correlation coefficients for the POWERbreathe® S-index indicated excellent (p 0.99 and during the Mueller maneuver (p > 0.99. The POWERbreathe® S-Index is a moderately reliable, but not equivalent, measure of MIP determined during a Mueller maneuver. Furthermore, repeated-sprint cycling does not induce globalized respiratory muscle fatigue in recreationally-active adults.

  3. Repeatability of measurements of packed cell volume and egg count as indicators of endoparasite load and their relationship with sheep productivity.

    Science.gov (United States)

    Bekele, T; Kasali, O B; Rege, J E

    1991-12-01

    Monthly measurements of packed cell volume (PCV) and nematode and trematode eggs per gram (EPG) were made in Ethiopian highland sheep at Debre Berhan, Dejen, Deneba, Tulu Meko and Wereilu from June 1988 to December 1989. High frequencies of low PCV, high nematode EPG and high trematode EPG were found at Tulu Meko. Among the productivity traits examined, body condition scores and live-weights were significantly (P less than 0.05) associated with differences in PCV and nematode and trematode EPG levels at most sites. The lambing interval was, however, not significantly (P greater than 0.05) affected by these variables. Monthly repeatabilities of PCV, body weight and body condition scores were 0.44 +/- 0.01, 0.71 +/- 0.01 and 0.35 +/- 0.01, respectively, while those of nematode (0.09 +/- 0.01) and trematode EPGs (0.20 +/- 0.02) were much lower. The high repeatability for PCV indicates that it was less affected by the variable factors influencing egg output, and hence it could be utilized in conjunction with nematode and trematode EPG levels for endoparasite monitoring. Repeatability of the lambing interval across parities was 0.43 +/- 0.14.

  4. Relationship between measures of aerobic fitness, speed and repeated sprint ability in full and part time youth soccer players.

    Science.gov (United States)

    Gibson, N; Currie, J; Johnston, R; Hill, J

    2013-02-01

    The aim of the study was to investigate the relationship between repeated sprint ability (RSA) involving changes in direction, short linear sprinting and aerobic capacity in young elite soccer players. A secondary aim was to assess any differences in performance of these assessments between players of different age groups. Thirty-two male adolescent soccer players belonging to the same elite club academy were assessed for RSA comprising 6 x 40m efforts interspersed by 25s recovery, linear sprinting speed over 15m, and aerobic capacity via the YYIE2 assessment. There was a significant correlation between performance in the YYIE2 and RSA total time, RSA fastest sprint and RSA percentage decrement (r = -0.71, -0.53, and -0.52 respectively. Psprint (Psprinting. Assessments of RSA over 40m and incorporating changes of direction appear to be significantly correlated with YYIE2 performance in young elite level soccer players. In addition older players performed significantly better in the YYIE2 assessment and RSA protocol but not in short linear sprinting. These results have implications for the design of assessment protocols for young elite soccer players of different ages.

  5. Very long Detection Times after High and repeated intake of Heroin and Methadone, measured in Oral Fluid

    Directory of Open Access Journals (Sweden)

    Vindenes V.

    2014-12-01

    Full Text Available When detection times for psychoactive drugs in oral fluid are reported, they are most often based on therapeutic doses administered in clinical studies. Repeated ingestions of high doses, as seen after drug abuse, are however likely to cause positive samples for extended time periods. Findings of drugs of abuse in oral fluid might lead to negative sanctions, and the knowledge of detection times of these drugs are important to ensure correct interpretation. The aim of this study was to investigate the detection times of opioids in oral fluid. 25 patients with a history of heavy drug abuse admitted to a detoxification ward were included. Oral fluid and urine were collected daily and, if the patient gave consent, a blood sample was drawn during the first five days after admission. Morphine, codeine and/or 6-monoacetyl morphine (6-MAM were found in oral fluid and/or urine from 20 patients. The maximum detection times in oral fluid for codeine, morphine and 6-MAM were 1, 3 and 8 days, respectively. Positive oral fluid samples were interspersed with negative samples, mainly for concentrations around cut off. Elimination curves for methadone in oral fluid were found for two subjects, and the detection times were 5 and 8 days. Oral fluid is likely to become a good method for detection of drug abuse in the future

  6. The reliability of repeated TMS measures in older adults and in patients with subacute and chronic stroke

    Directory of Open Access Journals (Sweden)

    Heidi M. Schambra

    2015-09-01

    Full Text Available The reliability of transcranial magnetic stimulation (TMS measures in healthy older adults and stroke patients has been insufficiently characterized. We determined whether common TMS measures could reliably evaluate change in individuals and in groups using the smallest detectable change (SDC, or could tell subjects apart using the intraclass correlation coefficient (ICC. We used a single-rater test-retest design in older healthy, subacute stroke, and chronic stroke subjects. At twice daily sessions on two consecutive days, we recorded resting motor threshold, test stimulus intensity, recruitment curves, short-interval intracortical inhibition and facilitation, and long-interval intracortical inhibition. Using variances estimated from a random effects model, we calculated the SDC and ICC for each TMS measure. For all TMS measures in all groups, SDCs for single subjects were large; only with modest group sizes did the SDCs become low. Thus, while these TMS measures cannot be reliably used as a biomarker to detect individual change, they can reliably detect change exceeding measurement noise in moderate-sized groups. For several of the TMS measures, ICCs were universally high, suggesting that they can reliably discriminate between subjects. Though most TMS measures have sufficient reliability in particular contexts, work establishing their validity, responsiveness, and clinical relevance is still needed.

  7. Comparison of intraclass correlation coefficient estimates and standard errors between using cross-sectional and repeated measurement data: the Safety Check cluster randomized trial.

    Science.gov (United States)

    Ip, Edward H; Wasserman, Richard; Barkin, Shari

    2011-03-01

    Designing cluster randomized trials in clinical studies often requires accurate estimates of intraclass correlation, which quantifies the strength of correlation between units, such as participants, within a cluster, such as a practice. Published ICC estimates, even when available, often suffer from the problem of wide confidence intervals. Using data from a national, randomized, controlled study concerning violence prevention for children--the Safety Check--we compare the ICC values derived from two approaches only baseline data and using both baseline and follow-up data. Using a variance component decomposition approach, the latter method allows flexibility in handling complex data sets. For example, it allows for shifts in the outcome variable over time and for an unbalanced cluster design. Furthermore, we evaluate the large-sample formula for ICC estimates and standard errors using the bootstrap method. Our findings suggest that ICC estimates range from 0.012 to 0.11 for providers within practice and range from 0.018 to 0.11 for families within provider. The estimates derived from the baseline-only and repeated-measurements approaches agree quite well except in cases in which variation over repeated measurements is large. The reductions in the widths of ICC confidence limits from using repeated measurement over baseline only are, respectively, 62% and 42% at the practice and provider levels. The contribution of this paper therefore includes two elements, which are a methodology for improving the accuracy of ICC, and the reporting of such quantities for pediatric and other researchers who are interested in designing clustered randomized trials similar to the current study.

  8. A genetic strategy to measure circulating Drosophila insulin reveals genes regulating insulin production and secretion.

    Science.gov (United States)

    Park, Sangbin; Alfa, Ronald W; Topper, Sydni M; Kim, Grace E S; Kockel, Lutz; Kim, Seung K

    2014-08-01

    Insulin is a major regulator of metabolism in metazoans, including the fruit fly Drosophila melanogaster. Genome-wide association studies (GWAS) suggest a genetic basis for reductions of both insulin sensitivity and insulin secretion, phenotypes commonly observed in humans with type 2 diabetes mellitus (T2DM). To identify molecular functions of genes linked to T2DM risk, we developed a genetic tool to measure insulin-like peptide 2 (Ilp2) levels in Drosophila, a model organism with superb experimental genetics. Our system permitted sensitive quantification of circulating Ilp2, including measures of Ilp2 dynamics during fasting and re-feeding, and demonstration of adaptive Ilp2 secretion in response to insulin receptor haploinsufficiency. Tissue specific dissection of this reduced insulin signaling phenotype revealed a critical role for insulin signaling in specific peripheral tissues. Knockdown of the Drosophila orthologues of human T2DM risk genes, including GLIS3 and BCL11A, revealed roles of these Drosophila genes in Ilp2 production or secretion. Discovery of Drosophila mechanisms and regulators controlling in vivo insulin dynamics should accelerate functional dissection of diabetes genetics.

  9. Compositional variability across Mercury's surface revealed by MESSENGER measurements of variations in thermal neutron count rates

    Science.gov (United States)

    Peplowski, P. N.; Lawrence, D. J.; Goldsten, J. O.; Nittler, L. R.; Solomon, S. C.

    2013-12-01

    Measurements by MESSENGER's Gamma-Ray and Neutron Spectrometer (GRNS) have revealed variations in the flux of thermal neutrons across Mercury's northern hemisphere. These variations are interpreted to originate from spatial variations in surface elemental composition. In particular, the measurements are sensitive to the near-surface abundances of elements that absorb thermal neutrons, including major rock-forming elements such as Fe and Ti, minor elements such as Mn and Cl, and rare-earth elements such as Gd and Sm. We have constructed a map of thermal neutron variability across the surface and compared it with known variations in elemental composition and with the distribution of geologic units. Development of the map included the derivation of the macroscopic thermal neutron absorption cross section across the surface, a quantity whose value and variability provides useful constraints on the formation and geochemical evolution of Mercury's crust. Finally, by combining the thermal neutron measurements with previously reported elemental measurements from the GRNS and MESSENGER's X-Ray Spectrometer, we have derived constraints on the abundances of neutron-absorbing elements, including previously unreported limits for some minor and rare-earth elements.

  10. The near-infrared spectroscopy-derived deoxygenated haemoglobin breaking-point is a repeatable measure that demarcates exercise intensity domains.

    Science.gov (United States)

    Iannetta, Danilo; Qahtani, Ahmad; Mattioni Maturana, Felipe; Murias, Juan Manuel

    2017-09-01

    A breaking-point in the near-infrared spectroscopy (NIRS)-derived deoxygenated haemoglobin ([HHb]) profile towards the end of a ramp incremental (RI) cycling test has been associated to the respiratory compensation point (RCP). Despite the physiological value of this measure, its repeatability remains unknown. The aim was to examine the repeatability of the [HHb] breaking-point ([HHb]BP) and its association to RCP during a RI cycling test. A repeated measures design was performed on 11 males (30.5±8.4 year; 76.5±8.4kg) and 4 females (30.5±5.9 year; 61.9±4.4 Kg). Gas exchange and NIRS [HHb] data were collected during RI tests performed on two different days separated by 48h. The [HHb]BP and the RCP were determined and compared for each trial. The [HHb]BP and the respiratory compensation point (RCP) occurred at the same VO2 in test 1 and test 2 ([HHb]BP: 3.49±0.52Lmin(-1) test 1; 3.48±0.45Lmin(-1) test 2; RCP: 3.38±0.40Lmin(-1) test 1; 3.38±0.44Lmin(-1) test 2) (P>0.05). The VO2 associated with the [HHb]BP and the VO2 at RCP were not significantly different from each other either in test 1 as well as in test 2 (P>0.05). Neither test 1 nor test 2 showed significant mean average error between the VO2 at the [HHb]BP and RCP using Bland & Altman plots. The [HHb]BP is a repeatable measure that consistently occurs towards the end of a RI test. The association between the [HHb]BP and the RCP reinforces the idea that these parameters may share similar mechanistic basis. Copyright © 2017 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  11. Variation in repeated mouth-opening measurements in head and neck cancer patients with and without trismus

    NARCIS (Netherlands)

    Jager-Wittenaar, H.; Dijkstra, P. U.; Vissink, A.; van Oort, R. P.; Roodenburg, J. L. N.

    2009-01-01

    Trismus after head and neck cancer treatment may severely limit mandibular functioning. Interventions aimed at reducing trismus can only be evaluated when the amount of variation associated with these measurements is known. The aim of this Study was to analyse the variation in mouth-opening measurem

  12. Repeated measurements of mite and pet allergen levels in house dust over a time period of 8 years

    NARCIS (Netherlands)

    Antens, C. J. M.; Oldenwening, M.; Wolse, A.; Gehring, U.; Smit, H. A.; Aalberse, R. C.; Kerkhof, M.; Gerritsen, J.; de Jongste, J. C.; Brunekreef, B.

    2006-01-01

    Background Studies of the association between indoor allergen exposure and the development of allergic diseases have often measured allergen exposure at one point in time. Objective We investigated the variability of house dust mite (Der p 1, Der f 1) and cat (Fel d 1) allergen in Dutch homes over a

  13. Variation in repeated mouth-opening measurements in head and neck cancer patients with and without trismus

    NARCIS (Netherlands)

    Jager-Wittenaar, H.; Dijkstra, P. U.; Vissink, A.; van Oort, R. P.; Roodenburg, J. L. N.

    2009-01-01

    Trismus after head and neck cancer treatment may severely limit mandibular functioning. Interventions aimed at reducing trismus can only be evaluated when the amount of variation associated with these measurements is known. The aim of this Study was to analyse the variation in mouth-opening measurem

  14. Variation in repeated mouth-opening measurements in head and neck cancer patients with and without trismus

    NARCIS (Netherlands)

    Jager-Wittenaar, H.; Dijkstra, P. U.; Vissink, A.; van Oort, R. P.; Roodenburg, J. L. N.

    Trismus after head and neck cancer treatment may severely limit mandibular functioning. Interventions aimed at reducing trismus can only be evaluated when the amount of variation associated with these measurements is known. The aim of this Study was to analyse the variation in mouth-opening

  15. Repeated measurements of mite and pet allergen levels in house dust over a time period of 8 years

    NARCIS (Netherlands)

    Antens, C. J. M.; Oldenwening, M.; Wolse, A.; Gehring, U.; Smit, H. A.; Aalberse, R. C.; Kerkhof, M.; Gerritsen, J.; de Jongste, J. C.; Brunekreef, B.

    2006-01-01

    Background Studies of the association between indoor allergen exposure and the development of allergic diseases have often measured allergen exposure at one point in time. Objective We investigated the variability of house dust mite (Der p 1, Der f 1) and cat (Fel d 1) allergen in Dutch homes over a

  16. Magnetization measurements reveal the local shear stiffness of hydrogels probed by ferromagnetic nanorods

    Energy Technology Data Exchange (ETDEWEB)

    Bender, P., E-mail: nano@p-bender.de; Tschöpe, A., E-mail: antsch@mx.uni-saarland.de; Birringer, R., E-mail: r.birringer@nano.uni-saarland.de

    2014-12-15

    The local mechanical coupling of ferromagnetic nanorods in hydrogels was characterized by magnetization measurements. Nickel nanorods were synthesized by the AAO-template method and embedded in gelatine hydrogels with mechanically soft or hard matrix properties determined by the gelatine weight fraction. By applying a homogeneous magnetic field during gelation the nanorods were aligned along the field resulting in uniaxially textured ferrogels. The magnetization curves of the soft ferrogel exhibited not only important similarities but also characteristic differences as compared to the hard ferrogel. The hystereses measured in a field parallel to the texture axis were almost identical for both samples indicating effective coupling of the nanorods with the polymer network. By contrast, measurements in a magnetic field perpendicular to the texture axis revealed a much higher initial susceptibility of the soft as compared to the hard ferrogel. This difference was attributed to the additional rotation of the nanorods allowed by the reduced shear modulus in the soft ferrogel matrix. Two methods for data analysis were presented which enabled us to determine the shear modulus of the gelatine matrix which was interpreted as a local rather than macroscopic quantity in consideration of the nanoscale of the probe particles. - Highlights: • Nanorods are embedded as magnetic probes in gelatine gels. • Elastic rotation of the rods can be induced by applying a homogeneous magnetic field. • Rod rotation has significant influence on the magnetization curves. • Two methods are presented to estimate the shear modulus of the matrix from the magnetization curves.

  17. Your mind wanders weakly, your mind wanders deeply: objective measures reveal mindless reading at different levels.

    Science.gov (United States)

    Schad, Daniel J; Nuthmann, Antje; Engbert, Ralf

    2012-11-01

    When the mind wanders, attention turns away from the external environment and cognitive processing is decoupled from perceptual information. Mind wandering is usually treated as a dichotomy (dichotomy-hypothesis), and is often measured using self-reports. Here, we propose the levels of inattention hypothesis, which postulates attentional decoupling to graded degrees at different hierarchical levels of cognitive processing. To measure graded levels of attentional decoupling during reading we introduce the sustained attention to stimulus task (SAST), which is based on psychophysics of error detection. Under experimental conditions likely to induce mind wandering, we found that subjects were less likely to notice errors that required high-level processing for their detection as opposed to errors that only required low-level processing. Eye tracking revealed that before errors were overlooked influences of high- and low-level linguistic variables on eye fixations were reduced in a graded fashion, indicating episodes of mindless reading at weak and deep levels. Individual fixation durations predicted overlooking of lexical errors 5s before they occurred. Our findings support the levels of inattention hypothesis and suggest that different levels of mindless reading can be measured behaviorally in the SAST. Using eye tracking to detect mind wandering online represents a promising approach for the development of new techniques to study mind wandering and to ameliorate its negative consequences. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Effects of ambient air pollution on functional status in patients with chronic congestive heart failure: a repeated-measures study

    Directory of Open Access Journals (Sweden)

    Phillips Russell S

    2007-09-01

    Full Text Available Abstract Background Studies using administrative data report a positive association between ambient air pollution and the risk of hospitalization for congestive heart failure (HF. Circulating levels of B-type natriuretic peptide (BNP are directly associated with cardiac hemodynamics and symptom severity in patients with HF and, therefore, serves as a marker of functional status. We tested the hypothesis that BNP levels would be positively associated with short-term changes in ambient pollution levels among 28 patients with chronic stable HF and impaired systolic function. Methods BNP was measured in whole blood at 0, 6, and 12 weeks. We used linear mixed models to evaluate the association between fine particulate matter (PM2.5, carbon monoxide, sulfur dioxide, nitrogen dioxide, ozone, and black carbon and log(BNP. Lags of 0 to 3 days were considered in separate models. We calculated the intraclass correlation coefficient and within-subject coefficient of variation as measures of reproducibility. Results We found no association between any pollutant and measures of BNP at any lag. For example, a 10 μg/m3 increase in PM2.5 was associated with a 0.8% (95% CI: -16.4, 21.5; p = 0.94 increase in BNP on the same day. The within-subject coefficient of variation was 45% on the natural scale and 9% on the log scale. Conclusion These results suggest that serial BNP measurements are unlikely to be useful in a longitudinal study of air pollution-related acute health effects. The magnitude of expected ambient air pollution health effects appears small in relation to the considerable within-person variability in BNP levels in this population.

  19. A technique for conditioning and calibrating force-sensing resistors for repeatable and reliable measurement of compressive force.

    Science.gov (United States)

    Hall, Rick S; Desmoulin, Geoffrey T; Milner, Theodore E

    2008-12-01

    Miniature sensors that could measure forces applied by the fingers and hand without interfering with manual dexterity or range of motion would have considerable practical value in ergonomics and rehabilitation. In this study, techniques have been developed to use inexpensive pressure-sensing resistors (FSRs) to accurately measure compression force. The FSRs are converted from pressure-sensing to force-sensing devices. The effects of nonlinear response properties and dependence on loading history are compensated by signal conditioning and calibration. A fourth-order polynomial relating the applied force to the current voltage output and a linearly weighted sum of prior outputs corrects for sensor hysteresis and drift. It was found that prolonged (>20h) shear force loading caused sensor gain to change by approximately 100%. Shear loading also had the effect of eliminating shear force effects on sensor output, albeit only in the direction of shear loading. By applying prolonged shear loading in two orthogonal directions, the sensors were converted into pure compression sensors. Such preloading of the sensor is, therefore, required prior to calibration. The error in compression force after prolonged shear loading and calibration was consistently industrial design applications where measurements of finger and hand force are needed.

  20. Repeated measures of body mass index and C-reactive protein in relation to all-cause mortality and cardiovascular disease

    DEFF Research Database (Denmark)

    O'Doherty, Mark G; Jørgensen, Torben; Borglykke, Anders

    2014-01-01

    Obesity has been linked with elevated levels of C-reactive protein (CRP), and both have been associated with increased risk of mortality and cardiovascular disease (CVD). Previous studies have used a single 'baseline' measurement and such analyses cannot account for possible changes in these which...... body mass index (BMI) and CRP with all-cause mortality and CVD. Being overweight (≥25-obese (≥30-....79-0.94) and 0.80 (0.72-0.89). A similar relationship was found, but only for overweight in Glostrup, HR (95 % CI) 0.88 (0.76-1.02); and moderately obese in Tromsø, HR (95 % CI) 0.79 (0.62-1.01). Associations were not evident between repeated measures of BMI and CVD. Conversely, increasing CRP concentrations...

  1. Fibrinogen adsorption mechanisms at the gold substrate revealed by QCM-D measurements and RSA modeling.

    Science.gov (United States)

    Kubiak, Katarzyna; Adamczyk, Zbigniew; Cieśla, Michał

    2016-03-01

    Adsorption kinetics of fibrinogen at a gold substrate at various pHs was thoroughly studied using the QCM-D method. The experimental were interpreted in terms of theoretical calculations performed according to the random sequential adsorption model (RSA). In this way, the hydration functions and water factors of fibrinogen monolayers were quantitatively evaluated at various pHs. It was revealed that for the lower range of fibrinogen coverage the hydration function were considerably lower than previously obtained for the silica sensor [33]. The lower hydration of fibrinogen monolayers on the gold sensor was attributed to its higher roughness. However, for higher fibrinogen coverage the hydration functions for both sensors became identical exhibiting an universal behavior. By using the hydration functions, the fibrinogen adsorption/desorption runs derived from QCM-D measurements were converted to the Γd vs. the time relationships. This allowed to precisely determine the maximum coverage that varied between 1.6mgm(-2) at pH 3.5 and 4.5mgm(-2) at pH 7.4 (for ionic strength of 0.15M). These results agree with theoretical eRSA modeling and previous experimental data derived by using ellipsometry, OWLS and TIRF. Various fibrinogen adsorption mechanisms were revealed by exploiting the maximum coverage data. These results allow one to develop a method for preparing fibrinogen monolayers of well-controlled coverage and molecule orientation. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Duct Leakage Repeatability Testing

    Energy Technology Data Exchange (ETDEWEB)

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    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.

