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Sample records for repeated pairs method

  1. Repeatedly pairing vagus nerve stimulation with a movement reorganizes primary motor cortex.

    Science.gov (United States)

    Porter, Benjamin A; Khodaparast, Navid; Fayyaz, Tabbassum; Cheung, Ryan J; Ahmed, Syed S; Vrana, William A; Rennaker, Robert L; Kilgard, Michael P

    2012-10-01

    Although sensory and motor systems support different functions, both systems exhibit experience-dependent cortical plasticity under similar conditions. If mechanisms regulating cortical plasticity are common to sensory and motor cortices, then methods generating plasticity in sensory cortex should be effective in motor cortex. Repeatedly pairing a tone with a brief period of vagus nerve stimulation (VNS) increases the proportion of primary auditory cortex responding to the paired tone (Engineer ND, Riley JR, Seale JD, Vrana WA, Shetake J, Sudanagunta SP, Borland MS, Kilgard MP. 2011. Reversing pathological neural activity using targeted plasticity. Nature. 470:101-104). In this study, we predicted that repeatedly pairing VNS with a specific movement would result in an increased representation of that movement in primary motor cortex. To test this hypothesis, we paired VNS with movements of the distal or proximal forelimb in 2 groups of rats. After 5 days of VNS movement pairing, intracranial microstimulation was used to quantify the organization of primary motor cortex. Larger cortical areas were associated with movements paired with VNS. Rats receiving identical motor training without VNS pairing did not exhibit motor cortex map plasticity. These results suggest that pairing VNS with specific events may act as a general method for increasing cortical representations of those events. VNS movement pairing could provide a new approach for treating disorders associated with abnormal movement representations.

  2. A COMPARISON OF PAIRS FIGURE SKATERS IN REPEATED JUMPS

    Directory of Open Access Journals (Sweden)

    William A. Sands

    2012-03-01

    Full Text Available Trends in pairs figure skating have shown that increasingly difficult jumps have become an essential aspect of high-level performance, especially in the latter part of a competitive program. We compared a repeated jump power index in a 60 s repeated jump test to determine the relationship of repeated jump test to competitive rank and to measure 2D hip, knee, and ankle angles and angular velocities at 0, 20, 40, and 60 s. Eighteen National Team Pairs Figure Skaters performed a 60 s repeated jump test on a large switch-mat with timing of flight and ground durations and digital video recording. Each 60-s period was divided into 6, 10-s intervals, with power indexes (W/kg calculated for each 10-s interval. Power index by 10-s interval repeated measures ANOVAs (RMANOVA showed that males exceeded females at all intervals, and the highest power index interval was during 10 to 20 s for both sexes. RMANOVAs of angles and angular velocities showed main effects for time only. Power index and jumping techniques among figure skaters showed rapid and steady declines over the test duration. Power index can predict approximately 50% of competitive rank variance, and sex differences in jumping technique were rare

  3. Investigation of the paired-gear method in selectivity studies

    DEFF Research Database (Denmark)

    Sistiaga, Manu; Herrmann, Bent; Larsen, R.B.

    2009-01-01

    was repeated throughout the eight cases in this investigation. When using the paired-gear method, the distribution of the estimated L50 and SR is wider; the distribution of the estimated split parameter has a higher variability than the true split; the estimated mean L50 and SR can be biased; the estimated...... recommend that the methodology used to obtain selectivity estimates using the paired-gear method be reviewed....

  4. Finding Maximal Pairs with Bounded Gap

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Lyngsø, Rune B.; Pedersen, Christian N. S.

    1999-01-01

    . In this paper we present methods for finding all maximal pairs under various constraints on the gap. In a string of length n we can find all maximal pairs with gap in an upper and lower bounded interval in time O(n log n+z) where z is the number of reported pairs. If the upper bound is removed the time reduces...... to O(n+z). Since a tandem repeat is a pair where the gap is zero, our methods can be seen as a generalization of finding tandem repeats. The running time of our methods equals the running time of well known methods for finding tandem repeats....

  5. A Golub-Kahan-type reduction method for matrix pairs

    NARCIS (Netherlands)

    Hochstenbach, M.E.; Reichel, L.; Yu, X.

    2015-01-01

    We describe a novel method for reducing a pair of large matrices {A;B} to a pair of small matrices {H;K}. The method is an extension of Golub-Kahan bidiagonalization to matrix pairs, and simplifies to the latter method when B is the identity matrix. Applications to Tikhonov regularization of large

  6. A Golub-Kahan-type reduction method for matrix pairs

    NARCIS (Netherlands)

    Hochstenbach, M.E.; Reichel, L.; Yu, X.

    2015-01-01

    We describe a novel method for reducing a pair of large matrices {A,B} to a pair of small matrices {H,K}. The method is an extension of Golub–Kahan bidiagonalization to matrix pairs, and simplifies to the latter method when B is the identity matrix. Applications to Tikhonov regularization of large

  7. What Is the Role of Paired Rapid Plasma Reagin Testing (Simultaneous Testing of Acute and Convalescent Samples) in the Diagnosis of Repeat Syphilis and the Follow-up of Syphilis?

    Science.gov (United States)

    Kenyon, Chris R; Osbak, Kara Krista; Van Esbroek, Marjan; Lynen, Lutgarde; Crucitti, Tania

    2018-01-01

    Repeat syphilis is playing an increasing role in syphilis transmission in several populations. The assessment of repeat syphilis and response to treatment depends on accurately measuring intraindividual changes in non-treponemal tests. For a 0- to 6-month delta rapid plasma reagin (RPR) to be determined by routine individual RPR testing, samples are tested 6 months apart with differences in reagent batches, environmental conditions, and observers all leading to measurement errors. We hypothesized that conducting paired RPR testing (simultaneous testing of acute and convalescent samples) would enable a more accurate determination of delta RPR compared with individual testing. A total of 120 study participants with a new diagnosis of syphilis were followed up at 0, 3, 6, 9, 12, 18, and 24 months, with RPR testing performed via individual testing at each study visit and at any suspected repeat syphilis. Rapid plasma reagin paired testing was performed on samples from 0 and 6 months and at any suspected repeat syphilis. The quantitative agreement ±1 dilution among paired and individual testing was 97.2%. There was no difference in the proportion with serofast status at 6 months: 21 (19.4%) and 19 (17.6%) according to paired and individual testing, respectively (P = 0.726). There was no statistically significant difference between 0- and 6-month delta RPR as determined by paired and individual testing in predicting seroresponse at 12 months (86.1% and 91.6% agreement with 12-month serofast/nonserofast classification, respectively; P = 0.262). In our setting, individual testing performed equally well compared with paired testing. Follow-up of syphilis will remain onerous for the patient and the health care provider until new tests that can more accurately assess the response to therapy and repeat syphilis/treatment failure are developed.

  8. On Solving Intransitivities in Repeated Pairwise Choices

    NARCIS (Netherlands)

    A. Maas (Arne); Th.G.G. Bezembinder (Thom); P.P. Wakker (Peter)

    1995-01-01

    textabstractAn operational method is presented for deriving a linear ranking of alternatives from repeated paired comparisons of the alternatives. Intransitivities in the observed preferences are cleared away by the introduction of decision errors of varying importance. An observed preference

  9. Synergistic enhancement of cellulase pairs linked by consensus ankyrin repeats: Determination of the roles of spacing, orientation, and enzyme identity.

    Science.gov (United States)

    Cunha, Eva S; Hatem, Christine L; Barrick, Doug

    2016-08-01

    Biomass deconstruction to small simple sugars is a potential approach to biofuels production; however, the highly recalcitrant nature of biomass limits the economic viability of this approach. Thus, research on efficient biomass degradation is necessary to achieve large-scale production of biofuels. Enhancement of cellulolytic activity by increasing synergism between cellulase enzymes holds promise in achieving high-yield biofuels production. Here we have inserted cellulase pairs from extremophiles into hyperstable α-helical consensus ankyrin repeat domain scaffolds. Such chimeric constructs allowed us to optimize arrays of enzyme pairs against a variety of cellulolytic substrates. We found that endocellulolytic domains CelA (CA) and Cel12A (C12A) act synergistically in the context of ankyrin repeats, with both three and four repeat spacing. The extent of synergy differs for different substrates. Also, having C12A N-terminal to CA provides greater synergy than the reverse construct, especially against filter paper. In contrast, we do not see synergy for these enzymes in tandem with CelK (CK) catalytic domain, a larger exocellulase, demonstrating the importance of enzyme identity in synergistic enhancement. Furthermore, we found endocellulases CelD and CA with three repeat spacing to act synergistically against filter paper. Importantly, connecting CA and C12A with a disordered linker of similar contour length shows no synergistic enhancement, indicating that synergism results from connecting these domains with folded ankyrin repeats. These results show that ankyrin arrays can be used to vary spacing and orientation between enzymes, helping to design and optimize artificial cellulosomes, providing a novel architecture for synergistic enhancement of enzymatic cellulose degradation. Proteins 2016; 84:1043-1054. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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

    Science.gov (United States)

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

    2017-10-03

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

  11. Question presentation methods for paired-associate learning

    NARCIS (Netherlands)

    Engel, F.L.; Geerings, M.P.W.

    1988-01-01

    Four different methods of question presentation, in interactive computeraided learning of Dutch-English word pairs are evaluated experimentally. These methods are: 1) the 'open-question method', 2) the 'multiple-choice method', 3) the 'sequential method' and 4) the 'true/ false method'. When

  12. Methods for analysing cardiovascular studies with repeated measures

    NARCIS (Netherlands)

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

    2009-01-01

    Background. Repeated measurements in a single subject are generally more similar than unrepeated measurements in different subjects. Unrepeated analyses of repeated data cause underestimation of the treatment effects. Objective. To review methods adequate for the analysis of cardiovascular studies

  13. Hepatitis c virus antibodies in mother-infant blood pair in Zaria

    African Journals Online (AJOL)

    2017-06-01

    Jun 1, 2017 ... Abstract: Objectives: To deter- mine the prevalence of Hepatitis. C virus (HCV) antibodies in mother-infant pair, and risk fac- tors for vertical transmission of. HCV in ABUTH Zaria. Method: One hundred mother- infant pair had serological deter- mination for HCV antibodies from birth to 28days and a repeat.

  14. The Impact of a Modified Repeated-Reading Strategy Paired with Optical Character Recognition on the Reading Rates of Students with Visual Impairments

    Science.gov (United States)

    Pattillo, Suzan Trefry; Heller, Kathryn Wolf; Smith, Maureen

    2004-01-01

    The repeated-reading strategy and optical character recognition were paired to demonstrate a functional relationship between the combined strategies and two factors: the reading rates of students with visual impairments and the students' self-perceptions, or attitudes, toward reading. The results indicated that all five students increased their…

  15. Pairing interaction method in crystal field theory

    International Nuclear Information System (INIS)

    Dushin, R.B.

    1989-01-01

    Expressions, permitting to describe matrix elements of secular equation for metal-ligand pairs via parameters of the method of pairing interactions, genealogical coefficients and Clebsch-Gordan coefficients, are given. The expressions are applicable to any level or term of f n and d n configurations matrix elements for the terms of the maximum multiplicity of f n and d n configurations and also for the main levels of f n configurations are tabulated

  16. METHODS OF STEREO PAIR IMAGES FORMATION WITH A GIVEN PARALLAX VALUE

    Directory of Open Access Journals (Sweden)

    Viktoriya G. Chafonova

    2014-11-01

    Full Text Available Two new complementary methods of stereo pair images formation are proposed. The first method is based on finding the maximum correlation between the gradient images of the left and right frames. The second one implies the finding of the shift between two corresponding key points of images for a stereo pair found by a detector of point features. These methods give the possibility to set desired values of vertical and horizontal parallaxes for the selected object in the image. Application of these methods makes it possible to measure the parallax values for the objects on the final stereo pair in pixels and / or the percentage of the total image size. It gives the possibility to predict the possible excesses in parallax values while stereo pair printing or projection. The proposed methods are easily automated after object selection, for which a predetermined value of the horizontal parallax will be exposed. Stereo pair images superposition using the key points takes less than one second. The method with correlation application requires a little bit more computing time, but makes it possible to control and superpose undivided anaglyph image. The proposed methods of stereo pair formation can find their application in programs for editing and processing images of a stereo pair, in the monitoring devices for shooting cameras and in the devices for video sequence quality assessment

  17. Repeatability and reproducibility of decisions by latent fingerprint examiners.

    Directory of Open Access Journals (Sweden)

    Bradford T Ulery

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

  18. Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method.

    Science.gov (United States)

    Neese, Frank; Wennmohs, Frank; Hansen, Andreas

    2009-03-21

    Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Moller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol(-1). Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500

  19. simple sequence repeats (EST-SSR)

    African Journals Online (AJOL)

    Yomi

    2012-01-19

    Jan 19, 2012 ... 212 primer pairs selected, based on repeat patterns of n≥8 for di-, tri-, tetra- and penta-nucleotide repeat ... Cluster analysis revealed a high genetic similarity among the sugarcane (Saccharum spp.) breeding lines which could reduce the genetic gain in ..... The multiple allele characteristic of SSR com-.

  20. THE USE OF PAIR COMPOSITION METHOD ON STUDENTS’ DESCRIPTIVE WRITING SKILL

    Directory of Open Access Journals (Sweden)

    Maya Nurmayanti

    2014-06-01

    Full Text Available This research was aimed to find out roles of pair composition method on students’ behaviour in learning processes and their writing assessment, and also to find out students’ attitude toward learning process of pair composition method in writing descriptive text in the classroom. Descriptive qualitative method was used in this research. The participants were 33 students of X grade of Senior High School. The data were collected from observation, the result of analysis showed that 66% of the seriousness of students during learning process was high, 78% of enthusiasm of students in doing task was high, and 58% of students’ participation was high. The increasing of students’ assessment was 18,7 from the average score before. The data collected from interview and questionnaire indicated that pair composition method provided the opportunities for sharing ideas, developing text, corresting writing errors, motivating students being active, and 50% students strongly agreed that pair composition method on writing descriptive text was lively and enjoyable.

  1. Construction of a quantum repeater with linear optics

    International Nuclear Information System (INIS)

    Kok, Pieter; Williams, Colin P.; Dowling, Jonathan P.

    2003-01-01

    We study the mechanism and complexity of an efficient quantum repeater, employing double-photon guns, for long-distance optical quantum communication. The guns create polarization-entangled photon pairs on demand. One such source might be a semiconducter quantum dot, which has the distinct advantage over parametric down-conversion that the probability of creating a photon pair is close to 1, while the probability of creating multiple pairs vanishes. The swapping and purifying components are implemented by polarizing beam splitters and probabilistic optical controlled-NOT gates. We also show that the bottleneck in the efficiency of this repeater is due to detector losses

  2. Repeatability of oral fluid collection methods for THC measurement

    NARCIS (Netherlands)

    Houwing, Sjoerd; Smink, Beitske E.; Legrand, Sara-Ann; Mathijssen, Rene P. M.; Verstraete, Alain G.; Brookhuis, Karel A.

    2012-01-01

    Study objectives: To determine the influence of sample collection for two different collection methods on THC concentrations and to compare THC concentrations collected by both methods. Methods: A total of 136 pairs of oral fluid samples from subjects who had recently smoked Cannabis were obtained

  3. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  4. Studies on the instrumental neutron activation analysis by cadmium ratio method and pair comparator method

    Energy Technology Data Exchange (ETDEWEB)

    Chao, H E; Lu, W D; Wu, S C

    1977-12-01

    The cadmium ratio method and pair comparator method provide a solution for the effects on the effective activation factors resulting from the variation of neutron spectrum at different irradiation positions as usually encountered in the single comparator method. The relations between the activation factors and neutron spectrum in terms of cadmium ratio of the comparator Au or of the activation factor of Co-Au pair for the elements, Sc, Cr, Mn, Co, La, Ce, Sm, and Th have been determined. The activation factors of the elements at any irradiation position can then be obtained from the cadmium ratio of the comparator and/or the activation factor of the comparator pair. The relations determined should be able to apply to different reactors and/or different positions of a reactor. It is shown that, for the isotopes /sup 46/Sc, /sup 51/Cr, /sup 56/Mn, /sup 60/Co, /sup 140/La, /sup 141/Ce, /sup 153/Sm and /sup 233/Pa, the thermal neutron activation factors determined by these two methods were generally in agreement with theoretical values. Their I/sub 0//sigma/sub th/ values appeared to agree with literature values also. The methods were applied to determine the contents of elements Sc, Cr, Mn, La, Ce, Sm, and Th in U.S.G.S. Standard Rock G-2, and the results were also in agreement with literature values. The cadmium ratio method and pair comparator method improved the single comparator method, and they are more suitable to analysis for multi-elements of a large number of samples.

  5. Repeatability of oral fluid collection methods for THC measurement.

    NARCIS (Netherlands)

    Houwing, S. Smink, B.E. Legrand, S.-A. Mathijssen, M.P.M. Verstraete, A.G. & Brookhuis, K.A.

    2013-01-01

    The study objective was to determine the influence of sample collection for two different collection methods on THC concentrations and to compare THC concentrations collected by both methods. A total of 136 pairs of oral fluid samples from subjects who had recently smoked Cannabis were obtained by

  6. SU-F-R-35: Repeatability of Texture Features in T1- and T2-Weighted MR Images

    International Nuclear Information System (INIS)

    Mahon, R; Weiss, E; Karki, K; Hugo, G; Ford, J

    2016-01-01

    Purpose: To evaluate repeatability of lung tumor texture features from inspiration/expiration MR image pairs for potential use in patient specific care models and applications. Repeatability is a desirable and necessary characteristic of features included in such models. Methods: T1-weighted Volumetric Interpolation Breath-Hold Examination (VIBE) and/or T2-weighted MRI scans were acquired for 15 patients with non-small cell lung cancer before and during radiotherapy for a total of 32 and 34 same session inspiration-expiration breath-hold image pairs respectively. Bias correction was applied to the VIBE (VIBE-BC) and T2-weighted (T2-BC) images. Fifty-nine texture features at five wavelet decomposition ratios were extracted from the delineated primary tumor including: histogram(HIST), gray level co-occurrence matrix(GLCM), gray level run length matrix(GLRLM), gray level size zone matrix(GLSZM), and neighborhood gray tone different matrix (NGTDM) based features. Repeatability of the texture features for VIBE, VIBE-BC, T2-weighted, and T2-BC image pairs was evaluated by the concordance correlation coefficient (CCC) between corresponding image pairs, with a value greater than 0.90 indicating repeatability. Results: For the VIBE image pairs, the percentage of repeatable texture features by wavelet ratio was between 20% and 24% of the 59 extracted features; the T2-weighted image pairs exhibited repeatability in the range of 44–49%. The percentage dropped to 10–20% for the VIBE-BC images, and 12–14% for the T2-BC images. In addition, five texture features were found to be repeatable in all four image sets including two GLRLM, two GLZSM, and one NGTDN features. No single texture feature category was repeatable among all three image types; however, certain categories performed more consistently on a per image type basis. Conclusion: We identified repeatable texture features on T1- and T2-weighted MRI scans. These texture features should be further investigated for use

  7. SU-F-R-35: Repeatability of Texture Features in T1- and T2-Weighted MR Images

    Energy Technology Data Exchange (ETDEWEB)

    Mahon, R; Weiss, E; Karki, K; Hugo, G [Virginia Commonwealth University, Richmond, VA (United States); Ford, J [University of Miami Miller School of Medicine, Miami, FL (United States)

    2016-06-15

    Purpose: To evaluate repeatability of lung tumor texture features from inspiration/expiration MR image pairs for potential use in patient specific care models and applications. Repeatability is a desirable and necessary characteristic of features included in such models. Methods: T1-weighted Volumetric Interpolation Breath-Hold Examination (VIBE) and/or T2-weighted MRI scans were acquired for 15 patients with non-small cell lung cancer before and during radiotherapy for a total of 32 and 34 same session inspiration-expiration breath-hold image pairs respectively. Bias correction was applied to the VIBE (VIBE-BC) and T2-weighted (T2-BC) images. Fifty-nine texture features at five wavelet decomposition ratios were extracted from the delineated primary tumor including: histogram(HIST), gray level co-occurrence matrix(GLCM), gray level run length matrix(GLRLM), gray level size zone matrix(GLSZM), and neighborhood gray tone different matrix (NGTDM) based features. Repeatability of the texture features for VIBE, VIBE-BC, T2-weighted, and T2-BC image pairs was evaluated by the concordance correlation coefficient (CCC) between corresponding image pairs, with a value greater than 0.90 indicating repeatability. Results: For the VIBE image pairs, the percentage of repeatable texture features by wavelet ratio was between 20% and 24% of the 59 extracted features; the T2-weighted image pairs exhibited repeatability in the range of 44–49%. The percentage dropped to 10–20% for the VIBE-BC images, and 12–14% for the T2-BC images. In addition, five texture features were found to be repeatable in all four image sets including two GLRLM, two GLZSM, and one NGTDN features. No single texture feature category was repeatable among all three image types; however, certain categories performed more consistently on a per image type basis. Conclusion: We identified repeatable texture features on T1- and T2-weighted MRI scans. These texture features should be further investigated for use

  8. Pairs Trading to the Commodities Futures Market Using Cointegration Method

    Directory of Open Access Journals (Sweden)

    Cüneyt Ungever

    2015-10-01

    Full Text Available This paper investigates pairs trading strategy by using the cointegration method among the 10 most popular agricultural future markets. It is found that only in 2 pairs shows trading signal. The pairs trading strategy is performed in two stages that are the formation period and the trading period with daily futures data from 2004 to 2015. After the formation period was constructed, it is assumed that the cointegration error continues to hold the trading period same as it does for the formation period. The pairs trading strategy is created by the long position cotton and the short position coffee and also long position cotton and short position the livecattle. It is found that the profitability of this strategy worked well in both formation period and trading period.

  9. Quantitative evaluation of pairs and RS steganalysis

    Science.gov (United States)

    Ker, Andrew D.

    2004-06-01

    We give initial results from a new project which performs statistically accurate evaluation of the reliability of image steganalysis algorithms. The focus here is on the Pairs and RS methods, for detection of simple LSB steganography in grayscale bitmaps, due to Fridrich et al. Using libraries totalling around 30,000 images we have measured the performance of these methods and suggest changes which lead to significant improvements. Particular results from the project presented here include notes on the distribution of the RS statistic, the relative merits of different "masks" used in the RS algorithm, the effect on reliability when previously compressed cover images are used, and the effect of repeating steganalysis on the transposed image. We also discuss improvements to the Pairs algorithm, restricting it to spatially close pairs of pixels, which leads to a substantial performance improvement, even to the extent of surpassing the RS statistic which was previously thought superior for grayscale images. We also describe some of the questions for a general methodology of evaluation of steganalysis, and potential pitfalls caused by the differences between uncompressed, compressed, and resampled cover images.

  10. Pair Programming as a Modern Method of Teaching Computer Science

    Directory of Open Access Journals (Sweden)

    Irena Nančovska Šerbec

    2008-10-01

    Full Text Available At the Faculty of Education, University of Ljubljana we educate future computer science teachers. Beside didactical, pedagogical, mathematical and other interdisciplinary knowledge, students gain knowledge and skills of programming that are crucial for computer science teachers. For all courses, the main emphasis is the absorption of professional competences, related to the teaching profession and the programming profile. The latter are selected according to the well-known document, the ACM Computing Curricula. The professional knowledge is therefore associated and combined with the teaching knowledge and skills. In the paper we present how to achieve competences related to programming by using different didactical models (semiotic ladder, cognitive objectives taxonomy, problem solving and modern teaching methodpair programming”. Pair programming differs from standard methods (individual work, seminars, projects etc.. It belongs to the extreme programming as a discipline of software development and is known to have positive effects on teaching first programming language. We have experimentally observed pair programming in the introductory programming course. The paper presents and analyzes the results of using this method: the aspects of satisfaction during programming and the level of gained knowledge. The results are in general positive and demonstrate the promising usage of this teaching method.

  11. Selection pressure on human STR loci and its relevance in repeat expansion disease

    KAUST Repository

    Shimada, Makoto K.; Sanbonmatsu, Ryoko; Yamaguchi-Kabata, Yumi; Yamasaki, Chisato; Suzuki, Yoshiyuki; Chakraborty, Ranajit; Gojobori, Takashi; Imanishi, Tadashi

    2016-01-01

    Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat

  12. Learning With Repeated-Game Strategies

    Directory of Open Access Journals (Sweden)

    Christos A. Ioannou

    2014-07-01

    Full Text Available We use the self-tuning Experience Weighted Attraction model with repeated-game strategies as a computer testbed to examine the relative frequency, speed of convergence and progression of a set of repeated-game strategies in four symmetric 2x2 games: Prisoner's Dilemma, Battle of the Sexes, Stag-Hunt, and Chicken. In the Prisoner's Dilemma game, we fi□nd that the strategy with the most occurrences is the Grim-Trigger. In the Battle of the Sexes game, a cooperative pair that alternates between the two pure-strategy Nash equilibria emerges as the one with the most occurrences. In the Stag-Hunt and Chicken games, the Win-Stay, Lose-Shift and Grim-Trigger strategies are the ones with the most occurrences. Overall, the pairs that converged quickly ended up at the cooperative outcomes, whereas the ones that were extremely slow to reach convergence ended up at non-cooperative outcomes.

  13. Repeatability in Color Measurements of a Spectrophotometer using Different Positioning Devices.

    Science.gov (United States)

    Hemming, Michael; Kwon, So Ran; Qian, Fang

    2015-12-01

    This study aimed to evaluate the repeatability of color measurements of an intraoral spectrophotometer with the use of three different methods by two operators. A total of 60 teeth were obtained, comprising 30 human maxillary teeth [central incisors (n = 10); canines (n = 10); molars (n = 10)] and 30 artificial teeth [lateral incisors (n = 10); premolar (n = 20)]. Multiple repeated color measurements were obtained from each tooth using three measuring methods by each of the two operators. Five typodonts with alternating artificial and human teeth were made. Measurements were taken by two operators with the Vita EasyShade spectrophotometer using the custom tray (CT), custom jig (CJ) and free hand (FH) method, twice, at an interval of 2 to 7 days. Friedman test was used to detect difference among the three color measuring methods. Post hoc Wilcoxon signed-rank test with Bonferroni correction applied was used for pair-wise comparison of color measurements among the three methods. Additionally, a paired-sample t-test was used to assess a significant difference between the two duplicated measurements made on the same tooth by the same operator for each color parameter and measuring method. For operator A, mean (SD) overall color change-ΔE* (SD) perceived for FH, CT and CJ were 2.21(2.00), 2.39 (1.58) and 2.86 (1.92), respectively. There was statistically significant difference in perceived ΔE* in FH vs CJ (p = 0.0107). However, there were no significant differences between FH and CT (p = 0.2829) or between CT and CJ (p = 0.1159). For operator B mean ΔE* (SD) for FH, CT and CJ were 3.24 (3.46), 1.95 (1.19) and 2.45 (1.56), respectively. There was a significant difference between FH and CT (p = 0.0031). However, there were no statistically significant differences in ΔE* in FH vs CJ (p = 0.3696) or CT vs CJ (p = 0.0809). The repeatability of color measurements was different among the three measuring methods by operators. Overall, the CT method worked well for both

  14. Nonrandom network connectivity comes in pairs

    Directory of Open Access Journals (Sweden)

    Felix Z. Hoffmann

    2017-02-01

    Full Text Available Overrepresentation of bidirectional connections in local cortical networks has been repeatedly reported and is a focus of the ongoing discussion of nonrandom connectivity. Here we show in a brief mathematical analysis that in a network in which connection probabilities are symmetric in pairs, Pij = Pji, the occurrences of bidirectional connections and nonrandom structures are inherently linked; an overabundance of reciprocally connected pairs emerges necessarily when some pairs of neurons are more likely to be connected than others. Our numerical results imply that such overrepresentation can also be sustained when connection probabilities are only approximately symmetric.

  15. An enquiry into the method of paired comparison: reliability, scaling, and Thurstone's Law of Comparative Judgment

    Science.gov (United States)

    Thomas C. Brown; George L. Peterson

    2009-01-01

    The method of paired comparisons is used to measure individuals' preference orderings of items presented to them as discrete binary choices. This paper reviews the theory and application of the paired comparison method, describes a new computer program available for eliciting the choices, and presents an analysis of methods for scaling paired choice data to...

  16. WTA estimates using the method of paired comparison: tests of robustness

    Science.gov (United States)

    Patricia A. Champ; John B. Loomis

    1998-01-01

    The method of paired comparison is modified to allow choices between two alternative gains so as to estimate willingness to accept (WTA) without loss aversion. The robustness of WTA values for two public goods is tested with respect to sensitivity of theWTA measure to the context of the bundle of goods used in the paired comparison exercise and to the scope (scale) of...

  17. Characteristics of intergenerational contractions of the CTG repeat in myotonic dystropy

    Energy Technology Data Exchange (ETDEWEB)

    Ashizawa, T.; Anvret, M.; Grandell, U.; Baiget, M.; Cobo, A.M.; Barcelo, J.M.; Korneluk, R.G.; Dallapiccola, B.; Novelli, G.; Fenwick, R.G. Jr. (and others)

    1994-03-01

    In myotonic dystropy (DM), the size of a CTG repeat in the DM kinase gene generally increases in successive generations with clinical evidence of anticipation. However, there have also been cases with an intergenerational contraction of the repeat. The authors have examined 1,489 DM parent-offspring pairs, of which 95 (6.4%) showed such contractions in peripheral blood leukocytes (PBL). In 56 of th 95 pairs, clinical data allowed an analysis of their anticipation status. It is surprising that anticipation occurred in 27 (48%) of these 56 pairs, while none clearly showed a later onset of DM in the asymptomatic offspring. The contraction occurred in 76 (10%) of 753 paternal transmission and in 19 (3%) of 736 maternal transmissions. Anticipation was observed more frequently in maternal (85%) than in paternal (37%) transmissions (P<.001). The parental repeat size correlated with the size of intergenerational contraction (r[sup 2] = .50, P [much lt].001), and the slope of linear regression was steeper in paternal ([minus].62) than in maternal ([minus].30) transmissions (P [much lt].001). Sixteen DM parents had multiple DM offspring with the CTG repeat contractions. This frequency was higher than the frequency expected from the probability of the repeat contractions (6.4%) and the size of DM sib population (1.54 DM offspring per DM parent, in 968 DM parents). The authors conclude that (1) intergenerational contraction of the CTG repeat in leukocyte DNA frequently accompanies apparent anticipation, especially when DM is maternally transmitted, and (2) the paternal origin of the repeat and the presence of the repeat contraction in a sibling increase the probability of the CTG repeat contraction. 43 refs., 1 fig., 4 tabs.

  18. The Effects of Reinforcer Pairing and Fading on Preschoolers' Snack Selections

    Science.gov (United States)

    Solberg, Katherine M.; Hanley, Gregory P.; Layer, Stacy A.; Ingvarsson, Einar T.

    2007-01-01

    The effects of reinforcement pairing and fading on preschoolers' snack selections were evaluated in a multiple baseline design. Baseline preferences for snack options were assessed via repeated paired-item preference assessments. Edible, social, and activity-based reinforcers were then exclusively paired with a less preferred snack option. Once…

  19. Trinucleotide repeat microsatellite markers for Black Poplar (Populus nigra L.)

    NARCIS (Netherlands)

    Smulders, M.J.M.; Schoot, van der J.; Arens, P.; Vosman, B.

    2001-01-01

    Using an enrichment procedure, we have cloned microsatellite repeats from black poplar (Populus nigra L.) and developed primers for microsatellite marker analysis. Ten primer pairs, mostly for trinucleotide repeats, produced polymorphic fragments in P. nigra. Some of them also showed amplification

  20. t2prhd: a tool to study the patterns of repeat evolution

    Directory of Open Access Journals (Sweden)

    Pénzes Zsolt

    2008-01-01

    Full Text Available Abstract Background The models developed to characterize the evolution of multigene families (such as the birth-and-death and the concerted models have also been applied on the level of sequence repeats inside a gene/protein. Phylogenetic reconstruction is the method of choice to study the evolution of gene families and also sequence repeats in the light of these models. The characterization of the gene family evolution in view of the evolutionary models is done by the evaluation of the clustering of the sequences with the originating loci in mind. As the locus represents positional information, it is straightforward that in the case of the repeats the exact position in the sequence should be used, as the simple numbering according to repeat order can be misleading. Results We have developed a novel rapid visual approach to study repeat evolution, that takes into account the exact repeat position in a sequence. The "pairwise repeat homology diagram" visualizes sequence repeats detected by a profile HMM in a pair of sequences and highlights their homology relations inferred by a phylogenetic tree. The method is implemented in a Perl script (t2prhd available for downloading at http://t2prhd.sourceforge.net and is also accessible as an online tool at http://t2prhd.brc.hu. The power of the method is demonstrated on the EGF-like and fibronectin-III-like (Fn-III domain repeats of three selected mammalian Tenascin sequences. Conclusion Although pairwise repeat homology diagrams do not carry all the information provided by the phylogenetic tree, they allow a rapid and intuitive assessment of repeat evolution. We believe, that t2prhd is a helpful tool with which to study the pattern of repeat evolution. This method can be particularly useful in cases of large datasets (such as large gene families, as the command line interface makes it possible to automate the generation of pairwise repeat homology diagrams with the aid of scripts.