  3. Repeated-measure validation of craniofacial metrics from three-dimensional surface scans: application to medical genetics

    Science.gov (United States)

    Lauer, Eric A.; Corner, Brian D.; Li, Peng; Beecher, Robert M.; Deutsch, Curtis

    2002-03-01

    Traditionally, medical geneticists have employed visual inspection (anthroposcopy) to clinically evaluate dysmorphology. In the last 20 years, there has been an increasing trend towards quantitative assessment to render diagnosis of anomalies more objective and reliable. These methods have focused on direct anthropometry, using a combination of classical physical anthropology tools and new instruments tailor-made to describe craniofacial morphometry. These methods are painstaking and require that the patient remain still for extended periods of time. Most recently, semiautomated techniques (e.g., structured light scanning) have been developed to capture the geometry of the face in a matter of seconds. In this paper, we establish that direct anthropometry and structured light scanning yield reliable measurements, with remarkably high levels of inter-rater and intra-rater reliability, as well as validity (contrasting the two methods).

  4. New Aspects of Photocurrent Generation at Graphene pn Junctions Revealed by Ultrafast Optical Measurements

    Science.gov (United States)

    Aivazian, Grant; Sun, Dong; Jones, Aaron; Ross, Jason; Yao, Wang; Cobden, David; Xu, Xiaodong

    2012-02-01

    The remarkable electrical and optical properties of graphene make it a promising material for new optoelectronic applications. However, one important, but so far unexplored, property is the role of hot carriers in charge and energy transport at graphene interfaces. Here we investigate the photocurrent (PC) dynamics at a tunable graphene pn junction using ultrafast scanning PC microscopy. Pump-probe measurements show a temperature dependent relaxation time of photogenerated carriers that increases from 1.5ps at 290K to 4ps at 20K; while the amplitude of the PC is independent of the lattice temperature. These observations imply that it is hot carriers, not phonons, which dominate ultrafast energy transport. Gate dependent measurements show many interesting features such as pump induced saturation, enhancement, and sign reversal of probe generated PC. These observations reveal that the underlying PC mechanism is a combination of the thermoelectric and built-in electric field effects. Our results enhance the understanding of non-equilibrium electron dynamics, electron-electron interactions, and electron-phonon interactions in graphene. They also determine fundamental limits on ultrafast device operation speeds (˜500 GHz) for graphene-based photodetectors.

  5. 躯体X线测量板的研制和应用%Validation and repeatability of Limb X Film Measuring Plate

    Institute of Scientific and Technical Information of China (English)

    卫小春; 柴旭峰; 许趁心

    2008-01-01

    Objective To study the efficacy and repeatability of the Limb X Film Measuring Plate (LXMP)in clinical x film measurement of lengths and angles of limbs.Methods The LXMP was de- signed and manufactured for testing.Three known points in 9 templates were taken as golden standards.which were to be compared with measuring results of these projected points on the X film for testing efficacy of LXMP.Twenty-one patients with knees osteoarthritis were selected.The lengths and angles of their lower limbs were measured twice with the help of LXMP by an observer at different time intervals for testing in. Tra-observer repeatability.Two observers measured once on films at the same time for testing inter-observer repeatability.The correlation coefficients,mean absolute difierences between the repeated measurements,and error rate were calculated. Results The points on LXMP could be seen clearly on X film.Validation tests showed the differences in angle measurement between golden standards and measuring results for those pro- jeted points on the X film were insignificant.with mean absolute difference being O.10.-0.21,error rate being 0.12%-3.15%and r being close to 1.The differences in length measurement were insignificant ei- ther,with mean absolute differenee being 0.05 cm-0.16 cm.error rate being 0.12%-o.28%and r being close to 1.The intra-observer repeatability test for beth angles and lengths showed that r was close to I.mean absolute diffefences 0.55.and 0.1-0.37cm and error rate 0.3l%-O.97%.while the inter-observer re- peatability test showed that r was close to 1.mean absolute difierences o.39.and0.05-0.13cm and error rate O.16%-O.35%. Conclusion The Limb X Film Measuring Plate Can be used for accurately mcasuring limb lengths and angles with good efficacy and repeatability.%目的 介绍躯体X线测量板的制作方法 ,探讨其有效性、重复性,为临床X线测量提供一套精确、实用、经济的方法 和工具.方法 设计和制作躯体X线

  6. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  7. Evaluation of Multiple Imputation in Missing Data Analysis: An Application on Repeated Measurement Data in Animal Science

    Directory of Open Access Journals (Sweden)

    Gazel Ser

    2015-12-01

    Full Text Available The purpose of this study was to evaluate the performance of multiple imputation method in case that missing observation structure is at random and completely at random from the approach of general linear mixed model. The application data of study was consisted of a total 77 heads of Norduz ram lambs at 7 months of age. After slaughtering, pH values measured at five different time points were determined as dependent variable. In addition, hot carcass weight, muscle glycogen level and fasting durations were included as independent variables in the model. In the dependent variable without missing observation, two missing observation structures including Missing Completely at Random (MCAR and Missing at Random (MAR were created by deleting the observations at certain rations (10% and 25%. After that, in data sets that have missing observation structure, complete data sets were obtained using MI (multiple imputation. The results obtained by applying general linear mixed model to the data sets that were completed using MI method were compared to the results regarding complete data. In the mixed model which was applied to the complete data and MI data sets, results whose covariance structures were the same and parameter estimations and standard estimations were rather close to the complete data are obtained. As a result, in this study, it was ensured that reliable information was obtained in mixed model in case of choosing MI as imputation method in missing observation structure and rates of both cases.

  8. Bayesian hierarchical joint modeling of repeatedly measured continuous and ordinal markers of disease severity: Application to Ugandan diabetes data.

    Science.gov (United States)

    Buhule, O D; Wahed, A S; Youk, A O

    2017-08-22

    Modeling of correlated biomarkers jointly has been shown to improve the efficiency of parameter estimates, leading to better clinical decisions. In this paper, we employ a joint modeling approach to a unique diabetes dataset, where blood glucose (continuous) and urine glucose (ordinal) measures of disease severity for diabetes are known to be correlated. The postulated joint model assumes that the outcomes are from distributions that are in the exponential family and hence modeled as multivariate generalized linear mixed effects model associated through correlated and/or shared random effects. The Markov chain Monte Carlo Bayesian approach is used to approximate posterior distribution and draw inference on the parameters. This proposed methodology provides a flexible framework to account for the hierarchical structure of the highly unbalanced data as well as the association between the 2 outcomes. The results indicate improved efficiency of parameter estimates when blood glucose and urine glucose are modeled jointly. Moreover, the simulation studies show that estimates obtained from the joint model are consistently less biased and more efficient than those in the separate models. Copyright © 2017 John Wiley & Sons, Ltd.

  9. Revealing time-unlocked brain activity from MEG measurements by common waveform estimation.

    Directory of Open Access Journals (Sweden)

    Yusuke Takeda

    Full Text Available Brain activities related to cognitive functions, such as attention, occur with unknown and variable delays after stimulus onsets. Recently, we proposed a method (Common Waveform Estimation, CWE that could extract such brain activities from magnetoencephalography (MEG or electroencephalography (EEG measurements. CWE estimates spatiotemporal MEG/EEG patterns occurring with unknown and variable delays, referred to here as unlocked waveforms, without hypotheses about their shapes. The purpose of this study is to demonstrate the usefulness of CWE for cognitive neuroscience. For this purpose, we show procedures to estimate unlocked waveforms using CWE and to examine their role. We applied CWE to the MEG epochs during Go trials of a visual Go/NoGo task. This revealed unlocked waveforms with interesting properties, specifically large alpha oscillations around the temporal areas. To examine the role of the unlocked waveform, we attempted to estimate the strength of the brain activity of the unlocked waveform in various conditions. We made a spatial filter to extract the component reflecting the brain activity of the unlocked waveform, applied this spatial filter to MEG data under different conditions (a passive viewing, a simple reaction time, and Go/NoGo tasks, and calculated the powers of the extracted components. Comparing the powers across these conditions suggests that the unlocked waveforms may reflect the inhibition of the task-irrelevant activities in the temporal regions while the subject attends to the visual stimulus. Our results demonstrate that CWE is a potential tool for revealing new findings of cognitive brain functions without any hypothesis in advance.

  10. Two to five repeated measurements per patient reduced the required sample size considerably in a randomized clinical trial for patients with inflammatory rheumatic diseases

    Directory of Open Access Journals (Sweden)

    Smedslund Geir

    2013-02-01

    Full Text Available Abstract Background Patient reported outcomes are accepted as important outcome measures in rheumatology. The fluctuating symptoms in patients with rheumatic diseases have serious implications for sample size in clinical trials. We estimated the effects of measuring the outcome 1-5 times on the sample size required in a two-armed trial. Findings In a randomized controlled trial that evaluated the effects of a mindfulness-based group intervention for patients with inflammatory arthritis (n=71, the outcome variables Numerical Rating Scales (NRS (pain, fatigue, disease activity, self-care ability, and emotional wellbeing and General Health Questionnaire (GHQ-20 were measured five times before and after the intervention. For each variable we calculated the necessary sample sizes for obtaining 80% power (α=.05 for one up to five measurements. Two, three, and four measures reduced the required sample sizes by 15%, 21%, and 24%, respectively. With three (and five measures, the required sample size per group was reduced from 56 to 39 (32 for the GHQ-20, from 71 to 60 (55 for pain, 96 to 71 (73 for fatigue, 57 to 51 (48 for disease activity, 59 to 44 (45 for self-care, and 47 to 37 (33 for emotional wellbeing. Conclusions Measuring the outcomes five times rather than once reduced the necessary sample size by an average of 27%. When planning a study, researchers should carefully compare the advantages and disadvantages of increasing sample size versus employing three to five repeated measurements in order to obtain the required statistical power.

  11. The Effects of Repeat Testing, Malingering, and Traumatic Brain Injury on Computerized Measures of Visuospatial Memory Span.

    Science.gov (United States)

    Woods, David L; Wyma, John M; Herron, Timothy J; Yund, E W

    2015-01-01

    Spatial span tests (SSTs) such as the Corsi Block Test (CBT) and the SST of the Wechsler Memory Scale are widely used to assess deficits in spatial working memory. We conducted three experiments to evaluate the test-retest reliability and clinical sensitivity of a new computerized spatial span test (C-SST) that incorporates psychophysical methods to improve the precision of spatial span measurement. In Experiment 1, we analyzed C-SST test-retest reliability in 49 participants who underwent three test sessions at weekly intervals. Intraclass correlation coefficients (ICC) were higher for a psychophysically derived mean span (MnS) metric (0.83) than for the maximal span and total correct metrics used in traditional spatial-span tests. Response times (ReTs) also showed high ICCs (0.93) that correlated negatively with MnS scores and correlated positively with response-time latencies from other tests of processing speed. Learning effects were insignificant. Experiment 2 examined the performance of Experiment 1 participants when instructed to feign symptoms of traumatic brain injury (TBI): 57% showed abnormal MnS z-scores. A MnS z-score cutoff of 3.0 correctly classified 36% of simulated malingerers and 91% of the subgroup of 11 control participants with abnormal spans. Malingerers also made more substitution errors than control participants with abnormal spans (sensitivity = 43%, specificity = 91%). In addition, malingerers showed no evidence of ReT slowing, in contrast to significant abnormalities seen on other malingered tests of processing speed. As a result, differences between ReT z-scores and z-scores on other processing speed tests showed very high sensitivity and specificity in distinguishing malingering and control participants with either normal or abnormal spans. Experiment 3 examined C-SST performance in a group of patients with predominantly mild TBI: neither MnS nor ReT z-scores showed significant group-level abnormalities. The C-SST improves the

  12. Teaching renewable energy using online PBL in investigating its effect on behaviour towards energy conservation among Malaysian students: ANOVA repeated measures approach

    Science.gov (United States)

    Nordin, Norfarah; Samsudin, Mohd Ali; Hadi Harun, Abdul

    2017-01-01

    This research aimed to investigate whether online problem based learning (PBL) approach to teach renewable energy topic improves students’ behaviour towards energy conservation. A renewable energy online problem based learning (REePBaL) instruction package was developed based on the theory of constructivism and adaptation of the online learning model. This study employed a single group quasi-experimental design to ascertain the changed in students’ behaviour towards energy conservation after underwent the intervention. The study involved 48 secondary school students in a Malaysian public school. ANOVA Repeated Measure technique was employed in order to compare scores of students’ behaviour towards energy conservation before and after the intervention. Based on the finding, students’ behaviour towards energy conservation improved after the intervention.

  13. The effect of technical replicate (repeats) on Nix Pro Color Sensor™ measurement precision for meat: A case-study on aged beef colour stability.

    Science.gov (United States)

    Holman, Benjamin W B; Collins, Damian; Kilgannon, Ashleigh K; Hopkins, David L

    2017-09-04

    The Nix Pro Colour Sensor™ (NIX) can be potentially used to measure meat colour, but procedural guidelines that assure measurement reproducibility and repeatability (precision) must first be established. Technical replicate number (r) will minimise response variation, measureable as standard error of predicted mean (SEM), and contribute to improved precision. Consequently, we aimed to explore the effects of r on NIX precision when measuring aged beef colour (colorimetrics; L*, a*, b*, hue and chroma values). Each colorimetric SEM declined with increasing r to indicate improved precision and followed a diminishing rate of improvement that allowed us to recommend r=7 for meat colour studies using the NIX. This definition was based on practical limitations and a* variability, as additional r would be required if other colorimetrics or advanced levels of precision are necessary. Beef ageing and display period, holding temperature, loin and sampled portion were also found to contribute to colorimetric variation, but were incorporated within our definition of r. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  14. Measurement of Surface Displacement and Deformation of Mass Movements Using Least Squares Matching of Repeat High Resolution Satellite and Aerial Images

    Directory of Open Access Journals (Sweden)

    Misganu Debella-Gilo

    2012-01-01

    Full Text Available Displacement and deformation are fundamental measures of Earth surface mass movements such as glacier flow, rockglacier creep and rockslides. Ground-based methods of monitoring such mass movements can be costly, time consuming and limited in spatial and temporal coverage. Remote sensing techniques, here matching of repeat optical images, are increasingly used to obtain displacement and deformation fields. Strain rates are usually computed in a post-processing step based on the gradients of the measured velocity field. This study explores the potential of automatically and directly computing velocity, rotation and strain rates on Earth surface mass movements simultaneously from the matching positions and the parameters of the geometric transformation models using the least squares matching (LSM approach. The procedures are exemplified using bi-temporal high resolution satellite and aerial images of glacier flow, rockglacier creep and land sliding. The results show that LSM matches the images and computes longitudinal strain rates, transverse strain rates and shear strain rates reliably with mean absolute deviations in the order of 10−4 (one level of significance below the measured values as evaluated on stable grounds. The LSM also improves the accuracy of displacement estimation of the pixel-precision normalized cross-correlation by over 90% under ideal (simulated circumstances and by about 25% for real multi-temporal images of mass movements.

  15. Lumbar spine and pelvic posture between standing and sitting: a radiologic investigation including reliability and repeatability of the lumbar lordosis measure.

    Science.gov (United States)

    De Carvalho, Diana E; Soave, David; Ross, Kim; Callaghan, Jack P

    2010-01-01

    Sitting has been identified as a cause of mechanical low back pain. The purpose of this study was to use plain film x-rays to measure lumbar spine and pelvic posture differences between standing and sitting. Eight male subjects were radiographed standing and sitting in an automobile seat. Measures of lumbar lordosis, intervertebral disk angles, lumbosacral angle, lumbosacral lordosis, and sacral tilt were completed. One-way analysis of variance (alpha = .05) was conducted on the variables stated above. A Bland-Altman analysis was conducted to assess agreement and repeatability of the lumbar lordosis angle using 2 raters. Lumbar lordosis values in standing (average, 63 degrees +/- 15 degrees ) and sacral inclination (average, 43 degrees +/- 10 degrees ) decreased by 43 degrees and 44 degrees , respectively, in sitting. Intervertebral joint angles in sitting underwent substantial flexion (L1/L2-5 degrees [+/-3 degrees ], L2/L3-7 degrees [+/-3 degrees ], L3/L4-8 degrees [+/-3 degrees ], L4/L5-13 degrees [+/-3 degrees ], and L5/S1-4 degrees [+/-10 degrees ]). Measures of lumbar lordosis; intervertebral disk angles between L2/L3, L3/L4, and L4/L5; lumbosacral lordosis; lumbosacral angle; and sacral tilt were significantly decreased between standing and sitting (P posture should be investigated because they may play a role in preventing injury and low back pain. Copyright 2010 National University of Health Sciences. Published by Mosby, Inc. All rights reserved.

  16. Seismic measurements to reveal short-term variations in the elastic properties of the Earth crust

    Science.gov (United States)

    Piccinini, Davide; Zaccarelli, Lucia; Pastori, Marina; Margheriti, Lucia; Pio Lucente, Francesco; De Gori, Pasquale; Faenza, Licia; Soldati, Gaia

    2013-04-01

    Since the late the late '60s-early '70s era seismologists started developed theories that included variations of the elastic property of the Earth crust and the state of stress and its evolution crust prior to the occurrence of a large earthquake. Among the others the theory of the dilatancy (Scholz et al., 1973): when a rock is subject to stress, the rock grains are shifted generating micro-cracks, thus the rock itself increases its volume. Inside the fractured rock, fluid saturation and pore pressure play an important role in earthquake nucleation, by modulating the effective stress. Thus measuring the variations of wave speed and of anisotropic parameter in time can be highly informative on how the stress leading to a major fault failure builds up. In 80s and 90s such kind of research on earthquake precursor slowed down and the priority was given to seismic hazard and ground motions studies, which are very important since these are the basis for the building codes in many countries. Today we have dense and sophisticated seismic networks to measure wave-fields characteristics: we archive continuous waveform data recorded at three components broad-band seismometers, we almost routinely obtain high resolution earthquake locations. Therefore we are ready to start to systematically look at seismic-wave propagation properties to possibly reveal short-term variations in the elastic properties of the Earth crust. One seismological quantity which, since the '70s, is recognized to be diagnostic of the level of fracturation and/or of the pore pressure in the rock, hence of its state of stress, is the ratio between the compressional (P-wave) and the shear (S-wave) seismic velocities, the Vp/Vs (Nur, 1972; Kisslinger and Engdahl, 1973). Variations of this ratio have been recently observed and measured during the preparatory phase of a major earthquake (Lucente et al. 2010). In active fault areas and volcanoes, tectonic stress variation influences fracture field orientation

  17. 基于同频RF直放站的回波测量方法%Technique of measuring the echo for RF repeaters in single frequency networks

    Institute of Scientific and Technical Information of China (English)

    陈哲; 宋葛

    2011-01-01

    直放站的同频转发模式存在收发天线间互耦的问题,接收天线在接收主基站的信号时,同时接收到直放站发射天线发射的信号,以同频RF直放站调试隔离度为技术背景,提出了同频RF直放站的回波测量方法.该方法利用CAZAC码实现的初估计快速地估计出回波信道的特性,自适应LMS算法的使用可以进一步跟踪信道的变化.通过MATLAB仿真后,在数字硬件平台上用FPGA实现该方法,并用数字电视信号CMMB做为信号源对系统进行了测试,结果说明此种测量方法准确、实用.%The signal transition mode of repeater which works on the same frequency has some troubles on signal coupling between receive and transmit aerials,the signal from transmit aerial may leak out into receive aerial. This paper presents a method of measuring the echo under the context of isolation test for RF repeaters in single frequency networks. The experimental apparatus firstly uses CAZAC code as the method of channel initial estimation, secondly uses LMS arithmetic to track the change of the channel. After the MATLAB simulation realization has been achieved by FPGA on real digital hardware board. The result of test which uses DTV signal (CMMB) as the source proves the function of method achieved accurately.

  18. Repeat, Low Altitude Measurements of Vegetation Status and Biomass Using Manned Aerial and UAS Imagery in a Piñon-Juniper Woodland

    Science.gov (United States)

    Krofcheck, D. J.; Lippitt, C.; Loerch, A.; Litvak, M. E.

    2015-12-01

    Measuring the above ground biomass of vegetation is a critical component of any ecological monitoring campaign. Traditionally, biomass of vegetation was measured with allometric-based approach. However, it is also time-consuming, labor-intensive, and extremely expensive to conduct over large scales and consequently is cost-prohibitive at the landscape scale. Furthermore, in semi-arid ecosystems characterized by vegetation with inconsistent growth morphologies (e.g., piñon-juniper woodlands), even ground-based conventional allometric approaches are often challenging to execute consistently across individuals and through time, increasing the difficulty of the required measurements and consequently the accuracy of the resulting products. To constrain the uncertainty associated with these campaigns, and to expand the extent of our measurement capability, we made repeat measurements of vegetation biomass in a semi-arid piñon-juniper woodland using structure-from-motion (SfM) techniques. We used high-spatial resolution overlapping aerial images and high-accuracy ground control points collected from both manned aircraft and multi-rotor UAS platforms, to generate digital surface model (DSM) for our experimental region. We extracted high-precision canopy volumes from the DSM and compared these to the vegetation allometric data, s to generate high precision canopy volume models. We used these models to predict the drivers of allometric equations for Pinus edulis and Juniperous monosperma (canopy height, diameter at breast height, and root collar diameter). Using this approach, we successfully accounted for the carbon stocks in standing live and standing dead vegetation across a 9 ha region, which contained 12.6 Mg / ha of standing dead biomass, with good agreement to our field plots. Here we present the initial results from an object oriented workflow which aims to automate the biomass estimation process of tree crown delineation and volume calculation, and partition

  19. Automated gray level index measurements reveal only minor cytoarchitectonic changes of Brodmann area 9 in schizophrenia.

    Science.gov (United States)

    Tepest, Ralf; Vogeley, Kai; Viebahn, Bettina; Schneider-Axmann, Thomas; Honer, William G; Falkai, Peter

    2008-07-15

    Using an automatized gray level index (GLI) method, we recently found cytoarchitectonic abnormalities in schizophrenia in Brodmann area 10 (BA10) [Vogeley, K., Tepest, R., Schneider-Axmann, T., Hutte, H., Zilles, K., Honer, W.G., Falkai, P., 2003. Automated image analysis of disturbed cytoarchitecture in Brodmann area 10 in schizophrenia, Schizophrenia Research 62, 133-140]. As another potential key region involved in the pathophysiology of schizophrenia, we have now investigated BA9 in the same sample consisting of 20 schizophrenic cases and 20 controls. The GLI value represents the area-percentage covered by perikarya in measuring fields of microscopic images. BA9 was analyzed with respect to the factors diagnosis and gender for six different compartments approximately corresponding to the neocortical layers. The main result in BA9 was a significant interaction of diagnosis and gender for GLI in layers IV and V on the left side. Subsequent analyses separately performed concerning gender revealed a significant GLI increase in layer V on the left side in male patients compared with controls. However, after an adjustment of error probabilities for multiple testing, differences did not reach significance. No GLI difference was observed in the sample between diagnostic groups for females and between the diagnostic groups in general. Comparisons with our BA10 results suggest that cytoarchitectural changes relevant to schizophrenia appear different in various Brodmann areas. Since increases in GLI were found only in selected layers (V and VI) of BA9, these findings do not support a generalized neuropil reduction across all cortical layers.

  20. Revealed Comparative Advantage and the Alternatives as Measures of International Specialization

    DEFF Research Database (Denmark)

    Laursen, Keld

    2015-01-01

    This paper provides an analysis of Balassa's 'revealed comparative advantage' (RCA). It shows that when using RCA, it should be adjusted such that it becomes symmetric around its neutral value. The proposed adjusted index is called 'revealed symmetric comparative advantage' (RSCA). The theoretical...

  1. All-photonic quantum repeaters

    Science.gov (United States)

    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

  2. Seasonal variation in objectively measured physical activity, sedentary time, cardio-respiratory fitness and sleep duration among 8–11 year-old Danish children: a repeated-measures study

    DEFF Research Database (Denmark)

    Hjorth, Mads F.; Chaput, Jean-Philippe; Michaelsen, Kim;

    2013-01-01

    BACKGROUND: Understanding fluctuations in lifestyle indicators is important to identify relevant time periods to intervene in order to promote a healthy lifestyle; however, objective assessment of multiple lifestyle indicators has never been done using a repeated-measures design. The primary aim...... was, therefore, to examine between-season and within-week variation in physical activity, sedentary behaviour, cardio-respiratory fitness and sleep duration among 8–11 year-old children. METHODS: A total of 1021 children from nine Danish schools were invited to participate and 834 accepted. Due...

  3. Evaluation of the running-based anaerobic sprint test as a measure of repeated sprint ability in collegiate-level soccer players.

    Science.gov (United States)

    Keir, Daniel A; Thériault, Francis; Serresse, Olivier

    2013-06-01

    Repeated sprint ability (RSA) refers to an individual's ability to perform maximal sprints of short duration in succession with little recovery between sprints. The running-based anaerobic sprint test (RAST) has been adapted from the Wingate anaerobic test (WAnT) protocol as a tool to assess RSA and anaerobic power. The purpose of this study was to evaluate the relationship between performance variables and physiological responses obtained during the RAST and the WAnT using 8 collegiate-level soccer players. Participants performed a single trial of both the WAnT and the RAST. Breath-by-breath gas exchange was monitored throughout each trial, and blood lactate (BL) measures were recorded postexercise. The oxygen uptake (VO2) profile suggested that the RAST required greater contributions from aerobic metabolism although there was no difference in VO2peak (p < 0.05). Peak BL values were also similar between the RAST and the WAnT (p < 0.05). Neither peak physiological values nor performance variables (peak and mean power) were significantly correlated between protocols. The weak association in physiological responses indicates that different combinations of metabolic contributions exist between protocols, suggesting that individual performances on each test are not related in collegiate soccer players. Further studies on these relationships with players of other competitive levels and team sport athletes are warranted.

  4. Using the American alligator and a repeated-measures design to place constraints on in vivo shoulder joint range of motion in dinosaurs and other fossil archosaurs.

    Science.gov (United States)

    Hutson, Joel D; Hutson, Kelda N

    2013-01-15

    Using the extant phylogenetic bracket of dinosaurs (crocodylians and birds), recent work has reported that elbow joint range of motion (ROM) studies of fossil dinosaur forearms may be providing conservative underestimates of fully fleshed in vivo ROM. As humeral ROM occupies a more central role in forelimb movements, the placement of quantitative constraints on shoulder joint ROM could improve fossil reconstructions. Here, we investigated whether soft tissues affect the more mobile shoulder joint in the same manner in which they affect elbow joint ROM in an extant archosaur. This test involved separately and repeatedly measuring humeral ROM in Alligator mississippiensis as soft tissues were dissected away in stages to bare bone. Our data show that the ROMs of humeral flexion and extension, as well as abduction and adduction, both show a statistically significant increase as flesh is removed, but then decrease when the bones must be physically articulated and moved until they separate from one another and/or visible joint surfaces. A similar ROM pattern is inferred for humeral pronation and supination. All final skeletonized ROMs were less than initial fully fleshed ROMs. These results are consistent with previously reported elbow joint ROM patterns from the extant phylogenetic bracket of dinosaurs. Thus, studies that avoid separation of complementary articular surfaces may be providing fossil shoulder joint ROMs that underestimate in vivo ROM in dinosaurs, as well as other fossil archosaurs.

  5. Knowledge and skill retention of in-service versus preservice nursing professionals following an informal training program in pediatric cardiopulmonary resuscitation: a repeated-measures quasiexperimental study.

    Science.gov (United States)

    Sankar, Jhuma; Vijayakanthi, Nandini; Sankar, M Jeeva; Dubey, Nandkishore

    2013-01-01

    Our objective was to compare the impact of a training program in pediatric cardiopulmonary resuscitation (CPR) on the knowledge and skills of in-service and preservice nurses at prespecified time points. This repeated-measures quasiexperimental study was conducted in the pediatric emergency and ICU of a tertiary care teaching hospital between January and March 2011. We assessed the baseline knowledge and skills of nursing staff (in-service nurses) and final year undergraduate nursing students (preservice nurses) using a validated questionnaire and a skill checklist, respectively. The participants were then trained on pediatric CPR using standard guidelines. The knowledge and skills were reassessed immediately after training and at 6 weeks after training. A total of 74 participants-28 in-service and 46 preservice professionals-were enrolled. At initial assessment, in-service nurses were found to have insignificant higher mean knowledge scores (6.6 versus 5.8, P = 0.08) while the preservice nurses had significantly higher skill scores (6.5 versus 3.2, P nurses performing better in knowledge test (10.5 versus 9.1, P = 0.01) and the preservice nurses performing better in skill test (9.8 versus 7.4, P skills of in-service and preservice nurses in pediatric CPR improved with training. In comparison to preservice nurses, the in-service nurses seemed to retain knowledge better with time than skills.

  6. Direct and accurate measurement of CAG repeat configuration in the ataxin-1 (ATXN-1) gene by "dual-fluorescence labeled PCR-restriction fragment length analysis".

    Science.gov (United States)

    Lin, Jiang X; Ishikawa, Kinya; Sakamoto, Masaki; Tsunemi, Taiji; Ishiguro, Taro; Amino, Takeshi; Toru, Shuta; Kondo, Ikuko; Mizusawa, Hidehiro

    2008-01-01

    Spinocerebellar ataxia type 1 (SCA1; OMIM: #164400) is an autosomal dominant cerebellar ataxia caused by an expansion of CAG repeat, which encodes polyglutamine, in the ataxin-1 (ATXN1) gene. Length of polyglutamine in the ATXN1 protein is the critical determinant of pathogenesis of this disease. Molecular diagnosis of SCA1 is usually undertaken by assessing the length of CAG repeat configuration using primers spanning this configuration. However, this conventional method may potentially lead to misdiagnosis in assessing polyglutamine-encoding CAG repeat length, since CAT interruptions may be present within the CAG repeat configuration, not only in normal controls but also in neurologically symptomatic subjects. We developed a new method for assessing actual CAG repeat numbers not interrupted by CAT sequences. Polymerase chain reaction using a primer pair labeled with two different fluorescences followed by restriction enzyme digestion with SfaNI which recognizes the sequence "GCATC(N)(5)", lengths of actual CAG repeats that encode polyglutamine were directly detected. We named this method "dual fluorescence labeled PCR-restriction fragment length analysis". We found that numbers of actual CAG repeat encoding polyglutamine do not overlap between our cohorts of normal chromosomes (n=385) and SCA1 chromosomes (n=5). We conclude that the present method is a useful way for molecular diagnosis of SCA1.

  7. Genome-wide Characterization of Long Terminal Repeat-retrotransposons in Apple Reveals the Differences in Heterogeneity and Copy Number between Ty1-copia and Ty3-gypsy Retrotransposons

    Institute of Scientific and Technical Information of China (English)

    Hai-Yue Sun; Hong-Yan Dai; Gui-Ling Zhao; Yue Ma; Chun-Qing Ou; He Li; Lin-Guang Li; Zhi-Hong Zhang

    2008-01-01

    The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of long terminal repeat (LTR) retrotransposons were isolated from the Malus domestica genome using degenerate oligonucleotide primers.Sequence analysis showed that 45% of Ty1-copia and 63% of Ty3-gypsy RT sequences contained premature stop codons and/or indels disrupting the reading frame.High heterogeneity among RT sequences of both Tyl-copia and Ty3-gypsy group retrotransposons was observed,but Ty3-gypsy group retrotransposons in the apple genome are less heterogeneous than Ty1-copia elements.Retrotransposon copy number was estimated by dot blot hybridizations for Ty1-copia (~500O) and Ty3-gypsy ( ~26000).All elements of the two types of LTR retrotransposons comprise approximately 38% of the M.domestica genome,with the Ty3-gypsy group contribution being higher (33.5%) than the Ty1-copia one (4.6%).Transcription was not detected by reverse transcription-polymerase chain reaction for either Tyl.copia or Ty3-gypsy retrotransposons in the leaves of plants in vitro or in leaf explants cultured on medium supplemented with high concentration benzylaminopurine.This research reveals the differences in heterogeneity and copy number between Ty1-copia and Ty3-gypsy retrotransposons in the apple genome.Ty1-copia retrotransposon has higher heterogeneity than Ty3-gypsy retrotransposon,but the latter has a higher copy number,which implies that Ty3-gypsy retrotransposons may play a more important role in the apple genome evolution.

  8. Origin of the Outbreak in France of Pseudomonas syringae pv. actinidiae Biovar 3, the Causal Agent of Bacterial Canker of Kiwifruit, Revealed by a Multilocus Variable-Number Tandem-Repeat Analysis

    Science.gov (United States)

    Cunty, A.; Cesbron, S.; Poliakoff, F.; Jacques, M.-A.

    2015-01-01

    The first outbreaks of bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae biovar 3 were detected in France in 2010. P. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. P. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. In order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in France, we developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). MLVA was conducted on 340 strains of P. syringae pv. actinidiae biovar 3 isolated in Chile, China, France, Italy, and New Zealand and on 39 strains of P. syringae pv. actinidifoliorum isolated in Australia, France, and New Zealand. Eleven polymorphic VNTR loci were identified in the genomes of P. syringae pv. actinidiae biovar 3 ICMP 18744 and of P. syringae pv. actinidifoliorum ICMP 18807. MLVA enabled the structuring of P. syringae pv. actinidiae biovar 3 and P. syringae pv. actinidifoliorum strains in 55 and 16 haplotypes, respectively. MLVA and discriminant analysis of principal components revealed that strains isolated in Chile, China, and New Zealand are genetically distinct from P. syringae pv. actinidiae strains isolated in France and in Italy, which appear to be closely related at the genetic level. In contrast, no structuring was observed for P. syringae pv. actinidifoliorum. We developed an MLVA scheme to explore the diversity within P. syringae pv. actinidiae biovar 3 and to trace the dispersal routes of epidemic P. syringae pv. actinidiae biovar 3 in Europe. We suggest using this MLVA scheme to trace the dispersal routes of P. syringae pv. actinidiae at a global level. PMID:26209667

  9. Simulated Conversations With Virtual Humans to Improve Patient-Provider Communication and Reduce Unnecessary Prescriptions for Antibiotics: A Repeated Measure Pilot Study

    Science.gov (United States)

    2017-01-01

    Background Despite clear evidence that antibiotics do not cure viral infections, the problem of unnecessary prescribing of antibiotics in ambulatory care persists, and in some cases, prescribing patterns have increased. The overuse of antibiotics for treating viral infections has created numerous economic and clinical consequences including increased medical costs due to unnecessary hospitalizations, antibiotic resistance, disruption of gut bacteria, and obesity. Recent research has underscored the importance of collaborative patient-provider communication as a means to reduce the high rates of unnecessary prescriptions for antibiotics. However, most patients and providers do not feel prepared to engage in such challenging conversations. Objectives The aim of this pilot study was to assess the ability of a brief 15-min simulated role-play conversation with virtual humans to serve as a preliminary step to help health care providers and patients practice, and learn how to engage in effective conversations about antibiotics overuse. Methods A total of 69 participants (35 providers and 34 patients) completed the simulation once in one sitting. A pre-post repeated measures design was used to assess changes in patients’ and providers’ self-reported communication behaviors, activation, and preparedness, intention, and confidence to effectively communicate in the patient-provider encounter. Changes in patients’ knowledge and beliefs regarding antibiotic use were also evaluated. Results Patients experienced a short-term positive improvement in beliefs about appropriate antibiotic use for infection (F1,30=14.10, P=.001). Knowledge scores regarding the correct uses of antibiotics improved immediately postsimulation, but decreased at the 1-month follow-up (F1,30=31.16, P.10) Patients with lower levels of activation exhibited positive, short-term benefits in increased intent and confidence to discuss their needs and ask questions in the clinic visit, positive attitudes

  10. Telomere shortening unrelated to smoking, body weight, physical activity, and alcohol intake: 4,576 general population individuals with repeat measurements 10 years apart.

    Directory of Open Access Journals (Sweden)

    Maren Weischer

    2014-03-01

    Full Text Available Cross-sectional studies have associated short telomere length with smoking, body weight, physical activity, and possibly alcohol intake; however, whether these associations are due to confounding is unknown. We tested these hypotheses in 4,576 individuals from the general population cross-sectionally, and with repeat measurement of relative telomere length 10 years apart. We also tested whether change in telomere length is associated with mortality and morbidity in the general population. Relative telomere length was measured with quantitative polymerase chain reaction. Cross-sectionally at the first examination, short telomere length was associated with increased age (P for trend across quartiles = 3 × 10(-77, current smoking (P = 8 × 10(-3, increased body mass index (P = 7 × 10(-14, physical inactivity (P = 4 × 10(-17, but not with increased alcohol intake (P = 0.10. At the second examination 10 years later, 56% of participants had lost and 44% gained telomere length with a mean loss of 193 basepairs. Change in leukocyte telomere length during 10 years was associated inversely with baseline telomere length (P<1 × 10(-300 and age at baseline (P = 1 × 10(-27, but not with baseline or 10-year inter-observational tobacco consumption, body weight, physical activity, or alcohol intake. Prospectively during a further 10 years follow-up after the second examination, quartiles of telomere length change did not associate with risk of all-cause mortality, cancer, chronic obstructive pulmonary disease, diabetes mellitus, ischemic cerebrovascular disease, or ischemic heart disease. In conclusion, smoking, increased body weight, and physical inactivity were associated with short telomere length cross-sectionally, but not with telomere length change during 10 years observation, and alcohol intake was associated with neither. Also, change in telomere length did not associate prospectively with mortality or morbidity in the general population.

  11. Joint modeling of repeated multivariate cognitive measures and competing risks of dementia and death: a latent process and latent class approach.

    Science.gov (United States)

    Proust-Lima, Cécile; Dartigues, Jean-François; Jacqmin-Gadda, Hélène

    2016-02-10

    Joint models initially dedicated to a single longitudinal marker and a single time-to-event need to be extended to account for the rich longitudinal data of cohort studies. Multiple causes of clinical progression are indeed usually observed, and multiple longitudinal markers are collected when the true latent trait of interest is hard to capture (e.g., quality of life, functional dependency, and cognitive level). These multivariate and longitudinal data also usually have nonstandard distributions (discrete, asymmetric, bounded, etc.). We propose a joint model based on a latent process and latent classes to analyze simultaneously such multiple longitudinal markers of different natures, and multiple causes of progression. A latent process model describes the latent trait of interest and links it to the observed longitudinal outcomes using flexible measurement models adapted to different types of data, and a latent class structure links the longitudinal and cause-specific survival models. The joint model is estimated in the maximum likelihood framework. A score test is developed to evaluate the assumption of conditional independence of the longitudinal markers and each cause of progression given the latent classes. In addition, individual dynamic cumulative incidences of each cause of progression based on the repeated marker data are derived. The methodology is validated in a simulation study and applied on real data about cognitive aging obtained from a large population-based study. The aim is to predict the risk of dementia by accounting for the competing death according to the profiles of semantic memory measured by two asymmetric psychometric tests.

  12. In situ measurements reveal extremely low pH in soil

    DEFF Research Database (Denmark)

    Nielsen, Knud Erik; Nielsen, Lars Peter; Damgaard, Christian Frølund

    2017-01-01

    We measured pH in situ in the top organic soil horizons in heathland and pine forest and found values between 2.6 and 3.2. This was 0.5e0.8 units lower than concurrent laboratory pH measurements of the same soil, which raises questions about the interpretation of pH measurements. We propose...... that the higher pH recorded by standard laboratory methods may be due to buffering ions from soil biota released from drying, grinding and rewetting of soil samples, whereas the in situ pH reflects the correct level of acidification....

  13. An evaluation of a structured learning program as a component of the clinical practicum in undergraduate nurse education: A repeated measures analysis.

    Science.gov (United States)

    Watt, Elizabeth; Murphy, Maria; MacDonald, Lee; Pascoe, Elizabeth; Storen, Heather; Scanlon, Andrew

    2016-01-01

    There is evidence that nursing students experience stress and anxiety and a reduction in self-efficacy when undertaking clinical placements. Previous reports have identified that a structured three-day program within the Bachelor of Nursing (BN) clinical practicum reduces the students self-report of anxiety and increases self-efficacy. However, it is unreported whether these improved outcomes are sustained for the duration of the clinical placement. The aim of this study was to evaluate the duration of the effect of a three-day structured learning program within the clinical placement on final year Bachelor of Nursing student's report of anxiety and self-efficacy pre- and post-program participation in this intervention and following completion of the clinical practicum. A repeated measures design. University-based Clinical School of Nursing, acute care clinical practicum. Final year Bachelor of Nursing students. The intervention comprised the three-day program on starting the clinical practicum. A questionnaire included the anxiety subscale of The Hospital Anxiety & Depression Scale (The HAD) and the General Self-Efficacy Scale (GSES-12). The questionnaire was completed on day one (time one), upon completion of the three-day program (time two) and upon completion of placement on day 18 (time three). The questionnaire response rate varied over time. There was a statistically significant effect in reducing anxiety over time: F(1.73,74.46)=25.20, plearning program and the benefit of the intervention is sustained for the clinical placement duration. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Which are the most useful scales for predicting repeat self-harm? A systematic review evaluating risk scales using measures of diagnostic accuracy

    Science.gov (United States)

    Quinlivan, L; Cooper, J; Davies, L; Hawton, K; Gunnell, D; Kapur, N

    2016-01-01

    Objectives The aims of this review were to calculate the diagnostic accuracy statistics of risk scales following self-harm and consider which might be the most useful scales in clinical practice. Design Systematic review. Methods We based our search terms on those used in the systematic reviews carried out for the National Institute for Health and Care Excellence self-harm guidelines (2012) and evidence update (2013), and updated the searches through to February 2015 (CINAHL, EMBASE, MEDLINE, and PsychINFO). Methodological quality was assessed and three reviewers extracted data independently. We limited our analysis to cohort studies in adults using the outcome of repeat self-harm or attempted suicide. We calculated diagnostic accuracy statistics including measures of global accuracy. Statistical pooling was not possible due to heterogeneity. Results The eight papers included in the final analysis varied widely according to methodological quality and the content of scales employed. Overall, sensitivity of scales ranged from 6% (95% CI 5% to 6%) to 97% (CI 95% 94% to 98%). The positive predictive value (PPV) ranged from 5% (95% CI 3% to 9%) to 84% (95% CI 80% to 87%). The diagnostic OR ranged from 1.01 (95% CI 0.434 to 2.5) to 16.3 (95%CI 12.5 to 21.4). Scales with high sensitivity tended to have low PPVs. Conclusions It is difficult to be certain which, if any, are the most useful scales for self-harm risk assessment. No scales perform sufficiently well so as to be recommended for routine clinical use. Further robust prospective studies are warranted to evaluate risk scales following an episode of self-harm. Diagnostic accuracy statistics should be considered in relation to the specific service needs, and scales should only be used as an adjunct to assessment. PMID:26873046

  15. Noninvasive neutron scattering measurements reveal slower cholesterol transport in model lipid membranes.

    Science.gov (United States)

    Garg, S; Porcar, L; Woodka, A C; Butler, P D; Perez-Salas, U

    2011-07-20

    Proper cholesterol transport is essential to healthy cellular activity and any abnormality can lead to several fatal diseases. However, complete understandings of cholesterol homeostasis in the cell remains elusive, partly due to the wide variability in reported values for intra- and intermembrane cholesterol transport rates. Here, we used time-resolved small-angle neutron scattering to measure cholesterol intermembrane exchange and intramembrane flipping rates, in situ, without recourse to any external fields or compounds. We found significantly slower transport kinetics than reported by previous studies, particularly for intramembrane flipping where our measured rates are several orders of magnitude slower. We unambiguously demonstrate that the presence of chemical tags and extraneous compounds employed in traditional kinetic measurements dramatically affect the system thermodynamics, accelerating cholesterol transport rates by an order of magnitude. To our knowledge, this work provides new insights into cholesterol transport process disorders, and challenges many of the underlying assumptions used in most cholesterol transport studies to date.

  16. Revealing the connectivity of groundwater and surface water using electromagnetic induction measurements

    Science.gov (United States)

    Binley, A. M.; McLachlan, P.; Chambers, J. E.; Uhlemann, S.

    2016-12-01

    It is now widely recognised that hydrological and biogeochemical processes that occur at the interface of groundwater (GW) and surface water (SW) can have a significant impact on catchment water quality and ecosystem health. Significant heterogeneity in the fabric of the subsurface at the GW-SW interface can lead to complex fluid flow pathways, both of which can exert a strong control on biogeochemical cycling. Revealing such heterogeneity remains a challenge because of the limitations of traditional field experimental processes. Such traditional techniques are often invasive, which often prevents their use in ecologically sensitive environments. Furthermore, they are often limited to localised characterisation. Studies to date have thus focussed on relatively small (easily accessible) stream environments, at short reach, or plot, scales. There is a clear demand for techniques that can capture the heterogeneity of sediments and pore fluids over larger scales. Geophysical methods may offer valuable information at such scales, particularly when used in combination with traditional sampling approaches. The value of electrical methods for revealing detailed information about the heterogeneity of sediments at the GW-SW interface has been demonstrated, and in a few studies such methods have assisted tracer tests in mapping the solute pathways. However, most investigations have been confined to relatively small scale (tens of metres). There is growing (and renewed) interest in the use of frequency domain electromagnetic induction (EMI) techniques in hydrogeophysics. At the GW-SW interface these methods allow rapid, non-invasive exploration of the top few metres. Relatively recent technological developments have provided multi-coil instrumentation, permitting rapid assessment of electrical conductivity at multiple depths of investigation. Here, we demonstrate the effectiveness of EMI for revealing the heterogeneity of sediments and flow pathways at the GW-SW interface. We

  17. Your Mind Wanders Weakly, Your Mind Wanders Deeply: Objective Measures Reveal Mindless Reading at Different Levels

    Science.gov (United States)

    Schad, Daniel J.; Nuthmann, Antje; Engbert, Ralf

    2012-01-01

    Time Factors (Learning);When the mind wanders, attention turns away from the external environment and cognitive processing is decoupled from perceptual information. Mind wandering is usually treated as a dichotomy (dichotomy-hypothesis), and is often measured using self-reports. Here, we propose the levels of inattention hypothesis, which…

  18. Measuring with the heart's rhythm: hidden particles reveal flow in chicken embryo hearts

    NARCIS (Netherlands)

    Van de Graaf, A.