  1. Calculations of pair production by Monte Carlo methods

    International Nuclear Information System (INIS)

    Bottcher, C.; Strayer, M.R.

    1991-01-01

    We describe some of the technical design issues associated with the production of particle-antiparticle pairs in very large accelerators. To answer these questions requires extensive calculation of Feynman diagrams, in effect multi-dimensional integrals, which we evaluate by Monte Carlo methods on a variety of supercomputers. We present some portable algorithms for generating random numbers on vector and parallel architecture machines. 12 refs., 14 figs

  2. Kinetics of electron-positron pair plasmas using an adaptive Monte Carlo method

    International Nuclear Information System (INIS)

    Pilla, R.P.; Shaham, J.

    1997-01-01

    A new algorithm for implementing the adaptive Monte Carlo method is given. It is used to solve the Boltzmann equations that describe the time evolution of a nonequilibrium electron-positron pair plasma containing high-energy photons. These are coupled nonlinear integro-differential equations. The collision kernels for the photons as well as pairs are evaluated for Compton scattering, pair annihilation and creation, bremsstrahlung, and Coulomb collisions. They are given as multidimensional integrals which are valid for all energies. For an homogeneous and isotropic plasma with no particle escape, the equilibrium solution is expressed analytically in terms of the initial conditions. For two specific cases, for which the photon and the pair spectra are initially constant or have a power-law distribution within the given limits, the time evolution of the plasma is analyzed using the new method. The final spectra are found to be in a good agreement with the analytical solutions. The new algorithm is faster than the Monte Carlo scheme based on uniform sampling and more flexible than the numerical methods used in the past, which do not involve Monte Carlo sampling. It is also found to be very stable. Some astrophysical applications of this technique are discussed. copyright 1997 The American Astronomical Society

  3. On a method for constructing the Lax pairs for nonlinear integrable equations

    International Nuclear Information System (INIS)

    Habibullin, I T; Poptsova, M N; Khakimova, A R

    2016-01-01

    We suggest a direct algorithm for searching the Lax pairs for nonlinear integrable equations. It is effective for both continuous and discrete models. The first operator of the Lax pair corresponding to a given nonlinear equation is found immediately, coinciding with the linearization of the considered nonlinear equation. The second one is obtained as an invariant manifold to the linearized equation. A surprisingly simple relation between the second operator of the Lax pair and the recursion operator is discussed: the recursion operator can immediately be found from the Lax pair. Examples considered in the article are convincing evidence that the found Lax pairs differ from the classical ones. The examples also show that the suggested objects are true Lax pairs which allow the construction of infinite series of conservation laws and hierarchies of higher symmetries. In the case of the hyperbolic type partial differential equation our algorithm is slightly modified; in order to construct the Lax pairs from the invariant manifolds we use the cutting off conditions for the corresponding infinite Laplace sequence. The efficiency of the method is illustrated by application to some equations given in the Svinolupov–Sokolov classification list for which the Lax pairs and the recursion operators have not been found earlier. (paper)

  4. An Improved Method of Training Overcomplete Dictionary Pair

    Directory of Open Access Journals (Sweden)

    Zhuozheng Wang

    2014-01-01

    Full Text Available Training overcomplete dictionary pair is a critical step of the mainstream superresolution methods. For the high time complexity and susceptible to corruption characteristics of training dictionary, an improved method based on lifting wavelet transform and robust principal component analysis is reported. The high-frequency components of example images are estimated through wavelet coefficients of 3-tier lifting wavelet transform decomposition. Sparse coefficients are similar in multiframe images. Accordingly, the inexact augmented Lagrange multiplier method is employed to achieve robust principal component analysis in the process of imposing global constraints. Experiments reveal that the new algorithm not only reduces the time complexity preserving the clarity but also improves the robustness for the corrupted example images.

  5. An entropy-based improved k-top scoring pairs (TSP) method for ...

    African Journals Online (AJOL)

    An entropy-based improved k-top scoring pairs (TSP) (Ik-TSP) method was presented in this study for the classification and prediction of human cancers based on gene-expression data. We compared Ik-TSP classifiers with 5 different machine learning methods and the k-TSP method based on 3 different feature selection ...

  6. Measurement System Analyses - Gauge Repeatability and Reproducibility Methods

    Science.gov (United States)

    Cepova, Lenka; Kovacikova, Andrea; Cep, Robert; Klaput, Pavel; Mizera, Ondrej

    2018-02-01

    The submitted article focuses on a detailed explanation of the average and range method (Automotive Industry Action Group, Measurement System Analysis approach) and of the honest Gauge Repeatability and Reproducibility method (Evaluating the Measurement Process approach). The measured data (thickness of plastic parts) were evaluated by both methods and their results were compared on the basis of numerical evaluation. Both methods were additionally compared and their advantages and disadvantages were discussed. One difference between both methods is the calculation of variation components. The AIAG method calculates the variation components based on standard deviation (then a sum of variation components does not give 100 %) and the honest GRR study calculates the variation components based on variance, where the sum of all variation components (part to part variation, EV & AV) gives the total variation of 100 %. Acceptance of both methods among the professional society, future use, and acceptance by manufacturing industry were also discussed. Nowadays, the AIAG is the leading method in the industry.

  7. Comparability and repeatability of three commonly used methods for measuring endurance capacity.

    Science.gov (United States)

    Baxter-Gilbert, James; Mühlenhaupt, Max; Whiting, Martin J

    2017-12-01

    Measures of endurance (time to exhaustion) have been used to address a wide range of questions in ecomorphological and physiological research, as well as being used as a proxy for survival and fitness. Swimming, stationary (circular) track running, and treadmill running are all commonly used methods for measuring endurance. Despite the use of these methods across a broad range of taxa, how comparable these methods are to one another, and whether they are biologically relevant, is rarely examined. We used Australian water dragons (Intellagama lesueurii), a species that is morphologically adept at climbing, swimming, and running, to compare these three methods of endurance and examined if there is repeatability within and between trial methods. We found that time to exhaustion was not highly repeatable within a method, suggesting that single measures or a mean time to exhaustion across trials are not appropriate. Furthermore, we compared mean maximal endurance times among the three methods, and found that the two running methods (i.e., stationary track and treadmill) were similar, but swimming was distinctly different, resulting in lower mean maximal endurance times. Finally, an individual's endurance rank was not repeatable across methods, suggesting that the three endurance trial methods are not providing similar information about an individual's performance capacity. Overall, these results highlight the need to carefully match a measure of performance capacity with the study species and the research questions being asked so that the methods being used are behaviorally, ecologically, and physiologically relevant. © 2018 Wiley Periodicals, Inc.

  8. The role of familiarity in associative recognition of unitized compound word pairs.

    Science.gov (United States)

    Ahmad, Fahad N; Hockley, William E

    2014-01-01

    This study examined the effect of unitization and contribution of familiarity in the recognition of word pairs. Compound words were presented as word pairs and were contrasted with noncompound word pairs in an associative recognition task. In Experiments 1 and 2, yes-no recognition hit and false-alarm rates were significantly higher for compound than for noncompound word pairs, with no difference in discrimination in both within- and between-subject comparisons. Experiment 2 also showed that item recognition was reduced for words from compound compared to noncompound word pairs, providing evidence of the unitization of the compound pairs. A two-alternative forced-choice test used in Experiments 3A and 3B provided evidence that the concordant effect for compound word pairs was largely due to familiarity. A discrimination advantage for compound word pairs was also seen in these experiments. Experiment 4A showed that a different pattern of results is seen when repeated noncompound word pairs are compared to compound word pairs. Experiment 4B showed that memory for the individual items of compound word pairs was impaired relative to items in repeated and nonrepeated noncompound word pairs, and Experiment 5 demonstrated that this effect is eliminated when the elements of compound word pairs are not unitized. The concordant pattern seen in yes-no recognition and the discrimination advantage in forced-choice recognition for compound relative to noncompound word pairs is due to greater reliance on familiarity at test when pairs are unitized.

  9. Simulation-based investigation of the paired-gear method in cod-end selectivity studies

    DEFF Research Database (Denmark)

    Herrmann, Bent; Frandsen, Rikke; Holst, René

    2007-01-01

    In this paper, the paired-gear and covered cod-end methods for estimating the selectivity of trawl cod-ends are compared. A modified version of the cod-end selectivity simulator PRESEMO is used to simulate the data that would be collected from a paired-gear experiment where the test cod-end also ...

  10. Multi-pair states in electron–positron pair creation

    Directory of Open Access Journals (Sweden)

    Anton Wöllert

    2016-09-01

    Full Text Available Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

  11. Multi-pair states in electron–positron pair creation

    Energy Technology Data Exchange (ETDEWEB)

    Wöllert, Anton, E-mail: woellert@mpi-hd.mpg.de; Bauke, Heiko, E-mail: heiko.bauke@mpi-hd.mpg.de; Keitel, Christoph H.

    2016-09-10

    Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

  12. Multi-pair states in electron–positron pair creation

    International Nuclear Information System (INIS)

    Wöllert, Anton; Bauke, Heiko; Keitel, Christoph H.

    2016-01-01

    Ultra strong electromagnetic fields can lead to spontaneous creation of single or multiple electron–positron pairs. A quantum field theoretical treatment of the pair creation process combined with numerical methods provides a description of the fermionic quantum field state, from which all observables of the multiple electron–positron pairs can be inferred. This allows to study the complex multi-particle dynamics of electron–positron pair creation in-depth, including multi-pair statistics as well as momentum distributions and spin. To illustrate the potential benefit of this approach, it is applied to the intermediate regime of pair creation between nonperturbative Schwinger pair creation and perturbative multiphoton pair creation where the creation of multi-pair states becomes nonnegligible but cascades do not yet set in. Furthermore, it is demonstrated how spin and helicity of the created electrons and positrons are affected by the polarization of the counterpropagating laser fields, which induce the creation of electron–positron pairs.

  13. Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

    Science.gov (United States)

    Chen, Jonathan L; VanEtten, Damian M; Fountain, Matthew A; Yildirim, Ilyas; Disney, Matthew D

    2017-07-11

    RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

  14. High spin exotic states and new method for pairing energy

    International Nuclear Information System (INIS)

    Molique, H.

    1996-01-01

    We present a new method called 'PSY-MB', initially developed in the framework of abstract group theory for the solution of the problem of strongly interacting multi-fermionic systems with particular to systems in an external rotating field. The validity of the new method (PSY-MB) is tested on model Hamiltonians. A detailed comparison between the obtained solutions and the exact ones is performed. The new method is used in the study of realistic nuclear Hamiltonians based on the Woods-Saxon potential within the cranking approximation to study the influence of residual monopole pairing interactions in the rare-earth mass region. In parallel with this new technique we present original results obtained with the Woods-Saxon mean-field and the self-consistent Hartree-Fock approximation in order to investigate such exotic effects as octupole deformations and hexadecapole C 4 -polarizing deformations in the framework of high-spin physics. By developing these three approaches in one single work we prepare the ground for the nuclear structure calculations of the new generation - where the residual two-body interactions are taken into account also in the weak pairing limit. (author)

  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. Performance of thallium bromide semiconductor detectors produced by repeated Bridgman method

    International Nuclear Information System (INIS)

    Santos, Robinson Alves dos; Costa, Fabio Eduardo da; Martins, Joao Francisco Trencher; Hamada, Margarida M.

    2009-01-01

    TlBr crystals have been grown by the Repeated Bridgman method from commercial TlBr materials and characterized to be used as radiation detectors. We have shown that the Repeated Bridgman is effective to reduce the concentration of impurities in TlBr. It was observed that detectors fabricated from higher purity crystal exhibit significant improvement in performance compared to those produced from low purity crystals. However, problems still exist in TlBr detectors, due to the low charge carrier collection efficiency, which is probably caused by additional impurities or defects incorporated during crystal growth and detector fabrication processes. (author)

  17. Development of a spatial analysis method using ground-based repeat photography to detect changes in the alpine treeline ecotone, Glacier National Park, Montana, U.S.A.

    Science.gov (United States)

    Roush, W.; Munroe, Jeffrey S.; Fagre, D.B.

    2007-01-01

    Repeat photography is a powerful tool for detection of landscape change over decadal timescales. Here a novel method is presented that applies spatial analysis software to digital photo-pairs, allowing vegetation change to be categorized and quantified. This method is applied to 12 sites within the alpine treeline ecotone of Glacier National Park, Montana, and is used to examine vegetation changes over timescales ranging from 71 to 93 years. Tree cover at the treeline ecotone increased in 10 out of the 12 photo-pairs (mean increase of 60%). Establishment occurred at all sites, infilling occurred at 11 sites. To demonstrate the utility of this method, patterns of tree establishment at treeline are described and the possible causes of changes within the treeline ecotone are discussed. Local factors undoubtedly affect the magnitude and type of the observed changes, however the ubiquity of the increase in tree cover implies a common forcing mechanism. Mean minimum summer temperatures have increased by 1.5??C over the past century and, coupled with variations in the amount of early spring snow water equivalent, likely account for much of the increase in tree cover at the treeline ecotone. Lastly, shortcomings of this method are presented along with possible solutions and areas for future research. ?? 2007 Regents of the University of Colorado.

  18. Differential Regulation of Strand-Specific Transcripts from Arabidopsis Centromeric Satellite Repeats.

    Directory of Open Access Journals (Sweden)

    2005-12-01

    Full Text Available Centromeres interact with the spindle apparatus to enable chromosome disjunction and typically contain thousands of tandemly arranged satellite repeats interspersed with retrotransposons. While their role has been obscure, centromeric repeats are epigenetically modified and centromere specification has a strong epigenetic component. In the yeast Schizosaccharomyces pombe, long heterochromatic repeats are transcribed and contribute to centromere function via RNA interference (RNAi. In the higher plant Arabidopsis thaliana, as in mammalian cells, centromeric satellite repeats are short (180 base pairs, are found in thousands of tandem copies, and are methylated. We have found transcripts from both strands of canonical, bulk Arabidopsis repeats. At least one subfamily of 180-base pair repeats is transcribed from only one strand and regulated by RNAi and histone modification. A second subfamily of repeats is also silenced, but silencing is lost on both strands in mutants in the CpG DNA methyltransferase MET1, the histone deacetylase HDA6/SIL1, or the chromatin remodeling ATPase DDM1. This regulation is due to transcription from Athila2 retrotransposons, which integrate in both orientations relative to the repeats, and differs between strains of Arabidopsis. Silencing lost in met1 or hda6 is reestablished in backcrosses to wild-type, but silencing lost in RNAi mutants and ddm1 is not. Twenty-four-nucleotide small interfering RNAs from centromeric repeats are retained in met1 and hda6, but not in ddm1, and may have a role in this epigenetic inheritance. Histone H3 lysine-9 dimethylation is associated with both classes of repeats. We propose roles for transcribed repeats in the epigenetic inheritance and evolution of centromeres.

  19. Repeated dose titration versus age-based method in electroconvulsive therapy: a pilot study

    NARCIS (Netherlands)

    Aten, J.J.; Oudega, M.L.; van Exel, E.; Stek, M.L.; van Waarde, J.A.

    2015-01-01

    In electroconvulsive therapy (ECT), a dose titration method (DTM) was suggested to be more individualized and therefore more accurate than formula-based dosing methods. A repeated DTM (every sixth session and dose adjustment accordingly) was compared to an age-based method (ABM) regarding treatment

  20. REPEATABILITY OF THE FRENCH HIGHER VEGETATION TYPES ACCORDING

    Directory of Open Access Journals (Sweden)

    H. BRISSE

    1998-04-01

    Full Text Available Higher vegetation types are generally determined by successive approximations and defined by a common consent. Instead, they might be statistically determined and repeated, according to a numerical method called ‘socio-ecology’. This method deals only with floristical data, but gives them an ecological meaning by a previous calibration of the relations between plants, computed as ecological indices. It is applied to a pair of two homologous samples, each having 2.000 relevés and coming from the 60.000 relevés stored in the French data bank ‘Sophy’. Each sample covers the main ecological gradients of the bank, it defines a hierarchy of vegetation types and it explains half the peculiarity of a type with only 10 to 30 discriminant plants, out of the 5.000 plants observed in the relevés. Results : 1 The discriminant plants may characterize the vegetation types, including the higher ones, in a coherent and readable form. 2 In the two independent classifications, having different structures, the same vegetation types are repeated. They are the reciprocal nearest types, in the socio-ecological space. Though the two classifications have no one relevé in common, the repeated types have nearly the same discriminant plants. 3 At the highest level, two clear-cut main types show the difference between light and shadow. The same herbaceous discriminant plants, for a type, and the ligneous or sciaphilous ones, for the other, have similar fidelities and constancies in the two classifications. 4 Such a numerical agreement, instead of common consent, appears again in the sub-types, which remind the classical ones, but which are repeatable.

  1. Pairing vibrational and isospin rotational states in a particle number and isospin projected generator coordinate method

    International Nuclear Information System (INIS)

    Chen, H.T.; Muether, H.; Faessler, A.

    1978-01-01

    Pairing vibrational and isospin rotational states are described in different approximations based on particle number and isospin projected, proton-proton, neutron-neutron and proton-neutron pairing wave functions and on the generator coordinate method (GCM). The investigations are performed in models for which an exact group theoretical solution exists. It turns out that a particle number and isospin projection is essential to yield a good approximation to the ground state or isospin yrast state energies. For strong pairing correlations (pairing force constant equal to the single-particle level distance) isospin cranking (-ωTsub(x)) yields with particle number projected pairing wave function also good agreement with the exact energies. GCM wave functions generated by particle number and isospin projected BCS functions with different amounts of pairing correlations yield for the lowest T=0 and T=2 states energies which are practically indistinguishable from the exact solutions. But even the second and third lowest energies of charge-symmetric states are still very reliable. Thus it is concluded that also in realistic cases isospin rotational and pairing vibrational states may be described in the framework of the GCM method with isospin and particle number projected generating wave functions. (Auth.)

  2. Crystal structure and pair potentials: A molecular-dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Parrinello, M.; Rahman, A.

    1980-10-06

    With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.

  3. Insertion device and method for accurate and repeatable target insertion

    Science.gov (United States)

    Gubeli, III, Joseph F.; Shinn, Michelle D.; Bevins, Michael E.; Dillon-Townes, Lawrence; Neil, George R.

    2017-07-04

    The present invention discloses a device and a method for inserting and positioning a target within a free electron laser, particle accelerator, or other such device that generates or utilizes a beam of energy or particles. The system includes a three-point registration mechanism that insures angular and translational accuracy and repeatability of positioning upon multiple insertions within the same structure.

  4. Ab initio pair potentials for FCC metals: An application of the method of Moebius transform

    International Nuclear Information System (INIS)

    Mookerjee, A.; Chen Nanxian; Kumar, V.; Satter, M.A.

    1991-10-01

    We use the method of Moebius transform introduced by one of us (Chen, Phys. Rev. Lett. 64, 1193 (1990)) to obtain pair potentials for fcc metals from first principles total energy calculations. The derivation is exact for radial potentials and it converges much faster than the earlier reported method of Carlsson-Gelatt-Ehrenreich. We have tested this formulation for Cu using the tight binding representation of the linear muffin tin orbital method. Our results agree with those obtained by Carlsson et al. and qualitatively with the other Morse-type pair potentials derived from effective medium theories. (author). 18 refs, 3 figs, 3 tabs

  5. System and method of detecting cavitation in pumps

    Science.gov (United States)

    Lu, Bin; Sharma, Santosh Kumar; Yan, Ting; Dimino, Steven A.

    2017-10-03

    A system and method for detecting cavitation in pumps for fixed and variable supply frequency applications is disclosed. The system includes a controller having a processor programmed to repeatedly receive real-time operating current data from a motor driving a pump, generate a current frequency spectrum from the current data, and analyze current data within a pair of signature frequency bands of the current frequency spectrum. The processor is further programmed to repeatedly determine fault signatures as a function of the current data within the pair of signature frequency bands, repeatedly determine fault indices based on the fault signatures and a dynamic reference signature, compare the fault indices to a reference index, and identify a cavitation condition in a pump based on a comparison between the reference index and a current fault index.

  6. Link-based quantitative methods to identify differentially coexpressed genes and gene Pairs

    Directory of Open Access Journals (Sweden)

    Ye Zhi-Qiang

    2011-08-01

    Full Text Available Abstract Background Differential coexpression analysis (DCEA is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones. Especially, the correlation-reversal is easily missed although it probably indicates remarkable biological significance. Results We developed two link-based quantitative methods, DCp and DCe, to identify differentially coexpressed genes and gene pairs (links. Bearing the uniqueness of exploiting the quantitative coexpression change of each gene pair in the coexpression networks, both methods proved to be superior to currently popular methods in simulation studies. Re-mining of a publicly available type 2 diabetes (T2D expression dataset from the perspective of differential coexpression analysis led to additional discoveries than those from differential expression analysis. Conclusions This work pointed out the critical weakness of current popular DCEA methods, and proposed two link-based DCEA algorithms that will make contribution to the development of DCEA and help extend it to a broader spectrum.

  7. Brucella 'HOOF-Prints': strain typing by multi-locus analysis of variable number tandem repeats (VNTRs

    Directory of Open Access Journals (Sweden)

    Halling Shirley M

    2003-07-01

    Full Text Available Abstract Background Currently, there are very few tools available for subtyping Brucella isolates for epidemiological trace-back. Subtyping is difficult because of the genetic homogeneity within the genus. Sequencing of the genomes from three Brucella species has facilitated the search for DNA sequence variability. Recently, hypervariability among short tandem repeat sequences has been exploited for strain-typing of several bacterial pathogens. Results An eight-base pair tandem repeat sequence was discovered in nine genomic loci of the B. abortus genome. Eight loci were hypervariable among the three Brucella species. A PCR-based method was developed to identify the number of repeat units (alleles at each locus, generating strain-specific fingerprints. None of the loci exhibited species- or biovar-specific alleles. Sometimes, a species or biovar contained a specific allele at one or more loci, but the allele also occurred in other species or biovars. The technique successfully differentiated the type strains for all Brucella species and biovars, among unrelated B. abortus biovar 1 field isolates in cattle, and among B. abortus strains isolated from bison and elk. Isolates from the same herd or from short-term in vitro passage exhibited little or no variability in fingerprint pattern. Sometimes, isolates from an animal would have multiple alleles at a locus, possibly from mixed infections in enzootic areas, residual disease from incomplete depopulation of an infected herd or molecular evolution within the strain. Therefore, a mixed population or a pool of colonies from each animal and/or tissue was tested. Conclusion This paper describes a new method for fingerprinting Brucella isolates based on multi-locus characterization of a variable number, eight-base pair, tandem repeat. We have named this technique "HOOF-Prints" for Hypervariable Octameric Oligonucleotide Finger-Prints. The technique is highly discriminatory among Brucella species, among

  8. Identification of apple cultivars on the basis of simple sequence repeat markers.

    Science.gov (United States)

    Liu, G S; Zhang, Y G; Tao, R; Fang, J G; Dai, H Y

    2014-09-12

    DNA markers are useful tools that play an important role in plant cultivar identification. They are usually based on polymerase chain reaction (PCR) and include simple sequence repeats (SSRs), inter-simple sequence repeats, and random amplified polymorphic DNA. However, DNA markers were not used effectively in the complete identification of plant cultivars because of the lack of known DNA fingerprints. Recently, a novel approach called the cultivar identification diagram (CID) strategy was developed to facilitate the use of DNA markers for separate plant individuals. The CID was designed whereby a polymorphic maker was generated from each PCR that directly allowed for cultivar sample separation at each step. Therefore, it could be used to identify cultivars and varieties easily with fewer primers. In this study, 60 apple cultivars, including a few main cultivars in fields and varieties from descendants (Fuji x Telamon) were examined. Of the 20 pairs of SSR primers screened, 8 pairs gave reproducible, polymorphic DNA amplification patterns. The banding patterns obtained from these 8 primers were used to construct a CID map. Each cultivar or variety in this study was distinguished from the others completely, indicating that this method can be used for efficient cultivar identification. The result contributed to studies on germplasm resources and the seedling industry in fruit trees.

  9. A natively paired antibody library yields drug leads with higher sensitivity and specificity than a randomly paired antibody library.

    Science.gov (United States)

    Adler, Adam S; Bedinger, Daniel; Adams, Matthew S; Asensio, Michael A; Edgar, Robert C; Leong, Renee; Leong, Jackson; Mizrahi, Rena A; Spindler, Matthew J; Bandi, Srinivasa Rao; Huang, Haichun; Tawde, Pallavi; Brams, Peter; Johnson, David S

    2018-04-01

    Deep sequencing and single-chain variable fragment (scFv) yeast display methods are becoming more popular for discovery of therapeutic antibody candidates in mouse B cell repertoires. In this study, we compare a deep sequencing and scFv display method that retains native heavy and light chain pairing with a related method that randomly pairs heavy and light chain. We performed the studies in a humanized mouse, using interleukin 21 receptor (IL-21R) as a test immunogen. We identified 44 high-affinity binder scFv with the native pairing method and 100 high-affinity binder scFv with the random pairing method. 30% of the natively paired scFv binders were also discovered with the randomly paired method, and 13% of the randomly paired binders were also discovered with the natively paired method. Additionally, 33% of the scFv binders discovered only in the randomly paired library were initially present in the natively paired pre-sort library. Thus, a significant proportion of "randomly paired" scFv were actually natively paired. We synthesized and produced 46 of the candidates as full-length antibodies and subjected them to a panel of binding assays to characterize their therapeutic potential. 87% of the antibodies were verified as binding IL-21R by at least one assay. We found that antibodies with native light chains were more likely to bind IL-21R than antibodies with non-native light chains, suggesting a higher false positive rate for antibodies from the randomly paired library. Additionally, the randomly paired method failed to identify nearly half of the true natively paired binders, suggesting a higher false negative rate. We conclude that natively paired libraries have critical advantages in sensitivity and specificity for antibody discovery programs.

  10. Repeated dose titration versus age-based method in electroconvulsive therapy: a pilot study.

    Science.gov (United States)

    Aten, Jan Jaap; Oudega, Mardien; van Exel, Eric; Stek, Max L; van Waarde, Jeroen A

    2015-06-01

    In electroconvulsive therapy (ECT), a dose titration method (DTM) was suggested to be more individualized and therefore more accurate than formula-based dosing methods. A repeated DTM (every sixth session and dose adjustment accordingly) was compared to an age-based method (ABM) regarding treatment characteristics, clinical outcome, and cognitive functioning after ECT. Thirty-nine unipolar depressed patients dosed using repeated DTM and 40 matched patients treated with ABM were compared. Montgomery-Åsberg Depression Rating Scale (MADRS) and Mini-Mental State Examination (MMSE) were assessed at baseline and at the end of the index course, as well as the total number of ECT sessions. Both groups were similar regarding age, sex, psychotic features, mean baseline MADRS, and median baseline MMSE. At the end of the index course, the two methods showed equal outcome (mean end MADRS, 11.6 ± 8.3 in DTM and 9.5 ± 7.6 in ABM (P = 0.26); median end MMSE, 28 (25-29) and 28 (25-29.8), respectively (P = 0.81). However, the median number of all ECT sessions differed 16 (11-22) in DTM versus 12 (10-14.8) in ABM; P = 0.02]. Using regression analysis, dosing method and age were independently associated with the total number of ECT sessions, with less sessions needed in ABM (P = 0.02) and in older patients (P = 0.001). In this comparative cohort study, ABM and DTM showed equal outcome for depression and cognition. However, the median ECT course duration in repeated DTM appeared longer. Additionally, higher age was associated with shorter ECT courses regardless of the dosing method. Further prospective studies are needed to confirm these findings.

  11. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

  12. Development and validation of rapid ion-pair RPLC method for simultaneous determination of certain B-complex vitamins along with vitamin C.

    Science.gov (United States)

    Patil, Suyog S; Srivastava, Ashiwini K

    2012-01-01

    A rapid, simple, and accurate ion-pair RPLC method has been developed for simultaneous analysis of vitamin C and major B-complex vitamins. An RP C18 column thermostated at 30 degrees C was used with gradient elution of mobile phase comprising 10 mM potassium dihydrogen phosphate buffer (containing 3 mM sodium hexane-1-sulfonate, adjusted to pH 2.80 with o-phosphoric acid) and methanol at a flow rate of 1.0 mL/min to achieve the best possible separation and resolution of all vitamins in about 11.00 min. The detection was performed at 274 nm. The method has been implemented successfully for simultaneous determination of vitamins present in 12 multivitamin/multimineral pharmaceutical preparations, as well as in human urine. Typical validation characteristics were evaluated in accordance with International Conference on Harmonization guidelines. Good linearity over the investigated concentration levels was observed. Intraday repeatability was vitamins. The method can be used for assay of these vitamins over a wide concentration range with good precision and accuracy; hence, it would be appropriate for routine QC as well as in clinical analysis.

  13. The repeatability of three diagnostic methods (visual using ICDAS II, laser fluorescence, and radiographic) for early caries detection

    Science.gov (United States)

    Sukmasari, S.; Lestari, W.; Ko, B. B.; Noh, Z.; Asmail, N.; Yaacob, N.

    2017-08-01

    Newly introduced ICDAS II as a visual method, laser fluorescence as another technique that have ability to quantify early mineral loss of tooth structure and intra oral radiograph, are methods can be used in the clinic. To provide standardization for comprehensive caries management at an early stage, all methods supposed to be tested between users. The objective of this research is to evaluate the repeatability of each system. It is a comparative cross sectional study using 100 extracted permanent teeth without obvious cavitation (premolar & molar) that were collected and stored in thymol solution. The teeth were embedded on the wax block and labeled with numbers. All 5 surfaces were examined by 5 examiners using visual (ICDAS II), laser fluorescence (LF) and radiographic examination. The data were then analyzed to measure intra and inter examiner repeatability using Cronbach’s alpha and inter-item correlation matrix. Intra-examiner repeatability for all examiners was >0.7. Chronbach’s a value for inter-examiner repeatability for ICDAS II was >0.8 on 3 surfaces except on buccal and lingual. LF exhibit repeatability of >0.8 on all surfaces. Radiograph shows a low value of inter examiner repeatability (students for inter-item correlation while the 2nd and 3rd reading of LF displays the best agreement. ICDAS II score favors more non-invasive treatment compared to LF. ICDAS II showed good repeatability except on buccal and lingual surfaces. In line with some of the previous study, ICDAS II is applicable for caries detection in daily clinical basis. Laser fluorescence exhibits the highest repeatability while the radiograph showed weak inter-examiner repeatability. Treatment decisions of ICDAS II propose more preventive treatment for early caries lesions compared to laser fluorescence.

  14. Lesser Neural Pattern Similarity across Repeated Tests Is Associated with Better Long-Term Memory Retention.

    Science.gov (United States)

    Karlsson Wirebring, Linnea; Wiklund-Hörnqvist, Carola; Eriksson, Johan; Andersson, Micael; Jonsson, Bert; Nyberg, Lars

    2015-07-01

    Encoding and retrieval processes enhance long-term memory performance. The efficiency of encoding processes has recently been linked to representational consistency: the reactivation of a representation that gets more specific each time an item is further studied. Here we examined the complementary hypothesis of whether the efficiency of retrieval processes also is linked to representational consistency. Alternatively, recurrent retrieval might foster representational variability--the altering or adding of underlying memory representations. Human participants studied 60 Swahili-Swedish word pairs before being scanned with fMRI the same day and 1 week later. On Day 1, participants were tested three times on each word pair, and on Day 7 each pair was tested once. A BOLD signal change in right superior parietal cortex was associated with subsequent memory on Day 1 and with successful long-term retention on Day 7. A representational similarity analysis in this parietal region revealed that beneficial recurrent retrieval was associated with representational variability, such that the pattern similarity on Day 1 was lower for retrieved words subsequently remembered compared with those subsequently forgotten. This was mirrored by a monotonically decreased BOLD signal change in dorsolateral prefrontal cortex on Day 1 as a function of repeated successful retrieval for words subsequently remembered, but not for words subsequently forgotten. This reduction in prefrontal response could reflect reduced demands on cognitive control. Collectively, the results offer novel insights into why memory retention benefits from repeated retrieval, and they suggest fundamental differences between repeated study and repeated testing. Repeated testing is known to produce superior long-term retention of the to-be-learned material compared with repeated encoding and other learning techniques, much because it fosters repeated memory retrieval. This study demonstrates that repeated memory

  15. Fine typing of methicillin-resistant Staphylococcus aureus isolates using direct repeat unit and staphylococcal interspersed repeat unit typing methods.