    2004-01-01

    Blood is said to be thicker than water, and it may come as a surprise to learn that red blood cells 8 micrometres across routinely manage to work their way through minute blood vessels no more than 5 micrometre in diameter. How they do so remains a mystery, but thanks to a noninvasive optical measur

  19. Measurement of refractive index by nanoparticle tracking analysis reveals heterogeneity in extracellular vesicles

    Directory of Open Access Journals (Sweden)

    Chris Gardiner

    2014-11-01

    Full Text Available Introduction: Optical techniques are routinely used to size and count extracellular vesicles (EV. For comparison of data from different methods and laboratories, suitable calibrators are essential. A suitable calibrator must have a refractive index (RI as close to that of EV as possible but the RI of EV is currently unknown. To measure EV, RI requires accurate knowledge of size and light scattering. These are difficult to measure as most EVs cannot be resolved by light microscopy and their diameter is smaller than the wavelength of visible light. However, nanoparticle tracking analysis (NTA provides both size and relative light scattering intensity (rLSI values. We therefore sought to determine whether it was possible to use NTA to measure the RI of individual EVs. Methods: NTA was used to measure the rLSI and size of polystyrene and silica microspheres of known size and RI (1.470 and 1.633, respectively and of EV isolated from a wide range of cells. We developed software, based on Mie scattering code, to calculate particle RI from the rLSI data. This modelled theoretical scattering intensities for polystyrene and silica microspheres of known size (100 and 200 nm and RI. The model was verified using data from the polystyrene and silica microspheres. Size and rLSI data for each vesicle were processed by the software to generate RI values. Results: The following modal RI measurements were obtained: fresh urinary EV 1.374, lyophilised urinary EV 1.367, neuroblastoma EV 1.393, blood EV 1.398, EV from activated platelets 1.390, small placental EV 1.364–1.375 and 1.398–1.414 for large placental EV (>200 nm. Large placental EV had a significantly higher RI than small placental EV (p1.40 were observed for some large (>200 nm microvesicles. Conclusion: This method for measuring EV RI will be useful for developing appropriate calibrators for EV measurement.

  20. Quantum criticality at the superconductor-insulator transition revealed by specific heat measurements.

    Science.gov (United States)

    Poran, S; Nguyen-Duc, T; Auerbach, A; Dupuis, N; Frydman, A; Bourgeois, Olivier

    2017-02-22

    The superconductor-insulator transition (SIT) is considered an excellent example of a quantum phase transition that is driven by quantum fluctuations at zero temperature. The quantum critical point is characterized by a diverging correlation length and a vanishing energy scale. Low-energy fluctuations near quantum criticality may be experimentally detected by specific heat, cp, measurements. Here we use a unique highly sensitive experiment to measure cp of two-dimensional granular Pb films through the SIT. The specific heat shows the usual jump at the mean field superconducting transition temperature marking the onset of Cooper pairs formation. As the film thickness is tuned towards the SIT, is relatively unchanged, while the magnitude of the jump and low-temperature specific heat increase significantly. This behaviour is taken as the thermodynamic fingerprint of quantum criticality in the vicinity of a quantum phase transition.

  1. Quantum criticality at the superconductor-insulator transition revealed by specific heat measurements

    Science.gov (United States)

    Poran, S.; Nguyen-Duc, T.; Auerbach, A.; Dupuis, N.; Frydman, A.; Bourgeois, Olivier

    2017-01-01

    The superconductor–insulator transition (SIT) is considered an excellent example of a quantum phase transition that is driven by quantum fluctuations at zero temperature. The quantum critical point is characterized by a diverging correlation length and a vanishing energy scale. Low-energy fluctuations near quantum criticality may be experimentally detected by specific heat, cp, measurements. Here we use a unique highly sensitive experiment to measure cp of two-dimensional granular Pb films through the SIT. The specific heat shows the usual jump at the mean field superconducting transition temperature marking the onset of Cooper pairs formation. As the film thickness is tuned towards the SIT, is relatively unchanged, while the magnitude of the jump and low-temperature specific heat increase significantly. This behaviour is taken as the thermodynamic fingerprint of quantum criticality in the vicinity of a quantum phase transition. PMID:28224994

  2. Direct measurements reveal non-Markovian fluctuations of DNA threading through a solid-state nanopore

    CERN Document Server

    Bell, Nicholas A W

    2016-01-01

    The threading of a polymer chain through a small pore is a classic problem in polymer dynamics and underlies nanopore sensing technology. However important experimental aspects of the polymer motion in a solid-state nanopore, such as an accurate measurement of the velocity variation during translocation, have remained elusive. In this work we analysed the translocation through conical quartz nanopores of a 7 kbp DNA double-strand labelled with six markers equally spaced along its contour. These markers, constructed from DNA hairpins, give direct experimental access to the translocation dynamics. On average we measure a 5% reduction in velocity during the translocation. We also find a striking correlation in velocity fluctuations with a decay constant of 100s of {\\mu}s. These results shed light on hitherto unresolved problems in the dynamics of DNA translocation and provide guidance for experiments seeking to determine positional information along a DNA strand.

  3. Orientation selective DEER measurements on vinculin tail at X-band frequencies reveal spin label orientations

    Science.gov (United States)

    Abé, Christoph; Klose, Daniel; Dietrich, Franziska; Ziegler, Wolfgang H.; Polyhach, Yevhen; Jeschke, Gunnar; Steinhoff, Heinz-Jürgen

    2012-03-01

    Double electron electron resonance (DEER) spectroscopy has been established as a valuable method to determine distances between spin labels bound to protein molecules. Caused by selective excitation of molecular orientations DEER primary data also depend on the mutual orientation of the spin labels. For a doubly spin labeled variant of the cytoskeletal protein vinculin tail strong orientation selection can be observed already at X-band frequencies, which allows us to reduce the problem to the relative orientation of two molecular axes and the spin-spin axis parameterized by three angles. A full grid search of parameter space reveals that the DEER experiment introduces parameter-space symmetry higher than the symmetry of the spin Hamiltonian. Thus, the number of equivalent parameter sets is twice as large as expected and the relative orientation of the two spin labels is ambiguous. Except for this inherent ambiguity the most probable relative orientation of the two spin labels can be determined with good confidence and moderate uncertainty by global fitting of a set of five DEER experiments at different offsets between pump and observer frequency. The experiment provides restraints on the angles between the z axis of the nitroxide molecular frame and the spin-spin vector and on the dihedral between the two z axes. When using the same type of label at both sites, assignment of the angle restraints is ambiguous and the sign of the dihedral restraint is also ambiguous.

  4. One-neutron removal measurement reveals 24O as a new doubly magic nucleus.

    Science.gov (United States)

    Kanungo, R; Nociforo, C; Prochazka, A; Aumann, T; Boutin, D; Cortina-Gil, D; Davids, B; Diakaki, M; Farinon, F; Geissel, H; Gernhäuser, R; Gerl, J; Janik, R; Jonson, B; Kindler, B; Knöbel, R; Krücken, R; Lantz, M; Lenske, H; Litvinov, Y; Lommel, B; Mahata, K; Maierbeck, P; Musumarra, A; Nilsson, T; Otsuka, T; Perro, C; Scheidenberger, C; Sitar, B; Strmen, P; Sun, B; Szarka, I; Tanihata, I; Utsuno, Y; Weick, H; Winkler, M

    2009-04-17

    The first measurement of the momentum distribution for one-neutron removal from (24)O at 920A MeV performed at GSI, Darmstadt is reported. The observed distribution has a width (FWHM) of 99 +/- 4 MeV/c in the projectile rest frame and a one-neutron removal cross section of 63 +/- 7 mb. The results are well explained with a nearly pure 2s_{1/2} neutron spectroscopic factor of 1.74 +/- 0.19 within the eikonal model. This large s-wave probability shows a spherical shell closure thereby confirming earlier suggestions that (24)O is a new doubly magic nucleus.

  5. Association of Repeatedly Measured High-Sensitivity-Assayed Troponin I with Cardiovascular Disease Events in a General Population from the MORGAM/BiomarCaRE Study

    DEFF Research Database (Denmark)

    Hughes, Maria F; Ojeda, Francisco; Saarela, Olli;

    2017-01-01

    BACKGROUND: High-sensitivity troponin I (hs-cTnI) concentrations reflect myocardial stress. The role of hs-cTnI in predicting long-term changes in the risk of cardiovascular disease (CVD) in general populations is not clearly defined. METHODS: We investigated whether the change in 3 repeated meas...

  6. Ex vivo measures of muscle mitochondrial capacity reveal quantitative limits of oxygen delivery by the circulation during exercise

    DEFF Research Database (Denmark)

    Boushel, Robert; Saltin, Bengt

    2013-01-01

    of the body mass will be discussed in relation to mitochondrial capacity measured ex vivo. These analyses reveal that as the mass of muscle engaged in exercise increases from one-leg knee extension, to 2-arm cranking, to 2-leg cycling and x-country skiing, the magnitude of blood flow and oxygen delivery...... decrease. Accordingly, a 2-fold higher oxygen delivery and oxygen uptake per unit muscle mass are seen in vivo during 1-leg exercise compared to 2-leg cycling indicating a significant limitation of the circulation during exercise with a large muscle mass. This analysis also reveals that mitochondrial......Muscle mitochondrial respiratory capacity measured ex vivo provides a physiological reference to assess cellular oxidative capacity as a component in the oxygen cascade in vivo. In this article, the magnitude of muscle blood flow and oxygen uptake during exercise involving a small-to-large fraction...

  7. Depth-dependence of post-seismic velocity changes in and near source area of the 2013 M7.0 Lushan earthquake revealed by S coda of repeating events

    Science.gov (United States)

    Li, Le

    2017-10-01

    I investigated postseismic velocity changes within focal area of the 2013 M7.0 Lushan earthquake using coda-wave data of repeating small earthquakes. I employed template matching and grid search methods to identify well-defined repeating earthquakes in order to minimize artifacts induced by variations in source location. I identified a total of 3 isolated patches in a two-month period after the M7.0 mainshock. I applied the coda wave interferometry technique to the waveform data of the identified repeating earthquakes to estimate velocity changes between the first and subsequent events in each cluster. Up to 0.1-0.2% velocity increase is observed from the S coda of repeating events occurred at regions surrounding the large coseismic slip area at seismogenic depths. My observations suggest that a large percent of velocity changes may occur at surface near the stations or shallow, however, healing along the propagation paths in the deep ( 5-20 km) is likely have contributed to the amount of velocity changes observed after the Lushan earthquake.

  8. Extended carrier lifetimes and diffusion in hybrid perovskites revealed by Hall effect and photoconductivity measurements

    Science.gov (United States)

    Chen, Y.; Yi, H. T.; Wu, X.; Haroldson, R.; Gartstein, Y. N.; Rodionov, Y. I.; Tikhonov, K. S.; Zakhidov, A.; Zhu, X.-Y.; Podzorov, V.

    2016-08-01

    Impressive performance of hybrid perovskite solar cells reported in recent years still awaits a comprehensive understanding of its microscopic origins. In this work, the intrinsic Hall mobility and photocarrier recombination coefficient are directly measured in these materials in steady-state transport studies. The results show that electron-hole recombination and carrier trapping rates in hybrid perovskites are very low. The bimolecular recombination coefficient (10-11 to 10-10 cm3 s-1) is found to be on par with that in the best direct-band inorganic semiconductors, even though the intrinsic Hall mobility in hybrid perovskites is considerably lower (up to 60 cm2 V-1 s-1). Measured here, steady-state carrier lifetimes (of up to 3 ms) and diffusion lengths (as long as 650 μm) are significantly longer than those in high-purity crystalline inorganic semiconductors. We suggest that these experimental findings are consistent with the polaronic nature of charge carriers, resulting from an interaction of charges with methylammonium dipoles.

  9. Measurement on isolated lithium iron phosphate particles reveals heterogeneity in material properties distribution

    Science.gov (United States)

    Snowden, Michael E.; Dayeh, Malak; Payne, Nicholas A.; Gervais, Simon; Mauzeroll, Janine; Schougaard, Steen B.

    2016-09-01

    We present herein localized galvanostatic and potentiodynamic measurements on lithium iron phosphate (LFP) particles, using the combination of a scanning micropipette contact method (SMCM) and scanning electron microscopy (SEM). The proposed technique allows small substrate areas (∼10 μm in diameter) decorated with LFP particles to be probed within a lithium electrolyte solution in organic carbonate solvents (0.1 M LiClO4 in propylene carbonate in the present study). SEM images of the scanned area allow the correlation of each electrochemical response to the number, and volume of the probed particles. Under favorable conditions, single particles are found within the measurement areas, thus enabling the determination of single particle properties in an anaerobic environment without the additional complications arising from the presence of binders and electronically conductive fillers. The ability to analyze a material with complementary experimental techniques at the single particle level should create new opportunities for fundamental studies and for the quality control of granular materials.

  10. Motor agency: a new and highly sensitive measure to reveal agency disturbances in early psychosis.

    Directory of Open Access Journals (Sweden)

    Hélène Wilquin

    Full Text Available BACKGROUND: Early diagnosis of young adults at risk of schizophrenia is essential for preventive approaches of the illness. Nevertheless, classic screening instruments are difficult to use because of the non-specific nature of the signs at this pre-onset phase of illness. The objective of the present contribution was to propose an innovating test that can probe the more specific symptom of psychosis, i.e., the sense of agency, which is defined as being the immediate experience of oneself as the cause of an action. More specifically, we tested whether motor agency is abnormal in early psychosis. METHODS: Thirty-two young symptomatic patients and their age-matched controls participated in the study. 15 of these patients were at ultra high-risk for developing psychosis (UHR, and 17 patients were suffering from first-episode psychosis (FEP. Patients' neurocognitive capacities were assessed through the use of seven neuropsychological tests. A motor agency task was also introduced to obtain an objective indicator of the degree of sense of agency, by contrasting force levels applied during other and self-produced collisions between a hand-held objet and a pendulum. RESULTS: As reported in the literature for adult controls, healthy adolescents used more efficient force levels in self than in other-imposed collisions. For both UHR and FEP patients, abnormally high levels of grip force were used for self-produced collisions, leading to an absence of difference between self and other. The normalized results revealed that motor agency differentiated patients from controls with a higher level of sensitivity than the more classic neuropsychological test battery. CONCLUSIONS: This study is in favour of the existence of an abnormal sense of agency early in the psychotic illness. Because it is quick and none verbal, motor agency may be a valuable tool to use in complement to classic interviews, especially when investigating complex ineffable experiences that are

  11. Repeated electromagnetic induction measurements for mapping soil moisture at the field scale: comparison with data from a wireless soil moisture monitoring network

    Science.gov (United States)

    Martini, Edoardo; Werban, Ulrike; Zacharias, Steffen; Pohle, Marco; Dietrich, Peter; Wollschläger, Ute

    2016-04-01

    Electromagnetic induction (EMI) methods are widely used for soil mapping, as they allow fast and relatively low-cost surveys of soil apparent electrical conductivity (ECa) at various scales. Soil ECa is well known to be influenced by both the volumetric content and the electrical conductivity (EC) of soil water, as well as by soil temperature and by the volume of the solid particles and their EC. Among other applications, EMI has become widely used to determine soil water content or to study hydrological processes within the field of hydrogeophysics. Although the use of non-invasive EMI for imaging soil spatial properties is very attractive, the dependence of ECa on several properties and states challenges any interpretation with respect to individual soil properties or states such as θ. The major aim of this study was to further investigate the potential of repeated EMI measurements to map soil moisture at the hillslope scale, with particular focus on the temporal variability of the spatial patterns of ECa and soil moisture, respectively, and on the stability of the ECa-soil moisture relationship over time. To this end, we compared time series of EMI measurements with high-resolution soil moisture data for a non-intensively managed hillslope area in the Schäfertal catchment (Central Germany) for which the spatial distribution of soil properties and soil water dynamics were known in detail. Soil water and temperature dynamics were observed in 40 soil profiles at hourly resolution during 14 months using a wireless monitoring network. During this period of time, ECa was mapped on seven occasions using an EM38-DD device. For the investigated site, ECa showed small temporal variations (ranging between 0 and 24 mS/m) whereas the temporal range of soil moisture was very large (from very dry to soil saturation). Furthermore, temporal changes of the spatial pattern of ECa differed from temporal changes of the spatial pattern of soil moisture. The ECa-soil moisture

  12. Atomic force microscopy measurements reveal multiple bonds between Helicobacter pylori blood group antigen binding adhesin and Lewis b ligand.

    Science.gov (United States)

    Parreira, P; Shi, Q; Magalhaes, A; Reis, C A; Bugaytsova, J; Borén, T; Leckband, D; Martins, M C L

    2014-12-01

    The strength of binding between the Helicobacter pylori blood group antigen-binding adhesin (BabA) and its cognate glycan receptor, the Lewis b blood group antigen (Le(b)), was measured by means of atomic force microscopy. High-resolution measurements of rupture forces between single receptor-ligand pairs were performed between the purified BabA and immobilized Le(b) structures on self-assembled monolayers. Dynamic force spectroscopy revealed two similar but statistically different bond populations. These findings suggest that the BabA may form different adhesive attachments to the gastric mucosa in ways that enhance the efficiency and stability of bacterial adhesion.

  13. How science maps reveal knowledge transfer: new measurement for a historical case

    CERN Document Server

    Soós, Sándor

    2014-01-01

    Modelling actors of science via science (overlay) maps has recently become a popular practice in Interdisciplinarity Research (IDR). The benefits of this toolkit have also been recognized for other areas of scientometrics, such as the study of science dynamics. In this paper we propose novel methods of measuring knowledge diffusion/integration based on previous applications of the overlay methodology. New indices called Mean Overlay Distance and Overlay Diversity Ratio, respectively, are being drawn from previous uses of the Stirling index as the main proxy for knowledge diversification. We demonstrate the added value of this proposal via a case study addressing the development of a rather complex discourse in biology, usually referred to as the Species Problem. The selected topic is known for a history connecting various research fields and traditions, being, therefore, both an ideal and challenging case for the study of knowledge diffusion.

  14. Using SKA Rotation Measures to Reveal the Mysteries of the Magnetised Universe

    CERN Document Server

    Johnston-Hollitt, Melanie; Beck, Rainer; Dehghan, Siamak; Pratley, Luke; Akahori, Takuya; Heald, George; Agudo, Ivan; Bonafede, Annalisa; Carretti, Ettore; Clarke, Tracy; Colafrancesco, Sergio; Enßlin, Torsten; Feretti, Luigina; Gaensler, Bryan; Haverkorn, Marijke; Mao, Sui Ann; Oppermann, Niels; Rudnick, Lawrence; Scaife, Anna; Schnitzeler, Dominic; Stil, Jeroen; Taylor, A Russ; Vacca, Valentina

    2015-01-01

    We know that magnetic fields are pervasive across all scales in the Universe and over all of cosmic time and yet our understanding of many of the properties of magnetic fields is still limited. We do not yet know when, where or how the first magnetic fields in the Universe were formed, nor do we fully understand their role in fundamental processes such as galaxy formation or cosmic ray acceleration or how they influence the evolution of astrophysical objects. The greatest challenge to addressing these issues has been a lack of deep, broad bandwidth polarimetric data over large areas of the sky. The Square Kilometre Array will radically improve this situation via an all-sky polarisation survey that delivers both high quality polarisation imaging in combination with observations of 7-14 million extragalactic rotation measures. Here we summarise how this survey will improve our understanding of a range of astrophysical phenomena on scales from individual Galactic objects to the cosmic web.

  15. Planetary science. Low-altitude magnetic field measurements by MESSENGER reveal Mercury's ancient crustal field.

    Science.gov (United States)

    Johnson, Catherine L; Phillips, Roger J; Purucker, Michael E; Anderson, Brian J; Byrne, Paul K; Denevi, Brett W; Feinberg, Joshua M; Hauck, Steven A; Head, James W; Korth, Haje; James, Peter B; Mazarico, Erwan; Neumann, Gregory A; Philpott, Lydia C; Siegler, Matthew A; Tsyganenko, Nikolai A; Solomon, Sean C

    2015-05-22

    Magnetized rocks can record the history of the magnetic field of a planet, a key constraint for understanding its evolution. From orbital vector magnetic field measurements of Mercury taken by the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft at altitudes below 150 kilometers, we have detected remanent magnetization in Mercury's crust. We infer a lower bound on the average age of magnetization of 3.7 to 3.9 billion years. Our findings indicate that a global magnetic field driven by dynamo processes in the fluid outer core operated early in Mercury's history. Ancient field strengths that range from those similar to Mercury's present dipole field to Earth-like values are consistent with the magnetic field observations and with the low iron content of Mercury's crust inferred from MESSENGER elemental composition data. Copyright © 2015, American Association for the Advancement of Science.