    Science.gov (United States)

    Ho, Cheng-Mao; Ho, Mao-Wang; Li, Chi-Yuan; Lu, Jang-Jih

    2015-08-01

    Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated. A total of 157 MRSA isolates from four different regions in Taiwan were typed with five different molecular methods, including SCCmec typing, multilocus sequence typing (MLST), spa typing, mec-associated direct repeat unit (dru) copy number determination, and staphylococcal interspersed repeat unit (SIRU) profiling. There were four SCCmec types, eight MLST types, 15 spa types, 11 dru types, and 31 SIRU profiles. The most common type determined by each molecular typing method was SCCmec III (115 isolates, 73.2%), ST239 (99 isolates, 63.1%), t037 (107 isolates, 68.2%), 14 dru copies (76 isolates, 48.4%), and SIRU profile 3013722 (102 isolates, 65%), respectively. When using the combination of MLST, spa typing, and dru copy number, ST5-t002-4 (n = 8), ST239-t037-14 (n = 68), ST59-t437-9 (n = 9), and ST59-t437-11 (n = 6) were found to be the most common types of SCCmec types II (n = 9), III (n = 115), IV (n = 21), and VT (n = 11) isolates, respectively. SCCmec type III isolates were further classified into 11 dru types. Of the 21 SCCmec type IV isolates, 14 SIRU profiles were found. Seven SIRU patterns were observed in the 11 SCCmec type VT isolates. Different typing methods showed a similar Hunter-Gaston discrimination index among the 157 MRSA isolates. However, dru and SIRU typing methods had a better discriminatory power for SCCmec type III and SCCmec types IV and VT isolates, respectively, suggesting that dru and SIRU can be used to further type these isolates. Copyright © 2013. Published by Elsevier B.V.

  16. Welfare Risks of Repeated Application of On-Farm Killing Methods for Poultry

    Directory of Open Access Journals (Sweden)

    Jessica E. Martin

    2018-03-01

    Full Text Available Council Regulation (EC no. 1099/2009 on the protection of animals at the time of killing restricts the use of manual cervical dislocation in poultry on farms in the European Union (EU to birds weighing up to 3 kg and 70 birds per person per day. However, few studies have examined whether repeated application of manual cervical dislocation has welfare implications and whether these are dependent on individual operator skill or susceptibility to fatigue. We investigated the effects of repeated application (100 birds at a fixed killing rate of 1 bird per 2 min and multiple operators on two methods of killing of broilers, laying hens, and turkeys in commercial settings. We compared the efficacy and welfare impact of repeated application of cervical dislocation and a percussive killer (Cash Poultry Killer, CPK, using 12 male stockworkers on three farms (one farm per bird type. Both methods achieved over 96% kill success at the first attempt. The killing methods were equally effective for each bird type and there was no evidence of reduced performance with time and/or bird number. Both methods of killing caused a rapid loss of reflexes, indicating loss of brain function. There was more variation in reflex durations and post-mortem damage in birds killed by cervical dislocation than that found using CPK. High neck dislocation was associated with improved kill success and more rapid loss of reflexes. The CPK caused damage to multiple brain areas with little variation. Overall, the CPK was associated with faster abolition of reflexes, with fewer birds exhibiting them at all, suggestive of better welfare outcomes. However, technical difficulties with the CPK highlighted the advantages of cervical dislocation, which can be performed immediately with no equipment. At the killing rates tested, we did not find evidence to justify the current EU limit on the number of birds that one operator can kill on–farm by manual cervical dislocation.

  17. Determinants and Experiences of Repeat Pregnancy among HIV-Positive Kenyan Women--A Mixed-Methods Analysis.

    Directory of Open Access Journals (Sweden)

    Victor Akelo

    Full Text Available To identify factors associated with repeat pregnancy subsequent to an index pregnancy among women living with HIV (WLWH in western Kenya who were enrolled in a 24-month phase-II clinical trial of triple-ART prophylaxis for prevention of mother-to-child transmission, and to contextualize social and cultural influences on WLWH's reproductive decision making.A mixed-methods approach was used to examine repeat pregnancy within a 24 month period after birth. Counselor-administered questionnaires were collected from 500 WLWH. Forty women (22 with a repeat pregnancy; 18 with no repeat pregnancy were purposively selected for a qualitative interview (QI. Simple and multiple logistic regression analyses were performed for quantitative data. Thematic coding and saliency analysis were undertaken for qualitative data.Eighty-eight (17.6% women had a repeat pregnancy. Median maternal age was 23 years (range 15-43 years and median gestational age at enrollment was 34 weeks. In multiple logistic regression analyses, living in the same compound with a husband (adjusted odds ratio (AOR: 2.33; 95% confidence interval (CI: 1.14, 4.75 was associated with increased odds of repeat pregnancy (p ≤ 0.05. Being in the 30-43 age group (AOR: 0.25; 95% CI: 0.07, 0.87, having talked to a partner about family planning (FP use (AOR: 0.53; 95% CI: 0.29, 0.98, and prior usage of FP (AOR: 0.45; 95% CI: 0.25, 0.82 were associated with a decrease in odds of repeat pregnancy. QI findings centered on concerns about modern contraception methods (side effects and views that they 'ruined the womb' and a desire to have the right number of children. Religious leaders, family, and the broader community were viewed as reinforcing cultural expectations for married women to have children. Repeat pregnancy was commonly attributed to contraception failure or to lack of knowledge about post-delivery fertility.In addition to cultural context, reproductive health programs for WLWH may need to

  18. Evaluative Conditioning Can Be Modulated by Memory of the CS-US Pairings at the Time of Testing

    Science.gov (United States)

    Gast, Anne; De Houwer, Jan; De Schryver, Maarten

    2012-01-01

    Evaluative conditioning (EC) is the valence change of a (typically neutral) stimulus (CS) that is due to the previous pairing with another (typically valent) stimulus (US). It has been repeatedly shown that EC effects are stronger or existent only if participants know which US was paired with which CS. Knowledge of the CS-US pairings is usually…

  19. Cortical Plasticity Induction by Pairing Subthalamic Nucleus Deep-Brain Stimulation and Primary Motor Cortical Transcranial Magnetic Stimulation in Parkinson's Disease.

    Science.gov (United States)

    Udupa, Kaviraja; Bahl, Nina; Ni, Zhen; Gunraj, Carolyn; Mazzella, Filomena; Moro, Elena; Hodaie, Mojgan; Lozano, Andres M; Lang, Anthony E; Chen, Robert

    2016-01-13

    Noninvasive brain stimulation studies have shown abnormal motor cortical plasticity in Parkinson's disease (PD). These studies used peripheral nerve stimulation paired with transcranial magnetic stimulation (TMS) to primary motor cortex (M1) at specific intervals to induce plasticity. Induction of cortical plasticity through stimulation of the basal ganglia (BG)-M1 connections has not been studied. In the present study, we used a novel technique of plasticity induction by repeated pairing of deep-brain stimulation (DBS) of the BG with M1 stimulation using TMS. We hypothesize that repeated pairing of subthalamic nucleus (STN)-DBS and M1-TMS at specific time intervals will lead to plasticity in the M1. Ten PD human patients with STN-DBS were studied in the on-medication state with DBS set to 3 Hz. The interstimulus intervals (ISIs) between STN-DBS and TMS that produced cortical facilitation were determined individually for each patient. Three plasticity induction conditions with repeated pairings (180 times) at specific ISIs (∼ 3 and ∼ 23 ms) that produced cortical facilitation and a control ISI of 167 ms were tested in random order. Repeated pairing of STN-DBS and M1-TMS at short (∼ 3 ms) and medium (∼ 23 ms) latencies increased M1 excitability that lasted for at least 45 min, whereas the control condition (fixed ISI of 167 ms) had no effect. There were no specific changes in motor thresholds, intracortical circuits, or recruitment curves. Our results indicate that paired-associative cortical plasticity can be induced by repeated STN and M1 stimulation at specific intervals. These results show that STN-DBS can modulate cortical plasticity. We introduced a new experimental paradigm to test the hypothesis that pairing subthalamic nucleus deep-brain stimulation (STN-DBS) with motor cortical transcranial magnetic stimulation (M1-TMS) at specific times can induce cortical plasticity in patients with Parkinson's disease (PD). We found that repeated pairing of STN

  20. 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

  1. How much will afforestation of former cropland influence soil C stocks? A synthesis of paired sampling, chronosequence sampling and repeated sampling studies

    Science.gov (United States)

    Vesterdal, Lars; Hansen, K.; Stupak, I.; Don, Axel; Poeplau, C.; Leifeld, Jens; van Wesemael, Bas

    2010-05-01

    The need for documentation of land-use change effects on soil C is high on the agenda in most signatory countries to the Kyoto Protocol. Large land areas in Europe have experienced land-use change from cropland to forest since 1990 by direct afforestation as well as abandonment and regrowth of marginally productive cropland. Soil C dynamics following land-use change remain highly uncertain due to a limited number of available studies and due to influence of interacting factors such as land use history, soil type, and climate. Common approaches for estimation of potential soil C changes following land-use change are i) paired sampling of plots with a long legacy of different land uses, ii) chronosequence studies of land-use change, and lastly iii) repeated sampling of plots subject to changed land use. This paper will synthesize the quantitative effects of cropland afforestation on soil C sequestration based on all three approaches and will report on related work within Cost 639. Paired plots of forest and cropland were used to study the general differences between soil C stocks in the two land uses. At 27 sites in Denmark distributed among different regions and soil types forest floor and mineral soil were sampled in and around soil pits. Soil C stocks were higher in forest than cropland (mean difference 22 Mg C ha-1 to 1 m depth). This difference was caused solely by the presence of a forest floor in forests; mineral soil C stocks were similar (108 vs. 109 Mg C ha-1) in the two land uses regardless of soil type and the soil layers considered. The chronosequence approach was employed in the AFFOREST project for evaluation of C sequestration in biomass and soils following afforestation of cropland. Two oak (Quercus robur) and four Norway spruce (Picea abies) afforestation chronosequences (age range 1 to 90 years) were studied in Denmark, Sweden and the Netherlands. Forest floor and mineral soil (0-25 cm) C contents were as a minimum unchanged and in most cases there

  2. Modified Extraction-Free Ion-Pair Methods for the Determination of Flunarizine Dihydrochloride in Bulk Drug, Tablets, and Human Urine

    Science.gov (United States)

    Prashanth, K. N.; Basavaiah, K.

    2018-01-01

    Two simple and sensitive extraction-free spectrophotometric methods are described for the determination of flunarizine dihydrochloride. The methods are based on the ion-pair complex formation between the nitrogenous compound flunarizine (FNZ), converted from flunarizine dihydrochloride (FNH), and the acidic dye phenol red (PR), in which experimental variables were circumvented. The first method (method A) is based on the formation of a yellow-colored ion-pair complex (1:1 drug:dye) between FNZ and PR in chloroform, which is measured at 415 nm. In the second method (method B), the formed drug-dye ion-pair complex is treated with ethanolic potassium hydroxide in an ethanolic medium, and the resulting base form of the dye is measured at 580 nm. The stoichiometry of the formed ion-pair complex between the drug and dye (1:1) is determined by Job's continuous variations method, and the stability constant of the complex is also calculated. These methods quantify FNZ over the concentration ranges 5.0-70.0 in method A and 0.5-7.0 μg/mL in method B. The calculated molar absorptivities are 6.17 × 103 and 5.5 × 104 L/mol·cm-1 for method A and method B, respectively, with corresponding Sandell sensitivity values of 0.0655 and 0.0074 μg/cm2. The methods are applied to the determination of FNZ in pure drug and human urine.

  3. Instability of (CTGn•(CAGn trinucleotide repeats and DNA synthesis

    Directory of Open Access Journals (Sweden)

    Liu Guoqi

    2012-02-01

    Full Text Available Abstract Expansion of (CTGn•(CAGn trinucleotide repeat (TNR microsatellite sequences is the cause of more than a dozen human neurodegenerative diseases. (CTGn and (CAGn repeats form imperfectly base paired hairpins that tend to expand in vivo in a length-dependent manner. Yeast, mouse and human models confirm that (CTGn•(CAGn instability increases with repeat number, and implicate both DNA replication and DNA damage response mechanisms in (CTGn•(CAGn TNR expansion and contraction. Mutation and knockdown models that abrogate the expression of individual genes might also mask more subtle, cumulative effects of multiple additional pathways on (CTGn•(CAGn instability in whole animals. The identification of second site genetic modifiers may help to explain the variability of (CTGn•(CAGn TNR instability patterns between tissues and individuals, and offer opportunities for prognosis and treatment.

  4. Image analysis as a non-destructive method to assess regrowth of weeds after repeated flame weeding

    DEFF Research Database (Denmark)

    Rask, Anne Merete; Kristoffersen, Palle; Andreasen, Christian

    2013-01-01

    picture of the long-term effect of repeated treatments. Image analysis was most useful for assessing the effect of repeated treatments when weed cover was relatively low (below 40%) and when plots contained relatively much withered plant material. However, when weed cover is close to 100%, dry weight......, and therefore it may influence the long-term effect of repeated treatments. Visual assessment of weed cover or image analysis do not affect the remaining parts of the weed plants after treatment, but the methods may have other disadvantages. In order to evaluate and compare three methods we measured changes...... in vegetation cover of perennial ryegrass after flaming by (1) a simple image analysis programme counting green pixels, (2) visual assessment of images and (3) by taking biomass samples. Plants were flame treated with eight different dosages (0, 20, 30, 35, 45, 60, 90 and 180 kg propane ha-1) and with various...

  5. Typing Method for the QUB11a Locus of Mycobacterium tuberculosis: IS6110 Insertions and Tandem Repeat Analysis

    Directory of Open Access Journals (Sweden)

    Eriko Maeda-Mitani

    2016-01-01

    Full Text Available QUB11a is used as a locus for variable number of tandem repeats (VNTR analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis. We established a method for determining both tandem repeat numbers and IS6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and BsmBI digestion. All 29 large QUB11a fragments (>1,200 bp investigated contained IS6110 insertions and varied in the number of repeats (18 patterns and location of IS6110 insertions. This method allows VNTR analysis with high discrimination.

  6. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma.

    Science.gov (United States)

    Hirao, Ichiro; Kimoto, Michiko

    2012-01-01

    Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.

  7. Repeatability of regional myocardial blood flow calculation in 82Rb PET imaging

    International Nuclear Information System (INIS)

    Knešaurek, Karin; Machac, Josef; Zhang, Zhuangyu

    2009-01-01

    We evaluated the repeatability of the calculation of myocardial blood flow (MBF) at rest and pharmacological stress, and calculated the coronary flow reserve (CFR) utilizing 82 Rb PET imaging. The aim of the research was to prove high repeatability for global MBF and CFR values and good repeatability for regional MBF and CFR values. The results will have significant impact on cardiac PET imaging in terms of making it more affordable and increasing its use. 12 normal volunteers were imaged at rest and during pharmacological stress, with 2220 MBq of 82 Rb each. A GE Advance PET system was used to acquire dynamic 50-frame studies. MBF was calculated with a 2-compartmental model using a modified PMOD program (PMOD; University Hospital Zurich, Zurich, Switzerland). Two differential equations, describing a 2-compartmental model, were solved by numerical integration and using Levenberg-Marquardt's method for fitting data. The PMOD program defines 16 standard segments and calculates myocardial flow for each segment, as well as average septal, anterior, lateral, inferior and global flow. Repeatability was evaluated according to the method of Bland and Altman. Global rest and stress MBF, as well as global CFR, showed very good repeatability. No significant differences were found between the paired resting global MBF (0.63 ± 0.13 vs. 0.64 ± 0.13 mL/min/g; mean difference, -1.0% ± 2.6%) and the stress global MBF (1.37 ± 0.23 vs. 1.37 ± 0.24; mean difference, 0.1% ± 2.3%). Global CFR was highly reproducible (2.25 ± 0.56 vs. 2.22 ± 0.54, P = not statistically significant; mean difference, 1.3% ± 14.3%). Repeatability coefficients for global rest MBF were 0.033 (5.2%) and stress MBF 0.062 (4.5%) mL/min/g. Regional rest and stress MBF and CFR have shown good reproducibility. The average per sector repeatability coefficients for rest MBF were 0.056 (8.5%) and stress MBF 0.089 (6.3%) mL/min/g, and average repeatability coefficient for CFR was 0.25 (10.6%). The results

  8. Determination of the pairing-strength constants in the isovector plus isoscalar pairing case

    Science.gov (United States)

    Mokhtari, D.; Fellah, M.; Allal, N. H.

    2016-05-01

    A method for the determination of the pairing-strength constants, in the neutron-proton (n-p) isovector plus isoscalar pairing case, is proposed in the framework of the BCS theory. It is based on the fitting of these constants to reproduce the experimentally known pairing gap parameters as well as the root-mean-squared (r.m.s) charge radii values. The method is applied to some proton-rich even-even nuclei. The single-particle energies used are those of a deformed Woods-Saxon mean field. It is shown that the obtained value of the ratio GnpT=0/G npT=1 is of the same order as the ones, arbitrary chosen, of some previous works. The effect of the inclusion of the isoscalar n-p pairing in the r.m.s matter radii is then numerically studied for the same nuclei.

  9. RePS: a sequence assembler that masks exact repeats identified from the shotgun data

    DEFF Research Database (Denmark)

    Wang, Jun; Wong, Gane Ka-Shu; Ni, Peixiang

    2002-01-01

    We describe a sequence assembler, RePS (repeat-masked Phrap with scaffolding), that explicitly identifies exact 20mer repeats from the shotgun data and removes them prior to the assembly. The established software is used to compute meaningful error probabilities for each base. Clone......-end-pairing information is used to construct scaffolds that order and orient the contigs. We show with real data for human and rice that reasonable assemblies are possible even at coverages of only 4x to 6x, despite having up to 42.2% in exact repeats. Udgivelsesdato: 2002-May...

  10. Repeatability of visual acuity measurement.

    Science.gov (United States)

    Raasch, T W; Bailey, I L; Bullimore, M A

    1998-05-01

    This study investigates features of visual acuity chart design and acuity testing scoring methods which affect the validity and repeatability of visual acuity measurements. Visual acuity was measured using the Sloan and British Standard letter series, and Landolt rings. Identifiability of the different letters as a function of size was estimated, and expressed in the form of frequency-of-seeing curves. These functions were then used to simulate acuity measurements with a variety of chart designs and scoring criteria. Systematic relationships exist between chart design parameters and acuity score, and acuity score repeatability. In particular, an important feature of a chart, that largely determines the repeatability of visual acuity measurement, is the amount of size change attributed to each letter. The methods used to score visual acuity performance also affect repeatability. It is possible to evaluate acuity score validity and repeatability using the statistical principles discussed here.

  11. Synergy between pair coupled cluster doubles and pair density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Garza, Alejandro J.; Bulik, Ireneusz W. [Department of Chemistry, Rice University, Houston, Texas 77251-1892 (United States); Henderson, Thomas M. [Department of Chemistry and Department of Physics and Astronomy, Rice University, Houston, Texas 77251-1892 (United States); Scuseria, Gustavo E. [Department of Chemistry and Department of Physics and Astronomy, Rice University, Houston, Texas 77251-1892 (United States); Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589 (Saudi Arabia)

    2015-01-28

    Pair coupled cluster doubles (pCCD) has been recently studied as a method capable of accounting for static correlation with low polynomial cost. We present three combinations of pCCD with Kohn–Sham functionals of the density and on-top pair density (the probability of finding two electrons on top of each other) to add dynamic correlation to pCCD without double counting. With a negligible increase in computational cost, these pCCD+DFT blends greatly improve upon pCCD in the description of typical problems where static and dynamic correlations are both important. We argue that—as a black-box method with low scaling, size-extensivity, size-consistency, and a simple quasidiagonal two-particle density matrix—pCCD is an excellent match for pair density functionals in this type of fusion of multireference wavefunctions with DFT.

  12. A Method against Interrupted-Sampling Repeater Jamming Based on Energy Function Detection and Band-Pass Filtering

    Directory of Open Access Journals (Sweden)

    Hui Yuan

    2017-01-01

    Full Text Available Interrupted-sampling repeater jamming (ISRJ is a new kind of coherent jamming to the large time-bandwidth linear frequency modulation (LFM signal. Many jamming modes, such as lifelike multiple false targets and dense false targets, can be made through setting up different parameters. According to the “storage-repeater-storage-repeater” characteristics of the ISRJ and the differences in the time-frequency-energy domain between the ISRJ signal and the target echo signal, one new method based on the energy function detection and band-pass filtering is proposed to suppress the ISRJ. The methods mainly consist of two parts: extracting the signal segments without ISRJ and constructing band-pass filtering function with low sidelobe. The simulation results show that the method is effective in the ISRJ with different parameters.

  13. Beyond Extinction: Prolonged Conditioning and Repeated Threat Exposure Abolish Contextual Renewal of Fear-Potentiated Startle Discrimination but Leave Expectancy Ratings Intact.

    Science.gov (United States)

    Leer, Arne; Haesen, Kim; Vervliet, Bram

    2018-01-01

    Extinction treatments decrease fear via repeated exposures to the conditioned stimulus (CS) and are associated with a return of fear. Alternatively, fear can be reduced via reductions in the perceived intensity of the unconditioned stimulus (US), e.g., through repeated exposures to the US. Promisingly, the few available studies show that repeated US exposures outperform standard extinction. US exposure treatments can decrease fear via two routes: (1) by weakening the CS-US association (extinction-like mechanism), and/or (2) by weakening the subjective US aversiveness (habituation-like mechanism). The current study further investigated the conditions under which US exposure treatment may reduce renewal, by adding a group in which CS-US pairings continued following fear acquisition. During acquisition, participants learned that one of two visual stimuli (CS+/CS-) predicted the occurrence of an aversive electrocutaneous stimulus (US). Next, the background context changed and participants received one of three interventions: repeated CS exposures, (2) repeated US exposures, or (3) continued CS-US pairings. Following repeated CS exposures, test presentations of the CSs in the original conditioning context revealed intact CS+/CS- differentiation in the fear-potentiated startle reflex, while the differentiation was abolished in the other two groups. Differential US expectancy ratings, on the other hand, were intact in all groups. Skin conductance data were inconclusive because standard context renewal following CS exposures did not occur. Unexpectedly, there was no evidence for a habituation-like process having taken place during US exposures or continued CS-US pairings. The results provide further evidence that US exposures outperform the standard extinction treatment and show that effects are similar when US exposures are part of CS-US pairings.

  14. Strong pairing approximation in comparison with the exact solutions to the pairing Hamiltonian

    Directory of Open Access Journals (Sweden)

    Lunyov A.V.

    2016-01-01

    Full Text Available Results of the Strong Pairing Approximation (SPA as a method with the exact particle number conservation are compared with those of the quasiparticle method (QM. It is shown that SPA comes to the same equations as QM for the gap parameter, chemical potential and one- and two-quasiparticle states. Calculations are performed for 14864Gd84 as an example, and compared with the exact solutions to the pairing Hamiltonian.

  15. Validation of the Rotation Ratios Method

    International Nuclear Information System (INIS)

    Foss, O.A.; Klaksvik, J.; Benum, P.; Anda, S.

    2007-01-01

    Background: The rotation ratios method describes rotations between pairs of sequential pelvic radiographs. The method seems promising but has not been validated. Purpose: To validate the accuracy of the rotation ratios method. Material and Methods: Known pelvic rotations between 165 radiographs obtained from five skeletal pelvises in an experimental material were compared with the corresponding calculated rotations to describe the accuracy of the method. The results from a clinical material of 262 pelvic radiographs from 46 patients defined the ranges of rotational differences compared. Repeated analyses, both on the experimental and the clinical material, were performed using the selected reference points to describe the robustness and the repeatability of the method. Results: The reference points were easy to identify and barely influenced by pelvic rotations. The mean differences between calculated and real pelvic rotations were 0.0 deg (SD 0.6) for vertical rotations and 0.1 deg (SD 0.7) for transversal rotations in the experimental material. The intra- and interobserver repeatability of the method was good. Conclusion: The accuracy of the method was reasonably high, and the method may prove to be clinically useful

  16. Contribution to the experimental study of excited levels of some light nuclei by using the method of angular correlation of internal conversion pairs and monopolar pairs; Contribution a l'etude experimentale de niveaux excites de quelques noyaux legers par la methode des Correlations angulaires des paires de conversion interne Et des paires monopolaires

    Energy Technology Data Exchange (ETDEWEB)

    Armbruster, Raymond

    1950-07-01

    In a first part, the author presents a brief theory of angular correlations of internal conversion pairs and monopolar pairs, and indicates the complete formulations which are used to compute all the angular correlations corresponding to the performed experiments. In a second part, he describes a beta spectrometer, outlines factors which govern the energy resolving power, and the peculiarity of summation of two pulses proportional to the energy of the electron and positron which build up an internal pair. In a third part, the author reports experiments of angular correlations, indicates the shapes of monopolar spectra for different angles between electron and positron emission directions, determines the multipolarity of gamma radiations from the first excited levels of {sup 13}C and {sup 12}C, and gives the angular moments, parity and isobaric spin of two excited levels of the {sup 12}C [French] Dans la premiere partie de notre travail, nous exposons une theorie sommaire des correlations angulaires des paires de conversion interne et des paires monopolaires. A la fin de cette premiere partie sont indiquees les formules completes, qui nous ont servi a calculer pratiquement toutes les correlations angulaires correspondant a nos experiences. Dans la deuxieme partie, nous decrivons un spectrometre beta a scintillation. Nous insistons surtout sur les elements qui determinent le pouvoir de resolution en energie et sur la particularite de sommation de deux impulsions proportionnelles a l'energie de l'electron et du positron formant une paire interne. Dans la troisieme partie, nous exposons nos experiences de correlations angulaires. Nous avons repris une mesure precise de la correlation angulaire des paires monopolaires provenant du niveau 6,05 Mev de l'Oxygene 16. Il nous a ete egalement possible de donner l'allure des spectres monopolaires pour differents angles formes par les directions d'emission de l'electron et du positron. Nous avons determine par la methode des

  17. Repeatability and variation of region-of-interest methods using quantitative diffusion tensor MR imaging of the brain

    International Nuclear Information System (INIS)

    Hakulinen, Ullamari; Brander, Antti; Ryymin, Pertti; Öhman, Juha; Soimakallio, Seppo; Helminen, Mika; Dastidar, Prasun; Eskola, Hannu

    2012-01-01

    Diffusion tensor imaging (DTI) is increasingly used in various diseases as a clinical tool for assessing the integrity of the brain’s white matter. Reduced fractional anisotropy (FA) and an increased apparent diffusion coefficient (ADC) are nonspecific findings in most pathological processes affecting the brain’s parenchyma. At present, there is no gold standard for validating diffusion measures, which are dependent on the scanning protocols, methods of the softwares and observers. Therefore, the normal variation and repeatability effects on commonly-derived measures should be carefully examined. Thirty healthy volunteers (mean age 37.8 years, SD 11.4) underwent DTI of the brain with 3T MRI. Region-of-interest (ROI) -based measurements were calculated at eleven anatomical locations in the pyramidal tracts, corpus callosum and frontobasal area. Two ROI-based methods, the circular method (CM) and the freehand method (FM), were compared. Both methods were also compared by performing measurements on a DTI phantom. The intra- and inter-observer variability (coefficient of variation, or CV%) and repeatability (intra-class correlation coefficient, or ICC) were assessed for FA and ADC values obtained using both ROI methods. The mean FA values for all of the regions were 0.663 with the CM and 0.621 with the FM. For both methods, the FA was highest in the splenium of the corpus callosum. The mean ADC value was 0.727 ×10 -3 mm 2 /s with the CM and 0.747 ×10 -3 mm 2 /s with the FM, and both methods found the ADC to be lowest in the corona radiata. The CV percentages of the derived measures were < 13% with the CM and < 10% with the FM. In most of the regions, the ICCs were excellent or moderate for both methods. With the CM, the highest ICC for FA was in the posterior limb of the internal capsule (0.90), and with the FM, it was in the corona radiata (0.86). For ADC, the highest ICC was found in the genu of the corpus callosum (0.93) with the CM and in the uncinate

  18. detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

    Science.gov (United States)

    Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

    2014-01-01

    Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.

  19. A comparative study between matched and mis-matched projection/back projection pairs used with ASIRT reconstruction method

    International Nuclear Information System (INIS)

    Guedouar, R.; Zarrad, B.

    2010-01-01

    For algebraic reconstruction techniques both forward and back projection operators are needed. The ability to perform accurate reconstruction relies fundamentally on the forward projection and back projection methods which are usually, the transpose of each other. Even though the mis-matched pairs may introduce additional errors during the iterative process, the usefulness of mis-matched projector/back projector pairs has been proved in image reconstruction. This work investigates the performance of matched and mis-matched reconstruction pairs using popular forward projectors and their transposes when used in reconstruction tasks with additive simultaneous iterative reconstruction techniques (ASIRT) in a parallel beam approach. Simulated noiseless phantoms are used to compare the performance of the investigated pairs in terms of the root mean squared errors (RMSE) which are calculated between reconstructed slices and the reference in different regions. Results show that mis-matched projection/back projection pairs can promise more accuracy of reconstructed images than matched ones. The forward projection operator performance seems independent of the choice of the back projection operator and vice versa.

  20. A comparative study between matched and mis-matched projection/back projection pairs used with ASIRT reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Guedouar, R., E-mail: raja_guedouar@yahoo.f [Higher School of Health Sciences and Techniques of Monastir, Av. Avicenne, 5060 Monastir, B.P. 128 (Tunisia); Zarrad, B., E-mail: boubakerzarrad@yahoo.f [Higher School of Health Sciences and Techniques of Monastir, Av. Avicenne, 5060 Monastir, B.P. 128 (Tunisia)

    2010-07-21

    For algebraic reconstruction techniques both forward and back projection operators are needed. The ability to perform accurate reconstruction relies fundamentally on the forward projection and back projection methods which are usually, the transpose of each other. Even though the mis-matched pairs may introduce additional errors during the iterative process, the usefulness of mis-matched projector/back projector pairs has been proved in image reconstruction. This work investigates the performance of matched and mis-matched reconstruction pairs using popular forward projectors and their transposes when used in reconstruction tasks with additive simultaneous iterative reconstruction techniques (ASIRT) in a parallel beam approach. Simulated noiseless phantoms are used to compare the performance of the investigated pairs in terms of the root mean squared errors (RMSE) which are calculated between reconstructed slices and the reference in different regions. Results show that mis-matched projection/back projection pairs can promise more accuracy of reconstructed images than matched ones. The forward projection operator performance seems independent of the choice of the back projection operator and vice versa.

  1. Parietal lesion effects on cued recall following pair associate learning.

    Science.gov (United States)

    Ben-Zvi, Shir; Soroker, Nachum; Levy, Daniel A

    2015-07-01

    We investigated the involvement of the posterior parietal cortex in episodic memory in a lesion-effects study of cued recall following pair-associate learning. Groups of patients who had experienced first-incident stroke, generally in middle cerebral artery territory, and exhibited damage that included lateral posterior parietal regions, were tested within an early post-stroke time window. In three experiments, patients and matched healthy comparison groups executed repeated study and cued recall test blocks of pairs of words (Experiment 1), pairs of object pictures (Experiment 2), or pairs of object pictures and environmental sounds (Experiment 3). Patients' brain CT scans were subjected to quantitative analysis of lesion volumes. Behavioral and lesion data were used to compute correlations between area lesion extent and memory deficits, and to conduct voxel-based lesion-symptom mapping. These analyses implicated lateral ventral parietal cortex, especially the angular gyrus, in cued recall deficits, most pronouncedly in the cross-modal picture-sound pairs task, though significant parietal lesion effects were also found in the unimodal word pairs and picture pairs tasks. In contrast to an earlier study in which comparable parietal lesions did not cause deficits in item recognition, these results indicate that lateral posterior parietal areas make a substantive contribution to demanding forms of recollective retrieval as represented by cued recall, especially for complex associative representations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. The leucine-rich repeat structure.

    Science.gov (United States)

    Bella, J; Hindle, K L; McEwan, P A; Lovell, S C

    2008-08-01

    The leucine-rich repeat is a widespread structural motif of 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucines. Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. Thousands of protein sequences containing leucine-rich repeats have been identified by automatic annotation methods. Three-dimensional structures of leucine-rich repeat domains determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. As the essential structural principles become well established, the leucine-rich repeat architecture is emerging as an attractive framework for structural prediction and protein engineering. This review presents an update of the current understanding of leucine-rich repeat structure at the primary, secondary, tertiary and quaternary levels and discusses specific examples from recently determined three-dimensional structures.

  3. A method for estimating the diffuse attenuation coefficient (KdPAR)from paired temperature sensors

    Science.gov (United States)

    Read, Jordan S.; Rose, Kevin C.; Winslow, Luke A.; Read, Emily K.

    2015-01-01

    A new method for estimating the diffuse attenuation coefficient for photosynthetically active radiation (KdPAR) from paired temperature sensors was derived. We show that during cases where the attenuation of penetrating shortwave solar radiation is the dominant source of temperature changes, time series measurements of water temperatures at multiple depths (z1 and z2) are related to one another by a linear scaling factor (a). KdPAR can then be estimated by the simple equation KdPAR ln(a)/(z2/z1). A suggested workflow is presented that outlines procedures for calculating KdPAR according to this paired temperature sensor (PTS) method. This method is best suited for conditions when radiative temperature gains are large relative to physical noise. These conditions occur frequently on water bodies with low wind and/or high KdPARs but can be used for other types of lakes during time periods of low wind and/or where spatially redundant measurements of temperatures are available. The optimal vertical placement of temperature sensors according to a priori knowledge of KdPAR is also described. This information can be used to inform the design of future sensor deployments using the PTS method or for campaigns where characterizing sub-daily changes in temperatures is important. The PTS method provides a novel method to characterize light attenuation in aquatic ecosystems without expensive radiometric equipment or the user subjectivity inherent in Secchi depth measurements. This method also can enable the estimation of KdPAR at higher frequencies than many manual monitoring programs allow.