  16. Simple pain measures reveal psycho-social pathology in patients with Crohn’s disease

    Science.gov (United States)

    Odes, Shmuel; Friger, Michael; Sergienko, Ruslan; Schwartz, Doron; Sarid, Orly; Slonim-Nevo, Vered; Singer, Terri; Chernin, Elena; Vardi, Hillel; Greenberg, Dan; Israel IBD Research Nucleus

    2017-01-01

    AIM To determine whether pain has psycho-social associations in adult Crohn’s disease (CD) patients. METHODS Patients completed demographics, disease status, Patient Harvey-Bradshaw Index (P-HBI), Short Form Health Survey (SF-36), Short Inflammatory Bowel Disease Questionnaire (SIBDQ), and five socio-psychological questionnaires: Brief Symptom Inventory, Brief COPE Inventory, Family Assessment Device, Satisfaction with Life Scale, and Work Productivity and Activity Impairment Questionnaire. Pain sub-scales in P-HBI, SF-36 and SIBDQ measures were recoded into 4 identical scores for univariate and multinomial logistic regression analysis of associations with psycho-social variables. RESULTS The cohort comprised 594 patients, mean age 38.6 ± 14.8 years, women 52.5%, P-HBI 5.76 ± 5.15. P-HBI, SF-36 and SIBDQ broadly agreed in their assessment of pain intensity. More severe pain was significantly associated with female gender, low socio-economic status, unemployment, Israeli birth and smoking. Higher pain scores correlated positively with psychological stress, dysfunctional coping strategies, poor family relationships, absenteeism, presenteeism, productivity loss and activity impairment and all WPAI sub-scores. Patients exhibiting greater satisfaction with life had less pain. The regression showed increasing odds ratios for psychological stress (lowest 2.26, highest 12.17) and female gender (highest 3.19) with increasing pain. Internet-recruited patients were sicker and differed from hardcopy questionnaire patients in their associations with pain. CONCLUSION Pain measures in P-HBI, SF-36 and SIBDQ correlate with psycho-social pathology in CD. Physicians should be aware also of these relationships in approaching CD patients with pain. PMID:28246482

  17. An Arctic sea ice thickness variability revealed from satellite altimetric measurements

    Institute of Scientific and Technical Information of China (English)

    BI Haibo; HUANG Haijun; SU Qiao; YAN Liwen; LIU Yanxia; XU Xiuli

    2014-01-01

    A modified algorithm taking into account the first year (FY) and multiyear (MY) ice densities is used to derive a sea ice thickness from freeboard measurements acquired by satellite altimetry ICESat (2003-2008). Estimates agree with various independent in situ measurements within 0.21 m. Both the fall and winter campaigns see a dramatic extent retreat of thicker MY ice that survives at least one summer melting sea-son. There were strong seasonal and interannual variabilities with regard to the mean thickness. Seasonal increases of 0.53 m for FY the ice and 0.29 m for the MY ice between the autumn and the winter ICESat campaigns, roughly 4-5 month separation, were found. Interannually, the significant MY ice thickness de-clines over the consecutive four ICESat winter campaigns (2005-2008) leads to a pronounced thickness drop of 0.8 m in MY sea ice zones. No clear trend was identified from the averaged thickness of thinner, FY ice that emerges in autumn and winter and melts in summer. Uncertainty estimates for our calculated thick-ness, caused by the standard deviations of multiple input parameters including freeboard, ice density, snow density, snow depth, show large errors more than 0.5 m in thicker MY ice zones and relatively small stan-dard deviations under 0.5 m elsewhere. Moreover, a sensitivity analysis is implemented to determine the separate impact on the thickness estimate in the dependence of an individual input variable as mentioned above. The results show systematic bias of the estimated ice thickness appears to be mainly caused by the variations of freeboard as well as the ice density whereas the snow density and depth brings about relatively insignificant errors.

  18. Airborne methane remote measurements reveal heavy-tail flux distribution in Four Corners region.

    Science.gov (United States)

    Frankenberg, C.

    2016-12-01

    Methane (CH4) impacts climate as the second strongest anthropogenic greenhouse gas and air quality by influencing tropospheric ozone levels. Space-based observations have identified the Four Corners region in the Southwest United States as an area of large CH4 enhancements. We conducted an airborne campaign in Four Corners during April 2015 with the next-generation Airborne Visible/Infrared Imaging Spectrometer (near-infrared) and Hyperspectral Thermal Emission Spectrometer (thermal infrared) imaging spectrometers to better understand the source of methane by measuring methane plumes at 1- to 3-m spatial resolution. Our analysis detected more than 250 individual methane plumes from fossil fuel harvesting, processing, and distributing infrastructures, spanning an emission range from the detection limit ˜ 2 kg/h to 5 kg/h through ˜ 5,000 kg/h. Observed sources include gas processing facilities, storage tanks, pipeline leaks, natural seeps and well pads, as well as a coal mine venting shaft. Overall, plume enhancements and inferred fluxes follow a lognormal distribution, with the top 10% emitters contributing 49 to 66% to the inferred total point source flux of 0.23 Tg/y to 0.39 Tg/y. We will summarize the campaign results and provide an overview of how airborne remote sensing can be used to detect and infer methane fluxes over widespread geographic areas and how new instrumentation could be used to perform similar observations from space.

  19. SANS measurements of semiflexible xyloglucan polysaccharide chains in water reveal their self-avoiding statistics.

    Science.gov (United States)

    Muller, François; Manet, Sabine; Jean, Bruno; Chambat, Gérard; Boué, François; Heux, Laurent; Cousin, Fabrice

    2011-09-12

    We explored the behavior and the characteristics of xyloglucan polysaccharide chains extracted from tamarind seeds in aqueous media. The initial solubilization is achieved by using a 0.01 M NaOH solution. The absence of compact aggregates in the solution and the average molecular mass of the individual chains were unambiguously demonstrated by size exclusion chromatography with multi-angle light scattering detection. The composition and the stability of the solution were quantitatively checked over weeks by using liquid state nuclear magnetic resonance with DMSO as internal standard. The conformational characteristics of the chains were measured using nondestructive small-angle neutron scattering (SANS). The unambiguous determination of the Flory exponent (ν = 0.588) by SANS enabled us to directly prove that xyloglucan chains in water behave like semiflexible worm-like chains with excluded volume statistics (good solvent), contrary to most of the neutral water-soluble polymer chains that rather exhibit Gaussian statistics (θ-solvent). In addition to the Flory exponent, the persistence length l(p) and the cross section of the chains were also determined by SANS with utmost precision, with values of 80 and of 7 Å, respectively, which provides a complete description of the conformational characteristics of XG chains at all relevant length scales.

  20. In God we trust? Neural measures reveal lower social conformity among non-religious individuals.

    Science.gov (United States)

    Thiruchselvam, Ravi; Gopi, Yashoda; Kilekwang, Leonard; Harper, Jessica; Gross, James J

    2017-02-21

    Even in predominantly religious societies, there are substantial individual differences in religious commitment. Why is this? One possibility is that differences in social conformity (i.e., the tendency to think and behave as others do) underlie inclination towards religiosity. However, the link between religiosity and conformity has not yet been directly examined. In this study, we tested the notion that non-religious individuals show dampened social conformity, using both self-reported and neural (EEG-based ERPs) measures of sensitivity to others' influence. Non-religious versus religious undergraduate subjects completed an experimental task that assessed levels of conformity in a domain unrelated to religion (i.e., in judgments of facial attractiveness). Findings showed that, although both groups yielded to conformity pressures at the self-report level, non-religious individuals did not yield to such pressures in their neural responses. These findings highlight a novel link between religiosity and social conformity, and hold implications for prominent theories about the psychological functions of religion.

  1. Urban eddy covariance measurements reveal significant missing NOx emissions in Central Europe.

    Science.gov (United States)

    Karl, T; Graus, M; Striednig, M; Lamprecht, C; Hammerle, A; Wohlfahrt, G; Held, A; von der Heyden, L; Deventer, M J; Krismer, A; Haun, C; Feichter, R; Lee, J

    2017-05-30

    Nitrogen oxide (NOx) pollution is emerging as a primary environmental concern across Europe. While some large European metropolitan areas are already in breach of EU safety limits for NO2, this phenomenon does not seem to be only restricted to large industrialized areas anymore. Many smaller scale populated agglomerations including their surrounding rural areas are seeing frequent NO2 concentration violations. The question of a quantitative understanding of different NOx emission sources is therefore of immanent relevance for climate and air chemistry models as well as air pollution management and health. Here we report simultaneous eddy covariance flux measurements of NOx, CO2, CO and non methane volatile organic compound tracers in a city that might be considered representative for Central Europe and the greater Alpine region. Our data show that NOx fluxes are largely at variance with modelled emission projections, suggesting an appreciable underestimation of the traffic related atmospheric NOx input in Europe, comparable to the weekend-weekday effect, which locally changes ozone production rates by 40%.

  2. Carrier behavior of HgTe under high pressure revealed by Hall effect measurement

    Institute of Scientific and Technical Information of China (English)

    胡廷静; 崔晓岩; 李雪飞; 王婧姝; 吕秀梅; 王棱升; 杨景海; 高春晓

    2015-01-01

    We investigate the carrier behavior of HgTe under high pressures up to 23 GPa using in situ Hall effect measurements. As the phase transitions from zinc blende to cinnabar, then to rock salt, and finally to Cmcm occur, all the parameters change discontinuously. The conductivity variation under compression is described by the carrier parameters. For the zinc blende phase, both the decrease of carrier concentration and the increase of mobility indicate the overlapped valence band and conduction band separates with pressure. Pressure causes an increase in the hole concentration of HgTe in the cinnabar phase, which leads to the carrier-type inversion and the lowest mobility at 5.6 GPa. In the phase transition process from zinc blende to rock salt, Te atoms are the major ones in atomic movements in the pressure regions of 1.0–1.5 GPa and 1.8–3.1 GPa, whereas Hg atoms are the major ones in the pressure regions of 1.5–1.8 GPa and 3.1–7.7 GPa. The polar optical scattering of the rock salt phase decreases with pressure.

  3. Gas-driven lava lake fluctuations at Erta 'Ale volcano (Ethiopia) revealed by MODIS measurements

    Science.gov (United States)

    Vergniolle, Sylvie; Bouche, Emmanuella

    2016-09-01

    The long-lived lava lake of Erta 'Ale volcano (Ethiopia) is remotely monitored by moderate resolution imaging spectroradiometers (MODIS) installed on satellites. The Normalised Thermal Index (NTI) (Wright et al. Remote Sens Environ 82:135-155 2002) is shown to be proportional to the volume of the lava lake based on visual observations. The lava lake's variable level can be plausibly related to a stable foam, i.e. a mixture composed of densely packed non-coalescing bubbles in suspension within a liquid. This foam is trapped at the top of the magma reservoir, and its thickness changes in response to the gas flux feeding the foam being successively turned on and off. The temporal evolution of the foam thickness, and the resulting variation of the volume of the lava lake, is calculated numerically by assuming that the gas flux feeding the foam, initially constant and homogeneous since December 9, 2002, is suddenly stopped on December 13, 2002 and not restarted before May 2003. The best fit between the theoretical foam thickness and the level of the lava lake deduced from the NTI provides an estimate of both the reservoir radius, 155-170 m, and the gas flux feeding the foam, 5.5×10-3-7.2×10-3 m 3 s -1 when existing. This is in agreement with previous estimates from acoustic measurements (Bouche et al. Earth Planet Sci Lett 295:37-48 2010). The very good agreement between the theoretical foam thickness and that deduced from MODIS data shows for the first time the existence of a regime based on the behaviour of a stable foam, whose spreading towards the conduit ("wide" conduit condition), can explain the long-lived activity. Our predictive model, which links the gas flux at the vent to the foam spreading, could potentially be used on any volcano with a long-lived activity. The underlying gas flux and the horizontal surface area of the magma reservoir can then be deduced by combining modelling to continuous measurements of gas flux. The lava lake, when high, often shows

  4. Airborne methane remote measurements reveal heavy-tail flux distribution in Four Corners region

    Science.gov (United States)

    Thorpe, Andrew K.; Thompson, David R.; Hulley, Glynn; Kort, Eric Adam; Vance, Nick; Borchardt, Jakob; Krings, Thomas; Gerilowski, Konstantin; Sweeney, Colm; Conley, Stephen; Bue, Brian D.; Aubrey, Andrew D.; Hook, Simon; Green, Robert O.

    2016-01-01

    Methane (CH4) impacts climate as the second strongest anthropogenic greenhouse gas and air quality by influencing tropospheric ozone levels. Space-based observations have identified the Four Corners region in the Southwest United States as an area of large CH4 enhancements. We conducted an airborne campaign in Four Corners during April 2015 with the next-generation Airborne Visible/Infrared Imaging Spectrometer (near-infrared) and Hyperspectral Thermal Emission Spectrometer (thermal infrared) imaging spectrometers to better understand the source of methane by measuring methane plumes at 1- to 3-m spatial resolution. Our analysis detected more than 250 individual methane plumes from fossil fuel harvesting, processing, and distributing infrastructures, spanning an emission range from the detection limit ∼ 2 kg/h to 5 kg/h through ∼ 5,000 kg/h. Observed sources include gas processing facilities, storage tanks, pipeline leaks, and well pads, as well as a coal mine venting shaft. Overall, plume enhancements and inferred fluxes follow a lognormal distribution, with the top 10% emitters contributing 49 to 66% to the inferred total point source flux of 0.23 Tg/y to 0.39 Tg/y. With the observed confirmation of a lognormal emission distribution, this airborne observing strategy and its ability to locate previously unknown point sources in real time provides an efficient and effective method to identify and mitigate major emissions contributors over a wide geographic area. With improved instrumentation, this capability scales to spaceborne applications [Thompson DR, et al. (2016) Geophys Res Lett 43(12):6571–6578]. Further illustration of this potential is demonstrated with two detected, confirmed, and repaired pipeline leaks during the campaign. PMID:27528660

  5. Physiological consequences of repeated exposures to conditioned fear.

    Science.gov (United States)

    Thompson, Robert S; Strong, Paul V; Fleshner, Monika

    2012-06-01

    Activation of the stress response evokes a cascade of physiological reactions that may be detrimental when repeated or chronic, and when triggered after exposure to psychological/emotional stressors. Investigation of the physiological mechanisms responsible for the health damaging effects requires animal paradigms that repeatedly evoke a response to psychological/emotional stressors. To this end, adult male Sprague Dawley rats were repeatedly exposed (2X per day for 20 days) to a context that they were conditioned to fear (conditioned fear test, CFT). Repeated exposure to CFT produced body weight loss, adrenal hypertrophy, thymic involution, and basal corticosterone elevation. In vivo biotelemetry measures revealed that CFT evokes sympathetic nervous system driven increases in heart rate (HR), mean arterial pressure (MAP), and core body temperature. Extinction of behavioral (freezing) and physiological responses to CFT was prevented using minimal reinstatement footshock. MAP responses to the CFT did not diminish across 20 days of exposure. In contrast, HR and cardiac contractility responses declined by day 15, suggesting a shift toward vascular-dominated MAP (a pre-clinical marker of CV dysfunction). Flattened diurnal rhythms, common to stress-related mood/anxiety disorders, were found for most physiological measures. Thus, repeated CFT produces adaptations indicative of the health damaging effects of psychological/emotional stress.

  6. Physiological Consequences of Repeated Exposures to Conditioned Fear

    Directory of Open Access Journals (Sweden)

    Robert S. Thompson

    2012-05-01

    Full Text Available Activation of the stress response evokes a cascade of physiological reactions that may be detrimental when repeated or chronic, and when triggered after exposure to psychological/emotional stressors. Investigation of the physiological mechanisms responsible for the health damaging effects requires animal paradigms that repeatedly evoke a response to psychological/emotional stressors. To this end, adult male Sprague Dawley rats were repeatedly exposed (2X per day for 20 days to a context that they were conditioned to fear (conditioned fear test, CFT. Repeated exposure to CFT produced body weight loss, adrenal hypertrophy, thymic involution, and basal corticosterone elevation. In vivo biotelemetry measures revealed that CFT evokes sympathetic nervous system driven increases in heart rate (HR, mean arterial pressure (MAP, and core body temperature. Extinction of behavioral (freezing and physiological responses to CFT was prevented using minimal reinstatement footshock. MAP responses to the CFT did not diminish across 20 days of exposure. In contrast, HR and cardiac contractility responses declined by day 15, suggesting a shift toward vascular-dominated MAP (a pre-clinical marker of CV dysfunction. Flattened diurnal rhythms, common to stress-related mood/anxiety disorders, were found for most physiological measures. Thus, repeated CFT produces adaptations indicative of the health damaging effects of psychological/emotional stress.

  7. Multiple measures reveal antiretroviral adherence successes and challenges in HIV-infected Ugandan children.

    Directory of Open Access Journals (Sweden)

    Jessica E Haberer

    Full Text Available BACKGROUND: Adherence to HIV antiretroviral therapy (ART among children in developing settings is poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: To understand the level, distribution, and correlates of ART adherence behavior, we prospectively determined monthly ART adherence through multiple measures and six-monthly HIV RNA levels among 121 Ugandan children aged 2-10 years for one year. Median adherence levels were 100% by three-day recall, 97.4% by 30-day visual analog scale, 97.3% by unannounced pill count/liquid formulation weights, and 96.3% by medication event monitors (MEMS. Interruptions in MEMS adherence of ≥ 48 hours were seen in 57.0% of children; 36.3% had detectable HIV RNA at one year. Only MEMS correlated significantly with HIV RNA levels (r = -0.25, p = 0.04. Multivariable regression found the following to be associated with <90% MEMS adherence: hospitalization of child (adjusted odds ratio [AOR] 3.0, 95% confidence interval [CI] 1.6-5.5; p = 0.001, liquid formulation use (AOR 1.4, 95%CI 1.0-2.0; p = 0.04, and caregiver's alcohol use (AOR 3.1, 95%CI 1.8-5.2; p<0.0001. Child's use of co-trimoxazole (AOR 0.5, 95%CI 0.4-0.9; p = 0.009, caregiver's use of ART (AOR 0.6, 95%CI 0.4-0.9; p = 0.03, possible caregiver depression (AOR 0.6, 95%CI 0.4-0.8; p = 0.001, and caregiver feeling ashamed of child's HIV status (AOR 0.5, 95%CI 0.3-0.6; p<0.0001 were protective against <90% MEMS adherence. Change in drug manufacturer (AOR 4.1, 95%CI 1.5-11.5; p = 0.009 and caregiver's alcohol use (AOR 5.5, 95%CI 2.8-10.7; p<0.0001 were associated with ≥ 48-hour interruptions by MEMS, while second-line ART (AOR 0.3, 95%CI 0.1-0.99; p = 0.049 and increasing assets (AOR 0.7, 95%CI 0.6-0.9; p = 0.0007 were protective against these interruptions. CONCLUSIONS/SIGNIFICANCE: Adherence success depends on a well-established medication taking routine, including caregiver support and adequate education on medication changes. Caregiver-reported depression and

  8. Strengthening concept learning by repeated testing.

    Science.gov (United States)

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

    2014-02-01

    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.

  9. Receiver-Operating-Characteristic Analysis Reveals Superiority of Scale-Dependent Wavelet and Spectral Measures for Assessing Cardiac Dysfunction

    CERN Document Server

    Thurner, S; Lowen, S B; Teich, M C; Thurner, Stefan; Feurstein, Markus C.; Lowen, Steven B.; Teich, Malvin C.

    1998-01-01

    Receiver-operating-characteristic (ROC) analysis was used to assess the suitability of various heart rate variability (HRV) measures for correctly classifying electrocardiogram records of varying lengths as normal or revealing the presence of heart failure. Scale-dependent HRV measures were found to be substantially superior to scale-independent measures (scaling exponents) for discriminating the two classes of data over a broad range of record lengths. The wavelet-coefficient standard deviation at a scale near 32 heartbeat intervals, and its spectral counterpart near 1/32 cycles per interval, provide reliable results using record lengths just minutes long. A jittered integrate-and-fire model built around a fractal Gaussian-noise kernel provides a realistic, though not perfect, simulation of heartbeat sequences.

  10. Quantum repeated games revisited

    CERN Document Server

    Frackiewicz, Piotr

    2011-01-01

    We present a scheme for playing quantum repeated 2x2 games based on the Marinatto and Weber's approach to quantum games. As a potential application, we study twice repeated Prisoner's Dilemma game. We show that results not available in 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.

  11. Discrepancies in reporting the CAG repeat lengths for Huntington's disease

    DEFF Research Database (Denmark)

    Quarrell, Oliver W; Handley, Olivia; O'Donovan, Kirsty

    2011-01-01

    Huntington's disease results from a CAG repeat expansion within the Huntingtin gene; this is measured routinely in diagnostic laboratories. The European Huntington's Disease Network REGISTRY project centrally measures CAG repeat lengths on fresh samples; these were compared with the original...

  12. Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site.

    Science.gov (United States)

    Hatoum-Aslan, Asma; Maniv, Inbal; Marraffini, Luciano A

    2011-12-27

    Precise RNA processing is fundamental to all small RNA-mediated interference pathways. In prokaryotes, clustered, regularly interspaced, short palindromic repeats (CRISPR) loci encode small CRISPR RNAs (crRNAs) that protect against invasive genetic elements by antisense targeting. CRISPR loci are transcribed as a long precursor that is cleaved within repeat sequences by CRISPR-associated (Cas) proteins. In many organisms, this primary processing generates crRNA intermediates that are subject to additional nucleolytic trimming to render mature crRNAs of specific lengths. The molecular mechanisms underlying this maturation event remain poorly understood. Here, we defined the genetic requirements for crRNA primary processing and maturation in Staphylococcus epidermidis. We show that changes in the position of the primary processing site result in extended or diminished maturation to generate mature crRNAs of constant length. These results indicate that crRNA maturation occurs by a ruler mechanism anchored at the primary processing site. We also show that maturation is mediated by specific cas genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci.

  13. Nitric oxide densities and their diurnal asymmetry in the upper middle atmosphere as revealed by ionospheric measurements

    Science.gov (United States)

    Laštovička, J.

    2001-01-01

    The nitric oxide (NO) density is of principal importance for the lower ionosphere as it is the source of the main ionized component. The mesospheric NO density climatology based on HALOE//UARS measurements (Siskind et al., Advances in Space Research 21 (1998) 1353-1362) and a comparison of the HALOE NO density data with some ionospheric data (Friedrich et al., Journal of Atmospheric and Solar-Terrestrial Physics 60 (1998) 1445-1457) revealed, among others, a large ``puzzling'' diurnal asymmetry of the NO density. In this paper, the existence of a diurnal asymmetry of the NO density is confirmed by independent data and is extended from the sunrise//sunset HALOE data to the entire daytime. We analyzed multi-frequency radio wave absorption measurements in the lower ionosphere over Central Europe, partly together with solar Lyman-/α and X-ray fluxes, in order to estimate the NO density. The results show that our ``ionospheric'' NO densities are comparable to, or somewhat higher than, the climatological NO densities of Siskind et al. (1998). They also show that the diurnal asymmetry in summer is a stable and regular feature of the lower ionosphere throughout the daytime, and that there is a substantial diurnal asymmetry in the NO density in the upper middle atmosphere that coincides with that revealed by the HALOE data and which is responsible for the asymmetry in the lower ionosphere.

  14. 重複觀測量數之分析:多群體多變項線性成長模式的估計Data Analysis of Repeated Measures: Estimating a Multi-Group Multivariate Linear Growth Model

    Directory of Open Access Journals (Sweden)

    溫福星 Fur-Hsing Wen

    2012-03-01

    Full Text Available 本研究利用「台灣教育長期追蹤資料庫」的一般分析能力與數學分析能力的四波調查結果,配合男、女學生樣本進行多群體多條追蹤資料的線性成長模式估計。在考慮重複觀測資料誤差項在不同時點的變異數非同質與不同時點間的共變數非獨立情況下,以及男、女學生的不同成長軌跡,將誤差項結構設為無限制結構,利用虛擬變項交互項法與虛擬變項多樣本法同時估計不同性別、不同能力的線性成長軌跡變化。由於全部追蹤資料樣本存在遺失值的情形,本研究以階層線性模式(hierarchical linear modeling, HLM)軟體對完整資料2,806位學生進行分析,其估計結果發現,在完整資料的兩條成長軌跡模式中,男、女學生誤差項共變異數矩陣結構相同,但線性成長軌跡不恆等。除此之外,本文並對競爭模式比較的結果在文章最後進行討論並提出相關的建議。 This paper demonstrates the data analysis of the repeated measures from the Taiwan Education Panel Survey (TEPS. Based on the four data waves on the TEPS, we consider two abilities (general and mathematic and two population groups (male and female students to construct a multi-group multivariate linear growth model. Because the two-group multivariate repeated measures belong to the different populations and the different research variables, the residual terms of linear growth models may imply heterogeneity of the error covariance structure. We treat the error covariance structure as an unrestricted structure to compare the various types of models. The results from the HLM on the complete data (2,806 students reveal that the male and female students in this study have the same error covariance structure but have distinct linear growth trajectories. In addition, comparisons of the competitive models and related suggestions are discussed in the results and conclusion

  15. An implicit measure of olfactory performance for non-human primates reveals aversive and pleasant odor conditioning.

    Science.gov (United States)

    Livneh, Uri; Paz, Rony

    2010-09-30

    We have little understanding of how odorants are processed in neural networks of the primate brain. Because chemo-stimuli are harder to control than physical stimuli (e.g. vision, audition), such research was limited by the temporal resolution, accuracy, and reliability of olfactometers (odor producing machines). Recent advances were able to create olfactometers that overcome these limitations, allowing their use together with neuroimaging techniques in humans. From the behavioral point of view, olfaction research requires a behavioral measure that can be used to quantify olfactory performance. This becomes a real problem when working with animals, where, unlike humans, explicit measures are harder to obtain. Furthermore, because odorants are powerful primitive reinforcers, such implicit measures can be beneficial to use in learning paradigms. Here we describe an olfactometer suitable for use in non-human primates, and an end-port design that allows the accurate measure of real-time respiratory modulations that are elicited in response to odor presentation. We demonstrate that this implicit measure is differentially modulated when experiencing pleasant or aversive odors. We then present an experimental paradigm in which monkeys learn to associate tones with odors, and show that the time delay from the conditioned stimuli to the next breath can be used to measure learning and memory expression in this paradigm. Using this construct, we reveal olfactory performance during acquisition and extinction of odor conditioning. These techniques can be used in electrophysiological recordings from relevant brain areas to shed light on neural networks involved in odor processing and reinforcement-learning.

  16. UK 2009-2010 repeat station report

    Directory of Open Access Journals (Sweden)

    Thomas J.G. Shanahan

    2013-03-01

    Full Text Available The British Geological Survey is responsible for conducting the UK geomagnetic repeat station programme. Measurements made at the UK repeat station sites are used in conjunction with the three UK magnetic observatories: Hartland, Eskdalemuir and Lerwick, to produce a regional model of the local field each year. The UK network of repeat stations comprises 41 stations which are occupied at approximately 3-4 year intervals. Practices for conducting repeat station measurements continue to evolve as advances are made in survey instrumentation and as the usage of the data continues to change. Here, a summary of the 2009 and 2010 UK repeat station surveys is presented, highlighting the measurement process and techniques, density of network, reduction process and recent results.

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

    Energy Technology Data Exchange (ETDEWEB)

    Provenzano, Virgil [National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Della Torre, Edward; Bennett, Lawrence H. [Department of Electrical and Computer Engineering, The George Washington University, Washington, DC 20052 (United States); ElBidweihy, Hatem, E-mail: Hatem@gwmail.gwu.edu [Department of Electrical and Computer Engineering, The George Washington University, Washington, DC 20052 (United States)

    2014-02-15

    The Gd{sub 5}Ge{sub 2}Si{sub 2} alloy and the off-stoichiometric Ni{sub 50}Mn{sub 35}In{sub 15} 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 Gd{sub 5}Ge{sub 2}Si{sub 2} and Ni{sub 50}Mn{sub 35}In{sub 15} 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.

  18. Reconfigurable multiport EPON repeater

    Science.gov (United States)

    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.

  19. Simple Sequence Repeats in Cultivated Peanut as Revealed by GenBank Inquiry%查询GenBank核酸数据库鉴定花生微卫星序列

    Institute of Scientific and Technical Information of China (English)

    杨新道; 王传堂; 陈殿绪; 张建成; 徐建志; 刘光臻

    2005-01-01

    运用SeqVerter和Tandem repeats finder软件,通过GenBank数据库查询了1,787条花生核酸序列,排除已报导微卫星序列后,获得了24条新的含有微卫星的花生序列.其中19条来自美国农业部Tifton实验站提交的花生未成熟荚果EST.本研究为开发多态性花生微卫星标记用于分子图谱构建提供了候选微卫星序列.

  20. First insight into genetic diversity of the Mycobacterium tuberculosis complex in Albania obtained by multilocus variable-number tandem-repeat analysis and spoligotyping reveals the presence of beijing multidrug-resistant isolates.

    Science.gov (United States)

    Tafaj, Silva; Zhang, Jian; Hauck, Yolande; Pourcel, Christine; Hafizi, Hasan; Zoraqi, Grigor; Sola, Christophe

    2009-05-01

    We characterized a set of 100 Mycobacterium tuberculosis complex clinical isolates from tuberculosis (TB) patients in Albania, typing them with a 24-locus variable-number tandem-repeat-spoligotyping scheme. Depending on the cluster definition, 43 to 49 patients were distributed into 15 to 16 clusters which were likely to be epidemiologically linked, indicative of a recent transmission rate of 28 to 34%. This result suggests that TB is under control in Albania. However, two multidrug-resistant (MDR) Beijing genotypes harboring the same S531A mutation on the rpoB gene were also found, suggesting a potential recent transmission of MDR TB. Three brand new genotypes, Albania-1 to Albania-3, are also described.

  1. Compositional variability on the surface of 4 Vesta revealed through GRaND measurements of high-energy gamma rays

    Science.gov (United States)

    Peplowski, Patrick N.; Lawrence, David J.; Prettyman, Thomas H.; Yamashita, Naoyuki; Bazell, Dave; Feldman, William C.; Le Corre, Lucille; McCoy, Timothy J.; Reddy, Vishnu; Reedy, Robert C.; Russell, Chris T.; Toplis, Michael J.

    2013-11-01

    Measurements of the high-energy gamma-ray flux emanating from asteroid 4 Vesta by the Dawn Gamma-Ray and Neutron Detector (GRaND) have revealed variability in the near-surface elemental composition of the Vestan surface. These observations are consistent with the presence of large (≥8 × 104 km2) regions with distinct, HED-like elemental compositions. The results agree broadly with other global measurements, such as the macroscopic neutron absorption cross section and spectral reflectance-derived mineralogic maps. Two distinct regions with eucrite-like elemental compositions have been identified, the first located primarily within the Lucaria and Marcia quadrangles and the second within Oppia quadrangle. The former region is collocated with some of the oldest, most heavily cratered terrain on Vesta. The interior of the 500 km diameter Rheasilvia impact basin is found to have a composition that is consistent with diogenite-like material. Taken together, these observations support the hypothesis that Vesta's original crust was composed of basaltic outflows in the form of eucritic-like material and that the Rheasilvia-basin-forming impact exposed lower-crustal, diogenite-like material. These measurements also constrain the maximum amount of mesosiderite-like material to <10% for each 15 × 15° surface element.

  2. A Repeating Fast Radio Burst

    CERN Document Server

    Spitler, L G; 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

    2016-01-01

    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 measures (i.e. integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of the fast radio bursts has led several authors to hypothesise that they originate in cataclysmic astrophysical events. Here we report the detection of ten additional bursts from the direction of FRB121102, using the 305-m Arecibo telescope. These new bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and wh...

  3. In-Plane Electronic Anisotropy of Underdoped ___122___ Fe-Arsenide Superconductors Revealed by Measurements of Detwinned Single Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Fisher, Ian Randal

    2012-05-08

    The parent phases of the Fe-arsenide superconductors harbor an antiferromagnetic ground state. Significantly, the Neel transition is either preceded or accompanied by a structural transition that breaks the four fold symmetry of the high-temperature lattice. Borrowing language from the field of soft condensed matter physics, this broken discrete rotational symmetry is widely referred to as an Ising nematic phase transition. Understanding the origin of this effect is a key component of a complete theoretical description of the occurrence of superconductivity in this family of compounds, motivating both theoretical and experimental investigation of the nematic transition and the associated in-plane anisotropy. Here we review recent experimental progress in determining the intrinsic in-plane electronic anisotropy as revealed by resistivity, reflectivity and ARPES measurements of detwinned single crystals of underdoped Fe arsenide superconductors in the '122' family of compounds.

  4. Recursive quantum repeater networks

    CERN Document Server

    Van Meter, Rodney; Horsman, Clare

    2011-01-01

    Internet-scale quantum repeater networks will be heterogeneous in physical technology, repeater functionality, and management. The classical control necessary to use the network will therefore face similar issues as Internet data transmission. Many scalability and management problems that arose during the development of the Internet might have been solved in a more uniform fashion, improving flexibility and reducing redundant engineering effort. Quantum repeater network development is currently at the stage where we risk similar duplication when separate systems are combined. We propose a unifying framework that can be used with all existing repeater designs. We introduce the notion of a Quantum Recursive Network Architecture, developed from the emerging classical concept of 'recursive networks', extending recursive mechanisms from a focus on data forwarding to a more general distributed computing request framework. Recursion abstracts independent transit networks as single relay nodes, unifies software layer...

  5. Temperature and light tolerance of representative brown,green and red algae in tumble culture revealed by chlorophyll fluorescence measurements

    Institute of Scientific and Technical Information of China (English)

    PANG Shaojun; SHAN Tifeng

    2008-01-01

    Laminaria japonica,Undaria pinnatifida,Ulva lactuca,Grateloupia turuturu and Palmaria palmata are suitable species that fit the requirements of a seaweed-animal integrated aquaculture system in terms of their viable biomass,rapid growth and promising nutrient uptake rates. In this investigation,the responses of the optimal chlorophyll fluolescence yield of the five algal species in tumble culture were assessed at a temperature range of 10~30℃.The results revealed that Ulva lactuca was the most resistant species to high temperature,withstanding 30℃ for 4 h without apparent decline in the optimal chlorophyll fluorescence yield. While the arctic alga Palmaria palmata was the most vulnerable one,showing significant decline in the optimal chlorophyll fluorescence yield at 25℃ for 2 h.The cold-water species Laminaria japonica,however,demonstrated strong ability to cope with higher temperature(24~26℃)for shorter time(within 24 h)without significant decline in the optimal chlorophyll fluorescence yield.Grateloupia turuturu showed a general decrease in the optimal chiorophyll fluores-cence yield with the rising temperature from 23 to 30℃,similar to the temperate kelp Undaria pinnatifida.Changes of chio-rophyll fluorescence yields of these algae were characterized differently indicating the existence of species-unique strategy to cope with high light.Measurements of the optimal chlorophyll fluorescence yield after short exposure to direct solar irradiance revealed how long these exposures could be without significant photoinhibition or with promising recovery in photosynthetic activities. Seasonal pattern of alternation of algal species in tank culture in the Northern Hemisphere at the latitude of 36°Nwas proposed according to these basic measurements.

  6. Repeatability of Harris Corner Detector

    Institute of Scientific and Technical Information of China (English)

    HU Lili

    2003-01-01

    Interest point detectors are commonly employed to reduce the amount of data to be processed. The ideal interest point detector would robustly select those features which are most appropriate or salient for the application and data at hand. This paper shows that interest points are geometrically stable under different transformations.This property makes interest points very successful in the context of image matching. To measure this property quantatively, we introduce a evaluation criterion: repeatability rate.

  7. Relationships between anthropometric measures and athletic performance, with special reference to repeated-sprint ability, in the Qatar national soccer team.

    Science.gov (United States)

    Brocherie, Franck; Girard, Olivier; Forchino, Fabricio; Al Haddad, Hani; Dos Santos, Gilvan A; Millet, Grégoire P

    2014-01-01

    The aim of this study was to determine potential relationships between anthropometric parameters and athletic performance with special consideration to repeated-sprint ability (RSA). Sixteen players of the senior male Qatar national soccer team performed a series of anthropometric and physical tests including countermovement jumps without (CMJ) and with free arms (CMJwA), straight-line 20 m sprint, RSA (6 × 35 m with 10 s recovery) and incremental field test. Significant (P sprinting times and r = 0.54 for maximal sprinting speed) with the exception of the sprint decrement score (Sdec). The sum of six skinfolds and adipose mass index were largely correlated with Sdec (r = 0.68, P 0.05, respectively) or any standard athletic tests. Multiple regression analyses indicated that muscular cross-sectional area for mid-thigh, adipose index, straight-line 20 m time, maximal sprinting speed and CMJwA are the strongest predictors of Sdec (r(2) = 0.89) and TT (r(2) = 0.95) during our RSA test. In the Qatar national soccer team, players' power-related qualities and RSA are associated with a high muscular profile and a low adiposity. This supports the relevance of explosive power for the soccer players and the larger importance of neuromuscular qualities determining the RSA.

  8. Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

    Directory of Open Access Journals (Sweden)

    Nelson Laura D

    2012-06-01

    Full Text Available Abstract Background Tri- and tetra-nucleotide repeats in mammalian genomes can induce formation of alternative non-B DNA structures such as triplexes and guanine (G-quadruplexes. These structures can induce mutagenesis, chromosomal translocations and genomic instability. We wanted to determine if proteins that bind triplex DNA structures are quantitatively or qualitatively different between colorectal tumor and adjacent normal tissue and if this binding activity correlates with patient clinical characteristics. Methods Extracts from 63 human colorectal tumor and adjacent normal tissues were examined by gel shifts (EMSA for triplex DNA-binding proteins, which were correlated with clinicopathological tumor characteristics using the Mann-Whitney U, Spearman’s rho, Kaplan-Meier and Mantel-Cox log-rank tests. Biotinylated triplex DNA and streptavidin agarose affinity binding were used to purify triplex-binding proteins in RKO cells. Western blotting and reverse-phase protein array were used to measure protein expression in tissue extracts. Results Increased triplex DNA-binding activity in tumor extracts correlated significantly with lymphatic disease, metastasis, and reduced overall survival. We identified three multifunctional splicing factors with biotinylated triplex DNA affinity: U2AF65 in cytoplasmic extracts, and PSF and p54nrb in nuclear extracts. Super-shift EMSA with anti-U2AF65 antibodies produced a shifted band of the major EMSA H3 complex, identifying U2AF65 as the protein present in the major EMSA band. U2AF65 expression correlated significantly with EMSA H3 values in all extracts and was higher in extracts from Stage III/IV vs. Stage I/II colon tumors (p = 0.024. EMSA H3 values and U2AF65 expression also correlated significantly with GSK3 beta, beta-catenin, and NF- B p65 expression, whereas p54nrb and PSF expression correlated with c-Myc, cyclin D1, and CDK4. EMSA values and expression of all three splicing factors correlated

  9. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF mediated gene expression pattern in Elaeis guineensis compared to other species.

    Directory of Open Access Journals (Sweden)

    Xintao Lei

    Full Text Available Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors of COG (Cluster of Orthologous Group annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR. CBFs reached maximum transcript level both at medium (4 h and long period time points (7 days, contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

  10. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

    Science.gov (United States)

    Lei, Xintao; Xiao, Yong; Xia, Wei; Mason, Annaliese S; Yang, Yaodong; Ma, Zilong; Peng, Ming

    2014-01-01

    Elaeis guineensis as a tropical oil-crop is particularly sensitive to low temperature. Improvement of cold-tolerance may significantly increase the total cultivation area of this tropical oil-crop worldwide. We sequenced cold-treated and control (untreated) samples of Elaeis guineensis. De novo assembly generated 51,452 unigenes with an average length of 703 bp. Subsequently, these expressed sequences were functionally annotated. In the K category (transcription factors) of COG (Cluster of Orthologous Group) annotation, the largest proportion of genes induced and repressed at least two-fold under cold stress were from the AP2/ERE family, indicating that C-repeat binding factor, (CBFs, members of the AP2/ERE family) may play a central role in cold tolerance in Elaeis guineensis. Subsequently, the CBF-mediated signal transduction pathway was reconstructed based on transcriptome data and the gene expression profile involving the pathway was examined using real-time quantitative RT-PCR (qRT-PCR). CBFs reached maximum transcript level both at medium (4 h) and long period time points (7 days), contrary to the expression pattern of CBFs in Arabidopsis and rice. Moreover, the promoters of downstream Cold Responsive gene (CORs) regulated by CBFs were analyzed. Conservation, mutation and absence of the DRE core motif were detected in the promoters of six CORs. These mutations in DRE motifs suggest that CORs may not be induced via cold stress in Elaeis guineensis.

  11. Color-Doppler sonographic tissue perfusion measurements reveal significantly diminished renal cortical perfusion in kidneys with vesicoureteral reflux.

    Science.gov (United States)

    Scholbach, T M; Sachse, C

    2016-01-01

    Vesicoureteral reflux (VUR) and its sequelae may lead to reduced renal perfusion and loss of renal function. Methods to describe and monitor tissue perfusion are needed. We investigated dynamic tissue perfusion measurement (DTPM) with the PixelFlux-software to measure microvascular changes in the renal cortex in 35 children with VUR and 28 healthy children. DTPM of defined horizontal slices of the renal cortex was carried out. A kidney was assigned to the "low grade reflux"-group if the reflux grade of the voiding cystourethrogram was 1 to 3 and to the "high grade reflux"-group if the reflux grade was 4 to 5. Kidneys with VUR showed a significantly reduced cortical perfusion. Compared to healthy kidneys, this decline reached in low and high grade refluxes within the proximal 50% of the cortex: 3% and 12 %, in the distal 50% of the cortex: 21% and 44 % and in the most distal 20 % of the cortex 41% and 44%. DTPM reveals a perfusion loss in kidneys depending on the degree of VUR, which is most pronounced in the peripheral cortex. Thus, DTPM offers the tool to evaluate microvascular perfusion, to help planning treatment decisions in children with VUR.

  12. Fine-resolution repeat topographic surveying of dryland landscapes using UAS-based structure-from-motion photogrammetry: Assessing accuracy and precision against traditional ground-based erosion measurements

    Science.gov (United States)

    Gillian, Jeffrey K.; Karl, Jason W.; Elaksher, Ahmed; Duniway, Michael C.

    2017-01-01

    Structure-from-motion (SfM) photogrammetry from unmanned aerial system (UAS) imagery is an emerging tool for repeat topographic surveying of dryland erosion. These methods are particularly appealing due to the ability to cover large landscapes compared to field methods and at reduced costs and finer spatial resolution compared to airborne laser scanning. Accuracy and precision of high-resolution digital terrain models (DTMs) derived from UAS imagery have been explored in many studies, typically by comparing image coordinates to surveyed check points or LiDAR datasets. In addition to traditional check points, this study compared 5 cm resolution DTMs derived from fixed-wing UAS imagery with a traditional ground-based method of measuring soil surface change called erosion bridges. We assessed accuracy by comparing the elevation values between DTMs and erosion bridges along thirty topographic transects each 6.1 m long. Comparisons occurred at two points in time (June 2014, February 2015) which enabled us to assess vertical accuracy with 3314 data points and vertical precision (i.e., repeatability) with 1657 data points. We found strong vertical agreement (accuracy) between the methods (RMSE 2.9 and 3.2 cm in June 2014 and February 2015, respectively) and high vertical precision for the DTMs (RMSE 2.8 cm). Our results from comparing SfM-generated DTMs to check points, and strong agreement with erosion bridge measurements suggests repeat UAS imagery and SfM processing could replace erosion bridges for a more synoptic landscape assessment of shifting soil surfaces for some studies. However, while collecting the UAS imagery and generating the SfM DTMs for this study was faster than collecting erosion bridge measurements, technical challenges related to the need for ground control networks and image processing requirements must be addressed before this technique could be applied effectively to large landscapes.

  13. Detection of the effects of repeated dose combined propoxur and heavy metal exposure by measurement of certain toxicological, haematological and immune function parameters in rats.

    Science.gov (United States)

    Institóris, L; Siroki, O; Undeger, U; Basaran, N; Banerjee, B D; Dési, I

    2001-06-21

    In the present study, an immunotoxicity test system, containing general toxicological (body weight gain, organ weights), haematological (WBC,RBC, Ht, mean cell volume of the RBCs, cell content of the femoral bone marrow), and immune function (PFC assay, DTH reaction) investigations, was used for detection the effects of a 4 weeks repeated low dose combined oral exposure of male Wistar rats with propoxur and the heavy metals arsenic or mercury. Two doses of the compounds were used: a higher one (the lowest dose which resulted in significant change of at least one parameter examined in previous dose-effect experiments), and a lower one (the highest dose which proved to be non-effective). The applied doses were: 8.51 and 0.851 mg kg(-1) of propoxur, 13.3 and 3.33 mg kg(-1) of NaAsO(2), and 3.20 and 0.40 mg kg(-1) of HgCl(2). In the combination treatment, the high dose of propoxur was combined with the low dose of arsenic or mercury, and the high doses of each heavy metals were combined with the low dose of propoxur. The main finding of this study was that some of the combinations significantly altered the relative weight of liver, adrenals and kidneys, related to both the untreated and the high dose internal control. Among the immune functions examined, only the PFC content of the spleen showed a trend of changes in certain combinations versus the corresponding high dose control. According to the present results, combined exposure with propoxur and the heavy metals examined can modify the detection limit of the single compounds and/or may alter their toxic effects.

  14. Dissolved Fe(II) in the Pacific Ocean: Measurements from the P16N CLIVAR/CO2 Repeat Hydrography Cruise

    Science.gov (United States)

    Hansard, S. P.; Landing, W. M.; Measures, C. I.