  4. Masonry fireplace emissions test method: Repeatability and sensitivity to fueling protocol.

    Science.gov (United States)

    Stern, C H; Jaasma, D R; Champion, M R

    1993-03-01

    A test method for masonry fireplaces has been evaluated during testing on six masonry fireplace configurations. The method determines carbon monoxide and particulate matter emission rates (g/h) and factors (g/kg) and does not require weighing of the appliance to determine the timing of fuel loading.The intralaboratory repeatability of the test method has been determined from multiple tests on the six fireplaces. For the tested fireplaces, the ratio of the highest to lowest measured PM rate averaged 1.17 and in no case was greater than 1.32. The data suggest that some of the variation is due to differences in fuel properties.The influence of fueling protocol on emissions has also been studied. A modified fueling protocol, tested in large and small fireplaces, reduced CO and PM emission factors by roughly 40% and reduced CO and PM rates from 0 to 30%. For both of these fireplaces, emission rates were less sensitive to fueling protocol than emission factors.

  5. The gut microbial community of Midas cichlid fish in repeatedly evolved limnetic-benthic species pairs.

    Science.gov (United States)

    Franchini, Paolo; Fruciano, Carmelo; Frickey, Tancred; Jones, Julia C; Meyer, Axel

    2014-01-01

    Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.

  6. Apomorphine conditioning and sensitization: the paired/unpaired treatment order as a new major determinant of drug conditioned and sensitization effects.

    Science.gov (United States)

    de Matos, Liana Wermelinger; Carey, Robert J; Carrera, Marinete Pinheiro

    2010-09-01

    Repeated treatments with psychostimulant drugs generate behavioral sensitization. In the present study we employed a paired/unpaired protocol to assess the effects of repeated apomorphine (2.0 mg/kg) treatments upon locomotion behavior. In the first experiment we assessed the effects of conditioning upon apomorphine sensitization. Neither the extinction of the conditioned response nor a counter-conditioning procedure in which we paired an inhibitory treatment (apomorphine 0.05 mg/kg) with the previously established conditioned stimulus modified the sensitization response. In the second experiment, we administered the paired/unpaired protocol in two phases. In the second phase, we reversed the paired/unpaired protocol. Following the first phase, the paired group alone exhibited conditioned locomotion in the vehicle test and a sensitization response. In the second phase, the initial unpaired group which received 5 paired apomorphine trials during the reversal phase did not develop a conditioned response but developed a potentiated sensitization response. This disassociation of the conditioned response from the sensitization response is attributed to an apomorphine anti-habituation effect that can generate a false positive Pavlovian conditioned response effect. The potentiated sensitization response induced by the treatment reversal protocol points to an important role for the sequential experience of the paired/unpaired protocol in behavioral sensitization. 2010 Elsevier Inc. All rights reserved.

  7. Think Pair Share (TPS as Method to Improve Student’s Learning Motivation and Learning Achievement

    Directory of Open Access Journals (Sweden)

    Hetika Hetika

    2018-03-01

    Full Text Available This research aims to find out the application of Think Pair Share (TPS learning method in improving learning motivation and learning achievement in the subject of Introduction to Accounting I of the Accounting Study Program students of Politeknik Harapan Bersama. The Method of data collection in this study used observation method, test method, and documentation method. The research instruments used observation sheet, questionnaire and test question. This research used Class Action Research Design which is an action implementation oriented research, with the aim of improving quality or problem solving in a group by carefully and observing the success rate due to the action. The method of analysis used descriptive qualitative and quantitative analysis method. The results showed that the application of Think Pair Share Learning (TPS Method can improve the Learning Motivation and Achievement. Before the implementation of the action, the obtained score is 67% then in the first cycle increases to 72%, and in the second cycle increasws to 80%. In addition, based on questionnaires distributed to students, it also increases the score of Accounting Learning Motivation where the score in the first cycle of 76% increases to 79%. In addition, in the first cycle, the score of pre test and post test of the students has increased from 68.86 to 76.71 while in the second cycle the score of pre test and post test of students has increased from 79.86 to 84.86.

  8. A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

    Science.gov (United States)

    Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

    2016-01-01

    Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

  9. Study of the processes of ion pairs formation by the method of ion-ion coincidence: I2 and chlorine-containing hydrocarbons

    International Nuclear Information System (INIS)

    Golovin, A.V.

    1991-01-01

    A method of ion-ion coincidences was suggested to study the process of ion pairs formation during molecule photoionization. The principle of action of ion-ion coincidence method is based on recording of only the negative and positive ions that formed as a result of a molecule decomposition. The flowsheet of the facility of ion-ion coincidences was presented. The processes of ion pairs formation in iodine, chloroform, propyl-, n-propenyl-, tert.butyl- and benzyl-chlorides were studied. A simple model permitting to evaluate the dependence of quantum yield of ion pair formation on excitation energy was suggested

  10. Pairing field methods to improve inference in wildlife surveys while accommodating detection covariance.

    Science.gov (United States)

    Clare, John; McKinney, Shawn T; DePue, John E; Loftin, Cynthia S

    2017-10-01

    It is common to use multiple field sampling methods when implementing wildlife surveys to compare method efficacy or cost efficiency, integrate distinct pieces of information provided by separate methods, or evaluate method-specific biases and misclassification error. Existing models that combine information from multiple field methods or sampling devices permit rigorous comparison of method-specific detection parameters, enable estimation of additional parameters such as false-positive detection probability, and improve occurrence or abundance estimates, but with the assumption that the separate sampling methods produce detections independently of one another. This assumption is tenuous if methods are paired or deployed in close proximity simultaneously, a common practice that reduces the additional effort required to implement multiple methods and reduces the risk that differences between method-specific detection parameters are confounded by other environmental factors. We develop occupancy and spatial capture-recapture models that permit covariance between the detections produced by different methods, use simulation to compare estimator performance of the new models to models assuming independence, and provide an empirical application based on American marten (Martes americana) surveys using paired remote cameras, hair catches, and snow tracking. Simulation results indicate existing models that assume that methods independently detect organisms produce biased parameter estimates and substantially understate estimate uncertainty when this assumption is violated, while our reformulated models are robust to either methodological independence or covariance. Empirical results suggested that remote cameras and snow tracking had comparable probability of detecting present martens, but that snow tracking also produced false-positive marten detections that could potentially substantially bias distribution estimates if not corrected for. Remote cameras detected marten

  11. Environmental manipulations alter age differences in attribution of incentive salience to reward-paired cues.

    Science.gov (United States)

    Anderson, Rachel I; Bush, Peter C; Spear, Linda P

    2013-11-15

    Cues repeatedly paired with rewards often themselves become imbued with enhanced motivational value, or incentive salience. During Pavlovian conditioned approach procedures, a cue repeatedly preceding reward delivery often elicits conditioned responses at either the reward delivery location ("goal-tracking") or the cue itself ("sign-tracking"). Sign-tracking behavior is thought to reflect the individual differences in attribution of incentive salience to reward-paired cues that may contribute to addiction vulnerability. Adolescent rats typically demonstrate less sign-tracking behavior than adult rats, a surprising finding given that adolescence is hypothesized to be a time of heightened addiction vulnerability. Given evidence that adult sign-tracking behavior can be influenced by environmental conditions, the present study compared the effects of isolate housing and food deprivation on expression of sign-tacking and goal-tracking behavior in adolescent and adult male rats across eight days of a Pavlovian conditioned approach procedure. Pair-housed adults exhibited more sign-tracking behavior than pair-housed adolescents; however, this age difference was not apparent in isolate-housed subjects. Adolescents often appeared more sensitive than adults to both food restriction- and isolate housing-induced changes in behavior, with food restriction promoting an increase in sign-tracking among isolate-housed adolescents and an increase in goal-tracking among pair-housed adolescents. For adults, food restriction resulted in a modest increase in overall expression of both sign- and goal-tracking behavior. To the extent that sign-tracking behavior reflects attribution of incentive salience to reward-paired cues, results from the present study provide evidence that reactivity to rewards during adolescence is strongly related to the nature of the surrounding environment. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Effect of Misalignment between Successive Corneal Videokeratography Maps on the Repeatability of Topography Data

    Science.gov (United States)

    Bao, FangJun; Wang, JunJie; Huang, JinHai; Yu, Ye; Deng, ManLi; Li, LinNa; Yu, AYong; Wang, QinMei; Davey, Pinakin Gunvant; Elsheikh, Ahmed

    2015-01-01

    Purpose To improve the reliability of corneal topographic data through the development of a method to estimate the magnitude of misalignment between successive corneal videokeratography (VK) maps and eliminate the effect of misalignment on the repeatability of topography data. Methods Anterior and posterior topography maps were recorded twice for 124 healthy eyes of 124 participants using a Pentacam, and the repeatability of measurements was assessed by calculating the differences in elevation between each two sets of data. The repeatability of measurements was re-assessed following the determination of the magnitude of misalignment components (translational displacements: x0, y0 and z0, and rotational displacements: α, β and γ) between each two data sets and using them to modify the second data set within each pair based on an Iterative Closest Point (ICP) algorithm. The method simultaneously considered the anterior and posterior maps taken for the same eye since they were assumed to have the same set of misalignment components. A new parameter, named Combined Misalignment parameter (CM), has been developed to combine the effect of all six misalignment components on topography data and so enable study of the association between misalignment and the data repeatability test results. Results The repeatability tests resulted in average root mean square (RMS) differences in elevation data of 8.46±2.75 μm before ICP map matching when simultaneously considering anterior and posterior surfaces. With map matching and misalignment correction, the differences decreased to 7.28±2.58 μm (P = 0.00). When applied to only the anterior maps, misalignment correction led to a more pronounced reduction in elevation data differences from 4.58±1.84 μm to 2.97±1.29 μm (P = 0.00). CM was found to be associated with the repeatability error (P = 0.00), with posterior maps being responsible for most of the error due to their relatively lower accuracy compared to anterior maps

  13. Pair shell model description of collective motions

    International Nuclear Information System (INIS)

    Chen Hsitseng; Feng Dahsuan

    1996-01-01

    The shell model in the pair basis has been reviewed with a case study of four particles in a spherical single-j shell. By analyzing the wave functions according to their pair components, the novel concept of the optimum pairs was developed which led to the proposal of a generalized pair mean-field method to solve the many-body problem. The salient feature of the method is its ability to handle within the framework of the spherical shell model a rotational system where the usual strong configuration mixing complexity is so simplified that it is now possible to obtain analytically the band head energies and the moments of inertia. We have also examined the effects of pair truncation on rotation and found the slow convergence of adding higher spin pairs. Finally, we found that when the SDI and Q .Q interactions are of equal strengths, the optimum pair approximation is still valid. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Odvody Gary N

    2008-11-01

    Full Text Available Abstract Background A recent outbreak of sorghum downy mildew in Texas has led to the discovery of both metalaxyl resistance and a new pathotype in the causal organism, Peronosclerospora sorghi. These observations and the difficulty in resolving among phylogenetically related downy mildew pathogens dramatically point out the need for simply scored markers in order to differentiate among isolates and species, and to study the population structure within these obligate oomycetes. Here we present the initial results from the use of a biotin capture method to discover, clone and develop PCR primers that permit the use of simple sequence repeats (microsatellites to detect differences at the DNA level. Results Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55% with dinucleotide repeats and 6 (11% with trinucleotide repeats. A total of 22 microsatellites with CA/AC or GT/TG repeats were the most abundant (40% and GA/AG or CT/TC types contribute 15% in our collection. When used to amplify DNA from 19 isolates from P. sorghi, as well as from 5 related species that cause downy mildew on other hosts, the number of different bands detected for each SSR primer pair using a LI-COR- DNA Analyzer ranged from two to eight. Successful cross-amplification for 12 primer pairs studied in detail using DNA from downy mildews that attack maize (P. maydis & P. philippinensis, sugar cane (P. sacchari, pearl millet (Sclerospora graminicola and rose (Peronospora sparsa indicate that the flanking regions are conserved in all these species. A total of 15 SSR amplicons unique to P. philippinensis (one of the potential threats to US maize production were detected, and these have potential for development of diagnostic tests. A total of 260 alleles were obtained using 54 microsatellites primer combinations, with an average of 4.8 polymorphic markers per SSR across 34

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

    Science.gov (United States)

    Perumal, Ramasamy; Nimmakayala, Padmavathi; Erattaimuthu, Saradha R; No, Eun-Gyu; Reddy, Umesh K; Prom, Louis K; Odvody, Gary N; Luster, Douglas G; Magill, Clint W

    2008-11-29

    A recent outbreak of sorghum downy mildew in Texas has led to the discovery of both metalaxyl resistance and a new pathotype in the causal organism, Peronosclerospora sorghi. These observations and the difficulty in resolving among phylogenetically related downy mildew pathogens dramatically point out the need for simply scored markers in order to differentiate among isolates and species, and to study the population structure within these obligate oomycetes. Here we present the initial results from the use of a biotin capture method to discover, clone and develop PCR primers that permit the use of simple sequence repeats (microsatellites) to detect differences at the DNA level. Among the 55 primers pairs designed from clones from pathotype 3 of P. sorghi, 36 flanked microsatellite loci containing simple repeats, including 28 (55%) with dinucleotide repeats and 6 (11%) with trinucleotide repeats. A total of 22 microsatellites with CA/AC or GT/TG repeats were the most abundant (40%) and GA/AG or CT/TC types contribute 15% in our collection. When used to amplify DNA from 19 isolates from P. sorghi, as well as from 5 related species that cause downy mildew on other hosts, the number of different bands detected for each SSR primer pair using a LI-COR- DNA Analyzer ranged from two to eight. Successful cross-amplification for 12 primer pairs studied in detail using DNA from downy mildews that attack maize (P. maydis & P. philippinensis), sugar cane (P. sacchari), pearl millet (Sclerospora graminicola) and rose (Peronospora sparsa) indicate that the flanking regions are conserved in all these species. A total of 15 SSR amplicons unique to P. philippinensis (one of the potential threats to US maize production) were detected, and these have potential for development of diagnostic tests. A total of 260 alleles were obtained using 54 microsatellites primer combinations, with an average of 4.8 polymorphic markers per SSR across 34 Peronosclerospora, Peronospora and Sclerospora

  16. Modeling of the phase equilibria of polystyrene in methylcyclohexane with semi-empirical quantum mechanical methods I

    DEFF Research Database (Denmark)

    Wilczura-Wachnik, H.; Jonsdottir, Svava Osk

    2003-01-01

    for the repeating unit of the polymer, the intermolecular interaction energies between the solvent molecule and the polymer were simulated. The semiempirical quantum mechanical method AM1, and a method for sampling relevant internal orientations for a pair of molecules developed previously were used. Interaction...

  17. Statistical deprojection of galaxy pairs

    Science.gov (United States)

    Nottale, Laurent; Chamaraux, Pierre

    2018-06-01

    Aims: The purpose of the present paper is to provide methods of statistical analysis of the physical properties of galaxy pairs. We perform this study to apply it later to catalogs of isolated pairs of galaxies, especially two new catalogs we recently constructed that contain ≈1000 and ≈13 000 pairs, respectively. We are particularly interested by the dynamics of those pairs, including the determination of their masses. Methods: We could not compute the dynamical parameters directly since the necessary data are incomplete. Indeed, we only have at our disposal one component of the intervelocity between the members, namely along the line of sight, and two components of their interdistance, i.e., the projection on the sky-plane. Moreover, we know only one point of each galaxy orbit. Hence we need statistical methods to find the probability distribution of 3D interdistances and 3D intervelocities from their projections; we designed those methods under the term deprojection. Results: We proceed in two steps to determine and use the deprojection methods. First we derive the probability distributions expected for the various relevant projected quantities, namely intervelocity vz, interdistance rp, their ratio, and the product rp v_z^2, which is involved in mass determination. In a second step, we propose various methods of deprojection of those parameters based on the previous analysis. We start from a histogram of the projected data and we apply inversion formulae to obtain the deprojected distributions; lastly, we test the methods by numerical simulations, which also allow us to determine the uncertainties involved.

  18. Dual market structures and the likelihood of repeated ties - evidence from pharmaceutical biotechnology

    NARCIS (Netherlands)

    Roijakkers, A.H.W.M.; Hagedoorn, J.; Kranenburg, van H.

    2005-01-01

    This paper analyses the role of repeated ties in the high-tech pharmaceutical biotechnology industry, a sector that is characterized by a strong dual market structure. Our most important finding is that previous ties in pairs of large pharmaceutical companies and small biotechnology firms have a

  19. Two-dimensional quantum repeaters

    Science.gov (United States)

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

    2016-11-01

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

  20. System and method for clock synchronization and position determination using entangled photon pairs

    Science.gov (United States)

    Shih, Yanhua (Inventor)

    2010-01-01

    A system and method for clock synchronization and position determination using entangled photon pairs is provided. The present invention relies on the measurement of the second order correlation function of entangled states. Photons from an entangled photon source travel one-way to the clocks to be synchronized. By analyzing photon registration time histories generated at each clock location, the entangled states allow for high accuracy clock synchronization as well as high accuracy position determination.

  1. Test–retest reliability and repeatability of renal diffusion tensor MRI in healthy subjects

    International Nuclear Information System (INIS)

    Cutajar, Marica; Clayden, Jonathan D.; Clark, Christopher A.; Gordon, Isky

    2011-01-01

    Purpose: This study assessed test–retest reliability and repeatability of diffusion tensor imaging (DTI) in the kidneys. Materials and methods: Seven healthy volunteers (age range, 19–31 years), were imaged three consecutive times on the same day (short-term reliability) and the same imaging protocol was repeated after a month (long-term reliability). Diffusion-weighted magnetic resonance imaging scans in the coronal-oblique projection of the kidney were acquired on a 1.5 T scanner using a multi-section echo-planar sequence; six contiguous slices each 5 mm thick, diffusion sensitisation along 20 non-collinear directions, TR = 730 ms, TE = 73 ms and 2 b-values (0 and 400 s mm −2 ). Volunteers were asked to hold their breath throughout each data acquisition (approx. 20 s). The apparent diffusion coefficient (ADC) and fractional anisotropy (FA) values were obtained from maps generated using dedicated software MIStar (Apollo Medical Imaging, Melbourne, Australia). Results: Statistical analyses of both short- and long-term repeats were carried out from which the within-subject coefficient of variation (wsCV) was calculated. The wsCV obtained for both the ADC and FA values were less than 10% in all the analyses carried out. In addition, paired (repeated measures) t-test was used to measure the variation between the diffusion parameters collected from the two scanning sessions a month apart. It showed no significant difference and the wsCV obtained after comparing the first and second scans were found to be smaller than 15% for both ADC and FA. Conclusion: Renal DTI produces reliable and repeatable results which make longitudinal investigation of patients viable.

  2. Frequent Pairs in Data Streams: Exploiting Parallelism and Skew

    DEFF Research Database (Denmark)

    Campagna, Andrea; Kutzkow, Konstantin; Pagh, Rasmus

    2011-01-01

    We introduce the Pair Streaming Engine (PairSE) that detects frequent pairs in a data stream of transactions. Our algorithm finds the most frequent pairs with high probability, and gives tight bounds on their frequency. It is particularly space efficient for skewed distribution of pair supports...... items mining in data streams. We show how to efficiently scale these approaches to handle large transactions. We report experimental results showcasing precision and recall of our method. In particular, we find that often our method achieves excellent precision, returning identical upper and lower...... bounds on the supports of the most frequent pairs....

  3. The influence of learning methods on collaboration: prior repeated retrieval enhances retrieval organization, abolishes collaborative inhibition, and promotes post-collaborative memory.

    Science.gov (United States)

    Congleton, Adam R; Rajaram, Suparna

    2011-11-01

    Research on collaborative memory has unveiled the counterintuitive yet robust phenomenon that collaboration impairs group recall. A candidate explanation for this collaborative inhibition effect is the disruption of people's idiosyncratic retrieval strategies during collaboration, and it is hypothesized that employing methods that improve one's organization protects against retrieval disruption. Here it is investigated how one's learning method during the study phase--defined as either repeatedly studying or repeatedly retrieving information--influences retrieval organization and what effects this has on collaborative recall and post-collaborative individual recall. Results show that repeated retrieval consistently eliminated collaborative inhibition. This enabled participants to gain the most from re-exposure to materials recalled by their partners that they themselves did not recall and led to improvements in their individual memory following collaboration. This repeated retrieval advantage stemmed from the preferential manner in which this learning method strengthened retrieval organization. Findings are also discussed that reveal a relationship between retrieval organization and the interaction observed between learning method and short versus long delay seen in the testing effect literature. Finally, results show that the elusive benefits of cross-cuing during collaboration may be best detected with a longer study-test delay. Together, these findings illuminate when and how collaboration can enhance memory.

  4. Validation of chimerism in pediatric recipients of allogeneic hematopoietic stem cell transplantation (HSCT) a comparison between two methods: real-time PCR (qPCR) vs. variable number tandem repeats PCR (VNTR PCR).

    Science.gov (United States)

    Kletzel, Morris; Huang, Wei; Olszewski, Marie; Khan, Sana

    2013-01-01

    Post-hematopoietic stem cell transplantation (HSCT) chimerism monitoring is important to assess relapse and therapeutic intervention. The purpose of our study is to compare two methods variable number tandem repeats (VNTR) vs. quantitative real- time polymerase chain reaction (qPCR) in terms of determining chimerism. 127 (peripheral blood n=112, bone marrow n=15) samples were simultaneously tested by VNTR using APO-B, D1S80, D1S111, D17S30, gene loci SRY and ZP3 and qPCR using 34 assays (CA001-CA034) that are designed to a bi-allelic insertion/deletion (indel) polymorphism in the human genome. Samples were separated in three subsets: total WBC, T-cell and Myeloid cells. Extraction of DNA was performed then quantified. We analyzed column statistics, paired t-test and regression analysis for both methods. There was complete correlation between the two methods. The simplicity and rapidity of the test results from the qPCR method is more efficient and accurate to assess chimerism.

  5. Node-pair reliability of network systems with small distances between adjacent nodes

    International Nuclear Information System (INIS)

    Malinowski, Jacek

    2007-01-01

    A new method for computing the node-pair reliability of network systems modeled by random graphs with nodes arranged in sequence is presented. It is based on a recursive algorithm using the 'sliding window' technique, the window being composed of several consecutive nodes. In a single step, the connectivity probabilities for all nodes included in the window are found. Subsequently, the window is moved one node forward. This process is repeated until, in the last step, the window reaches the terminal node. The connectivity probabilities found at that point are used to compute the node-pair reliability of the network system considered. The algorithm is designed especially for graphs with small distances between adjacent nodes, where the distance between two nodes is defined as the absolute value of the difference between the nodes' numbers. The maximal distance between any two adjacent nodes is denoted by Γ(G), where G symbolizes a random graph. If Γ(G)=2 then the method can be applied for directed as well as undirected graphs whose nodes and edges are subject to failure. This is important in view of the fact that many algorithms computing network reliability are designed for graphs with failure-prone edges and reliable nodes. If Γ(G)=3 then the method's applicability is limited to undirected graphs with reliable nodes. The main asset of the presented algorithms is their low numerical complexity-O(n), where n denotes the number of nodes

  6. Isolation and characterization of repeat elements of the oak genome and their application in population analysis

    International Nuclear Information System (INIS)

    Fluch, S.; Burg, K.

    1998-01-01

    Four minisatellite sequence elements have been identified and isolated from the genome of the oak species Quercus petraea and Quercus robur. Minisatellites 1 and 2 are putative members of repeat families, while minisatellites 3 and 4 show repeat length variation among individuals of test populations. A 590 base pair (bp) long element has also been identified which reveals individual-specific autoradiographic patterns when used as probe in Southern hybridisations of genomic oak DNA. (author)

  7. Revisiting Slow Slip Events Occurrence in Boso Peninsula, Japan, Combining GPS Data and Repeating Earthquakes Analysis

    Science.gov (United States)

    Gardonio, B.; Marsan, D.; Socquet, A.; Bouchon, M.; Jara, J.; Sun, Q.; Cotte, N.; Campillo, M.

    2018-02-01

    Slow slip events (SSEs) regularly occur near the Boso Peninsula, central Japan. Their time of recurrence has been decreasing from 6.4 to 2.2 years from 1996 to 2014. It is important to better constrain the slip history of this area, especially as models show that the recurrence intervals could become shorter prior to the occurrence of a large interplate earthquake nearby. We analyze the seismic waveforms of more than 2,900 events (M≥1.0) taking place in the Boso Peninsula, Japan, from 1 April 2004 to 4 November 2015, calculating the correlation and the coherence between each pair of events in order to define groups of repeating earthquakes. The cumulative number of repeating earthquakes suggests the existence of two slow slip events that have escaped detection so far. Small transient displacements observed in the time series of nearby GPS stations confirm these results. The detection scheme coupling repeating earthquakes and GPS analysis allow to detect small SSEs that were not seen before by classical methods. This work brings new information on the diversity of SSEs and demonstrates that the SSEs in Boso area present a more complex history than previously considered.

  8. Gene conversion homogenizes the CMT1A paralogous repeats

    Directory of Open Access Journals (Sweden)

    Hurles Matthew E

    2001-12-01

    Full Text Available Abstract Background Non-allelic homologous recombination between paralogous repeats is increasingly being recognized as a major mechanism causing both pathogenic microdeletions and duplications, and structural polymorphism in the human genome. It has recently been shown empirically that gene conversion can homogenize such repeats, resulting in longer stretches of absolute identity that may increase the rate of non-allelic homologous recombination. Results Here, a statistical test to detect gene conversion between pairs of non-coding sequences is presented. It is shown that the 24 kb Charcot-Marie-Tooth type 1A paralogous repeats (CMT1A-REPs exhibit the imprint of gene conversion processes whilst control orthologous sequences do not. In addition, Monte Carlo simulations of the evolutionary divergence of the CMT1A-REPs, incorporating two alternative models for gene conversion, generate repeats that are statistically indistinguishable from the observed repeats. Bounds are placed on the rate of these conversion processes, with central values of 1.3 × 10-4 and 5.1 × 10-5 per generation for the alternative models. Conclusions This evidence presented here suggests that gene conversion may have played an important role in the evolution of the CMT1A-REP paralogous repeats. The rates of these processes are such that it is probable that homogenized CMT1A-REPs are polymorphic within modern populations. Gene conversion processes are similarly likely to play an important role in the evolution of other segmental duplications and may influence the rate of non-allelic homologous recombination between them.

  9. Debiasing egocentrism and optimism biases in repeated competitions

    Directory of Open Access Journals (Sweden)

    Jason P. Rose

    2012-11-01

    Full Text Available When judging their likelihood of success in competitive tasks, people tend to be overoptimistic for easy tasks and overpessimistic for hard tasks (the shared circumstance effect; SCE. Previous research has shown that feedback and experience from repeated-play competitions has a limited impact on SCEs. However, in this paper, we suggest that competitive situations, in which the shared difficulty or easiness of the task is more transparent, will be more amenable to debiasing via repeated play. Pairs of participants competed in, made predictions about, and received feedback on, multiple rounds of a throwing task involving both easy- and hard-to-aim objects. Participants initially showed robust SCEs, but they also showed a significant reduction in bias after only one round of feedback. These and other results support a more positive view (than suggested from past research on the potential for SCEs to be debiased through outcome feedback.

  10. Dependence between the colour of galaxies in pairs (Holmberg effect)

    International Nuclear Information System (INIS)

    Demin, V.V.; Zasov, A.V.; Dibaj, Eh.A.; Tomov, A.N.

    1984-01-01

    Proceeding from the data of photoelectric photometpy by Tomov, the colours of galaxies in double systems are studied For the most of the paips formed by elliptical (EE) or by spiral (SS) galaxies, the difference between the corrected colour indices (B-V)sub(T)sup(0) of components does not exceed 0.10 and does not depend on the difference ΔT of their morphological types The correlation between the colours of galaxies in EE-pairs can be explained by the similaritins of element abundances but not of the luminosities of galaxies. The elliptical and SO-galaxies in pairs with the spiral galaxies ape noticeably bluep on the avepage. The relation between the colours of galaxies in ES-pairs is possible. The colours of early-type spiral galaxies (T < 4) in most of the SS-systems are more blue as compared to the mean colours of galaxies of the same type T. A similarity of the colours of the galaxies in many of the SS-pairs can be a result of the periodically repeated bursts of star formation which take place in both galaxies simultaneously

  11. Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation.

    Directory of Open Access Journals (Sweden)

    Noorain Khan

    2015-04-01

    Full Text Available Conformational polymorphism of DNA is a major causative factor behind several incurable trinucleotide repeat expansion disorders that arise from overexpansion of trinucleotide repeats located in coding/non-coding regions of specific genes. Hairpin DNA structures that are formed due to overexpansion of CAG repeat lead to Huntington's disorder and spinocerebellar ataxias. Nonetheless, DNA hairpin stem structure that generally embraces B-form with canonical base pairs is poorly understood in the context of periodic noncanonical A…A mismatch as found in CAG repeat overexpansion. Molecular dynamics simulations on DNA hairpin stems containing A…A mismatches in a CAG repeat overexpansion show that A…A dictates local Z-form irrespective of starting glycosyl conformation, in sharp contrast to canonical DNA duplex. Transition from B-to-Z is due to the mechanistic effect that originates from its pronounced nonisostericity with flanking canonical base pairs facilitated by base extrusion, backbone and/or base flipping. Based on these structural insights we envisage that such an unusual DNA structure of the CAG hairpin stem may have a role in disease pathogenesis. As this is the first study that delineates the influence of a single A…A mismatch in reversing DNA helicity, it would further have an impact on understanding DNA mismatch repair.

  12. Heritability of cortical thickness changes over time in twin pairs discordant for schizophrenia.

    Science.gov (United States)

    Hedman, Anna M; van Haren, Neeltje E M; van Baal, G Caroline M; Brouwer, Rachel M; Brans, Rachel G H; Schnack, Hugo G; Kahn, René S; Hulshoff Pol, Hilleke E

    2016-06-01

    Cortical thickness and surface area changes have repeatedly been found in schizophrenia. Whether progressive loss in cortical thickness and surface area are mediated by genetic or disease related factors is unknown. Here we investigate to what extent genetic and/or environmental factors contribute to the association between change in cortical thickness and surface area and liability to develop schizophrenia. Longitudinal magnetic resonance imaging study over a 5-year interval. Monozygotic (MZ) and dizygotic (DZ) twin pairs discordant for schizophrenia were compared with healthy control twin pairs using repeated measures analysis of variance (RM-ANOVA) and structural equation modeling (SEM). Twins discordant for schizophrenia and healthy control twins were recruited from the twin cohort at the University Medical Centre Utrecht, The Netherlands. A total of 90 individuals from 46 same sex twin pairs were included: 9 MZ and 10 DZ discordant for schizophrenia and 14 MZ and 13 (11 complete and 2 incomplete) DZ healthy twin-pairs. Age varied between 19 and 57years. Higher genetic liability for schizophrenia was associated with progressive global thinning of the cortex, particularly of the left superior temporal cortex. Higher environmental liability for schizophrenia was associated with global attenuated thinning of the cortex, and including of the left superior temporal cortex. Cortical surface area change was heritable, but not significantly associated with higher genetic or environmental liability for schizophrenia. Excessive cortical thinning, particularly of the left superior temporal cortex, may represent a genetic risk marker for schizophrenia. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Improved drug loading and antibacterial activity of minocycline-loaded PLGA nanoparticles prepared by solid/oil/water ion pairing method

    Science.gov (United States)

    Kashi, Tahereh Sadat Jafarzadeh; Eskandarion, Solmaz; Esfandyari-Manesh, Mehdi; Marashi, Seyyed Mahmoud Amin; Samadi, Nasrin; Fatemi, Seyyed Mostafa; Atyabi, Fatemeh; Eshraghi, Saeed; Dinarvand, Rassoul

    2012-01-01

    Background Low drug entrapment efficiency of hydrophilic drugs into poly(lactic-co-glycolic acid) (PLGA) nanoparticles is a major drawback. The objective of this work was to investigate different methods of producing PLGA nanoparticles containing minocycline, a drug suitable for periodontal infections. Methods Different methods, such as single and double solvent evaporation emulsion, ion pairing, and nanoprecipitation were used to prepare both PLGA and PEGylated PLGA nanoparticles. The resulting nanoparticles were analyzed for their morphology, particle size and size distribution, drug loading and entrapment efficiency, thermal properties, and antibacterial activity. Results The nanoparticles prepared in this study were spherical, with an average particle size of 85–424 nm. The entrapment efficiency of the nanoparticles prepared using different methods was as follows: solid/oil/water ion pairing (29.9%) > oil/oil (5.5%) > water/oil/water (4.7%) > modified oil/water (4.1%) > nano precipitation (0.8%). Addition of dextran sulfate as an ion pairing agent, acting as an ionic spacer between PEGylated PLGA and minocycline, decreased the water solubility of minocycline, hence increasing the drug entrapment efficiency. Entrapment efficiency was also increased when low molecular weight PLGA and high molecular weight dextran sulfate was used. Drug release studies performed in phosphate buffer at pH 7.4 indicated slow release of minocycline from 3 days to several weeks. On antibacterial analysis, the minimum inhibitory concentration and minimum bactericidal concentration of nanoparticles was at least two times lower than that of the free drug. Conclusion Novel minocycline-PEGylated PLGA nanoparticles prepared by the ion pairing method had the best drug loading and entrapment efficiency compared with other prepared nanoparticles. They also showed higher in vitro antibacterial activity than the free drug. PMID:22275837

  14. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

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

  15. Automated Potentiometric Titrations in KCl/Water-Saturated Octanol: Method for Quantifying Factors Influencing Ion-Pair Partitioning

    Science.gov (United States)

    2009-01-01

    The knowledge base of factors influencing ion pair partitioning is very sparse, primarily because of the difficulty in determining accurate log PI values of desirable low molecular weight (MW) reference compounds. We have developed a potentiometric titration procedure in KCl/water-saturated octanol that provides a link to log PI through the thermodynamic cycle of ionization and partitioning. These titrations have the advantage of being independent of the magnitude of log P, while maintaining a reproducibility of a few hundredths of a log P in the calculated difference between log P neutral and log P ion pair (diff (log PN − I)). Simple model compounds can be used. The titration procedure is described in detail, along with a program for calculating pKa′′ values incorporating the ionization of water in octanol. Hydrogen bonding and steric factors have a greater influence on ion pairs than they do on neutral species, yet these factors are missing from current programs used to calculate log PI and log D. In contrast to the common assumption that diff (log PN − I) is the same for all amines, they can actually vary more than 3 log units, as in our examples. A major factor affecting log PI is the ability of water and the counterion to approach the charge center. Bulky substituents near the charge center have a negative influence on log PI. On the other hand, hydrogen bonding groups near the charge center have the opposite effect by lowering the free energy of the ion pair. The use of this titration method to determine substituent ion pair stabilization values (IPS) should bring about more accurate log D calculations and encourage species-specific QSAR involving log DN and log DI. This work also brings attention to the fascinating world of nature’s highly stabilized ion pairs. PMID:19265385

  16. Automated potentiometric titrations in KCl/water-saturated octanol: method for quantifying factors influencing ion-pair partitioning.

    Science.gov (United States)

    Scherrer, Robert A; Donovan, Stephen F

    2009-04-01

    The knowledge base of factors influencing ion pair partitioning is very sparse, primarily because of the difficulty in determining accurate log P(I) values of desirable low molecular weight (MW) reference compounds. We have developed a potentiometric titration procedure in KCl/water-saturated octanol that provides a link to log P(I) through the thermodynamic cycle of ionization and partitioning. These titrations have the advantage of being independent of the magnitude of log P, while maintaining a reproducibility of a few hundredths of a log P in the calculated difference between log P neutral and log P ion pair (diff (log P(N - I))). Simple model compounds can be used. The titration procedure is described in detail, along with a program for calculating pK(a)'' values incorporating the ionization of water in octanol. Hydrogen bonding and steric factors have a greater influence on ion pairs than they do on neutral species, yet these factors are missing from current programs used to calculate log P(I) and log D. In contrast to the common assumption that diff (log P(N - I)) is the same for all amines, they can actually vary more than 3 log units, as in our examples. A major factor affecting log P(I) is the ability of water and the counterion to approach the charge center. Bulky substituents near the charge center have a negative influence on log P(I). On the other hand, hydrogen bonding groups near the charge center have the opposite effect by lowering the free energy of the ion pair. The use of this titration method to determine substituent ion pair stabilization values (IPS) should bring about more accurate log D calculations and encourage species-specific QSAR involving log D(N) and log D(I). This work also brings attention to the fascinating world of nature's highly stabilized ion pairs.

  17. A Multipoint Method for Detecting Genotyping Errors and Mutations in Sibling-Pair Linkage Data

    OpenAIRE

    Douglas, Julie A.; Boehnke, Michael; Lange, Kenneth

    2000-01-01

    The identification of genes contributing to complex diseases and quantitative traits requires genetic data of high fidelity, because undetected errors and mutations can profoundly affect linkage information. The recent emphasis on the use of the sibling-pair design eliminates or decreases the likelihood of detection of genotyping errors and marker mutations through apparent Mendelian incompatibilities or close double recombinants. In this article, we describe a hidden Markov method for detect...

  18. Sets of RNA repeated tags and hybridization-sensitive fluorescent probes for distinct images of RNA in a living cell.

    Directory of Open Access Journals (Sweden)

    Takeshi Kubota

    Full Text Available BACKGROUND: Imaging the behavior of RNA in a living cell is a powerful means for understanding RNA functions and acquiring spatiotemporal information in a single cell. For more distinct RNA imaging in a living cell, a more effective chemical method to fluorescently label RNA is now required. In addition, development of the technology labeling with different colors for different RNA would make it easier to analyze plural RNA strands expressing in a cell. METHODOLOGY/PRINCIPAL FINDINGS: Tag technology for RNA imaging in a living cell has been developed based on the unique chemical functions of exciton-controlled hybridization-sensitive oligonucleotide (ECHO probes. Repetitions of selected 18-nucleotide RNA tags were incorporated into the mRNA 3'-UTR. Pairs with complementary ECHO probes exhibited hybridization-sensitive fluorescence emission for the mRNA expressed in a living cell. The mRNA in a nucleus was detected clearly as fluorescent puncta, and the images of the expression of two mRNAs were obtained independently and simultaneously with two orthogonal tag-probe pairs. CONCLUSIONS/SIGNIFICANCE: A compact and repeated label has been developed for RNA imaging in a living cell, based on the photochemistry of ECHO probes. The pairs of an 18-nt RNA tag and the complementary ECHO probes are highly thermostable, sequence-specifically emissive, and orthogonal to each other. The nucleotide length necessary for one tag sequence is much shorter compared with conventional tag technologies, resulting in easy preparation of the tag sequences with a larger number of repeats for more distinct RNA imaging.

  19. Innovation of Methods for Measurement and Modelling of Twisted Pair Parameters

    Directory of Open Access Journals (Sweden)

    Lukas Cepa

    2011-01-01

    Full Text Available The goal of this paper is to optimize a measurement methodology for the most accurate broadband modelling of characteristic impedance and other parameters for twisted pairs. Measured values and theirs comparison is presented in this article. Automated measurement facility was implemented at the Department of telecommunication of Faculty of electrical engineering of Czech technical university in Prague. Measurement facility contains RF switches allowing measurements up to 300 MHz or 1GHz. Measured twisted pair’s parameters can be obtained by measurement but for purposes of fundamental characteristics modelling is useful to define functions that model the properties of the twisted pair. Its primary and secondary parameters depend mostly on the frequency. For twisted pair deployment, we are interested in a frequency band range from 1 MHz to 100 MHz.

  20. A comparative analysis of Painleve, Lax pair, and similarity transformation methods in obtaining the integrability conditions of nonlinear Schroedinger equations

    International Nuclear Information System (INIS)

    Al Khawaja, U.

    2010-01-01

    We derive the integrability conditions of nonautonomous nonlinear Schroedinger equations using the Lax pair and similarity transformation methods. We present a comparative analysis of these integrability conditions with those of the Painleve method. We show that while the Painleve integrability conditions restrict the dispersion, nonlinearity, and dissipation/gain coefficients to be space independent and the external potential to be only a quadratic function of position, the Lax Pair and the similarity transformation methods allow for space-dependent coefficients and an external potential that is not restricted to the quadratic form. The integrability conditions of the Painleve method are retrieved as a special case of our general integrability conditions. We also derive the integrability conditions of nonautonomous nonlinear Schroedinger equations for two- and three-spacial dimensions.

  1. Pavlovian conditioned approach, extinction, and spontaneous recovery to an audiovisual cue paired with an intravenous heroin infusion.

    Science.gov (United States)

    Peters, Jamie; De Vries, Taco J

    2014-01-01

    Novel stimuli paired with exposure to addictive drugs can elicit approach through Pavlovian learning. While such approach behavior, or sign tracking, has been documented for cocaine and alcohol, it has not been shown to occur with opiate drugs like heroin. Most Pavlovian conditioned approach paradigms use an operandum as the sign, so that sign tracking can be easily automated. We were interested in assessing whether approach behavior occurs to an audiovisual cue paired with an intravenous heroin infusion. If so, would this behavior exhibit characteristics of other Pavlovian conditioned behaviors, such as extinction and spontaneous recovery? Rats were repeatedly exposed to an audiovisual cue, similar to that used in standard self-administration models, along with an intravenous heroin infusion. Sign tracking was measured in an automated fashion by analyzing motion pixels within the cue zone during each cue presentation. We were able to observe significant sign tracking after only five pairings of the conditioned stimulus (CS) with the unconditioned stimulus (US). This behavior rapidly extinguished over 2 days, but exhibited pronounced spontaneous recovery 3 weeks later. We conclude that sign tracking measured by these methods exhibits all the characteristics of a classically conditioned behavior. This model can be used to examine the Pavlovian component of drug memories, alone, or in combination with self-administration methods.

  2. Detection-Discrimination Method for Multiple Repeater False Targets Based on Radar Polarization Echoes

    Directory of Open Access Journals (Sweden)

    Z. W. ZONG

    2014-04-01

    Full Text Available Multiple repeat false targets (RFTs, created by the digital radio frequency memory (DRFM system of jammer, are widely used in practical to effectively exhaust the limited tracking and discrimination resource of defence radar. In this paper, common characteristic of radar polarization echoes of multiple RFTs is used for target recognition. Based on the echoes from two receiving polarization channels, the instantaneous polarization radio (IPR is defined and its variance is derived by employing Taylor series expansion. A detection-discrimination method is designed based on probability grids. By using the data from microwave anechoic chamber, the detection threshold of the method is confirmed. Theoretical analysis and simulations indicate that the method is valid and feasible. Furthermore, the estimation performance of IPRs of RFTs due to the influence of signal noise ratio (SNR is also covered.

  3. Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription

    NARCIS (Netherlands)

    Berkhout, B.; Vastenhouw, N. L.; Klasens, B. I.; Huthoff, H.

    2001-01-01

    Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There

  4. An efficient quantum mechanical method for radical pair recombination reactions.

    Science.gov (United States)

    Lewis, Alan M; Fay, Thomas P; Manolopoulos, David E

    2016-12-28

    The standard quantum mechanical expressions for the singlet and triplet survival probabilities and product yields of a radical pair recombination reaction involve a trace over the states in a combined electronic and nuclear spin Hilbert space. If this trace is evaluated deterministically, by performing a separate time-dependent wavepacket calculation for each initial state in the Hilbert space, the computational effort scales as O(Z 2 log⁡Z), where Z is the total number of nuclear spin states. Here we show that the trace can also be evaluated stochastically, by exploiting the properties of spin coherent states. This results in a computational effort of O(MZlog⁡Z), where M is the number of Monte Carlo samples needed for convergence. Example calculations on a strongly coupled radical pair with Z>10 6 show that the singlet yield can be converged to graphical accuracy using just M=200 samples, resulting in a speed up by a factor of >5000 over a standard deterministic calculation. We expect that this factor will greatly facilitate future quantum mechanical simulations of a wide variety of radical pairs of interest in chemistry and biology.

  5. An Intelligent Model for Pairs Trading Using Genetic Algorithms.

    Science.gov (United States)

    Huang, Chien-Feng; Hsu, Chi-Jen; Chen, Chi-Chung; Chang, Bao Rong; Li, Chen-An

    2015-01-01

    Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

  6. Multicritical phase diagrams of the Blume-Emery-Griffiths model with repulsive biquadratic coupling including metastable phases: the pair approximation and the path probability method with pair distribution

    International Nuclear Information System (INIS)

    Keskin, Mustafa; Erdinc, Ahmet

    2004-01-01

    As a continuation of the previously published work, the pair approximation of the cluster variation method is applied to study the temperature dependences of the order parameters of the Blume-Emery-Griffiths model with repulsive biquadratic coupling on a body centered cubic lattice. We obtain metastable and unstable branches of the order parameters besides the stable branches and phase transitions of these branches are investigated extensively. We study the dynamics of the model by the path probability method with pair distribution in order to make sure that we find and define the metastable and unstable branches of the order parameters completely and correctly. We present the metastable phase diagram in addition to the equilibrium phase diagram and also the first-order phase transition line for the unstable branches of the quadrupole order parameter is superimposed on the phase diagrams. It is found that the metastable phase diagram and the first-order phase boundary for the unstable quadrupole order parameter always exist at the low temperatures which are consistent with experimental and theoretical works

  7. Deformed nuclear state as a quasiparticle-pair

    International Nuclear Information System (INIS)

    Dobaczewski, J.; Skalski, J.

    1988-01-01

    The deformed nuclear states, obtained in terms of the Hartree-Fock plus BCS method with the Skyrme SIII interaction, are approximated by condensates of the low-angular-momentum quasiparticle and particle pairs. The optimal pairs are determined by the variation after truncation method. The influence of the truncation on the deformation energy and the importance of the core-polarization effects are investigated

  8. QUANTITATIVE ION-PAIR EXTRACTION OF 4(5)-METHYLIMIDAZOLE FROM CARAMEL COLOR AND ITS DETERMINATION BY REVERSED-PHASE ION-PAIR LIQUID-CHROMATOGRAPHY

    DEFF Research Database (Denmark)

    Thomsen, Mohens; Willumsen, Dorthe

    1981-01-01

    A procedure for quantitative ion-pair extraction of 4(5)-methylimidazole from caramel colour using bis(2-ethylhexyl)phosphoric acid as ion-pairing agent has been developed. Furthermore, a reversed-phase ion-pair liquid chromatographic separation method has been established to analyse the content...

  9. Determination of subjective similarity for pairs of masses and pairs of clustered microcalcifications on mammograms: Comparison of similarity ranking scores and absolute similarity ratings

    International Nuclear Information System (INIS)

    Muramatsu, Chisako; Li Qiang; Schmidt, Robert A.; Shiraishi, Junji; Suzuki, Kenji; Newstead, Gillian M.; Doi, Kunio

    2007-01-01

    The presentation of images that are similar to that of an unknown lesion seen on a mammogram may be helpful for radiologists to correctly diagnose that lesion. For similar images to be useful, they must be quite similar from the radiologists' point of view. We have been trying to quantify the radiologists' impression of similarity for pairs of lesions and to establish a ''gold standard'' for development and evaluation of a computerized scheme for selecting such similar images. However, it is considered difficult to reliably and accurately determine similarity ratings, because they are subjective. In this study, we compared the subjective similarities obtained by two different methods, an absolute rating method and a 2-alternative forced-choice (2AFC) method, to demonstrate that reliable similarity ratings can be determined by the responses of a group of radiologists. The absolute similarity ratings were previously obtained for pairs of masses and pairs of microcalcifications from five and nine radiologists, respectively. In this study, similarity ranking scores for eight pairs of masses and eight pairs of microcalcifications were determined by use of the 2AFC method. In the first session, the eight pairs of masses and eight pairs of microcalcifications were grouped and compared separately for determining the similarity ranking scores. In the second session, another similarity ranking score was determined by use of mixed pairs, i.e., by comparison of the similarity of a mass pair with that of a calcification pair. Four pairs of masses and four pairs of microcalcifications were grouped together to create two sets of eight pairs. The average absolute similarity ratings and the average similarity ranking scores showed very good correlations in the first study (Pearson's correlation coefficients: 0.94 and 0.98 for masses and microcalcifications, respectively). Moreover, in the second study, the correlations between the absolute ratings and the ranking scores were also

  10. Franchise Values in North American Professional Sports Leagues: Evidence from a Repeat Sales Method

    OpenAIRE

    Brad R. Humphreys; Yang Seung Lee

    2009-01-01

    The paper develops a quality adjusted professional sports franchise price index for North America based on a repeat sale method. This index reflects trends in the general price of sports franchises holding local market, facility, and team characteristics constant. The price index exhibits considerable volatility but no upward trend over time, unlike previous quality adjusted price indexes based on hedonic models in the literature. The lack of an upward trend in this quality adjusted price ind...

  11. Film repeats in radiology department

    International Nuclear Information System (INIS)

    Suwan, A. Z.; Al-Shakharah, A. I

    1997-01-01

    During a one year period, 4910 radiographs of 55780 films were repeated. The objective of our study was to analyse and to classify the causes in order to minimize the repeats, cut the expenses and to provide optimal radiographs for accurate diagnosis. Analysis of the different factors revealed that, 43.6% of film repeats in our service were due to faults in exposure factors, centering comprises 15.9% of the repeats, while too much collimation was responsible for 7.6% of these repeats. All of which can be decreased by awareness and programmed training of technicians. Film blurring caused by patient motion was also responsible for 4.9% for radiographs reexamination, which can be minimized by detailed explanation to the patient and providing the necessary privacy. Fogging of X-Ray films by improper storage or inadequate handling or processing faults were responsible for 14.5% in repeats in our study. Methods and criteria for proper storage and handling of films were discussed. Recommendation for using modern day-light and laser processor has been high lighted. Artefacts are noticeably high in our cases, due to spinal dresses and frequent usage of precious metals for c osmotic purposes in this part of the world. The repeated films comprise 8.8% of all films We conclude that, the main factor responsible for repeats of up to 81.6% of cases was the technologists, thus emphasizing the importance of adequate training of the technologists. (authors). 15 refs., 9 figs., 1 table

  12. A simple and efficient method for assembling TALE protein based on plasmid library.

    Science.gov (United States)

    Zhang, Zhiqiang; Li, Duo; Xu, Huarong; Xin, Ying; Zhang, Tingting; Ma, Lixia; Wang, Xin; Chen, Zhilong; Zhang, Zhiying

    2013-01-01

    DNA binding domain of the transcription activator-like effectors (TALEs) from Xanthomonas sp. consists of tandem repeats that can be rearranged according to a simple cipher to target new DNA sequences with high DNA-binding specificity. This technology has been successfully applied in varieties of species for genome engineering. However, assembling long TALE tandem repeats remains a big challenge precluding wide use of this technology. Although several new methodologies for efficiently assembling TALE repeats have been recently reported, all of them require either sophisticated facilities or skilled technicians to carry them out. Here, we described a simple and efficient method for generating customized TALE nucleases (TALENs) and TALE transcription factors (TALE-TFs) based on TALE repeat tetramer library. A tetramer library consisting of 256 tetramers covers all possible combinations of 4 base pairs. A set of unique primers was designed for amplification of these tetramers. PCR products were assembled by one step of digestion/ligation reaction. 12 TALE constructs including 4 TALEN pairs targeted to mouse Gt(ROSA)26Sor gene and mouse Mstn gene sequences as well as 4 TALE-TF constructs targeted to mouse Oct4, c-Myc, Klf4 and Sox2 gene promoter sequences were generated by using our method. The construction routines took 3 days and parallel constructions were available. The rate of positive clones during colony PCR verification was 64% on average. Sequencing results suggested that all TALE constructs were performed with high successful rate. This is a rapid and cost-efficient method using the most common enzymes and facilities with a high success rate.

  13. 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.

  14. Intra-examiner repeatability and agreement in accommodative response measurements.

    Science.gov (United States)

    Antona, B; Sanchez, I; Barrio, A; Barra, F; Gonzalez, E

    2009-11-01

    Clinical measurement of the accommodative response (AR) identifies the focusing plane of a subject with respect to the accommodative target. To establish whether a significant change in AR has occurred, it is important to determine the repeatability of this measurement. This study had two aims: First, to determine the intraexaminer repeatability of AR measurements using four clinical methods: Nott retinoscopy, monocular estimate method (MEM) retinoscopy, binocular crossed cylinder test (BCC) and near autorefractometry. Second, to study the level of agreement between AR measurements obtained with the different methods. The AR of the right eye at one accommodative demand of 2.50 D (40 cm) was measured on two separate occasions in 61 visually normal subjects of mean age 19.7 years (range 18-32 years). The intraexaminer repeatability of the tests, and agreement between them, were estimated by the Bland-Altman method. We determined mean differences (MD) and the 95% limits of agreement [coefficient of repeatability (COR) and coefficient of agreement (COA)]. Nott retinoscopy and BCC offered the best repeatability, showing the lowest MD and narrowest 95% interval of agreement (Nott: -0.10 +/- 0.66 D, BCC: -0.05 +/- 0.75 D). The 95% limits of agreement for the four techniques were similar (COA = +/- 0.92 to +/-1.00 D) yet clinically significant, according to the expected values of the AR. The two dynamic retinoscopy techniques (Nott and MEM) had a better agreement (COA = +/-0.64 D) although this COA must be interpreted in the context of the low MEM repeatability (COR = +/-0.98 D). The best method of assessing AR was Nott retinoscopy. The BCC technique was also repeatable, and both are recommended as suitable methods for clinical use. Despite better agreement between MEM and Nott, agreement among the remaining methods was poor such that their interchangeable use in clinical practice is not recommended.

  15. Behavioral sensitization after repeated formaldehyde exposure in rats.

    Science.gov (United States)

    Sorg, B A; Hochstatter, T

    1999-01-01

    Multiple chemical sensitivity (MCS) is a phenomenon whereby individuals report increased sensitivity to chemicals in the environment, and attribute their sensitivities to prior exposure to the same or often structurally unrelated chemicals. A leading hypothesis suggests that MCS is akin to behavioral sensitization observed in rodents after repeated exposure to drugs of abuse or environmental stressors. Sensitization occurring within limbic circuitry of the central nervous system (CNS) may explain the multisymptom complaints in individuals with MCS. The present studies represent the continuing development of an animal model for MCS, the basis of which is the CNS sensitization hypothesis. Three behaviors were assessed in rats repeatedly exposed to formaldehyde (Form) inhalation. In the first series of experiments, rats were given high-dose Form exposure (11 parts per million [ppm]; 1 h/day x 7 days) or low-dose Form exposure (1 ppm; either 1 h/day x 7 days or 1 h/day x 5 days/week x 4 weeks). Within a few days after discontinuing daily Form, cocaine-induced locomotor activity was elevated after high-dose Form or 20 days of low-dose Form inhalation. Approximately 1 month later, cocaine-induced locomotor activity remained significantly elevated in the 20-day Form-exposed rats. The second experiment assessed whether prior exposure to Form (20 days, as above) would alter the ability to condition to an odor (orange oil) paired with footshock. The results suggested a tendency to increase the conditioned fear response to the odor but not the context of the footshock box, and a decreased tendency to extinguish the conditioned fear response to odor. The third experiment examined whether CNS sensitization to daily cocaine or stress would alter subsequent avoidance responding to odor (Form). Daily cocaine significantly elevated approach responses to Form, while daily stress pretreatment produced a trend in the opposite direction, producing greater avoidance of Form. Preliminary

  16. Paired-Associate Learning in Young and Old Adults as Related to Stimulus Concreteness and Presentation Method

    Science.gov (United States)

    Witte, Kenneth L.; Freund, Joel S.

    1976-01-01

    Investigated the learning of young and old adults as related to two variables, stimulus concreteness (low vs. high) and presentation method (recall vs. multiple choice vs. associate matching). Main findings were: (a) the elderly did not perform as well as young adults, (b) for both groups, performance was better for the pairs with concrete…

  17. In situ detection of tandem DNA repeat length

    Energy Technology Data Exchange (ETDEWEB)

    Yaar, R.; Szafranski, P.; Cantor, C.R.; Smith, C.L. [Boston Univ., MA (United States)

    1996-11-01

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

  18. 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.

  19. Ion-pair cloud-point extraction: a new method for the determination of water-soluble vitamins in plasma and urine.

    Science.gov (United States)

    Heydari, Rouhollah; Elyasi, Najmeh S

    2014-10-01

    A novel, simple, and effective ion-pair cloud-point extraction coupled with a gradient high-performance liquid chromatography method was developed for determination of thiamine (vitamin B1 ), niacinamide (vitamin B3 ), pyridoxine (vitamin B6 ), and riboflavin (vitamin B2 ) in plasma and urine samples. The extraction and separation of vitamins were achieved based on an ion-pair formation approach between these ionizable analytes and 1-heptanesulfonic acid sodium salt as an ion-pairing agent. Influential variables on the ion-pair cloud-point extraction efficiency, such as the ion-pairing agent concentration, ionic strength, pH, volume of Triton X-100, extraction temperature, and incubation time have been fully evaluated and optimized. Water-soluble vitamins were successfully extracted by 1-heptanesulfonic acid sodium salt (0.2% w/v) as ion-pairing agent with Triton X-100 (4% w/v) as surfactant phase at 50°C for 10 min. The calibration curves showed good linearity (r(2) > 0.9916) and precision in the concentration ranges of 1-50 μg/mL for thiamine and niacinamide, 5-100 μg/mL for pyridoxine, and 0.5-20 μg/mL for riboflavin. The recoveries were in the range of 78.0-88.0% with relative standard deviations ranging from 6.2 to 8.2%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Tetranucleotide repeat polymorphism at the human prostatic acid phosphatase (ACPP) gene

    Energy Technology Data Exchange (ETDEWEB)

    Polymeropoulos, M H; Xiao, Hong; Rath, D S; Merril, C R [National Inst. of Mental Health Neuroscience Center, Washington, DC (United States)

    1991-09-11

    The polymorphic (AAAT){sub n} repeat begins at base pair 2342 of the human prostatic acid phosphatase gene on chromosome 3q21-qter. The polymorphism can be typed using the polymerase chain reaction (PCR) as described previously. The predicted length of the amplified sequence was 275 bp. Co-dominant segregation was observed in two informative families. The human prostatic acid phosphatase gene has been assigned to chromosome 3q21-qter.

  1. Identification and characterization of short tandem repeats in the Tibetan macaque genome based on resequencing data.

    Science.gov (United States)

    Liu, San-Xu; Hou, Wei; Zhang, Xue-Yan; Peng, Chang-Jun; Yue, Bi-Song; Fan, Zhen-Xin; Li, Jing

    2018-07-18

    The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (lobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (Pgenome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.

  2. Neurobiology of pair bonding in fishes; convergence of neural mechanisms across distant vertebrate lineages

    KAUST Repository

    Nowicki, Jessica; Pratchett, Morgan; Walker, Stefan; Coker, Darren James; O'Connell, Lauren A.

    2017-01-01

    Pair bonding has independently evolved numerous times among vertebrates. The governing neural mechanisms of pair bonding have only been studied in depth in the mammalian model species, the prairie vole, Microtus ochrogaster. In this species, oxytocin (OT), arginine vasopressin (AVP), dopamine (DA), and opioid (OP) systems play key roles in signaling in the formation and maintenance of pair bonding by targeting specific social and reward-mediating brain regions. By contrast, the neural basis of pair bonding is poorly studied in other vertebrates, and especially those of early origins, limiting our understanding of the evolutionary history of pair bonding regulatory mechanisms. We compared receptor gene expression between pair bonded and solitary individuals across eight socio-functional brain regions. We found that in females, ITR and V1aR receptor expression varied in the lateral septum-like region (the Vv/Vl), while in both sexes D1R, D2R, and MOR expression varied within the mesolimbic reward system, including a striatum-like region (the Vc); mirroring sites of action in M. ochrogaster. This study provides novel insights into the neurobiology of teleost pair bonding. It also reveals high convergence in the neurochemical mechanisms governing pair bonding across actinopterygians and sarcopterygians, by repeatedly co-opting and similarly assembling deep neurochemical and neuroanatomical homologies that originated in ancestral osteithes.

  3. Neurobiology of pair bonding in fishes; convergence of neural mechanisms across distant vertebrate lineages

    KAUST Repository

    Nowicki, Jessica

    2017-11-14

    Pair bonding has independently evolved numerous times among vertebrates. The governing neural mechanisms of pair bonding have only been studied in depth in the mammalian model species, the prairie vole, Microtus ochrogaster. In this species, oxytocin (OT), arginine vasopressin (AVP), dopamine (DA), and opioid (OP) systems play key roles in signaling in the formation and maintenance of pair bonding by targeting specific social and reward-mediating brain regions. By contrast, the neural basis of pair bonding is poorly studied in other vertebrates, and especially those of early origins, limiting our understanding of the evolutionary history of pair bonding regulatory mechanisms. We compared receptor gene expression between pair bonded and solitary individuals across eight socio-functional brain regions. We found that in females, ITR and V1aR receptor expression varied in the lateral septum-like region (the Vv/Vl), while in both sexes D1R, D2R, and MOR expression varied within the mesolimbic reward system, including a striatum-like region (the Vc); mirroring sites of action in M. ochrogaster. This study provides novel insights into the neurobiology of teleost pair bonding. It also reveals high convergence in the neurochemical mechanisms governing pair bonding across actinopterygians and sarcopterygians, by repeatedly co-opting and similarly assembling deep neurochemical and neuroanatomical homologies that originated in ancestral osteithes.

  4. Selection of candidate plus phenotypes of Jatropha curcas L. using method of paired comparisons

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, D.K. [Silviculture Division, Arid Forest Research Institute, P.O. Krishi Mandi, New Pali Road, Jodhpur 342005, Rajasthan (India)

    2009-03-15

    Jatropha curcas L. (Euphorbiaceae) is an oil bearing species with multiple uses and considerable potential as a biodiesel crop. The present communication deals with the method of selecting plus phenotypes of J. curcas for exploiting genetic variability for further improvement. Candidate plus tree selection is the first and most important stage in any tree improvement programme. The selection of candidate plus plants (CPPs) is based upon various important attributes associated with the species and their relative ranking. Relative preference between various traits and scoring for each trait has been worked out by using the method of paired comparisons for the selection of CPP in J. curcas L. The most important ones are seed and oil yields. (author)

  5. Nuclear scissors mode with pairing

    International Nuclear Information System (INIS)

    Balbutsev, E. B.; Malov, L. A.; Schuck, P.; Urban, M.; Vinas, X.

    2008-01-01

    The coupled dynamics of the scissors mode and the isovector giant quadrupole resonance are studied using a generalized Wigner function moments method, taking into account pair correlations. Equations of motion for angular momentum, quadrupole moment, and other relevant collective variables are derived on the basis of the time-dependent Hartree-Fock-Bogolyubov equations. Analytical expressions for energy centroids and transition probabilities are found for the harmonic-oscillator model with the quadrupole-quadrupole residual interaction and monopole pairing force. Deformation dependences of energies and B(M1) values are correctly reproduced. The inclusion of pair correlations leads to a drastic improvement in the description of qualitative and quantitative characteristics of the scissors mode.

  6. Selection pressure on human STR loci and its relevance in repeat expansion disease

    KAUST Repository

    Shimada, Makoto K.

    2016-06-11

    Short Tandem Repeats (STRs) comprise repeats of one to several base pairs. Because of the high mutability due to strand slippage during DNA synthesis, rapid evolutionary change in the number of repeating units directly shapes the range of repeat-number variation according to selection pressure. However, the remaining questions include: Why are STRs causing repeat expansion diseases maintained in the human population; and why are these limited to neurodegenerative diseases? By evaluating the genome-wide selection pressure on STRs using the database we constructed, we identified two different patterns of relationship in repeat-number polymorphisms between DNA and amino-acid sequences, although both patterns are evolutionary consequences of avoiding the formation of harmful long STRs. First, a mixture of degenerate codons is represented in poly-proline (poly-P) repeats. Second, long poly-glutamine (poly-Q) repeats are favored at the protein level; however, at the DNA level, STRs encoding long poly-Qs are frequently divided by synonymous SNPs. Furthermore, significant enrichments of apoptosis and neurodevelopment were biological processes found specifically in genes encoding poly-Qs with repeat polymorphism. This suggests the existence of a specific molecular function for polymorphic and/or long poly-Q stretches. Given that the poly-Qs causing expansion diseases were longer than other poly-Qs, even in healthy subjects, our results indicate that the evolutionary benefits of long and/or polymorphic poly-Q stretches outweigh the risks of long CAG repeats predisposing to pathological hyper-expansions. Molecular pathways in neurodevelopment requiring long and polymorphic poly-Q stretches may provide a clue to understanding why poly-Q expansion diseases are limited to neurodegenerative diseases. © 2016, Springer-Verlag Berlin Heidelberg.

  7. Unique TTC repeat base pair loss mutation in cases of pure neural leprosy: A survival strategy of Mycobacterium leprae?

    Directory of Open Access Journals (Sweden)

    Abhishek De

    2015-01-01

    Full Text Available Background: Genomic reduction helps obligate intracellular microbes to survive difficult host niches. Adaptation of Mycobacterium leprae in cases of pure neural leprosy (PNL in the intracellular niche of peripheral nerves can be associated with some gene loss. Recently, a stable but variable number of tandem repefzats (TTC have been reported in strains of M. leprae. FolP and rpoB genes are the two common mutation sites which deal with the susceptibility of the bacteria to drugs. Aim: We attempted to find if genomic reduction of M. leprae in context of these TTC repeats or mutations in folP1 and rpoB can be the reason for the restriction of M. leprae in the nerves in PNL. Materials and Methods: DNA extracts taken from fine needle aspiration of affected nerves of 24 PNL cases were studied for tandem repeats with 21TTC primer in multiplex-PCR. Mutations were also studied by PCR Amplification of SRDR (Sulphone Resistance Determining Region of the folP1 and multiple primer PCR amplification refractory mutation system (MARS of the rpoB. Results: Of the 24 PNL, only 1 patient showed mutation in the rpoB gene and none in the folp1 gene. Studying the mutation in TTC region of the M. leprae gene we found that all the cases have a loss of a few bases in the sequence. Conclusion: We can conclude that there is consistent loss in the bases in the TTC region in all cases of pure neural Hansen and we postulate that it may be an adaptive response of the bacteria to survive host niche resulting in its restriction to peripheral nerves.