    2006-12-01

    Vertical profiles of seawater Fe(II) concentration were obtained for 37 stations sampled in early 2006, in conjunction with the CLIVAR Repeat Hydrography P16N transect (152° W, Tahiti to Alaska). At each station, seawater samples were collected from 12 target depths (0-1000 m) using trace-metal clean Go-Flo bottles. Upon recovery, Go-Flo bottles were immediately transferred to a Class 100 clean van and sub-sampled for Fe(II) by passing sample water through a 0.2 μm Supor (polyethersulfone) cartridge filter into 125 mL containers, pre-loaded with 25 μL of 6M quartz-distilled HCl (final pH ~~ 6) to slow oxidation. Samples were immediately analyzed for Fe(II) using a luminol-based chemiluminescence method. Total dissolved iron was also determined shipboard by spectrophotometric flow injection analysis. The data collected from this cruise will be presented, along with corroborating data from another North Pacific cruise (PO2). Concentrations of Fe(II) ranged from below detection (meters. Photoreduction of Fe(III) has been cited as a source of Fe(II) in surface waters, and the pattern of attenuation with depth is consistent with this mechanism. Many samples collected at or near the bottom of the profile (500-1000 m) exhibited elevated Fe(II) relative to the mid-depths of the profile. Due to the higher total dissolved iron at depth, the percentage of Fe(II) was low in these samples. Recent studies support the presence of Fe(II) at depth, in association with low or suboxic conditions. In situ processes such as the remineralization of sinking biogenic particles may provide a source for this Fe(II).

  15. Intra-genomic variation in the ribosomal repeats of nematodes.

    Directory of Open Access Journals (Sweden)

    Holly M Bik

    Full Text Available 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

  16. Two to five repeated measurements per patient reduced the required sample size considerably in a randomized clinical trial for patients with inflammatory rheumatic diseases

    OpenAIRE

    Smedslund Geir; Zangi Heidi Andersen; Mowinckel Petter; Hagen Kåre Birger

    2013-01-01

    Abstract Background Patient reported outcomes are accepted as important outcome measures in rheumatology. The fluctuating symptoms in patients with rheumatic diseases have serious implications for sample size in clinical trials. We estimated the effects of measuring the outcome 1-5 times on the sample size required in a two-armed trial. Findings In a randomized controlled trial that evaluated the effects of a mindfulness-based group intervention for patients with inflammatory arthritis (n=71)...

  17. Repeating the Past

    Science.gov (United States)

    Moore, John W.

    1998-05-01

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

  18. Repeatability and Minimal Detectable Change in Longitudinal Median Nerve Excursion Measures During Upper Limb Neurodynamic Techniques in a Mixed Population: A Pilot Study Using Musculoskeletal Ultrasound Imaging.

    Science.gov (United States)

    Paquette, Philippe; Lamontagne, Martin; Higgins, Johanne; Gagnon, Dany H

    2015-07-01

    This study determined test-retest reliability and minimum detectable change in longitudinal median nerve excursion during upper limb neurodynamic tests (ULNTs). Seven participants with unilateral or bilateral carpal tunnel syndrome and 11 healthy participants were randomly tested with two ULNTs (i.e., tensioner and slider). Each ULNT was performed three times each at 45° and 90° of shoulder abduction on two separate visits. Video sequences of median nerve excursion, recorded by a physical therapist using ultrasound imaging, were quantified using computer software. The generalizability theory, encompassing a G-Study and a D-study, measured the dependability coefficient (Φ) along with standard error of measurement (SEM) accuracy and allowed various testing protocols to be proposed. The highest reliability (Φ = 0.84) and lowest minimal measurement error (SEM = 0.58 mm) of the longitudinal median nerve excursion were reached during the ULNT-slider performed with 45° of shoulder abduction and when measures obtained from three different image sequences recorded during a single visit were averaged. It is recommended that longitudinal median nerve excursion measures computed from three separate image sequences recorded during a single visit be averaged in clinical practice. Ideally, adding a second visit (six image sequences) is also suggested in research protocols.

  19. Behavioral manifestations of audiometrically-defined "slight" or "hidden" hearing loss revealed by measures of binaural detection.

    Science.gov (United States)

    Bernstein, Leslie R; Trahiotis, Constantine

    2016-11-01

    This study assessed whether audiometrically-defined "slight" or "hidden" hearing losses might be associated with degradations in binaural processing as measured in binaural detection experiments employing interaurally delayed signals and maskers. Thirty-one listeners participated, all having no greater than slight hearing losses (i.e., no thresholds greater than 25 dB HL). Across the 31 listeners and consistent with the findings of Bernstein and Trahiotis [(2015). J. Acoust. Soc. Am. 138, EL474-EL479] binaural detection thresholds at 500 Hz and 4 kHz increased with increasing magnitude of interaural delay, suggesting a loss of precision of coding with magnitude of interaural delay. Binaural detection thresholds were consistently found to be elevated for listeners whose absolute thresholds at 4 kHz exceeded 7.5 dB HL. No such elevations were observed in conditions having no binaural cues available to aid detection (i.e., "monaural" conditions). Partitioning and analyses of the data revealed that those elevated thresholds (1) were more attributable to hearing level than to age and (2) result from increased levels of internal noise. The data suggest that listeners whose high-frequency monaural hearing status would be classified audiometrically as being normal or "slight loss" may exhibit substantial and perceptually meaningful losses of binaural processing.

  20. SHARP - II: Revealing a bias in observational measurements of dark matter substructure with gravitational lens flux ratios

    CERN Document Server

    Hsueh, J - W; Vegetti, S; McKean, J P; Spingola, C; Auger, M W; Koopmans, L V E; Lagattuta, D J

    2016-01-01

    Gravitational lens flux-ratio anomalies provide a powerful technique for measuring dark matter substructure in distant galaxies. However, before using these flux-ratio anomalies to test galaxy formation models, it is imperative to ascertain that the given anomalies are indeed due to the presence of dark matter substructure and not due to some other component of the lensing galaxy halo or to propagation effects. Here we present the case of CLASS~B1555+375, which has a strong radio-wavelength flux-ratio anomaly. Our high-resolution near-infrared Keck~II adaptive optics imaging and archival Hubble Space Telescope data reveal the lensing galaxy in this system to have a clear edge-on disc component that crosses directly over the pair of images that exhibit the flux-ratio anomaly. We find simple models that include the disc can reproduce the cm-wavelength flux-ratio anomaly without requiring additional dark matter substructure. Although further studies are required, our results suggest the assumption that all flux-...

  1. Impact of volunteer-related and methodology-related factors on the reproducibility of brachial artery flow-mediated vasodilation: analysis of 672 individual repeated measurements.

    NARCIS (Netherlands)

    Mil, A.C.C.M. van; Greyling, A.; Zock, P.L.; Geleijnse, J.M.; Hopman, M.T.E.; Mensink, R.P.; Reesink, K.D.; Green, D.J.; Ghiadoni, L.; Thijssen, D.H.J.

    2016-01-01

    OBJECTIVES: Brachial artery flow-mediated dilation (FMD) is a popular technique to examine endothelial function in humans. Identifying volunteer and methodological factors related to variation in FMD is important to improve measurement accuracy and applicability. METHODS: Volunteer-related and

  2. 数字光纤直放站中的时延测量与校正%The Measurement and Adjustment of Time Delay in Digital Optical Fiber Repeater

    Institute of Scientific and Technical Information of China (English)

    金绍春

    2011-01-01

    提出了应用于数字光纤直放站的时延测量与校正方法。阐述了数字光纤直放站的结构、时延测量的目的与原理、时延校正的计算。时延测量以CPRI协议为基础,包括光纤时延测量、转发时延测量。时延校正分下行时延校正和上行时延校正。下行时延校正是使同一台REC送出的IQ信号在不同的RE中能够同时射频发送出去。上行时延校正是使不同的RE接收到的IQ信号能够正确进行功率合成。%The Method of measurement and adjustment of time delay which applies to digital optical fiber repeater has been presented. The structure of digital optical fiber repeater, the purpose and principle of time delay measurement, the calculation of time delay adjustment, has been represented. The measurement of time delay that based on CPRI protocol includes the measurement of optical fiber time delay and the measurement of forward time delay. The time delay adjustment includes uplink time delay adjustment and downlink time delay adjustment. The purpose of downlink time delay adjustment is to ensure IQ signals in different REs which comes from the same REC transmit synchronously by radio frequency signals. The purpose of uplink time delay adjustment is to ensure received IQ signals by different REs synthesize correctly by power.

  3. All-optical repeater.

    Science.gov (United States)

    Silberberg, Y

    1986-06-01

    An all-optical device containing saturable gain, saturable loss, and unsaturable loss is shown to transform weak, distorted optical pulses into uniform standard-shape pulses. The proposed device performs thresholding, amplification, and pulse shaping as required from an optical repeater. It is shown that such a device could be realized by existing semiconductor technology.

  4. Bidirectional Manchester repeater

    Science.gov (United States)

    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.

  5. Whole scalp resting state EEG of oscillatory brain activity shows no parametric relationship with psychoacoustic and psychosocial assessment of tinnitus: A repeated measures study.

    Science.gov (United States)

    Pierzycki, Robert H; McNamara, Adam J; Hoare, Derek J; Hall, Deborah A

    2016-01-01

    Tinnitus is a perception of sound that can occur in the absence of an external stimulus. A brief review of electroencephalography (EEG) and magnetoencephalography (MEG) literature demonstrates that there is no clear relationship between tinnitus presence and frequency band power in whole scalp or source oscillatory activity. Yet a preconception persists that such a relationship exists and that resting state EEG could be utilised as an outcome measure for clinical trials of tinnitus interventions, e.g. as a neurophysiological marker of therapeutic benefit. To address this issue, we first examined the test-retest correlation of EEG band power measures in tinnitus patients (n = 42). Second we examined the evidence for a parametric relationship between numerous commonly used tinnitus variables (psychoacoustic and psychosocial) and whole scalp EEG power spectra, directly and after applying factor reduction techniques. Test-retest correlation for both EEG band power measures and tinnitus variables were high. Yet we found no relationship between whole scalp EEG band powers and psychoacoustic or psychosocial variables. We conclude from these data that resting state whole scalp EEG should not be used as a biomarker for tinnitus and that greater caution should be exercised in regard to reporting of findings to avoid confirmation bias. The data was collected during a randomised controlled trial registered at ClinicalTrials.gov (Identifier: NCT01541969).

  6. Repetibilidade e número mínimo de medições para caracteres de cacho de bacabi (Oenocarpus mapora Repeatability and minimum number of measurements for characters of bacabi palm (Oenocarpus mapora racemes

    Directory of Open Access Journals (Sweden)

    Maria do Socorro Padilha de Oliveira

    2010-12-01

    potential for commercial and food uses, but has not been well studied. The objectives of this study were to estimate the repeatability coefficients, determine predictability and the number of measurements needed for raceme characters of this palm. 27 individuals of bacabi that belong to the Germplasm Bank of Oenocarpus/Jessenia at Embrapa Eastern Amazon, in Belém, PA, Brazil were evaluated. Three fully matured racemes from each plant were sampled to measure six characters: total weight of raceme (TWR and fruit weight per raceme (FWR, number of rachillae per raceme (NRR, rachis length per raceme (RLR, weight of 100 fruits (WHF and fruit yield per raceme (FER. The repeatability estimates were obtained by three statistical methods: analysis of variance; principal components; and structural analysis. For all characters, the estimates of repeatability coefficients presented values with very similar magnitudes in the three methods. The estimates of repeatability coefficients and determination coefficients were relatively high (r 0.60 and R2 81.7% for the characters FER and NRR, showing genotype regularity for these raceme measurements. For these characters, the minimum number of racemes necessary to estimate the true character value of the genotypes was thirteen (FER and five (NRR, with 95% reliability. The remaining characters showed repeatabilities and determination coefficients with medium to low values, indicating the need for better environmental control to make the measurements.

  7. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  8. The child accident repeater: a review.

    Science.gov (United States)

    Jones, J G

    1980-04-01

    The child accident repeater is defined as one who has at least three accidents that come to medical attention within a year. The accident situation has features in common with those of the child who has a single accident through simple "bad luck", but other factors predispose him to repeated injury. In the child who has a susceptible personality, a tendency for accident repetition may be due to a breakdown in adjustment to a stressful environment. Prevention of repeat accidents should involve the usual measures considered appropriate for all children as well as an attempt to provide treatment of significant maladjustment and modification of a stressful environment.

  9. Burnout as a risk factor for antidepressant treatment - a repeated measures time-to-event analysis of 2936 Danish human service workers

    DEFF Research Database (Denmark)

    Madsen, Ida E H; Lange, Theis; Borritz, Marianne

    2015-01-01

    Burnout is a state of emotional exhaustion, feelings of reduced personal accomplishment, and withdrawal from work thought to occur as a consequence of prolonged occupational stress. The condition is not included in the diagnostic classifications, but is considered likely to develop into depressive...... disorder in some cases. We examined the prospective association between burnout and antidepressant treatment, as an indicator of clinically significant mental disorder. We further investigated potential effect-modifiers of the association, to identify factors that may prevent this progression of burnout...... modeling, examining the risk of entering antidepressant treatment in relation to the level of work-related burnout measured by the Copenhagen Burnout inventory. As effect-modifiers we examined both sociodemographic factors and a range of psychosocial work environment factors. The level of burnout predicted...

  10. County level socioeconomic position, work organization and depression disorder: a repeated measures cross-classified multilevel analysis of low-income nursing home workers.

    Science.gov (United States)

    Muntaner, Carles; Li, Yong; Xue, Xiaonan; Thompson, Theresa; O'Campo, Patricia; Chung, Haejoo; Eaton, William W

    2006-12-01

    This study simultaneously tests the effect of county, organizational, workplace, and individual level variables on depressive disorders among low-income nursing assistants employed in US nursing homes. A total of 482 observations are used from two waves of survey data collection, with an average two-year interval between initial and follow-up surveys. The overall response rate was 62 percent. The hierarchically structured data was analyzed using multilevel modeling to account for cross-classifications across levels of data. Nursing assistants working in nursing homes covered by a single union in three states were asked about aspects of their working conditions, job stress, physical and mental health status, individual and family health-care needs, household economics and household strain. The 241 nursing assistants who participated in this study were employed in 34 nursing homes and lived in 49 counties of West Virginia, Ohio and Kentucky. The study finds that emotional strain, related to providing direct care to elderly and disabled clients, is associated with depressive disorder, as is nursing home ownership type (for-profit versus not-for-profit). However, when controlling for county level socioeconomic variables (Gini index and proportion of African Americans living in the county), neither workplace nor organizational level variables were found to be statistically significant associated with depressive disorder. This study supports previous findings that emotional demand in health-care environments is an important correlate of mental health. It also adds empirical evidence to support a link between financial strain and depression in US women. While this study does not find that lack of a seniority wage benefits--a factor that can conceivably exacerbate financial strain over time--is associated with depressive disorder among low-income health-care workers, it does find county level measures of poverty to be statistically significant predictors of depressive

  11. Dynamics of Graft Function Measured by DNA-Technology in a Patient with Severe Aplastic Anemia and Repeated Stem Cell Transplantation

    Directory of Open Access Journals (Sweden)

    Anna Karastaneva

    2014-01-01

    Full Text Available Although bone marrow transplantation (BMT from an HLA identical sibling is considered as treatment of choice in pediatric patients with severe aplastic anemia (SAA, a significant number of them experience graft failure (GF after BMT. We report a case of an 8-year-old male patient with SAA who presented with a complicated posttransplant course due to parvovirus B19 infection and GF. A subsequent attempt to support the graft by antithymocyte globulin (ATG and a peripheral stem cell boost resulted in transitory autologous recovery of hematopoiesis followed by mixed chimerism, supported by donor lymphocyte infusions (DLIs and finally graft rejection with relapse of SAA. Permanent complete chimerism was achieved by a second BMT. Dynamics of graft function, measured by a single nucleotide polymorphism (SNPs analysis, are discussed.

  12. Long-term aerobic exercise and omega-3 supplementation modulate osteoporosis through inflammatory mechanisms in post-menopausal women: a randomized, repeated measures study

    Directory of Open Access Journals (Sweden)

    Kanaley Jill

    2011-10-01

    Full Text Available Abstract Background Evidence indicates that dietary fats and physical activity influence bone health. The purpose of this study was to examine the effects of long-term aerobic exercise and omega-3 (N-3 supplementation on serum inflammatory markers, bone mineral density (BMD, and bone biomarkers in post-menopausal women. Methods Seventy-nine healthy sedentary post-menopausal women aged 58-78 years participated in this study. Subjects were randomized to one of 4 groups: exercise + supplement (E+S, n = 21, exercise (E, n = 20, supplement (S, n = 20, and control (Con, n = 18 groups. The subjects in the E+S and E groups performed aerobic exercise training (walking and jogging up to 65% of HRmax, three times a week for 24 weeks. Subjects in the E+S and S groups consumed 1000 mg/d N-3 for 24 weeks. The lumbar spine (L2-L4 and femoral neck BMD, serum tumor necrosis factor (TNF α, interleukin (IL 6, prostaglandin (PG E2, estrogen, osteocalcin, 1, 25-dihydroxyvitamin D3 (1, 25 Vit D, C-telopeptide (CTX, parathyroid hormone (PTH and calcitonin (CT were measured at baseline, the end of week 12 and 24. Results Serum estrogen, osteocalcin, 1, 25 Vit D, CT, L2-L4 and femoral neck BMD measures increased (P 2 decreased (P 2-L4 and femoral neck BMD, estrogen, osteocalcin, and CT were negatively (P 2. PTH and CT were correlated positively and negatively with IL-6, respectively (P Conclusions The present study demonstrates that long-term aerobic exercise training plus N-3 supplementation have a synergistic effect in attenuating inflammation and augmenting BMD in post-menopausal osteoporosis.

  13. Thyroid nodules with nondiagnostic results on repeat fine-needle aspiration biopsy: which nodules should be considered for repeat biopsy or surgery rather than follow-up?

    Science.gov (United States)

    2016-01-01

    Purpose: The goal of this study was to assess the clinicopathologic and ultrasonographic features of thyroid nodules with nondiagnostic results on repeat ultrasonography (US)-guided fineneedle aspiration biopsy (FNAB) according to size and the number of suspicious findings and to determine the proper management of nodules with consecutive nondiagnostic results. Methods: This retrospective study included 297 nodules with nondiagnostic results on repeat FNAB that were evaluated by US over the course of at least 12 months of follow-up, a follow-up biopsy, or an operation. We compared clinical and US variables between benign and malignant nodules in thyroid nodules with repeat nondiagnostic results. Results: The comparison of benign and malignant nodules with repeat nondiagnostic results revealed that age, marked hypoechogenicity, irregular or microlobulated margins, microcalcifications, and nonparallel shape were significantly associated with malignancy. Multivariate logistic regression analysis in malignant nodules revealed that microcalcifications and irregular or microlobulated margins were independently associated with malignancy. Among them, only irregular or microlobulated margins were independently significant as a predictor of malignancy in repeatedly nondiagnostic nodules measuring >10 mm. Using receiver operating characteristic analysis, the best cutoff value for the “number of suspicious findings” between benign and malignant nodules was three in nodules of all sizes, three in nodules measuring ≤10 mm, and two in nodules measuring >10 mm. Conclusion: Irregular or microlobulated margins may be the most frequent US features in repeatedly nondiagnostic nodules >10 mm. The presence of “two or more suspicious findings” can be used as the cutoff for distinguishing benign and malignant nodules. PMID:27068131

  14. Thyroid nodules with nondiagnostic results on repeat fine-needle aspiration biopsy: which nodules should be considered for repeat biopsy or surgery rather than follow-up?

    Directory of Open Access Journals (Sweden)

    Na Lae Eun

    2016-07-01

    Full Text Available Purpose: The goal of this study was to assess the clinicopathologic and ultrasonographic features of thyroid nodules with nondiagnostic results on repeat ultrasonography (US-guided fineneedle aspiration biopsy (FNAB according to size and the number of suspicious findings and to determine the proper management of nodules with consecutive nondiagnostic results. Methods: This retrospective study included 297 nodules with nondiagnostic results on repeat FNAB that were evaluated by US over the course of at least 12 months of follow-up, a follow-up biopsy, or an operation. We compared clinical and US variables between benign and malignant nodules in thyroid nodules with repeat nondiagnostic results. Results: The comparison of benign and malignant nodules with repeat nondiagnostic results revealed that age, marked hypoechogenicity, irregular or microlobulated margins, microcalcifications, and nonparallel shape were significantly associated with malignancy. Multivariate logistic regression analysis in malignant nodules revealed that microcalcifications and irregular or microlobulated margins were independently associated with malignancy. Among them, only irregular or microlobulated margins were independently significant as a predictor of malignancy in repeatedly nondiagnostic nodules measuring >10 mm. Using receiver operating characteristic analysis, the best cutoff value for the “number of suspicious findings” between benign and malignant nodules was three in nodules of all sizes, three in nodules measuring ≤10 mm, and two in nodules measuring >10 mm. Conclusion: Irregular or microlobulated margins may be the most frequent US features in repeatedly nondiagnostic nodules >10 mm. The presence of “two or more suspicious findings” can be used as the cutoff for distinguishing benign and malignant nodules.

  15. Thyroid nodules with nondiagnostic results on repeat fine-needle aspiration biopsy: which nodules should be considered for repeat biopsy or surgery rather than follow-up?

    Energy Technology Data Exchange (ETDEWEB)

    Eun, Na Lae; Chang, Hang Seok; Gweon, Hye Mi; Kim, Jeong Ah; Youk, Ji Hyun; Son, Eun Jun [Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of); Yoo, Mi Ri [Dept. of Radiology, Dongjak Kyunghee Hospital, Seoul (Korea, Republic of); Park, Ah Young [Dept. of Radiology, Korea University Ansan Hospital, Korea University College of Medicine, Ansan (Korea, Republic of); Moon, Hee Jung [Dept. of Radiology and Research Institute of Radiological Science, Severance Hospital, Yonsei University College of Medicine, Seoul (Korea, Republic of)

    2016-07-15

    The goal of this study was to assess the clinicopathologic and ultrasonographic features of thyroid nodules with nondiagnostic results on repeat ultrasonography (US)-guided fineneedle aspiration biopsy (FNAB) according to size and the number of suspicious findings and to determine the proper management of nodules with consecutive nondiagnostic results. This retrospective study included 297 nodules with nondiagnostic results on repeat FNAB that were evaluated by US over the course of at least 12 months of follow-up, a follow-up biopsy, or an operation. We compared clinical and US variables between benign and malignant nodules in thyroid nodules with repeat nondiagnostic results. The comparison of benign and malignant nodules with repeat nondiagnostic results revealed that age, marked hypoechogenicity, irregular or microlobulated margins, microcalcifications, and nonparallel shape were significantly associated with malignancy. Multivariate logistic regression analysis in malignant nodules revealed that microcalcifications and irregular or microlobulated margins were independently associated with malignancy. Among them, only irregular or microlobulated margins were independently significant as a predictor of malignancy in repeatedly nondiagnostic nodules measuring >10 mm. Using receiver operating characteristic analysis, the best cutoff value for the “number of suspicious findings” between benign and malignant nodules was three in nodules of all sizes, three in nodules measuring ≤10 mm, and two in nodules measuring >10 mm. Irregular or microlobulated margins may be the most frequent US features in repeatedly nondiagnostic nodules >10 mm. The presence of “two or more suspicious findings” can be used as the cutoff for distinguishing benign and malignant nodules.

  16. Perfusion CT measurements in healthy cervical spinal cord: feasibility and repeatability of the study as well as interchangeability of the perfusion estimates using two commercially available software packages

    Energy Technology Data Exchange (ETDEWEB)

    Bisdas, Sotirios [Johann Wolfgang University Hospital, Department of Radiology, Frankfurt (Germany); Medical University of South Carolina, Department of Radiology, Charleston, SC (United States); Johann Wolfgang Goethe University Hospital, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Rumboldt, Zoran; Deveikis, John; Spampinato, Maria Vittoria [Medical University of South Carolina, Department of Radiology, Charleston, SC (United States); Surlan, Katarina [Clinical Centre Ljubljana, Department of Clinical Radiology, Ljubljana (Slovenia); Koh, Tong San [Nanyang Technological University, School of Electrical and Electronic Engineering, Singapore (Singapore)

    2008-10-15

    Our purpose was to examine the feasibility and reproducibility of perfusion CT studies in the cervical spinal cord and the interchangeability of the values obtained by two post-processing methods. The perfusion CT studies of 40 patients with neck tumours were post-processed using two software packages (Software-1: deconvolution-based analysis with adiabatic tissue homogeneity approach and Software-2: maximum-slope-model with Patlak analysis). Eight patients were examined twice for assessing the reproducibility of the technique. Two neuroradiologists separately post-processed the images with two arterial input functions (AIFs): (1) the internal carotid artery (ICA) and (2) the vertebral artery (VA). Maps of blood flow (F) in ml/min/100 g, blood volume (V) in ml/100 g, mean transit time (MTT) in seconds (s) and permeability (PS) in ml/min/100 g were generated. The mean F, V, MTT and PS (Software-1) with VA-AIF and ICA-AIF were 8.93, 1.12, 16.3, 1.88 and 8.57, 1.19, 16.85 and 1.94, respectively. The reproducibility of the techniques was satisfactory, while the V and MTT values (in Software-1) and the F and V values (in Software-2) were dependent on the site of the AIF (p{>=}0.03 and p=0.02, respectively). The interobserver agreement was very good. The significant differences in measurements for a single patient (%) using Software-1/Software-2 were {+-}120%/110%, 90%/80%, 180% and 250%/130% for F, V, MTT and PS, respectively. Only F and PS values in the healthy tissue seemed to be interchangeable. Our results were in essential agreement with those derived by invasive measurements in animals. The cervical spine perfusion CT studies are feasible and reproducible. The present knowledge has to be validated with studies in spinal cord tumours in order to decide the usefulness of the perfusion CT in this field. (orig.)

  17. Evaluation of repeated measurements of radon-222 concentrations in well water sampled from bedrock aquifers of the Piedmont near Richmond, Virginia, USA: effects of lithology and well characteristics.

    Science.gov (United States)

    Harris, Shelley A; Billmeyer, Ernest R; Robinson, Michael A

    2006-07-01

    Radon (222Rn) concentrations in 26 ground water wells of two distinct lithologies in the Piedmont of Virginia were measured to assess variation in ground water radon concentrations (GWRC), to evaluate differences in concentrations related to well characteristics, lithology, and spatial distributions, and to assess the feasibility of predicting GWRC. Wells were sampled in accordance with American Public Health Association Method 7500 Rn-B, with modifications to include a well shaft profile analysis that determined the minimum purge time sufficient to remove the equivalent of one column of water from each well. Statistically significant differences in GWRC were found in the Trssu (1482 +/- 1711 pCi/L) and Mpg (7750 +/- 5188 pCi/L) lithologies, however, no significant differences were found among GWRC at each well over time. Using multiple regression, 86% of the variability (R2) in the GWRC was explained by the lithology, latitudinal class, and water table elevation of the wells. The GWRC in a majority of the wells studied exceed US Environmental Protection Agency designated maximum contaminant level and AMCL. Results support modifications to sampling procedures and indicate that, in previous studies, variations in GWRC concentrations over time may have been due in part to differences in sampling procedures and not in source water.

  18. Redox-controlled backbone dynamics of human cytochrome c revealed by {sup 15}N NMR relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Sakamoto, Koichi [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Kamiya, Masakatsu [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Uchida, Takeshi [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan); Kawano, Keiichi [Graduate School of Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810 (Japan); Ishimori, Koichiro, E-mail: koichiro@sci.hokudai.ac.jp [Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo 060-0810 (Japan); Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810 (Japan)

    2010-07-23

    Research highlights: {yields} The dynamic parameters for the backbone dynamics in Cyt c were determined. {yields} The backbone mobility of Cyt c is highly restricted due to the covalently bound heme. {yields} The backbone mobility of Cyt c is more restricted upon the oxidation of the heme. {yields} The redox-dependent dynamics are shown in the backbone of Cyt c. {yields} The backbone dynamics of Cyt c would regulate the electron transfer from Cyt c. -- Abstract: Redox-controlled backbone dynamics in cytochrome c (Cyt c) were revealed by 2D {sup 15}N NMR relaxation experiments. {sup 15}N T{sub 1} and T{sub 2} values and {sup 1}H-{sup 15}N NOEs of uniformly {sup 15}N-labeled reduced and oxidized Cyt c were measured, and the generalized order parameters (S{sup 2}), the effective correlation time for internal motion ({tau}{sub e}), the {sup 15}N exchange broadening contributions (R{sub ex}) for each residue, and the overall correlation time ({tau}{sub m}) were estimated by model-free dynamics formalism. These dynamic parameters clearly showed that the backbone dynamics of Cyt c are highly restricted due to the covalently bound heme that functions as the stable hydrophobic core. Upon oxidation of the heme iron in Cyt c, the average S{sup 2} value was increased from 0.88 {+-} 0.01 to 0.92 {+-} 0.01, demonstrating that the mobility of the backbone is further restricted in the oxidized form. Such increases in the S{sup 2} values were more prominent in the loop regions, including amino acid residues near the thioether bonds to the heme moiety and positively charged region around Lys87. Both of the regions are supposed to form the interaction site for cytochrome c oxidase (CcO) and the electron pathway from Cyt c to CcO. The redox-dependent mobility of the backbone in the interaction site for the electron transfer to CcO suggests an electron transfer mechanism regulated by the backbone dynamics in the Cyt c-CcO system.

  19. Relative contributions of interface pressure, shear stress, and temperature on ischemic-induced, skin-reactive hyperemia in healthy volunteers: a repeated measures laboratory study.

    Science.gov (United States)

    Lachenbruch, Charlie; Tzen, Yi-Ting; Brienza, David; Karg, Patricia E; Lachenbruch, Peter A

    2015-02-01

    Although the primary risk factors for pressure ulcer development - pressure, shear, skin temperature, moisture, and friction - have been identified for decades, the relative contribution of each to this risk remains unclear. To confirm the results of and expand upon earlier research into the relative contributions of interface pressures, shear stress, and skin temperature among 4 healthy volunteers, a study involving 6 additional healthy 40- to 75-year-old volunteers was conducted and results of the 2 studies were pooled. All 3 variables (interface pressures, shear stress, and skin temperature) were systematically and randomly varied. In the prone position, volunteers each underwent 18 test conditions representing different combinations of temperature (28˚ C, 32˚ C, 36˚ C), pressure (8.0 and 13.3 kPa), and shear (0, 6.7, and 14.0 kPa) using a computer-controlled indenter applied to the sacrum for 20 minutes exerting weights of 100 g and 200 g to induce 0.98 N and 1.96 N of shear force, respectively. Each condition was tested twice, resulting in a total of 360 trials. Magnitude of postload reactive hyperemia as an index of ischemia was measured by laser Doppler flowmetry. Fixed effects regression models were used to predict 3 different indices of reactive hyperemic magnitude. Friedman tests were performed to compare the reactive hyperemia among 3 different skin temperatures or shear stresses under the same amount of localized pressure. In all regression models, pressure and temperature were highly significant predictors of the extent of reactive hyperemia (P pressure and shear stress, and the difference was more profound between 32˚ C and 36˚ C than between 28˚ C and 32˚ C. These results confirm that, in laboratory settings, temperature is an important factor in tissue ischemia. Additional studies examining the relative importance of pressure, shear, and temperature and potential effects of lowering temperature on tissue ischemia in healthy volunteers and

  20. Repetibilidade da mensuração de imagens das características de carcaça obtidas por ultrassonografia em fêmeas Nelore Repeatability of ultrasound image measurements of carcass traits in Nellore cattle

    Directory of Open Access Journals (Sweden)

    Maria Eugênia Zerlotti Mercadante

    2010-04-01

    Full Text Available Avaliou-se a repetibilidade da mensuração de imagens de ultrassom da área do músculo longissimus dorsi (AOL e das espessuras de gordura subcutânea do lombo (EGL e da garupa (EGG. Imagens de ultrassom tomadas no lombo (entre a 12ª e a 13ª costela e na garupa (entre os músculos gluteus medium e biceps femoris de novilhas Nelore de 14 a 22 meses de idade foram classificadas em aceitáveis, marginais e rejeitáveis. As imagens aceitáveis e marginais foram mensuradas duas vezes por três técnicos em diferentes níveis de treinamento. Foram estimadas as repetibilidades entre e dentro de técnicos por classe de qualidade da imagem, para determinação do efeito da qualidade da imagem e do técnico no valor absoluto da diferença entre a primeira e a segunda mensuração dessas características. A repetibilidade para as imagens aceitáveis foi maior que para imagens marginais, tanto entre como dentro de técnicos. Na análise da diferença absoluta entre a primeira e a segunda interpretação, foram significativos os efeitos de técnico para AOL e EGL e de classe de qualidade da imagem para AOL. Em geral, o técnico com maior experiência apresentou maiores valores de repetibilidade. É recomendável que a mensuração de imagens de animais de mesmo grupo contemporâneo seja feita por um único técnico.The repeatability of ultrasound image measurements of the longissimus dorsi muscle (AOL and of the rumpfat (EGG and backfat (EGL subcutaneous thickness was evaluated. Ultrasound images taken from the back (between 12th and 13th ribs and from the rump (between gluteus medium and biceps femoris muscles of Nelore heifers at 14 and 22 months of age were classified as acceptable, marginal and rejected. The acceptable and marginal images were measured twice by three technicians at different levels of training. It was estimated repeatabilities among and within technicians by class of image quality in order to determine effect of image quality and of

  1. Crowding by a repeating pattern.

    Science.gov (United States)

    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.

  2. Repeatability of peripheral aberrations in young emmetropes.

    Science.gov (United States)

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

    2010-10-01

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

  3. 超高分辨率OCT角膜上皮厚度自动测量的重复性研究%Study of repeatability of corneal epithelium thickness profiles automatically measured by ultra -high resolution OCT system

    Institute of Scientific and Technical Information of China (English)

    徐肃仲; 叶欣杰; 许哲; 杨纯; 沈梅晓

    2013-01-01

    目的:研究基于自动分层算法的超高分辨率谱域 OCT ( UHR-OCT)用于角膜上皮厚度测量的重复性。  方法:使用自行搭建的UHR-OCT系统采集18例健康受试者(年龄23.2±0.9岁)左眼的图像,应用一种基于轴向梯度信息和最短路径的分层算法对得到的SD-OCT图像进行边界探测获取角膜上皮厚度。  结果:自动与手动的上皮分层的位置有很好的相关性(P>0.05,配对t检验)。自动算法获取的6 mm范围平均上皮厚度为52.1±2.1μm,范围从50.3±1.8μm 到53.2±2.4μm,与手动分层之间的角膜上皮厚度差异为0.4±0.3μm。UHR-OCT自动算法重复测量上皮厚度的组内相关系数ICC和可重复性系数CoR分别为0.90±0.05,1.44±0.01μm。  结论:对于超高分辨率OCT,自动分层方法在角膜上皮厚度测量中有着很好的准确性和可重复性。%AIM:To assess the repeatability of thickness profiles of corneal epithelium produced by aautomatic hierarchic algorithm that was applied to images obtained by a custom-built ultra-high resolution OCT ( UHR-OCT ) system. METHODS:Eighteen left eyes of 18 subjects (23.2±0.9) years;mean age±standard deviation) were imaged twice on non-consecutive days by a custom-built ultra-high resolution OCT ( UHR -OCT ) system. A hierarchic algorithm based on the axial gradient information and a shortest path search was developed to measure the corneal epithelial thickness profiles from the SD-OCT images. RESULTS: There was good correlation between theautomatic and manual hierarchy positions of the epithelium ( p >0.05, paired t -test ). The average epithelial thickness of the 6mm central corneal region determined by the automatic hierarchic algorithm was 52.1±2.1μm, ranging from 50.3 ±1.8μm to 53.2 ±2.4μm along the horizontal meridian. The epithelial thickness differences between automatic and manual hierarchy by the UHR-OCT systems were 0.4 ±0

  4. Repeatability of Cryogenic Multilayer Insulation

    Science.gov (United States)

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

    2017-01-01

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

  5. Repeated Measurement of Divers’ Word Fluency.

    Science.gov (United States)

    1987-04-01

    function (Fillskov & Boll, -V 1981). One type of test with clinical significance reflects Word Fluency (Borkowski, Benton & Spreen, 1967; Lezak, 1983). Word...Fluency is "the facility to produce words that fit one or more structural, phonetic , or orthographic restrictions that are not relevant to the meaning...toxic chemical exposure (Anger, 1984) and closed head injury (Borkowski et al, 1967). Word Fluency reflects mild linguistic deficits in expressive speech

  6. Surface structure of CdSe Nanorods revealed by combined X-rayabsorption fine structure measurements and ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois; Galli, Giulia; Alivisatos, A. Paul

    2006-01-27

    We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.

  7. Quantum Key Distribution over Probabilistic Quantum Repeaters

    CERN Document Server

    Amirloo, Jeyran; Majedi, A Hamed

    2010-01-01

    A feasible route towards 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 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 of with and without a repeater node. We find the cross-over distance beyond which the repeater system outperforms the non-repeater one. That provides us with the optimum inter-node distancing in quantum repeater systems. We also find the optimal exci...

  8. Whole-brain analytic measures of network communication reveal increased structure-function correlation in right temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Jonathan Wirsich

    2016-01-01

    In rTLE patients, we found a widespread hypercorrelated functional network. Network communication analysis revealed greater unspecific branching of the shortest path (search information in the structural connectome and a higher global correlation between the structural and functional connectivity for the patient group. We also found evidence for a preserved structural rich-club in the patient group. In sum, global augmentation of structure-function correlation might be linked to a smaller functional repertoire in rTLE patients, while sparing the central core of the brain which may represent a pathway that facilitates the spread of seizures.

  9. Sample Entropy and Traditional Measures of Heart Rate Dynamics Reveal Different Modes of Cardiovascular Control During Low Intensity Exercise

    Directory of Open Access Journals (Sweden)

    Matthias Weippert

    2014-10-01

    Full Text Available Nonlinear parameters of heart rate variability (HRV have proven their prognostic value in clinical settings, but their physiological background is not very well established. We assessed the effects of low intensity isometric (ISO and dynamic (DYN exercise of the lower limbs on heart rate matched intensity on traditional and entropy measures of HRV. Due to changes of afferent feedback under DYN and ISO a distinct autonomic response, mirrored by HRV measures, was hypothesized. Five-minute inter-beat interval measurements of 43 healthy males (26.0 ± 3.1 years were performed during rest, DYN and ISO in a randomized order. Blood pressures and rate pressure product were higher during ISO vs. DYN (p < 0.001. HRV indicators SDNN as well as low and high frequency power were significantly higher during ISO (p < 0.001 for all measures. Compared to DYN, sample entropy (SampEn was lower during ISO (p < 0.001. Concluding, contraction mode itself is a significant modulator of the autonomic cardiovascular response to exercise. Compared to DYN, ISO evokes a stronger blood pressure response and an enhanced interplay between both autonomic branches. Non-linear HRV measures indicate a more regular behavior under ISO. Results support the view of the reciprocal antagonism being only one of many modes of autonomic heart rate control. Under different conditions; the identical “end product” heart rate might be achieved by other modes such as sympathovagal co-activation as well.

  10. Random Number Simulations Reveal How Random Noise Affects the Measurements and Graphical Portrayals of Self-Assessed Competency

    Directory of Open Access Journals (Sweden)

    Edward Nuhfer

    2016-01-01

    Full Text Available Self-assessment measures of competency are blends of an authentic self-assessment signal that researchers seek to measure and random disorder or "noise" that accompanies that signal. In this study, we use random number simulations to explore how random noise affects critical aspects of self-assessment investigations: reliability, correlation, critical sample size, and the graphical representations of self-assessment data. We show that graphical conventions common in the self-assessment literature introduce artifacts that invite misinterpretation. Troublesome conventions include: (y minus x vs. (x scatterplots; (y minus x vs. (x column graphs aggregated as quantiles; line charts that display data aggregated as quantiles; and some histograms. Graphical conventions that generate minimal artifacts include scatterplots with a best-fit line that depict (y vs. (x measures (self-assessed competence vs. measured competence plotted by individual participant scores, and (y vs. (x scatterplots of collective average measures of all participants plotted item-by-item. This last graphic convention attenuates noise and improves the definition of the signal. To provide relevant comparisons across varied graphical conventions, we use a single dataset derived from paired measures of 1154 participants' self-assessed competence and demonstrated competence in science literacy. Our results show that different numerical approaches employed in investigating and describing self-assessment accuracy are not equally valid. By modeling this dataset with random numbers, we show how recognizing the varied expressions of randomness in self-assessment data can improve the validity of numeracy-based descriptions of self-assessment.

  11. Verificação da prótese auditiva realizada face a face e via teleconsulta: medidas repetidas Telecounselling and face to face hearing aid verification: repeated measures

    Directory of Open Access Journals (Sweden)

    Deborah Viviane Ferrari

    2012-12-01

    Full Text Available OBJETIVO: avaliar as medidas repetidas da resposta de ressonância da orelha externa sem (REUR e com uso de amplificação (REAR e o ganho de inserção (REIG, realizados face a face e via teleconsulta. MÉTODO: estudo prospectivo longitudinal. Foram realizadas quatro repetições da REUR, REAR e REIG (com estímulo speech noise apresentado em 65 dB NPS e 0º azimute em 19 orelhas de adultos ouvintes normais, via face a face (F e teleconsulta síncrona por controle remoto de aplicativo (T e vídeo interativo. O software Polycom PVX foi utilizado para compartilhamento e transmissão de áudio e vídeo. A conexão foi realizada via LAN (Local Area Network USP na velocidade de 384 kbps Foi calculado o erro causal (Dalhberg entre as quatro medidas para frequências de 250 a 8000 Hz. RESULTADOS: os erros casuais entre as medidas F e T foram muito semelhantes, sendo maiores nas frequências acima de 4 kHz. As diferenças e variações entre as medidas F e T estavam dentro da magnitude de variabilidade do procedimento de medidas com microfone sonda. CONCLUSÃO: as medidas com microfone sonda via teleconsulta fornece resultados confiáveis e similares aos obtidos pelo procedimento padrão.PURPOSE: to evaluate the repeated measurements of the real ear unaided response (REUR, real ear aided response (REAR and insertion gain (REIG conducted as face to face (F and via telecounselling (T. METHOD: longitudinal prospective study. Four measures of REUR, REAR and REIG (carried out with speech noise stimulus presented at 65 dB SPL at 0° azimuth were obtained in 19 ears in normal hearing adults, face to face and via synchronous telecounsellings with remote control of the real ear equipment and interactive video. Polycom PVX software was used for desktop sharing and video and audio transmission. The Loca Area Network (LAN USP was used for the connection (transmission rate: 384 kbps. Dahlberg’s casual errors were calculated for obtaining the measures for

  12. Reliability and criterion-related validity of a new repeated agility test

    Directory of Open Access Journals (Sweden)

    MS Fessi

    2016-04-01

    Full Text Available The study aimed to assess the reliability and the criterion-related validity of a new repeated sprint T-test (RSTT that includes intense multidirectional intermittent efforts. The RSTT consisted of 7 maximal repeated executions of the agility T-test with 25 s of passive recovery rest in between. Forty-five team sports players performed two RSTTs separated by 3 days to assess the reliability of best time (BT and total time (TT of the RSTT. The intra-class correlation coefficient analysis revealed a high relative reliability between test and retest for BT and TT (>0.90. The standard error of measurement (<0.50 showed that the RSTT has a good absolute reliability. The minimal detectable change values for BT and TT related to the RSTT were 0.09 s and 0.58 s, respectively. To check the criterion-related validity of the RSTT, players performed a repeated linear sprint (RLS and a repeated sprint with changes of direction (RSCD. Significant correlations between the BT and TT of the RLS, RSCD and RSTT were observed (p<0.001. The RSTT is, therefore, a reliable and valid measure of the intermittent repeated sprint agility performance. As this ability is required in all team sports, it is suggested that team sports coaches, fitness coaches and sports scientists consider this test in their training follow-up.

  13. Thermal stability of chicken brain {alpha}-spectrin repeat 17: a spectroscopic study

    Energy Technology Data Exchange (ETDEWEB)

    Brenner, Annette K. [University of Bergen, Department of Chemistry (Norway); Kieffer, Bruno [Ecole Superieure de Biotechnologie de Strasbourg, IGBMC Biomolecular NMR Group, CNRS UMR 7104 (France); Trave, Gilles [Ecole Superieure de Biotechnologie de Strasbourg, Equipe Oncoproteines, IREBS, UMR 7242 (France); Froystein, Nils Age [University of Bergen, Department of Chemistry (Norway); Raae, Arnt J., E-mail: arnt.raae@mbi.uib.no [University of Bergen, Department of Molecular Biology (Norway)

    2012-06-15

    Spectrin is a rod-like multi-modular protein that is mainly composed of triple-helical repeats. These repeats show very similar 3D-structures but variable conformational and thermodynamical stabilities, which may be of great importance for the flexibility and dynamic behaviour of spectrin in the cell. For instance, repeat 17 (R17) of the chicken brain spectrin {alpha}-chain is four times less stable than neighbouring repeat