  8. Repeatability of tumour hypoxia imaging using [{sup 18}F]EF5 PET/CT in head and neck cancer

    Energy Technology Data Exchange (ETDEWEB)

    Silvoniemi, Antti [University of Turku, Turku PET Centre (Finland); Turku University Hospital, Department of Otorhinolaryngology - Head and Neck Surgery (Finland); Suilamo, Sami [Turku University Hospital, Department of Oncology and Radiotherapy (Finland); Turku University Hospital, Department of Medical Physics (Finland); Laitinen, Timo; Forsback, Sarita; Solin, Olof [University of Turku, Turku PET Centre (Finland); Loeyttyniemi, Eliisa [University of Turku, Department of Biostatistics, Turku (Finland); Vaittinen, Samuli [Turku University Hospital, Department of Pathology (Finland); Saunavaara, Virva [University of Turku, Turku PET Centre (Finland); Turku University Hospital, Department of Medical Physics (Finland); Groenroos, Tove J.; Minn, Heikki [University of Turku, Turku PET Centre (Finland); Turku University Hospital, Department of Oncology and Radiotherapy (Finland)

    2018-02-15

    Hypoxia contributes to radiotherapy resistance and more aggressive behaviour of several types of cancer. This study was designed to evaluate the repeatability of intratumour uptake of the hypoxia tracer [{sup 18}F]EF5 in paired PET/CT scans. Ten patients with newly diagnosed head and neck cancer (HNC) received three static PET/CT scans before chemoradiotherapy: two with [{sup 18}F]EF5 a median of 7 days apart and one with [{sup 18}F]FDG. Metabolically active primary tumour volumes were defined in [{sup 18}F]FDG images and transferred to co-registered [{sup 18}F]EF5 images for repeatability analysis. A tumour-to-muscle uptake ratio (TMR) of 1.5 at 3 h from injection of [{sup 18}F]EF5 was used as a threshold representing hypoxic tissue. In 10 paired [{sup 18}F]EF5 PET/CT image sets, SUVmean, SUVmax, and TMR showed a good correlation with the intraclass correlation coefficients of 0.81, 0.85, and 0.87, respectively. The relative coefficients of repeatability for these parameters were 15%, 17%, and 10%, respectively. Fractional hypoxic volumes of the tumours in the repeated scans had a high correlation using the Spearman rank correlation test (r = 0.94). In a voxel-by-voxel TMR analysis between the repeated scans, the mean of Pearson correlation coefficients of individual patients was 0.65. The mean (± SD) difference of TMR in the pooled data set was 0.03 ± 0.20. Pretreatment [{sup 18}F]EF5 PET/CT within one week shows high repeatability and is feasible for the guiding of hypoxia-targeted treatment interventions in HNC. (orig.)

  9. Percutaneous evacuation (PEVAC) of multivesicular echinococcal cysts with or without cystobiliary fistulas which contain non-drainable material: first results of a modified PAIR method

    NARCIS (Netherlands)

    Schipper, H. G.; Laméris, J. S.; van Delden, O. M.; Rauws, E. A.; Kager, P. A.

    2002-01-01

    Background: Surgery is the treatment of choice in echinococcal cysts with cystobiliary fistulas. PAIR (puncture, aspiration, injection, and reaspiration of scolecidals) is contraindicated in these cases. Aim: To evaluate a modified PAIR method for percutoneous treatment of multivesicular

  10. Repeat Assessed Values Model for Housing Price Index

    Directory of Open Access Journals (Sweden)

    Carini Manuela

    2017-12-01

    Full Text Available This study proposes an innovative methodology, named Repeat Appraised Price Model (RAV, useful for determining the price index numbers for real estate markets and the corresponding index numbers of hedonic prices of main real estate characteristics in the case of a lack of data. The methodological approach proposed in this paper aims to appraise the time series of price index numbers. It integrates the principles of the method of repeat sales with the peculiarities of the Hedonic Price Method, overcoming the problem of an almost total absence of repeat sales for the same property in a given time range; on the other hand, the technique aims to overcome the limitation of the repeat sales technique concerning the inability to take into account the characteristics of individual properties.

  11. A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions.

    Science.gov (United States)

    Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon

    2017-07-17

    Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

  12. NxRepair: error correction in de novo sequence assembly using Nextera mate pairs

    Directory of Open Access Journals (Sweden)

    Rebecca R. Murphy

    2015-06-01

    Full Text Available Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.

  13. High spin exotic states and new method for pairing energy; Etats exotiques a hauts spins et nouvelle methode pour l`energie d`appariement nucleaire

    Energy Technology Data Exchange (ETDEWEB)

    Molique, H.

    1996-01-19

    We present a new method called `PSY-MB`, initially developed in the framework of abstract group theory for the solution of the problem of strongly interacting multi-fermionic systems with particular to systems in an external rotating field. The validity of the new method (PSY-MB) is tested on model Hamiltonians. A detailed comparison between the obtained solutions and the exact ones is performed. The new method is used in the study of realistic nuclear Hamiltonians based on the Woods-Saxon potential within the cranking approximation to study the influence of residual monopole pairing interactions in the rare-earth mass region. In parallel with this new technique we present original results obtained with the Woods-Saxon mean-field and the self-consistent Hartree-Fock approximation in order to investigate such exotic effects as octupole deformations and hexadecapole C{sub 4}-polarizing deformations in the framework of high-spin physics. By developing these three approaches in one single work we prepare the ground for the nuclear structure calculations of the new generation - where the residual two-body interactions are taken into account also in the weak pairing limit. (author). 2370refs.

  14. [Comparative study on promoting blood effects of Danshen-Honghua herb pair with different preparations based on chemometrics and multi-attribute comprehensive index methods].

    Science.gov (United States)

    Qu, Cheng; Tang, Yu-Ping; Shi, Xu-Qin; Zhou, Gui-Sheng; Shang, Er-Xin; Shang, Li-Li; Guo, Jian-Ming; Liu, Pei; Zhao, Jing; Zhao, Bu-Chang; Duan, Jin-Ao

    2017-08-01

    To evaluate the promoting blood circulation and removing blood stasis effects of Danshen-Honghua(DH) herb pair with different preparations (alcohol, 50% alcohol and water) on blood rheology and coagulation functions in acute blood stasis rats, and optimize the best preparation method of DH based on principal component analysis(PCA), hierarchical cluster heatmap analysis and multi-attribute comprehensive index methods. Ice water bath and subcutaneous injection of adrenaline were both used to establish the acute blood stasis rat model. Then the blood stasis rats were administrated intragastrically with DH (alcohol, 50% alcohol and water) extracts. The whole blood viscosity(WBV), plasma viscosity(PV), erythrocyte sedimentation rate(ESR) and haematocrit(HCT) were tested to observe the effects of DH herb pair with different preparations and doses on hemorheology of blood stasis rats; the activated partial thromboplastin time(APTT), thrombin time(TT), prothrombin time(PT), and plasma fibrinogen(FIB) were tested to observe the effects of DH herb pair with different preparations on blood coagulation function and platelet aggregation of blood stasis rats. Then PCA, hierarchical cluster heatmap analysis and multi-attribute comprehensive index methods were all used to comprehensively evaluate the total promoting blood circulation and removing blood stasis effects of DH herb pair with different preparations. The hemorheological indexes and coagulation parameters of model group had significant differences with normal blank group. As compared with the model group, the DH herb pair with different preparations at low, middle and high doses could improve the blood hemorheology indexes and coagulation parameters in acute blood stasis rats with dose-effect relation. Based on the PCA, hierarchical cluster heatmap analysis and multi-attribute comprehensive index methods, the high dose group of 50% alcohol extract had the best effect of promoting blood circulation and removing blood

  15. Clinical oversight and the avoidance of repeat induced abortion.

    Science.gov (United States)

    Jacovetty, Erica L; Clare, Camille A; Squire, Mary-Beatrice; Kubal, Keshar P; Liou, Sherry; Inchiosa, Mario A

    2018-06-03

    To evaluate the impact of patient counseling, demographics, and contraceptive methods on repeat induced abortion in women attending family planning clinics. A retrospective chart review of repeat induced abortions was performed. The analysis included patients with an initial induced abortion obtained between January 1, 2001, and March 31, 2014, at New York City Health + Hospitals/Metropolitan. The duration of involvement in the family planning program, the use of contraceptive interventions, and 18 patient factors were analyzed for their correlation with the incidence of repeat induced abortions per year of follow-up. A decreased rate of repeat induced abortions was associated with a longer duration of clinical oversight (r 2 =0.449, Pabortions. By determining the patient characteristics that most influence repeat induced abortion rates, providers can best choose the most efficacious method of contraception available. © 2018 International Federation of Gynecology and Obstetrics.

  16. Modeling age differences in effects of pair repetition and proactive interference using a single parameter.

    Science.gov (United States)

    Stephens, Joseph D W; Overman, Amy A

    2018-02-01

    In this article, we apply the REM model (Shiffrin & Steyvers, 1997) to age differences in associative memory. Using Criss and Shiffrin's (2005) associative version of REM, we show that in a task with pairs repeated across 2 study lists, older adults' reduced benefit of pair repetition can be produced by a general reduction in the diagnosticity of information stored in memory. This reduction can be modeled similarly well by reducing the overall distinctiveness of memory features, or by reducing the accuracy of memory encoding. We report a new experiment in which pairs are repeated across 3 study lists and extend the model accordingly. Finally, we extend the model to previously reported data using the same task paradigm, in which the use of a high-association strategy introduced proactive interference effects in young adults but not older adults. Reducing the diagnosticity of information in memory also reduces the proactive interference effect. Taken together, the modeling and empirical results reported here are consistent with the claim that some age differences that appear to be specific to associative information can be produced via general degradation of information stored in memory. The REM model provides a useful framework for examining age differences in memory as well as harmonizing seemingly conflicting prior modeling approaches for the associative deficit. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  17. Pairing in Cold Atoms and other Applications for Quantum Monte Carlo methods

    International Nuclear Information System (INIS)

    Bajdich, Michal; Kolorenc, Jindrich; Mitas, Lubos; Reynolds, P.J.

    2010-01-01

    We discuss the importance of the fermion nodes for the quantum Monte Carlo (QMC) methods and find two cases of the exact nodes. We describe the structure of the generalized pairing wave functions in Pfaffian antisymmetric form and demonstrate their equivalency with certain class of configuration interaction wave functions. We present the QMC calculations of a model fermion system at unitary limit. We find the system to have the energy of E = 0.425Efree and the condensate fraction of = 0.48. Further we also perform the QMC calculations of the potential energy surface and the electric dipole moment along that surface of the LiSr molecule. We estimate the vibrationally averaged dipole moment to be D =0 = 0.4(2).

  18. Lax pairs: a novel type of separability

    International Nuclear Information System (INIS)

    Fokas, A S

    2009-01-01

    An attempt is made to place into historical context the fundamental concept of Lax pairs. For economy of presentation, emphasis is placed on the effectiveness of Lax pairs for the analysis of integrable nonlinear evolution PDEs. It is argued that Lax pairs provide a deeper type of separability than the classical separation of variables. Indeed, it is shown that: (a) the solution of the Cauchy problem of evolution equations is based on the derivation of a nonlinear Fourier transform pair, and this is achieved by employing the spectral analysis of one of the two eigenvalue equations forming a Lax pair; thus, although this methodology still follows the reverent philosophy of the classical separation of variables and transform methods, it can be applied to a class of nonlinear PDEs. (b) The solution of initial-boundary-value problems of evolution equations is based on the simultaneous spectral analysis of both equations forming a Lax pair and hence, in a sense, it employs the synthesis instead of the separation of variables; this methodology does not have a direct classical analogue, however, it can be considered as the nonlinearization of a method which combines Green's function classical integral representations with an analogue of the method of images, but which are now formulated in the spectral (Fourier) instead of the physical space. In addition to presenting a general methodology for analysing initial- and initial-boundary-value problems for nonlinear integrable evolution equations in one and two spatial variables, recent progress is reviewed for the derivation and the solution of integrable nonlinear evolution PDEs formulated in higher than two spatial dimensions. (topical review)

  19. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

    Science.gov (United States)

    Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

    2017-04-01

    There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

  20. Non-radioactive detection of trinucleotide repeat size variability.

    Science.gov (United States)

    Tomé, Stéphanie; Nicole, Annie; Gomes-Pereira, Mario; Gourdon, Genevieve

    2014-03-06

    Many human diseases are associated with the abnormal expansion of unstable trinucleotide repeat sequences. The mechanisms of trinucleotide repeat size mutation have not been fully dissected, and their understanding must be grounded on the detailed analysis of repeat size distributions in human tissues and animal models. Small-pool PCR (SP-PCR) is a robust, highly sensitive and efficient PCR-based approach to assess the levels of repeat size variation, providing both quantitative and qualitative data. The method relies on the amplification of a very low number of DNA molecules, through sucessive dilution of a stock genomic DNA solution. Radioactive Southern blot hybridization is sensitive enough to detect SP-PCR products derived from single template molecules, separated by agarose gel electrophoresis and transferred onto DNA membranes. We describe a variation of the detection method that uses digoxigenin-labelled locked nucleic acid probes. This protocol keeps the sensitivity of the original method, while eliminating the health risks associated with the manipulation of radiolabelled probes, and the burden associated with their regulation, manipulation and waste disposal.

  1. Vital signs: Repeat births among teens - United States, 2007-2010.

    Science.gov (United States)

    2013-04-05

    Teen childbearing has potential negative health, economic, and social consequences for mother and child. Repeat teen childbearing further constrains the mother's education and employment possibilities. Rates of preterm and low birth weight are higher in teens with a repeat birth, compared with first births. To assess patterns of repeat childbearing and postpartum contraceptive use among teens, CDC analyzed natality data from the National Vital Statistics System (NVSS) and the Pregnancy Risk Assessment Monitoring System (PRAMS) from 2007-2010. Based on 2010 NVSS data from all 50 states and the District of Columbia, of more than 367,000 births to teens aged 15-19 years, 18.3% were repeat births. The percentage of teen births that represented repeat births decreased by 6.2% between 2007 and 2010. Disparities in repeat teen births exist by race/ethnicity, with the highest percentages found among American Indian/Alaska Natives (21.6%), Hispanics (20.9%), and non-Hispanic blacks (20.4%) and lowest among non-Hispanic whites (14.8%). Wide geographic disparities in the percentage of teen births that were repeat births also exist, ranging from 22% in Texas to 10% in New Hampshire. PRAMS data from 16 reporting areas (15 states and New York City) indicate that 91.2% of teen mothers used a contraceptive method 2-6 months after giving birth, but only 22.4% of teen mothers used the most effective methods. Teens with a previous live birth were significantly more likely to use the most effective methods postpartum compared with those with no prior live birth (29.6% versus 20.9%, respectively). Non-Hispanic white and Hispanic teens were significantly more likely to use the most effective methods than non-Hispanic black teens (24.6% and 27.9% versus 14.3%, respectively). The percentage of teens reporting postpartum use of the most effective methods varied greatly geographically across the PRAMS reporting areas, ranging from 50.3% in Colorado to 7.2% in New York State. Although the

  2. A new image reconstruction method for 3-D PET based upon pairs of near-missing lines of response

    Energy Technology Data Exchange (ETDEWEB)

    Kawatsu, Shoji [Department of Radiology, Kyoritu General Hospital, 4-33 Go-bancho, Atsuta-ku, Nagoya-shi, Aichi 456-8611 (Japan) and Department of Brain Science and Molecular Imaging, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 36-3, Gengo Moriaka-cho, Obu-shi, Aichi 474-8522 (Japan)]. E-mail: b6rgw@fantasy.plala.or.jp; Ushiroya, Noboru [Department of General Education, Wakayama National College of Technology, 77 Noshima, Nada-cho, Gobo-shi, Wakayama 644-0023 (Japan)

    2007-02-01

    We formerly introduced a new image reconstruction method for three-dimensional positron emission tomography, which is based upon pairs of near-missing lines of response. This method uses an elementary geometric property of lines of response, namely that two lines of response which originate from radioactive isotopes located within a sufficiently small voxel, will lie within a few millimeters of each other. The effectiveness of this method was verified by performing a simulation using GATE software and a digital Hoffman phantom.

  3. Evaluation of tetranucleotide repeat locus D7S809 (wg1g9) in the Japanese population.

    Science.gov (United States)

    Tamaki, K; Huang, X L; Nozawa, H; Yamamoto, T; Uchihi, R; Katsumata, Y; Armour, J A

    1996-08-15

    The tetrameric short tandem repeat (STR) locus (D7S809) has been evaluated in the Japanese population. In order to detect the alleles, PCR was carried out using primers, one of which was end labelled with 32P, and PCR products were separated by electrophoresis on a denaturing polyacrylamide gel. Using this method, accurate genotypes could be determined from as little as 0.5 ng of genomic DNA. Thirteen different alleles were identified on 256 chromosomes tested. All alleles differed in size by one (4 bp) repeat unit, and no "interalleles' were found. The estimated heterozygosity and the polymorphism information content (PIC) were 0.86 and 0.83, respectively. We observed 42 of the 91 possible different genotypes. The power of discrimination (PD) was 0.96, and no significant deviations from the Hardy-Weinberg equilibrium were found. We retyped all apparently homozygous samples using an alternative pair of flanking primers in order to confirm homozygosity. We also demonstrated a typing result involving sexual assault. D7S809 appears to be a very useful STR locus for forensic practice in Japanese.

  4. Paired-pulse flash-visual evoked potentials: new methods revive an old test.

    Science.gov (United States)

    Cantello, Roberto; Strigaro, Gionata; Prandi, Paolo; Varrasi, Claudia; Mula, Marco; Monaco, Francesco

    2011-08-01

    We aimed at reviving with modern technology the paired flash-visual evoked potential (F-VEP) testing of the visual system excitability. In the 1960s, methodological problems hindered this test, which was expected to provide important physiologic information. We studied 22 consenting healthy subjects (10 men). We recorded F-VEPs from electrodes over occipital and central brain regions. We delivered single flashes, mixed at random to flash pairs at the interstimulus interval (ISI) of 333, 125, 62.5, 50, 33, and 16.5 ms, (i.e. an internal frequency (IF) of 3, 8, 16, 20, 30, and 60 Hz). Recordings were performed with the subject's eyes closed and opened. The F-VEP was split into a "main complex" and an "afterdischarge", which we analyzed statistically in relation to the eye state (closed or open) and to the changes due to paired stimulation. The eye state affected the single F-VEP size, latency and shape significantly (p<0.05). On paired stimulation, the test (second) F-VEP exhibited significant (p<0.05), ISI-dependent size changes, such as a progressive decrease for ISIs from 62.5 to 16.5 ms (IFs of 16-60 Hz), whose timing/amount varied significantly (p<0.05) according to the eye state and to the F-VEP epoch considered. Suppression of the test F-VEP was never complete, even for the shortest ISI (ISI=16.5 ms, IF=60 Hz). The eye state (closed or open) must be considered meticulously when studying F-VEPs. F-VEP changes on paired stimulation express neural inhibition within the visual system, which can be depicted as ISI-dependent curves. Modern equipment and simplified measures render this an easy test, with statistical validity, providing specific information on the excitability properties of the visual system. Copyright © 2011 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  5. Plasmid P1 replication: negative control by repeated DNA sequences.

    OpenAIRE

    Chattoraj, D; Cordes, K; Abeles, A

    1984-01-01

    The incompatibility locus, incA, of the unit-copy plasmid P1 is contained within a fragment that is essentially a set of nine 19-base-pair repeats. One or more copies of the fragment destabilizes the plasmid when present in trans. Here we show that extra copies of incA interfere with plasmid DNA replication and that a deletion of most of incA increases plasmid copy number. Thus, incA is not essential for replication but is required for its control. When cloned in a high-copy-number vector, pi...

  6. Design of a rotary dielectric elastomer actuator using a topology optimization method based on pairs of curves

    Science.gov (United States)

    Wang, Nianfeng; Guo, Hao; Chen, Bicheng; Cui, Chaoyu; Zhang, Xianmin

    2018-05-01

    Dielectric elastomers (DE), known as electromechanical transducers, have been widely used in the field of sensors, generators, actuators and energy harvesting for decades. A large number of DE actuators including bending actuators, linear actuators and rotational actuators have been designed utilizing an experience design method. This paper proposes a new method for the design of DE actuators by using a topology optimization method based on pairs of curves. First, theoretical modeling and optimization design are discussed, after which a rotary dielectric elastomer actuator has been designed using this optimization method. Finally, experiments and comparisons between several DE actuators have been made to verify the optimized result.

  7. The benefits of paired-agent imaging in molecular-guided surgery: an update on methods and applications (Conference Presentation)

    Science.gov (United States)

    Tichauer, Kenneth M.

    2016-03-01

    One of the major complications with conventional imaging-agent-based molecular imaging, particularly for cancer imaging, is variability in agent delivery and nonspecific retention in biological tissue. Such factors can account to "swamp" the signal arising from specifically bound imaging agent, which is presumably indicative of the concentration of targeted biomolecule. In the 1950s, Pressman et al. proposed a method of accounting for these delivery and retention effects by normalizing targeted antibody retention to the retention of a co-administered "untargeted"/control imaging agent [1]. Our group resurrected the approach within the last 5 years, finding ways to utilize this so-called "paired-agent" imaging approach to directly quantify biomolecule concentration in tissue (in vitro, ex vivo, and in vivo) [2]. These novel paired-agent imaging approaches capable of quantifying biomolecule concentration provide enormous potential for being adapted to and optimizing molecular-guided surgery, which has a principle goal of identifying distinct biological tissues (tumor, nerves, etc…) based on their distinct molecular environment. This presentation will cover the principles and nuances of paired-agent imaging, as well as the current status of the field and future applications. [1] D. Pressman, E. D. Day, and M. Blau, "The use of paired labeling in the determination of tumor-localizing antibodies," Cancer Res, 17(9), 845-50 (1957). [2] K. M. Tichauer, Y. Wang, B. W. Pogue et al., "Quantitative in vivo cell-surface receptor imaging in oncology: kinetic modeling and paired-agent principles from nuclear medicine and optical imaging," Phys Med Biol, 60(14), R239-69 (2015).

  8. Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography—Tandem Mass Spectrometry

    Science.gov (United States)

    Tabb, David L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Variyath, Asokan Mulayath; Ham, Amy-Joan L.; Bunk, David M.; Kilpatrick, Lisa E.; Billheimer, Dean D.; Blackman, Ronald K.; Cardasis, Helene L.; Carr, Steven A.; Clauser, Karl R.; Jaffe, Jacob D.; Kowalski, Kevin A.; Neubert, Thomas A.; Regnier, Fred E.; Schilling, Birgit; Tegeler, Tony J.; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fisher, Susan J.; Gibson, Bradford W.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Steven E.; Tempst, Paul; Paulovich, Amanda G.; Liebler, Daniel C.; Spiegelman, Cliff

    2009-01-01

    The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35–60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind

  9. Recommendations for analysis of repeated-measures designs: testing and correcting for sphericity and use of manova and mixed model analysis.

    Science.gov (United States)

    Armstrong, Richard A

    2017-09-01

    A common experimental design in ophthalmic research is the repeated-measures design in which at least one variable is a within-subject factor. This design is vulnerable to lack of 'sphericity' which assumes that the variances of the differences among all possible pairs of within-subject means are equal. Traditionally, this design has been analysed using a repeated-measures analysis of variance (RM-anova) but increasingly more complex methods such as multivariate anova (manova) and mixed model analysis (MMA) are being used. This article surveys current practice in the analysis of designs incorporating different factors in research articles published in three optometric journals, namely Ophthalmic and Physiological Optics (OPO), Optometry and Vision Science (OVS), and Clinical and Experimental Optometry (CXO), and provides advice to authors regarding the analysis of repeated-measures designs. Of the total sample of articles, 66% used a repeated-measures design. Of those articles using a repeated-measures design, 59% and 8% analysed the data using RM-anova or manova respectively and 33% used MMA. The use of MMA relative to RM-anova has increased significantly since 2009/10. A further search using terms to select those papers testing and correcting for sphericity ('Mauchly's test', 'Greenhouse-Geisser', 'Huynh and Feld') identified 66 articles, 62% of which were published from 2012 to the present. If the design is balanced without missing data then manova should be used rather than RM-anova as it gives better protection against lack of sphericity. If the design is unbalanced or with missing data then MMA is the method of choice. However, MMA is a more complex analysis and can be difficult to set up and run, and care should be taken first, to define appropriate models to be tested and second, to ensure that sample sizes are adequate. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

  10. Changing US Attributes After CS-US Pairings Changes CS-Attribute-Assessments: Evidence for CS-US Associations in Attribute Conditioning.

    Science.gov (United States)

    Förderer, Sabine; Unkelbach, Christian

    2016-03-01

    Attribute Conditioning (AC) refers to people's changed assessments of stimuli's (CSs) attributes due to repeated pairing with stimuli (USs) possessing these attributes; for example, when an athletic person (US) is paired with a neutral person (CS), the neutral person is judged to be more athletic after the pairing. We hypothesize that this AC effect is due to CSs' associations with USs rather than direct associations with attributes. Three experiments test this hypothesis by changing US attributes after CS-US pairings. Experiments 1 and 2 conditioned athleticism by pairing neutral men (CSs) with athletic and non-athletic USs. Post-conditioning, USs' athleticism was reversed, which systematically influenced participants' assessment of CS athleticism. Experiment 3 conditioned athleticism and changed USs' musicality after CS-US pairings. This post-conditioning change affected musicality assessments of CSs but did not influence athleticism-assessments. The results indicate that AC effects are based on an associative CS-US-attribute structure. © 2016 by the Society for Personality and Social Psychology, Inc.

  11. Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.

    Directory of Open Access Journals (Sweden)

    Gabriela Moura

    Full Text Available BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.

  12. Pairing renormalization and regularization within the local density approximation

    International Nuclear Information System (INIS)

    Borycki, P.J.; Dobaczewski, J.; Nazarewicz, W.; Stoitsov, M.V.

    2006-01-01

    We discuss methods used in mean-field theories to treat pairing correlations within the local density approximation. Pairing renormalization and regularization procedures are compared in spherical and deformed nuclei. Both prescriptions give fairly similar results, although the theoretical motivation, simplicity, and stability of the regularization procedure make it a method of choice for future applications

  13. Repeatability and heritability of reproductive traits in free-ranging snakes.

    Science.gov (United States)

    Brown, G P; Shine, R

    2007-03-01

    The underlying genetic basis of life-history traits in free-ranging animals is critical to the effects of selection on such traits, but logistical constraints mean that such data are rarely available. Our long-term ecological studies on free-ranging oviparous snakes (keelbacks, Tropidonophis mairii (Gray, 1841), Colubridae) on an Australian floodplain provide the first such data for any tropical reptile. All size-corrected reproductive traits (egg mass, clutch size, clutch mass and post-partum maternal mass) were moderately repeatable between pairs of clutches produced by 69 female snakes after intervals of 49-1152 days, perhaps because maternal body condition was similar between clutches. Parent-offspring regression of reproductive traits of 59 pairs of mothers and daughters revealed high heritability for egg mass (h2= 0.73, SE=0.24), whereas heritability for the other three traits was low (snakes occurs because each female snake must allocate a finite amount of energy into eggs of a genetically determined size.

  14. Alternative Conformations of the Tau Repeat Domain in Complex with an Engineered Binding Protein*

    Science.gov (United States)

    Grüning, Clara S. R.; Mirecka, Ewa A.; Klein, Antonia N.; Mandelkow, Eckhard; Willbold, Dieter; Marino, Stephen F.; Stoldt, Matthias; Hoyer, Wolfgang

    2014-01-01

    The aggregation of Tau into paired helical filaments is involved in the pathogenesis of several neurodegenerative diseases, including Alzheimer disease. The aggregation reaction is characterized by conformational conversion of the repeat domain, which partially adopts a cross-β-structure in the resulting amyloid-like fibrils. Here, we report the selection and characterization of an engineered binding protein, β-wrapin TP4, targeting the Tau repeat domain. TP4 was obtained by phage display using the four-repeat Tau construct K18ΔK280 as a target. TP4 binds K18ΔK280 as well as the longest isoform of human Tau, hTau40, with nanomolar affinity. NMR spectroscopy identified two alternative TP4-binding sites in the four-repeat domain, with each including two hexapeptide motifs with high β-sheet propensity. Both binding sites contain the aggregation-determining PHF6 hexapeptide within repeat 3. In addition, one binding site includes the PHF6* hexapeptide within repeat 2, whereas the other includes the corresponding hexapeptide Tau(337–342) within repeat 4, denoted PHF6**. Comparison of TP4-binding with Tau aggregation reveals that the same regions of Tau are involved in both processes. TP4 inhibits Tau aggregation at substoichiometric concentration, demonstrating that it interferes with aggregation nucleation. This study provides residue-level insight into the interaction of Tau with an aggregation inhibitor and highlights the structural flexibility of Tau. PMID:24966331

  15. Galactic Pairs in the Early Universe

    Science.gov (United States)

    Kohler, Susanna

    2018-02-01

    ,000 objects. They find that roughly 50 have a redshift of z 7, and 22 have a redshift of z 8. None of the galaxies at z 7 are in pairs, but the sample at z 8 includes three groups for which the distance between galaxies is less than 1 arcsecond.But are these three pairs actual merging galaxies?Conclusions from StatisticsTop: Gas density at z 7.7 in the authors simulation output. Bottom: Mock observations of this output withHubbles WFC3 (left) and JWSTs NIRCam (right). [Adapted from Chaikin et al. 2018]To answer this question, the authors next perform numerical simulations of galaxy formation and produce mock observations showing what the simulatedfield would look like in an equivalent deep Hubble exposure.Based on their simulation statistics, Chaikin and collaborators argue that the three pairs at z 8 do represent an unusually high merger fraction but projection coincidences or lensing are far less likely scenarios to account for all three pairs. If the three pairs are indeed all merging galaxies, it could indicate that this Hubble field corresponds to a local overdensity at a redshift of z 8.Looking AheadThe best way to improve on these measurements is to repeat this study with more advanced telescopes. Chaikin and collaborators demonstrate the superiority of the observations that the upcoming James Webb Space Telescope (JWST) will provide. They also point out the potential power of the Wide Field Infrared Survey Telescope (WFIRST) currently under threat under the proposed 2019 federal budget to extend the observational horizon well into the epoch of reionization.Continued studies backed by the power of these future telescopes are sure to discover a wealth of additional distant galactic duos, helping us to characterize the universe in its early stages.CitationEvgenii A. Chaikin et al 2018 ApJ 853 81. doi:10.3847/1538-4357/aaa196

  16. Reject/repeat analysis and the effect prior film viewing has on a department's reject/repeat rate

    International Nuclear Information System (INIS)

    Clark, P.A.; Hogg, P.

    2003-01-01

    Purpose: Achieving cost-effectiveness within the NHS is an old initiative but one that has again been highlighted by recent government policies (The New NHS-Modern and Dependable, Stationary Office, London, 1997). It has been reiterated that it is the responsibility of individual Trusts to devise means to provide such a service. Reject/repeat analyses have long been the primary tool used to assess the cost-effectiveness of radiography departments (Quality Assurance in Diagnostic Radiology, WHO, Geneva, 1982). This research paper examines an in-house initiative (viewing patients' previous films) commonly employed in other Health Trusts in order to reduce departmental repeat/reject rates. Method: Three hundred orthopaedic patients with hip, knee and ankle prostheses were included in a reject/repeat analysis. The aim was to investigate whether or not viewing patient's previous relevant radiographs would be advantageous to the practicing radiographer. This was done through an audit cycle consisting of two audit periods each lasting for 3 months. The primary audit period recorded the baseline repeat/reject rate, with the secondary audit period recording the repeat/reject rate under an experimental condition of viewing the relevant radiographs. Results: The baseline audit revealed repeat rates of 33% in orthopaedic patients with hip, knee and ankle prostheses. The availability of prior film viewing to the radiographer reduced this repeat rate to 10.6%. Conclusion: Prior film viewing dramatically reduced the department's repeat/reject rate by 22.4%. This provides scope for significant patient dose reductions as well as reducing departmental film expenses. This is an underestimated initiative and should be used appropriately in routine clinical practice

  17. Rank error-correcting pairs

    DEFF Research Database (Denmark)

    Martinez Peñas, Umberto; Pellikaan, Ruud

    2017-01-01

    Error-correcting pairs were introduced as a general method of decoding linear codes with respect to the Hamming metric using coordinatewise products of vectors, and are used for many well-known families of codes. In this paper, we define new types of vector products, extending the coordinatewise ...

  18. Pairing gaps from nuclear mean-field models

    International Nuclear Information System (INIS)

    Bender, M.; Rutz, K.; Maruhn, J.A.

    2000-01-01

    We discuss the pairing gap, a measure for nuclear pairing correlations, in chains of spherical, semi-magic nuclei in the framework of self-consistent nuclear mean-field models. The equations for the conventional BCS model and the approximate projection-before-variation Lipkin-Nogami method are formulated in terms of local density functionals for the effective interaction. We calculate the Lipkin-Nogami corrections of both the mean-field energy and the pairing energy. Various definitions of the pairing gap are discussed as three-point, four-point and five-point mass-difference formulae, averaged matrix elements of the pairing potential, and single-quasiparticle energies. Experimental values for the pairing gap are compared with calculations employing both a delta pairing force and a density-dependent delta interaction in the BCS and Lipkin-Nogami model. Odd-mass nuclei are calculated in the spherical blocking approximation which neglects part of the the core polarization in the odd nucleus. We find that the five-point mass difference formula gives a very robust description of the odd-even staggering, other approximations for the gap may differ from that up to 30% for certain nuclei. (orig.)

  19. Transient Analysis of Dispersive Power-Ground Plate Pairs With Arbitrarily Shaped Antipads by the DGTD Method With Wave Port Excitation

    KAUST Repository

    Li, Ping; Jiang, Li Jun; Bagci, Hakan

    2016-01-01

    A discontinuous Galerkin time-domain (DGTD) method analyzing signal/power integrity on multilayered power-ground parallel plate pairs is proposed. The excitation is realized by introducing wave ports on the antipads where electric/magnetic current

  20. Facile fabrication of controllable zinc oxide nanorod clusters on polyacrylonitrile nanofibers via repeatedly alternating immersion method

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Ying; Li, Xia; Yu, Hou-Yong, E-mail: phdyu@zstu.edu.cn [Zhejiang Sci-Tech University, The Key Laboratory of Advanced Textile Materials and Manufacturing Technology of Ministry of Education, College of Materials and Textiles (China); Hu, Guo-Liang; Yao, Ju-Ming, E-mail: yaoj@zstu.edu.cn [Zhejiang Sci-Tech University, National Engineering Lab for Textile Fiber Materials and Processing Technology (China)

    2016-12-15

    Polyacrylonitrile/zinc oxide (PAN/ZnO) composite nanofiber membranes with different ZnO morphologies were fabricated by repeatedly alternating hot–cold immersion and single alternating hot–cold immersion methods. The influence of the PAN/ZnCl{sub 2} ratio and different immersion methods on the morphology, microstructure, and properties of the nanofiber membranes was investigated by using field-emission scanning electron microscopy (FE-SEM), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) analysis, thermogravimetric analysis (TGA), and ultraviolet–visible (UV–Vis) spectroscopy. A possible mechanism for different morphologies of PAN/ZnO nanofiber membranes with different PAN/ZnCl{sub 2} ratio through different immersion processes was presented, and well-dispersed ZnO nanorod clusters with smallest average dimeter of 115 nm and hexagonal wurtzite structure were successfully anchored onto the PAN nanofiber surface for R-7/1 nanofiber membrane. Compared to S-5/1 prepared by single alternating hot–cold immersion method, the PAN/ZnO nanofiber membrane fabricated by repeatedly alternating hot–cold immersion method (especially for R-7/1) showed improved thermal stability and high photocatalytic activity for methylene blue (MB). Compared to S-5/1, decomposition temperature at 5% weight loss (T{sub 5%}) was increased by 43 °C from 282 to 325 °C for R-7/1; meanwhile, R-7/1 showed higher photocatalytic degradation ratio of approximately 100% (after UV light irradiation for 8 h) than 65% for S-5/1 even after irradiation for 14 h. Moreover, the degradation efficiency of R-7/1 with good reuse stability remained above 94% after 3 cycles.

  1. Variable flip angle 3D ultrashort echo time (UTE) T1 mapping of mouse lung: A repeatability assessment.

    Science.gov (United States)

    Alamidi, Daniel F; Smailagic, Amir; Bidar, Abdel W; Parker, Nicole S; Olsson, Marita; Hockings, Paul D; Lagerstrand, Kerstin M; Olsson, Lars E

    2018-03-08

    Lung T 1 is a potential translational biomarker of lung disease. The precision and repeatability of variable flip angle (VFA) T 1 mapping using modern 3D ultrashort echo time (UTE) imaging of the whole lung needs to be established before it can be used to assess response to disease and therapy. To evaluate the feasibility of regional lung T 1 quantification with VFA 3D-UTE and to investigate long- and short-term T 1 repeatability in the lungs of naive mice. Prospective preclinical animal study. Eight naive mice and phantoms. 3D free-breathing radial UTE (8 μs) at 4.7T. VFA 3D-UTE T 1 calculations were validated against T 1 values measured with inversion recovery (IR) in phantoms. Lung T 1 and proton density (S 0 ) measurements of whole lung and muscle were repeated five times over 1 month in free-breathing naive mice. Two consecutive T 1 measurements were performed during one of the imaging sessions. Agreement in T 1 between VFA 3D-UTE and IR in phantoms was assessed using Bland-Altman and Pearson 's correlation analysis. The T 1 repeatability in mice was evaluated using coefficient of variation (CV), repeated-measures analysis of variance (ANOVA), and paired t-test. Good T 1 agreement between the VFA 3D-UTE and IR methods was found in phantoms. T 1 in lung and muscle showed a 5% and 3% CV (1255 ± 63 msec and 1432 ± 42 msec, respectively, mean ± SD) with no changes in T 1 or S 0 over a month. Consecutive measurements resulted in an increase of 2% in both lung T 1 and S 0 . VFA 3D-UTE shows promise as a reliable T 1 mapping method that enables full lung coverage, high signal-to-noise ratio (∼25), and spatial resolution (300 μm) in freely breathing animals. The precision of the VFA 3D-UTE method will enable better design and powering of studies. 1 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

  2. Classical reconstruction of interference patterns of position-wave-vector-entangled photon pairs by the time-reversal method

    Science.gov (United States)

    Ogawa, Kazuhisa; Kobayashi, Hirokazu; Tomita, Akihisa

    2018-02-01

    The quantum interference of entangled photons forms a key phenomenon underlying various quantum-optical technologies. It is known that the quantum interference patterns of entangled photon pairs can be reconstructed classically by the time-reversal method; however, the time-reversal method has been applied only to time-frequency-entangled two-photon systems in previous experiments. Here, we apply the time-reversal method to the position-wave-vector-entangled two-photon systems: the two-photon Young interferometer and the two-photon beam focusing system. We experimentally demonstrate that the time-reversed systems classically reconstruct the same interference patterns as the position-wave-vector-entangled two-photon systems.

  3. Patterns of hand preference for pairs of actions and the classification of handedness.

    Science.gov (United States)

    Annett, Marian

    2009-08-01

    Pairs of actions such as write x throw and throw x racquet were examined for items of the Annett hand preference questionnaire (AHPQ). Right (R) and left (L) responses were described for frequencies of RR, RL, LR, and LL pairings (write x throw etc.) in a large representative combined sample with the aim of discovering the distribution over the population as a whole. The frequencies of RL pairings varied significantly over the different item pairs but the frequencies of LR pairings were fairly constant. An important difference was found between primary actions (originally write, throw, racquet, match, toothbrush, hammer with the later addition of scissors for right-handers) and non-primary actions (needle and thread, broom, spade, dealing playing cards, and unscrewing the lid of a jar). For primary actions, there were similar numbers of right and left writers using the 'other' hand. For non-primary actions more right-handers used the left hand than for primary actions but more left-handers did not use the right hand. That is, different frequencies of response to primary versus non-primary actions were found for right-handers but not for left-handers. The pattern of findings was repeated for a corresponding analysis of left-handed throwing x AHPQ actions. The findings have implications for the classification of hand preferences and for analyses of the nature of hand skill.

  4. Effect of pairing on nuclear dynamics

    International Nuclear Information System (INIS)

    Scamps, Guillaume

    2014-01-01

    Pairing correlations is an essential component for the description of the atomic nuclei. The effects of pairing on static property of nuclei are now well known. In this thesis, the effect of pairing on nuclear dynamics is investigated. Theories that includes pairing are benchmarked in a model case. The TDHF+BCS theory turns out to be a good compromise between the physics taken into account and the numerical cost. This TDHF+BCS theory was retained for realistic calculations. Nevertheless, the application of pairing in the BCS approximation may induce new problems due to (1) the particle number symmetry breaking, (2) the non-conservation of the continuity equation. These difficulties are analysed in detail and solutions are proposed. In this thesis, a 3 dimensional TDHF+BCS code is developed to simulate the nuclear dynamic. Applications to giant resonances show that pairing modify only the low lying peaks. The high lying collective components are only affected by the initial conditions. An exhaustive study of the giant quadrupole resonances with the TDHF+BCS theory is performed on more than 700 spherical or deformed nuclei. Is is shown that the TDHF+BCS theory reproduces well the collective energy of the resonance. After validation on the small amplitude limit problem, the approach was applied to study nucleon transfer in heavy ion reactions. A new method to extract transfer probabilities is introduced. It is demonstrated that pairing significantly increases the two-nucleon transfer probability. (author) [fr

  5. Performance Comparisons of Improved Regular Repeat Accumulate (RA and Irregular Repeat Accumulate (IRA Turbo Decoding

    Directory of Open Access Journals (Sweden)

    Ahmed Abdulkadhim Hamad

    2017-08-01

    Full Text Available In this paper, different techniques are used to improve the turbo decoding of regular repeat accumulate (RA and irregular repeat accumulate (IRA codes. The adaptive scaling of a-posteriori information produced by Soft-output Viterbi decoder (SOVA is proposed. The encoded pilots are another scheme that applied for short length RA codes. This work also suggests a simple and a fast method to generate a random interleaver having a free 4 cycle Tanner graph. Progressive edge growth algorithm (PEG is also studied and simulated to create the Tanner graphs which have a great girth.

  6. Modulation of Human Corticospinal Excitability by Paired Associative Stimulation

    Directory of Open Access Journals (Sweden)

    Richard G. Carson

    2013-12-01

    Full Text Available Paired Associative Stimulation (PAS has come to prominence as a potential therapeutic intervention for the treatment of brain injury/disease, and as an experimental method with which to investigate Hebbian principles of neural plasticity in humans. Prototypically, a single electrical stimulus is directed to a peripheral nerve in advance of transcranial magnetic stimulation (TMS delivered to the contralateral primary motor cortex (M1. Repeated pairing of the stimuli (i.e. association over an extended period may increase or decrease the excitability of corticospinal projections from M1, in manner that depends on the interstimulus interval (ISI. It has been suggested that these effects represent a form of associative long-term potentiation (LTP and depression (LTD that bears resemblance to spike-timing dependent plasticity (STDP as it has been elaborated in animal models. With a large body of empirical evidence having emerged since the cardinal features of PAS were first described, and in light of the variations from the original protocols that have been implemented, it is opportune to consider whether the phenomenology of PAS remains consistent with the characteristic features that were initially disclosed. This assessment necessarily has bearing upon interpretation of the effects of PAS in relation to the specific cellular pathways that are putatively engaged, including those that adhere to the rules of STDP. The balance of evidence suggests that the mechanisms that contribute to the LTP- and LTD-type responses to PAS differ depending on the precise nature of the induction protocol that is used. In addition to emphasising the requirement for additional explanatory models, in the present analysis we highlight the key features of the PAS phenomenology that require interpretation.

  7. Generalized pairing strategies-a bridge from pairing strategies to colorings

    Directory of Open Access Journals (Sweden)

    Győrffy Lajos

    2016-12-01

    Full Text Available In this paper we define a bridge between pairings and colorings of the hypergraphs by introducing a generalization of pairs called t-cakes for t ∈ ℕ, t ≥ 2. For t = 2 the 2-cakes are the same as the well-known pairs of system of distinct representatives, that can be turned to pairing strategies in Maker-Breaker hypergraph games, see Hales and Jewett [12]. The two-colorings are the other extremity of t-cakes, in which the whole ground set of the hypergraph is one big cake that we divide into two parts (color classes. Starting from the pairings (2-cake placement and two-colorings we define the generalized t-cake placements where we pair p elements by q elements (p, q ∈ ℕ, 1 ≤ p, q < t, p + q = t.

  8. Isovectorial pairing in solvable and algebraic models

    International Nuclear Information System (INIS)

    Lerma, Sergio; Vargas, Carlos E; Hirsch, Jorge G

    2011-01-01

    Schematic interactions are useful to gain some insight in the behavior of very complicated systems such as the atomic nuclei. Prototypical examples are, in this context, the pairing interaction and the quadrupole interaction of the Elliot model. In this contribution the interplay between isovectorial pairing, spin-orbit, and quadrupole terms in a harmonic oscillator shell (the so-called pairing-plus-quadrupole model) is studied by algebraic methods. The ability of this model to provide a realistic description of N = Z even-even nuclei in the fp-shell is illustrated with 44 Ti. Our calculations which derive from schematic and simple terms confirm earlier conclusions obtained by using realistic interactions: the SU(3) symmetry of the quadrupole term is broken mainly by the spin-orbit term, but the energies depends strongly on pairing.

  9. Repeatability of cervical joint flexion and extension within and between days

    DEFF Research Database (Denmark)

    Wang, Xu; Lindstroem, René; Plocharski, Maciej

    2018-01-01

    OBJECTIVE: The purpose of this study was to investigate within- and between-day repeatability of free and unrestricted healthy cervical flexion and extension motion when assessing dynamic cervical spine motion. METHODS: Fluoroscopy videos of 2 repeated cervical flexion and 2 repeated extension...

  10. Impaired intracortical transmission in G2019S leucine rich-repeat kinase Parkinson patients.

    Science.gov (United States)

    Ponzo, Viviana; Di Lorenzo, Francesco; Brusa, Livia; Schirinzi, Tommaso; Battistini, Stefania; Ricci, Claudia; Sambucci, Manolo; Caltagirone, Carlo; Koch, Giacomo

    2017-05-01

    A mutation in leucine-rich repeat kinase 2 is the most common cause of hereditary Parkinson's disease (PD), yet the neural mechanisms and the circuitry potentially involved are poorly understood. We used different transcranial magnetic stimulation protocols to explore in the primary motor cortex the activity of intracortical circuits and cortical plasticity (long-term potentiation) in patients with the G2019S leucine-rich repeat kinase 2 gene mutation when compared with idiopathic PD patients and age-matched healthy subjects. Paired pulse transcranial magnetic stimulation was used to investigate short intracortical inhibition and facilitation and short afferent inhibition. Intermittent theta burst stimulation, a form of repetitive transcranial magnetic stimulation, was used to test long-term potentiation-like cortical plasticity. Leucine-rich repeat kinase 2 and idiopathic PD were tested both in ON and in OFF l-dopa therapy. When compared with idiopathic PD and healthy subjects, leucine-rich repeat kinase 2 PD patients showed a remarkable reduction of short intracortical inhibition in both ON and in OFF l-dopa therapy. This reduction was paralleled by an increase of intracortical facilitation in OFF l-dopa therapy. Leucine-rich repeat kinase 2 PD showed abnormal long-term potentiation-like cortical plasticity in ON l-dopa therapy. The motor cortex in leucine-rich repeat kinase 2 mutated PD patients is strongly disinhibited and hyperexcitable. These abnormalities could be a result of an impairment of inhibitory (gamma-Aminobutyric acid) transmission eventually related to altered neurotransmitter release. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

  11. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats.

    Science.gov (United States)

    Armour, John A L; Palla, Raquel; Zeeuwen, Patrick L J M; den Heijer, Martin; Schalkwijk, Joost; Hollox, Edward J

    2007-01-01

    Recent work has demonstrated an unexpected prevalence of copy number variation in the human genome, and has highlighted the part this variation may play in predisposition to common phenotypes. Some important genes vary in number over a high range (e.g. DEFB4, which commonly varies between two and seven copies), and have posed formidable technical challenges for accurate copy number typing, so that there are no simple, cheap, high-throughput approaches suitable for large-scale screening. We have developed a simple comparative PCR method based on dispersed repeat sequences, using a single pair of precisely designed primers to amplify products simultaneously from both test and reference loci, which are subsequently distinguished and quantified via internal sequence differences. We have validated the method for the measurement of copy number at DEFB4 by comparison of results from >800 DNA samples with copy number measurements by MAPH/REDVR, MLPA and array-CGH. The new Paralogue Ratio Test (PRT) method can require as little as 10 ng genomic DNA, appears to be comparable in accuracy to the other methods, and for the first time provides a rapid, simple and inexpensive method for copy number analysis, suitable for application to typing thousands of samples in large case-control association studies.

  12. Efficient genome editing by FACS enrichment of paired D10A Cas9 nickases coupled with fluorescent proteins.

    Science.gov (United States)

    Gopalappa, Ramu; Song, Myungjae; Chandrasekaran, Arun Pandian; Das, Soumyadip; Haq, Saba; Koh, Hyun Chul; Ramakrishna, Suresh

    2018-05-31

    Targeted genome editing by clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) raised concerns over off-target effects. The use of double-nicking strategy using paired Cas9 nickase has been developed to minimize off-target effects. However, it was reported that the efficiency of paired nickases were comparable or lower than that of either corresponding nuclease alone. Recently, we conducted a systematic comparison of the efficiencies of several paired Cas9 with their corresponding Cas9 nucleases and showed that paired D10A Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption. However, sometimes the designed paired Cas9 nickases exhibited significantly lower mutation frequencies than nucleases, hampering the generation of cells containing paired Cas9 nickase-induced mutations. Here we implemented IRES peptide-conjugation of fluorescent protein to Cas9 nickase and subjected for fluorescence-activated cell sorting. The sorted cell populations are highly enriched with cells containing paired Cas9 nickase-induced mutations, by a factor of up to 40-fold as compared with the unsorted population. Furthermore, gene-disrupted single cell clones using paired nickases followed by FACS sorting strategy were generated highly efficiently, without compromising with its low off-target effects. We envision that our fluorescent protein coupled paired nickase-mediated gene disruption, facilitating efficient and highly specific genome editing in medical research.

  13. Repeat-aware modeling and correction of short read errors.

    Science.gov (United States)

    Yang, Xiao; Aluru, Srinivas; Dorman, Karin S

    2011-02-15

    High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors

  14. [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.

  15. English for au pairs the au pair's guide to learning English

    CERN Document Server

    Curtis, Lucy

    2014-01-01

    English for Au Pairs has interlinked stories about a group of au pairs new to England. Marta, an 18-year-old from Poland arrives in the UK to work as an au pair. Throughout her year-long stay she has many different experiences - some bad, some good - but with the support of her host family she finds new friends and improves her English. English for Au Pairs offers insight into the joys and difficulties of being an au pair while at the same time reinforcing English language learning through grammar explanations and exercises.

  16. Emergency Department Referrals for Adolescent Urgent Psychiatric Consultation: Comparison of Clinical Characteristics of Repeat-presentations and Single-presentation.

    Science.gov (United States)

    Roberts, Nasreen; Nesdole, Robert; Hu, Tina

    2018-01-01

    a) to examine the demographic and clinical characteristics of repeat-presentations to an adolescent urgent psychiatric clinic, and b) to compare them with single-time presentation. This 18-month retrospective study compared repeat-presenters to age and gender matched single-time presenters. Demographic variables included age gender and ethnicity. Clinical variables included reason for referral, family history, diagnosis, recommendations and compliance. Data were analyzed using descriptive statistics, McNemar's Chi-square tests for matched pairs, and conditional logistic regression. Of 624 assessments 24% (N=151) were repeat-presentations. Compared with single-presentation, repeat-presentation group had a higher proportion of Aboriginal youth (X2 (1) = 108.28 p presentation group had higher odds of past hospital admission (OR: 3.50, p presentations for urgent psychiatric consultation constitute a quarter of referrals to the urgent psychiatric clinic. Identifying and addressing factors that contribute to repeat-presentations may, assist in improving treatment compliance by ensuring focused interventions and service delivery for these youth. In turn, this will improve access to the limited urgent services for other youth.

  17. Considerations on Velocities and Accelerations in Higher Pairs Mechanisms

    Directory of Open Access Journals (Sweden)

    Florina-Carmen Ciornei

    2015-12-01

    Full Text Available The paper proposes a method for finding the velocities and accelerations in the pairs from a mechanism with higher pairs in the case when the curvature radii of the curves achieving the higher pair are finite. There are obtained the characteristic equations of the motion in the higher pair for the case that one of the curves has zero curvature radius, condition characteristic to the knife edge follower. The relations are required to justify the difference between the particular cases of knife edge follower and flat face follower. The methodology is exemplified through an actual example.

  18. On the restoration of symmetry in paired Fermion systems

    International Nuclear Information System (INIS)

    Flocard, H.

    1997-01-01

    We consider the problem of symmetry restoration as treated by the method of variation after projection (VAP) on good quantum numbers. We show that for compact groups, the convergence of the connected-linked expansion of the VAP kernels over the physically relevant interval of integration of the pairing gauge angle is not guaranteed. We propose instead a method which generates approximations of increasing precision which are periodic with respect to the gauge angle while differing from truncations of the Fourier expansion of the VAP kernels. For the projection on good particle number in paired fermion systems, this new approach is shown to be equivalent to an expansion in powers of the pairing tensor. For the lowest order approximation, an analytical integration over the gauge angle is performed explicitly. It provides the algebraic forms of the single particle Hamiltonian and of the pairing field entering generalized Hartree endash Fock endash Bogoljubov equations. Contrary to most approximations, the validity of the expressions for the energy and mean values of operators thus obtained is not a priori restricted where the fluctuation of the operator associated with the broken symmetry is large. We also derive the first-order correction to the pairing-order parameter. We test the quality of the proposed method on a non-trivial soluble model. copyright 1997 Academic Press, Inc

  19. Genetic diversity studies in pea (Pisum sativum L.) using simple sequence repeat markers.

    Science.gov (United States)

    Kumari, P; Basal, N; Singh, A K; Rai, V P; Srivastava, C P; Singh, P K

    2013-03-13

    The genetic diversity among 28 pea (Pisum sativum L.) genotypes was analyzed using 32 simple sequence repeat markers. A total of 44 polymorphic bands, with an average of 2.1 bands per primer, were obtained. The polymorphism information content ranged from 0.657 to 0.309 with an average of 0.493. The variation in genetic diversity among these cultivars ranged from 0.11 to 0.73. Cluster analysis based on Jaccard's similarity coefficient using the unweighted pair-group method with arithmetic mean (UPGMA) revealed 2 distinct clusters, I and II, comprising 6 and 22 genotypes, respectively. Cluster II was further differentiated into 2 subclusters, IIA and IIB, with 12 and 10 genotypes, respectively. Principal component (PC) analysis revealed results similar to those of UPGMA. The first, second, and third PCs contributed 21.6, 16.1, and 14.0% of the variation, respectively; cumulative variation of the first 3 PCs was 51.7%.

  20. Towards accurate de novo assembly for genomes with repeats

    NARCIS (Netherlands)

    Bucur, Doina

    2017-01-01

    De novo genome assemblers designed for short k-mer length or using short raw reads are unlikely to recover complex features of the underlying genome, such as repeats hundreds of bases long. We implement a stochastic machine-learning method which obtains accurate assemblies with repeats and

  1. Environmentally benign working pairs for adsorption refrigeration

    International Nuclear Information System (INIS)

    Cui Qun; Tao Gang; Chen Haijun; Guo Xinyue; Yao Huqing

    2005-01-01

    This paper begins from adsorption working pairs: water and ethanol were selected as refrigerants; 13x molecular sieve, silica gel, activated carbon, adsorbent NA and NB, proposed by authors, were selected as adsorbents, and the performance of adsorption working pairs in adsorption refrigeration cycle was studied. The adsorption isotherms of adsorbents (NA and NB) were obtained by high-vacuum gravimetric method. Desorption properties of adsorbents were analyzed and compared by thermal analysis method. The performance of adsorption refrigeration was studied on simulation device of adsorption refrigeration cycle. After presentation of adsorption isotherms, the thermodynamic performance for their use in adsorption refrigeration system was calculated. The results show: (1) the maximum adsorption capacity of water on adsorbent NA reaches 0.7 kg/kg, and the maximum adsorption capacity of ethanol on adsorbent NB is 0.68 kg/kg, which is three times that of ethanol on activated carbon, (2) the refrigeration capacity of NA-water working pair is 922 kJ/kg, the refrigeration capacity of NB-ethanol is 2.4 times that of activated carbon-methanol, (3) as environmental friendly and no public hazard adsorption working pair, NA-H 2 O and NB-ethanol can substitute activated carbon-methanol in adsorption refrigeration system using low-grade heat source

  2. Poor methodological detail precludes experimental repeatability and hampers synthesis in ecology.

    Science.gov (United States)

    Haddaway, Neal R; Verhoeven, Jos T A

    2015-10-01

    Despite the scientific method's central tenets of reproducibility (the ability to obtain similar results when repeated) and repeatability (the ability to replicate an experiment based on methods described), published ecological research continues to fail to provide sufficient methodological detail to allow either repeatability of verification. Recent systematic reviews highlight the problem, with one example demonstrating that an average of 13% of studies per year (±8.0 [SD]) failed to report sample sizes. The problem affects the ability to verify the accuracy of any analysis, to repeat methods used, and to assimilate the study findings into powerful and useful meta-analyses. The problem is common in a variety of ecological topics examined to date, and despite previous calls for improved reporting and metadata archiving, which could indirectly alleviate the problem, there is no indication of an improvement in reporting standards over time. Here, we call on authors, editors, and peer reviewers to consider repeatability as a top priority when evaluating research manuscripts, bearing in mind that legacy and integration into the evidence base can drastically improve the impact of individual research reports.

  3. Pair creation by dynamic field configurations

    International Nuclear Information System (INIS)

    Aoyama, H.

    1982-01-01

    This thesis deals with the dynamics of the classical configuration of a quantum field unstable due to pair creation. The effective action method is developed first to treat such problems for a simple two-field model. Physical quantities such as pair creation probabilities are related to a complex function called the effective configuration, which is defined to minimize the effective action. Unitarity of the S-matrix is verified at the lowest order of the weak-field approximation. At the same order, the real valued vacuum expectation value of the quantum field, named the real configuration, is constructed in terms of the effective configuration. An integro-differential equation for the real configuration is given and is used to show that the real configuration is causal, while the effective configuration is not. Two practical applications of the effective action method are discussed. The first deals with pair creation in an anisotropic universe, and the real geometry is given in terms of the effective geometry in the samll anisotropy limit. The second deals with expanding vacuum bubbles. Corresponding to three possible situations, three kinds of field equations of each of the effective configuration and the real configuration are obtained. The behavior of the bubble is also studied by a semi-classical method, and one of the three situations is suggested to be plausible

  4. Ex vivo mammalian prions are formed of paired double helical prion protein fibrils.

    Science.gov (United States)

    Terry, Cassandra; Wenborn, Adam; Gros, Nathalie; Sells, Jessica; Joiner, Susan; Hosszu, Laszlo L P; Tattum, M Howard; Panico, Silvia; Clare, Daniel K; Collinge, John; Saibil, Helen R; Wadsworth, Jonathan D F

    2016-05-01

    Mammalian prions are hypothesized to be fibrillar or amyloid forms of prion protein (PrP), but structures observed to date have not been definitively correlated with infectivity and the three-dimensional structure of infectious prions has remained obscure. Recently, we developed novel methods to obtain exceptionally pure preparations of prions from mouse brain and showed that pathogenic PrP in these high-titre preparations is assembled into rod-like assemblies. Here, we have used precise cell culture-based prion infectivity assays to define the physical relationship between the PrP rods and prion infectivity and have used electron tomography to define their architecture. We show that infectious PrP rods isolated from multiple prion strains have a common hierarchical assembly comprising twisted pairs of short fibres with repeating substructure. The architecture of the PrP rods provides a new structural basis for understanding prion infectivity and can explain the inability to systematically generate high-titre synthetic prions from recombinant PrP. © 2016 The Authors.

  5. REPEATABILITY OF FRUIT QUALITY TRAITS OF CACTUS PEAR

    Directory of Open Access Journals (Sweden)

    VALTÂNIA XAVIER NUNES

    2017-12-01

    Full Text Available ABSTRACT Repeatability analysis has been used to study traits in several crops, assisting in the definition of the minimum number needed to evaluate genotypes more efficiently and with less time and resource consumption. So far, however, no repeatability studies on cactus pear have been found in the literature. The objective of this study was to determine the coefficient of repeatability for cactus pear fruits traits and the minimum number of evaluations (fruit that can provide acceptable accuracy for the prediction of the true value. The experiment was conducted at the Federal Institute of Bahia/Campus Guanambi, with 150 fruits collected from three municipalities in the state of Bahia. The coefficients of repeatability were estimated by the methods of analysis of variance, principal components based on the covariance (PCCV and correlation (PCC matrices, and structural analysis based on the correlation matrix (SA. The analysis of variance showed that, except for fruit diameter, the effect of the production site (municipality was significant for all traits evaluated. The PCCV method was proven the most suitable for studying the repeatability of quality traits of cactus pear fruits. Seven fruits were required to determine, with 90% confidence, the traits length, diameter, fruit firmness, skin thickness, number of seeds, fruit mass, bark mass, pulp mass, pH, titratable acidity, soluble solids, SS/AT ratio, and pulp yield.

  6. Isolation of human simple repeat loci by hybridization selection.

    Science.gov (United States)

    Armour, J A; Neumann, R; Gobert, S; Jeffreys, A J

    1994-04-01

    We have isolated short tandem repeat arrays from the human genome, using a rapid method involving filter hybridization to enrich for tri- or tetranucleotide tandem repeats. About 30% of clones from the enriched library cross-hybridize with probes containing trimeric or tetrameric tandem arrays, facilitating the rapid isolation of large numbers of clones. In an initial analysis of 54 clones, 46 different tandem arrays were identified. Analysis of these tandem repeat loci by PCR showed that 24 were polymorphic in length; substantially higher levels of polymorphism were displayed by the tetrameric repeat loci isolated than by the trimeric repeats. Primary mapping of these loci by linkage analysis showed that they derive from 17 chromosomes, including the X chromosome. We anticipate the use of this strategy for the efficient isolation of tandem repeats from other sources of genomic DNA, including DNA from flow-sorted chromosomes, and from other species.

  7. Comparative analysis of main bio-active components in the herb pair Danshen-Honghua and its single herbs by ultra-high performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry.

    Science.gov (United States)

    Qu, Cheng; Pu, Zong-Jin; Zhou, Gui-Sheng; Wang, Jun; Zhu, Zhen-Hua; Yue, Shi-Jun; Li, Jian-Ping; Shang, Li-Li; Tang, Yu-Ping; Shi, Xu-Qin; Liu, Pei; Guo, Jian-Ming; Sun, Jing; Tang, Zhi-Shu; Zhao, Jing; Zhao, Bu-Chang; Duan, Jin-Ao

    2017-09-01

    A sensitive, reliable, and powerful ultra-high performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry method was developed for simultaneous quantification of the 15 main bio-active components including phenolic acids and flavonoids within 13 min for the first time. The proposed method was first reported and validated by good linearity (r 2  > 0.9975), limit of detection (1.12-7.01 ng/mL), limit of quantification (3.73-23.37 ng/mL), intra- and inter-day precisions (RSD ≤ 1.92%, RSD ≤ 2.45%), stability (RSD ≤ 5.63%), repeatability (RSD ≤ 4.34%), recovery (96.84-102.12%), and matrix effects (0.92-1.02). The established analytical methodology was successfully applied to comparative analysis of main bio-active components in the herb pair Danshen-Honghua and its single herbs. Compared to the single herb, the content of most flavonoid glycosides was remarkably increased in their herb pair, and main phenolic acids were decreased, conversely. The content changes of the main components in the herb pair supported the synergistic effects on promoting blood circulation and removing blood stasis. The results provide a scientific basis and reference for the quality control of Danshen-Honghua herb pair and the drug interactions based on variation of bio-active components in herb pairs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Diversity analysis in Cannabis sativa based on large-scale development of expressed sequence tag-derived simple sequence repeat markers.

    Science.gov (United States)

    Gao, Chunsheng; Xin, Pengfei; Cheng, Chaohua; Tang, Qing; Chen, Ping; Wang, Changbiao; Zang, Gonggu; Zhao, Lining

    2014-01-01

    Cannabis sativa L. is an important economic plant for the production of food, fiber, oils, and intoxicants. However, lack of sufficient simple sequence repeat (SSR) markers has limited the development of cannabis genetic research. Here, large-scale development of expressed sequence tag simple sequence repeat (EST-SSR) markers was performed to obtain more informative genetic markers, and to assess genetic diversity in cannabis (Cannabis sativa L.). Based on the cannabis transcriptome, 4,577 SSRs were identified from 3,624 ESTs. From there, a total of 3,442 complementary primer pairs were designed as SSR markers. Among these markers, trinucleotide repeat motifs (50.99%) were the most abundant, followed by hexanucleotide (25.13%), dinucleotide (16.34%), tetranucloetide (3.8%), and pentanucleotide (3.74%) repeat motifs, respectively. The AAG/CTT trinucleotide repeat (17.96%) was the most abundant motif detected in the SSRs. One hundred and seventeen EST-SSR markers were randomly selected to evaluate primer quality in 24 cannabis varieties. Among these 117 markers, 108 (92.31%) were successfully amplified and 87 (74.36%) were polymorphic. Forty-five polymorphic primer pairs were selected to evaluate genetic diversity and relatedness among the 115 cannabis genotypes. The results showed that 115 varieties could be divided into 4 groups primarily based on geography: Northern China, Europe, Central China, and Southern China. Moreover, the coefficient of similarity when comparing cannabis from Northern China with the European group cannabis was higher than that when comparing with cannabis from the other two groups, owing to a similar climate. This study outlines the first large-scale development of SSR markers for cannabis. These data may serve as a foundation for the development of genetic linkage, quantitative trait loci mapping, and marker-assisted breeding of cannabis.

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

    International Nuclear Information System (INIS)

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

    1989-01-01

    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 [ 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

  10. 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.

  11. Mahonian pairs

    OpenAIRE

    Sagan, Bruce E.; Savage, Carla D.

    2012-01-01

    We introduce the notion of a Mahonian pair. Consider the set, P^*, of all words having the positive integers as alphabet. Given finite subsets S,T of P^*, we say that (S,T) is a Mahonian pair if the distribution of the major index, maj, over S is the same as the distribution of the inversion number, inv, over T. So the well-known fact that maj and inv are equidistributed over the symmetric group, S_n, can be expressed by saying that (S_n,S_n) is a Mahonian pair. We investigate various Mahonia...

  12. SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data

    Science.gov (United States)

    Miller, Mark P.; Knaus, Brian J.; Mullins, Thomas D.; Haig, Susan M.

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

  13. SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.

    Science.gov (United States)

    Miller, Mark P; Knaus, Brian J; Mullins, Thomas D; Haig, Susan M

    2013-01-01

    SSR_pipeline is a flexible set of programs designed to efficiently identify simple sequence repeats (e.g., microsatellites) from paired-end high-throughput Illumina DNA sequencing data. The program suite contains 3 analysis modules along with a fourth control module that can automate analyses of large volumes of data. The modules are used to 1) identify the subset of paired-end sequences that pass Illumina quality standards, 2) align paired-end reads into a single composite DNA sequence, and 3) identify sequences that possess microsatellites (both simple and compound) conforming to user-specified parameters. The microsatellite search algorithm is extremely efficient, and we have used it to identify repeats with motifs from 2 to 25 bp in length. Each of the 3 analysis modules can also be used independently to provide greater flexibility or to work with FASTQ or FASTA files generated from other sequencing platforms (Roche 454, Ion Torrent, etc.). We demonstrate use of the program with data from the brine fly Ephydra packardi (Diptera: Ephydridae) and provide empirical timing benchmarks to illustrate program performance on a common desktop computer environment. We further show that the Illumina platform is capable of identifying large numbers of microsatellites, even when using unenriched sample libraries and a very small percentage of the sequencing capacity from a single DNA sequencing run. All modules from SSR_pipeline are implemented in the Python programming language and can therefore be used from nearly any computer operating system (Linux, Macintosh, and Windows).

  14. Paired motor cortex and cervical epidural electrical stimulation timed to converge in the spinal cord promotes lasting increases in motor responses.

    Science.gov (United States)

    Mishra, Asht M; Pal, Ajay; Gupta, Disha; Carmel, Jason B

    2017-11-15

    Pairing motor cortex stimulation and spinal cord epidural stimulation produced large augmentation in motor cortex evoked potentials if they were timed to converge in the spinal cord. The modulation of cortical evoked potentials by spinal cord stimulation was largest when the spinal electrodes were placed over the dorsal root entry zone. Repeated pairing of motor cortex and spinal cord stimulation caused lasting increases in evoked potentials from both sites, but only if the time between the stimuli was optimal. Both immediate and lasting effects of paired stimulation are likely mediated by convergence of descending motor circuits and large diameter afferents onto common interneurons in the cervical spinal cord. Convergent activity in neural circuits can generate changes at their intersection. The rules of paired electrical stimulation are best understood for protocols that stimulate input circuits and their targets. We took a different approach by targeting the interaction of descending motor pathways and large diameter afferents in the spinal cord. We hypothesized that pairing stimulation of motor cortex and cervical spinal cord would strengthen motor responses through their convergence. We placed epidural electrodes over motor cortex and the dorsal cervical spinal cord in rats; motor evoked potentials (MEPs) were measured from biceps. MEPs evoked from motor cortex were robustly augmented with spinal epidural stimulation delivered at an intensity below the threshold for provoking an MEP. Augmentation was critically dependent on the timing and position of spinal stimulation. When the spinal stimulation was timed to coincide with the descending volley from motor cortex stimulation, MEPs were more than doubled. We then tested the effect of repeated pairing of motor cortex and spinal stimulation. Repetitive pairing caused strong augmentation of cortical MEPs and spinal excitability that lasted up to an hour after just 5 min of pairing. Additional physiology

  15. Identifying uniformly mutated segments within repeats.

    Science.gov (United States)

    Sahinalp, S Cenk; Eichler, Evan; Goldberg, Paul; Berenbrink, Petra; Friedetzky, Tom; Ergun, Funda

    2004-12-01

    Given a long string of characters from a constant size alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source. More specifically, consider all possible n-coin models for generating a binary string S, where each bit of S is generated via an independent toss of one of the n coins in the model. The choice of which coin to toss is decided by a random walk on the set of coins where the probability of a coin change is much lower than the probability of using the same coin repeatedly. We present a procedure to evaluate the likelihood of a n-coin model for given S, subject a uniform prior distribution over the parameters of the model (that represent mutation rates and probabilities of copying events). In the absence of detailed prior knowledge of these parameters, the algorithm can be used to determine whether the a posteriori probability for n=1 is higher than for any other n>1. Our algorithm runs in time O(l4logl), where l is the length of S, through a dynamic programming approach which exploits the assumed convexity of the a posteriori probability for n. Our test can be used in the analysis of long alignments between pairs of genomic sequences in a number of ways. For example, functional regions in genome sequences exhibit much lower mutation rates than non-functional regions. Because our test provides means for determining variations in the mutation rate, it may be used to distinguish functional regions from non-functional ones. Another application is in determining whether two highly similar, thus evolutionarily related, genome segments are the result of a single copy event or of a complex series of copy events. This is particularly an issue in evolutionary studies of genome regions rich with repeat segments (especially tandemly repeated segments).

  16. New method for remote and repeatable monitoring of intraocular pressure variations.

    Science.gov (United States)

    Margalit, Israel; Beiderman, Yevgeny; Skaat, Alon; Rosenfeld, Elkanah; Belkin, Michael; Tornow, Ralf-Peter; Mico, Vicente; Garcia, Javier; Zalevsky, Zeev

    2014-02-01

    We present initial steps toward a new measurement device enabling high-precision, noncontact remote and repeatable monitoring of intraocular pressure (IOP)-based on an innovative measurement principle. Using only a camera and a laser source, the device measures IOP by tracking the secondary speckle pattern trajectories produced by the reflection of an illuminating laser beam from the iris or the sclera. The device was tested on rabbit eyes using two different methods to modify IOP: via an infusion bag and via mechanical pressure. In both cases, the eyes were stimulated with increasing and decreasing ramps of the IOP. As IOP variations changed the speckle distributions reflected back from the eye, data were recorded under various optical configurations to define and optimize the best experimental configuration for the IOP extraction. The association between the data provided by our proposed device and that resulting from controlled modification of the IOP was assessed, revealing high correlation (R2=0.98) and sensitivity and providing a high-precision measurement (5% estimated error) for the best experimental configuration. Future steps will be directed toward applying the proposed measurement principle in clinical trials for monitoring IOP with human subjects.

  17. A repeatable and scalable fabrication method for sharp, hollow silicon microneedles

    Science.gov (United States)

    Kim, H.; Theogarajan, L. S.; Pennathur, S.

    2018-03-01

    Scalability and manufacturability are impeding the mass commercialization of microneedles in the medical field. Specifically, microneedle geometries need to be sharp, beveled, and completely controllable, difficult to achieve with microelectromechanical fabrication techniques. In this work, we performed a parametric study using silicon etch chemistries to optimize the fabrication of scalable and manufacturable beveled silicon hollow microneedles. We theoretically verified our parametric results with diffusion reaction equations and created a design guideline for a various set of miconeedles (80-160 µm needle base width, 100-1000 µm pitch, 40-50 µm inner bore diameter, and 150-350 µm height) to show the repeatability, scalability, and manufacturability of our process. As a result, hollow silicon microneedles with any dimensions can be fabricated with less than 2% non-uniformity across a wafer and 5% deviation between different processes. The key to achieving such high uniformity and consistency is a non-agitated HF-HNO3 bath, silicon nitride masks, and surrounding silicon filler materials with well-defined dimensions. Our proposed method is non-labor intensive, well defined by theory, and straightforward for wafer scale mass production, opening doors to a plethora of potential medical and biosensing applications.

  18. A novel multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) method for Propionibacterium acnes.

    Science.gov (United States)

    Hauck, Yolande; Soler, Charles; Gérôme, Patrick; Vong, Rithy; Macnab, Christine; Appere, Géraldine; Vergnaud, Gilles; Pourcel, Christine

    2015-07-01

    Propionibacterium acnes plays a central role in the pathogenesis of acne and is responsible for severe opportunistic infections. Numerous typing schemes have been developed that allow the identification of phylotypes, but they are often insufficient to differentiate subtypes. To better understand the genetic diversity of this species and to perform epidemiological analyses, high throughput discriminant genotyping techniques are needed. Here we describe the development of a multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) method. Thirteen VNTRs were identified in the genome of P. acnes and were used to genotype a collection of clinical isolates. In addition, publically available sequencing data for 102 genomes were analyzed in silico, providing an MLVA genotype. The clustering of MLVA data was in perfect congruence with whole genome based clustering. Analysis of the clustered regularly interspaced short palindromic repeat (CRISPR) element uncovered new spacers, a supplementary source of genotypic information. The present MLVA13 scheme and associated internet database represents a first line genotyping assay to investigate large number of isolates. Particular strains may then be submitted to full genome sequencing in order to better analyze their pathogenic potential. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Pair correlations in nuclei

    International Nuclear Information System (INIS)

    Shimizu, Yoshifumi

    2009-01-01

    Except for the closed shell nuclei, almost all nuclei are in the superconducting state at their ground states. This well-known pair correlation in nuclei causes various interesting phenomena. It is especially to be noted that the pair correlation becomes weak in the excited states of nuclei with high angular momentum, which leads to the pair phase transition to the normal state in the high spin limit. On the other hand, the pair correlation becomes stronger in the nuclei with lower nucleon density than in those with normal density. In the region of neutron halo or skin state of unstable nuclei, this phenomenon is expected to be further enhanced to be observed compared to the ground state of stable nuclei. An overview of those interesting aspects caused via the pair correlation is presented here in the sections titled 'pair correlations in ground states', pair correlations in high spin states' and 'pair correlations in unstable nuclei' focusing on the high spin state. (S. Funahashi)

  20. Experimental many-pairs nonlocality

    Science.gov (United States)

    Poh, Hou Shun; Cerè, Alessandro; Bancal, Jean-Daniel; Cai, Yu; Sangouard, Nicolas; Scarani, Valerio; Kurtsiefer, Christian

    2017-08-01

    Collective measurements on large quantum systems together with a majority voting strategy can lead to a violation of the Clauser-Horne-Shimony-Holt Bell inequality. In the presence of many entangled pairs, this violation decreases quickly with the number of pairs and vanishes for some critical pair number that is a function of the noise present in the system. Here we show that a different binning strategy can lead to a more substantial Bell violation when the noise is sufficiently small. Given the relation between the critical pair number and the source noise, we then present an experiment where the critical pair number is used to quantify the quality of a high visibility photon pair source. Our results demonstrate nonlocal correlations using collective measurements operating on clusters of more than 40 photon pairs.

  1. Repeating and non-repeating fast radio bursts from binary neutron star mergers

    Science.gov (United States)

    Yamasaki, Shotaro; Totani, Tomonori; Kiuchi, Kenta

    2018-04-01

    Most fast radio bursts (FRB) do not show evidence of repetition, and such non-repeating FRBs may be produced at the time of a merger of binary neutron stars (BNS), provided that the BNS merger rate is close to the high end of the currently possible range. However, the merger environment is polluted by dynamical ejecta, which may prohibit the radio signal from propagating. We examine this by using a general-relativistic simulation of a BNS merger, and show that the ejecta appears about 1 ms after the rotation speed of the merged star becomes the maximum. Therefore there is a time window in which an FRB signal can reach outside, and the short duration of non-repeating FRBs can be explained by screening after ejecta formation. A fraction of BNS mergers may leave a rapidly rotating and stable neutron star, and such objects may be the origin of repeating FRBs like FRB 121102. We show that a merger remnant would appear as a repeating FRB on a time scale of ˜1-10 yr, and expected properties are consistent with the observations of FRB 121102. We construct an FRB rate evolution model that includes these two populations of repeating and non-repeating FRBs from BNS mergers, and show that the detection rate of repeating FRBs relative to non-repeating ones rapidly increases with improving search sensitivity. This may explain why only the repeating FRB 121102 was discovered by the most sensitive FRB search with Arecibo. Several predictions are made, including the appearance of a repeating FRB 1-10 yr after a BNS merger that is localized by gravitational waves and subsequent electromagnetic radiation.

  2. Ocular surface sensitivity repeatability with Cochet-Bonnet esthesiometer.

    Science.gov (United States)

    Chao, Cecilia; Stapleton, Fiona; Badarudin, Ezailina; Golebiowski, Blanka

    2015-02-01

    To determine the repeatability of ocular surface threshold measurements using the Cochet-Bonnet esthesiometer on the same day and 3 months apart. Two separate studies were conducted to determine the repeatability of ocular surface threshold measurements made on the same day (n = 20 subjects) and 3 months apart (n = 29 subjects). The Cochet-Bonnet esthesiometer was used to measure corneal and inferior conjunctival thresholds using the ascending method of limits. The pressure exerted by the Cochet-Bonnet esthesiometer was determined using an analytical balance, for both the 0.08- and 0.12-mm-diameter filaments. This calibration was then used to convert filament length measurements to pressure. Repeatability was determined using a Bland and Altman analysis. The pressure exerted at each filament length differed between the two filament diameters. The measured pressure also differed from values provided by the manufacturer. Repeatability of threshold measurements at the central cornea was shown to be good, with better repeatability for same-day measurements (coefficient of repeatability [CoR] = ±0.23 g/mm²) than for those 3 months apart (CoR = ±0.52 g/mm²). Threshold measurements at the inferior conjunctiva, in contrast, were poorly repeatable (CoR = ±12.78 g/mm²). Cochet-Bonnet esthesiometry is repeatable when performed on the central cornea on the same day and 3 months apart, but this instrument is not recommended for conjunctival threshold measurements.

  3. Au pair trajectories

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2015-01-01

    pair-sending families in the Philippines, this dissertation examines the long-term trajectories of these young Filipinas. It shows how the au pairs’ local and transnational family relations develop over time and greatly influence their life trajectories. A focal point of the study is how au pairs...... that Filipina au pairs see their stay abroad as an avenue of personal development and social recognition, I examine how the au pairs re-position themselves within their families at home through migration, and how they navigate between the often conflicting expectations of participation in the sociality......Since 2000, thousands of young Filipino migrants have come to Denmark as au pairs. Officially, they are there to “broaden their cultural horizons” by living temporarily with a Danish host family, but they also conduct domestic labor in exchange for food and money, which allows them to send...

  4. Nonlinear electrostatic structures in homogeneous and inhomogeneous pair-ion plasmas

    International Nuclear Information System (INIS)

    Mahmood, S.; Ur-Rehman, H.; Shah, A.; Haque, Q.

    2012-01-01

    The nonlinear electrostatic structures such as solitons, shocks were studied in homogeneous, unmagnetized pair-ion plasma. The dissipation in the system was taken through kinematic viscosities of both pair-ion species. The one dimensional (Korteweg-de Vries-Burgers) KdVB equation was derived using reductive perturbation method. The analytical solution of KdVB equation was obtained using tanh method. It was found that solitons and monotonic shocks structures were formed in such type of plasmas depending on the value of dissipation in the system. Both compressive and refractive structures of solitons and monotonic shocks were obtained depending on the temperatures of negative and positive ions. The oscillatory shock structures in pair-ion plasmas were also obtained and its necessary conditions of formation were discussed. The acoustic solitons were also investigated in inhomogeneous unmagnetized pair-ion plasmas. The Korteweg-de Vries (KdV) like equation with an additional term due to density gradients was obtained by employing the reductive perturbation technique. It was found that amplitude of both compressive and refractive solitons was found to be enhanced as the density gradient parameter was increased. The Landau damping rates of electrostatic ion waves were studied for non-Maxwellian or Lorentzian pair-ion plasmas. The Val sov equation was solved analytically for weak damping effects in pair-ion plasma. It was found that Landau damping rate of ion plasma wave was increased in Lorentzian case in comparison with Maxwellian pair-ion plasmas. The numerical results were obtained by taking into account the parameters of pair-ion plasmas produced in laboratory experiments in Japan. (orig./A.B.)

  5. A stochastic model for identifying differential gene pair co-expression patterns in prostate cancer progression

    Directory of Open Access Journals (Sweden)

    Mao Yu

    2009-07-01

    Full Text Available Abstract Background The identification of gene differential co-expression patterns between cancer stages is a newly developing method to reveal the underlying molecular mechanisms of carcinogenesis. Most researches of this subject lack an algorithm useful for performing a statistical significance assessment involving cancer progression. Lacking this specific algorithm is apparently absent in identifying precise gene pairs correlating to cancer progression. Results In this investigation we studied gene pair co-expression change by using a stochastic process model for approximating the underlying dynamic procedure of the co-expression change during cancer progression. Also, we presented a novel analytical method named 'Stochastic process model for Identifying differentially co-expressed Gene pair' (SIG method. This method has been applied to two well known prostate cancer data sets: hormone sensitive versus hormone resistant, and healthy versus cancerous. From these data sets, 428,582 gene pairs and 303,992 gene pairs were identified respectively. Afterwards, we used two different current statistical methods to the same data sets, which were developed to identify gene pair differential co-expression and did not consider cancer progression in algorithm. We then compared these results from three different perspectives: progression analysis, gene pair identification effectiveness analysis, and pathway enrichment analysis. Statistical methods were used to quantify the quality and performance of these different perspectives. They included: Re-identification Scale (RS and Progression Score (PS in progression analysis, True Positive Rate (TPR in gene pair analysis, and Pathway Enrichment Score (PES in pathway analysis. Our results show small values of RS and large values of PS, TPR, and PES; thus, suggesting that gene pairs identified by the SIG method are highly correlated with cancer progression, and highly enriched in disease-specific pathways. From

  6. A rational repeating template method for synthesis of 2D hexagonally ordered mesoporous precious metals.

    Science.gov (United States)

    Takai, Azusa; Doi, Yoji; Yamauchi, Yusuke; Kuroda, Kazuyuki

    2011-03-01

    A repeating template method is presented for the synthesis of mesoporous metals with 2D hexagonal mesostructures. First, a silica replica (i.e., silica nanorods arranged periodically) is prepared by using 2D hexagonally ordered mesoporous carbon as the template. After that, the obtained silica replica is used as the second template for the preparation of mesoporous ruthenium. After the ruthenium species are introduced into the silica replica, the ruthenium species are then reduced by a vapor-infiltration method by using the reducing agent dimethylamine borane. After the ruthenium deposition, the silica is chemically removed. Analysis by transmission and scanning electron microscopies, a nitrogen-adsorption-desorption isotherm, and small-angle X-ray scattering revealed that the mesoporous ruthenium had a 2D hexagonal mesostructure, although the mesostructural ordering is decreased compared to that of the original mesoporous carbon template. This method is widely applicable to other metal systems. By changing the metal species introduced into the silica replica, several mesoporous metals (palladium and platinum) can be synthesized. Ordered mesoporous ruthenium and palladium, which are not easily attainable by the soft-templating methods, can be prepared. This study has overcome the composition variation limitations of the soft-templating method. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Development of double-pair double difference location algorithm and its application to the regular earthquakes and non-volcanic tremors

    Science.gov (United States)

    Guo, H.; Zhang, H.

    2016-12-01

    Relocating high-precision earthquakes is a central task for monitoring earthquakes and studying the structure of earth's interior. The most popular location method is the event-pair double-difference (DD) relative location method, which uses the catalog and/or more accurate waveform cross-correlation (WCC) differential times from event pairs with small inter-event separations to the common stations to reduce the effect of the velocity uncertainties outside the source region. Similarly, Zhang et al. [2010] developed a station-pair DD location method which uses the differential times from common events to pairs of stations to reduce the effect of the velocity uncertainties near the source region, to relocate the non-volcanic tremors (NVT) beneath the San Andreas Fault (SAF). To utilize advantages of both DD location methods, we have proposed and developed a new double-pair DD location method to use the differential times from pairs of events to pairs of stations. The new method can remove the event origin time and station correction terms from the inversion system and cancel out the effects of the velocity uncertainties near and outside the source region simultaneously. We tested and applied the new method on the northern California regular earthquakes to validate its performance. In comparison, among three DD location methods, the new double-pair DD method can determine more accurate relative locations and the station-pair DD method can better improve the absolute locations. Thus, we further proposed a new location strategy combining station-pair and double-pair differential times to determine accurate absolute and relative locations at the same time. For NVTs, it is difficult to pick the first arrivals and derive the WCC event-pair differential times, thus the general practice is to measure station-pair envelope WCC differential times. However, station-pair tremor locations are scattered due to the low-precision relative locations. The ability that double-pair data

  8. Scaling Professional Problems of Teachers in Turkey with Paired Comparison Method

    Directory of Open Access Journals (Sweden)

    Yasemin Duygu ESEN

    2017-03-01

    Full Text Available In this study, teachers’ professional problems was investigated and the significance level of them was measured with the paired comparison method. The study was carried out in survey model. The study group consisted of 484 teachers working in public schools which are accredited by Ministry of National Education (MEB in Turkey. “The Teacher Professional Problems Survey” developed by the researchers was used as a data collection tool. In data analysis , the scaling method with the third conditional equation of Thurstone’s law of comparative judgement was used. According to the results of study, the teachers’ professional problems include teacher training and the quality of teacher, employee rights and financial problems, decrease of professional reputation, the problems with MEB policies, the problems with union activities, workload, the problems with administration in school, physical conditions and the lack of infrastructure, the problems with parents, the problems with students. According to teachers, the most significant problem is MEB educational policies. This is followed by decrease of professional reputation, physical conditions and the lack of infrastructure, the problems with students, employee rights and financial problems, the problems with administration in school, teacher training and the quality of teacher, the problems with parents, workload, and the problems with union activities. When teachers’ professional problems were analyzed seniority variable, there was little difference in scale values. While the teachers with 0-10 years experience consider decrease of professional reputation as the most important problem, the teachers with 11-45 years experience put the problems with MEB policies at the first place.

  9. Dislocation processes in quasicrystals-Kink-pair formation control or jog-pair formation control

    International Nuclear Information System (INIS)

    Takeuchi, Shin

    2005-01-01

    A computer simulation of dislocation in a model quasiperiodic lattice indicates that the dislocation feels a large Peierls potential when oriented in particular directions. For a dislocation with a high Peierls potential, the glide velocity and the climb velocity of the dislocation can be described almost in parallel in terms of the kink-pair formation followed by kink motion and the jog-pair formation followed by jog motion, respectively. The activation enthalpy of the kink-pair formation is the sum of the kink-pair formation enthalpy and the atomic jump activation enthalpy, while the activation enthalpy of the jog-pair formation involves the jog-pair enthalpy and the self-diffusion enthalpy. Since the kink-pair energy can be considerably larger than the jog-pair energy, the climb velocity can be faster than the glide velocity, so that the plastic deformation of quasicrystals can be brought not by dislocation glide but by dislocation climb at high temperatures

  10. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    International Nuclear Information System (INIS)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E.; Eghbalnia, Hamid R.

    2012-01-01

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ( 1 H– 15 N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy ( 1 H– 1 H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a

  11. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts

    Energy Technology Data Exchange (ETDEWEB)

    Bahrami, Arash; Clos, Lawrence J.; Markley, John L.; Butcher, Samuel E. [National Magnetic Resonance Facility at Madison (United States); Eghbalnia, Hamid R., E-mail: eghbalhd@uc.edu [University of Cincinnati, Department of Molecular and Cellular Physiology (United States)

    2012-04-15

    The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear multiple quantum correlation ({sup 1}H-{sup 15}N 2D HMQC) and proton-proton nuclear Overhauser enhancement spectroscopy ({sup 1}H-{sup 1}H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%. RNA-PAIRS yielded accurate assignments and base pairings consistent with imino

  12. Highly sensitive detection of individual HEAT and ARM repeats with HHpred and COACH.

    Science.gov (United States)

    Kippert, Fred; Gerloff, Dietlind L

    2009-09-24

    HEAT and ARM repeats occur in a large number of eukaryotic proteins. As these repeats are often highly diverged, the prediction of HEAT or ARM domains can be challenging. Except for the most clear-cut cases, identification at the individual repeat level is indispensable, in particular for determining domain boundaries. However, methods using single sequence queries do not have the sensitivity required to deal with more divergent repeats and, when applied to proteins with known structures, in some cases failed to detect a single repeat. Testing algorithms which use multiple sequence alignments as queries, we found two of them, HHpred and COACH, to detect HEAT and ARM repeats with greatly enhanced sensitivity. Calibration against experimentally determined structures suggests the use of three score classes with increasing confidence in the prediction, and prediction thresholds for each method. When we applied a new protocol using both HHpred and COACH to these structures, it detected 82% of HEAT repeats and 90% of ARM repeats, with the minimum for a given protein of 57% for HEAT repeats and 60% for ARM repeats. Application to bona fide HEAT and ARM proteins or domains indicated that similar numbers can be expected for the full complement of HEAT/ARM proteins. A systematic screen of the Protein Data Bank for false positive hits revealed their number to be low, in particular for ARM repeats. Double false positive hits for a given protein were rare for HEAT and not at all observed for ARM repeats. In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries. A protocol is presented for the identification of individual HEAT or ARM repeats which is straightforward to implement. It provides high

  13. Comparison of a Variable-Number Tandem-Repeat (VNTR) Method for Typing Mycobacterium avium with Mycobacterial Interspersed Repetitive-Unit-VNTR and IS1245 Restriction Fragment Length Polymorphism Typing▿ †

    OpenAIRE

    Inagaki, Takayuki; Nishimori, Kei; Yagi, Tetsuya; Ichikawa, Kazuya; Moriyama, Makoto; Nakagawa, Taku; Shibayama, Takami; Uchiya, Kei-ichi; Nikai, Toshiaki; Ogawa, Kenji

    2009-01-01

    Mycobacterium avium complex (MAC) infections are increasing annually in various countries, including Japan, but the route of transmission and pathophysiology of the infection remain unclear. Currently, a variable-number tandem-repeat (VNTR) typing method using the Mycobacterium avium tandem repeat (MATR) loci (MATR-VNTR) is employed in Japan for epidemiological studies using clinical isolates of M. avium. In this study, the usefulness of this MATR-VNTR typing method was compared with that of ...

  14. Improvement of the repeatability of parallel transmission at 7T using interleaved acquisition in the calibration scan.

    Science.gov (United States)

    Kameda, Hiroyuki; Kudo, Kohsuke; Matsuda, Tsuyoshi; Harada, Taisuke; Iwadate, Yuji; Uwano, Ikuko; Yamashita, Fumio; Yoshioka, Kunihiro; Sasaki, Makoto; Shirato, Hiroki

    2017-12-04

    Respiration-induced phase shift affects B 0 /B 1 + mapping repeatability in parallel transmission (pTx) calibration for 7T brain MRI, but is improved by breath-holding (BH). However, BH cannot be applied during long scans. To examine whether interleaved acquisition during calibration scanning could improve pTx repeatability and image homogeneity. Prospective. Nine healthy subjects. 7T MRI with a two-channel RF transmission system was used. Calibration scanning for B 0 /B 1 + mapping was performed under sequential acquisition/free-breathing (Seq-FB), Seq-BH, and interleaved acquisition/FB (Int-FB) conditions. The B 0 map was calculated with two echo times, and the B 1 + map was obtained using the Bloch-Siegert method. Actual flip-angle imaging (AFI) and gradient echo (GRE) imaging were performed using pTx and quadrature-Tx (qTx). All scans were acquired in five sessions. Repeatability was evaluated using intersession standard deviation (SD) or coefficient of variance (CV), and in-plane homogeneity was evaluated using in-plane CV. A paired t-test with Bonferroni correction for multiple comparisons was used. The intersession CV/SDs for the B 0 /B 1 + maps were significantly smaller in Int-FB than in Seq-FB (Bonferroni-corrected P FB, Seq-BH, and qTx than in Seq-FB (Bonferroni-corrected P FB, Int-FB, and Seq-BH were significantly smaller than in qTx (Bonferroni-corrected P < 0.01 for all). Using interleaved acquisition during calibration scans of pTx for 7T brain MRI improved the repeatability of B 0 /B 1 + mapping, AFI, and GRE images, without BH. 1 Technical Efficacy Stage 1 J. Magn. Reson. Imaging 2017. © 2017 International Society for Magnetic Resonance in Medicine.

  15. Dictionary Pair Learning on Grassmann Manifolds for Image Denoising.

    Science.gov (United States)

    Zeng, Xianhua; Bian, Wei; Liu, Wei; Shen, Jialie; Tao, Dacheng

    2015-11-01

    Image denoising is a fundamental problem in computer vision and image processing that holds considerable practical importance for real-world applications. The traditional patch-based and sparse coding-driven image denoising methods convert 2D image patches into 1D vectors for further processing. Thus, these methods inevitably break down the inherent 2D geometric structure of natural images. To overcome this limitation pertaining to the previous image denoising methods, we propose a 2D image denoising model, namely, the dictionary pair learning (DPL) model, and we design a corresponding algorithm called the DPL on the Grassmann-manifold (DPLG) algorithm. The DPLG algorithm first learns an initial dictionary pair (i.e., the left and right dictionaries) by employing a subspace partition technique on the Grassmann manifold, wherein the refined dictionary pair is obtained through a sub-dictionary pair merging. The DPLG obtains a sparse representation by encoding each image patch only with the selected sub-dictionary pair. The non-zero elements of the sparse representation are further smoothed by the graph Laplacian operator to remove the noise. Consequently, the DPLG algorithm not only preserves the inherent 2D geometric structure of natural images but also performs manifold smoothing in the 2D sparse coding space. We demonstrate that the DPLG algorithm also improves the structural SIMilarity values of the perceptual visual quality for denoised images using the experimental evaluations on the benchmark images and Berkeley segmentation data sets. Moreover, the DPLG also produces the competitive peak signal-to-noise ratio values from popular image denoising algorithms.

  16. 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.

  17. SparseMaps—A systematic infrastructure for reduced-scaling electronic structure methods. III. Linear-scaling multireference domain-based pair natural orbital N-electron valence perturbation theory

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Yang; Sivalingam, Kantharuban; Neese, Frank, E-mail: Frank.Neese@cec.mpg.de [Max Planck Institut für Chemische Energiekonversion, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr (Germany); Valeev, Edward F. [Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24014 (United States)

    2016-03-07

    Multi-reference (MR) electronic structure methods, such as MR configuration interaction or MR perturbation theory, can provide reliable energies and properties for many molecular phenomena like bond breaking, excited states, transition states or magnetic properties of transition metal complexes and clusters. However, owing to their inherent complexity, most MR methods are still too computationally expensive for large systems. Therefore the development of more computationally attractive MR approaches is necessary to enable routine application for large-scale chemical systems. Among the state-of-the-art MR methods, second-order N-electron valence state perturbation theory (NEVPT2) is an efficient, size-consistent, and intruder-state-free method. However, there are still two important bottlenecks in practical applications of NEVPT2 to large systems: (a) the high computational cost of NEVPT2 for large molecules, even with moderate active spaces and (b) the prohibitive cost for treating large active spaces. In this work, we address problem (a) by developing a linear scaling “partially contracted” NEVPT2 method. This development uses the idea of domain-based local pair natural orbitals (DLPNOs) to form a highly efficient algorithm. As shown previously in the framework of single-reference methods, the DLPNO concept leads to an enormous reduction in computational effort while at the same time providing high accuracy (approaching 99.9% of the correlation energy), robustness, and black-box character. In the DLPNO approach, the virtual space is spanned by pair natural orbitals that are expanded in terms of projected atomic orbitals in large orbital domains, while the inactive space is spanned by localized orbitals. The active orbitals are left untouched. Our implementation features a highly efficient “electron pair prescreening” that skips the negligible inactive pairs. The surviving pairs are treated using the partially contracted NEVPT2 formalism. A detailed

  18. 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 measured on a COBAS Mira autoanalyser from Roche. The main findings were that samples for analysis of creatinine should be kept at a temperature of -20 degrees C or lower and frozen and thawed only once. The limit of detection, determined as 3 x SD of 20 determinations of a sample at a low concentration (6...

  19. AudioPairBank: Towards A Large-Scale Tag-Pair-Based Audio Content Analysis

    OpenAIRE

    Sager, Sebastian; Elizalde, Benjamin; Borth, Damian; Schulze, Christian; Raj, Bhiksha; Lane, Ian

    2016-01-01

    Recently, sound recognition has been used to identify sounds, such as car and river. However, sounds have nuances that may be better described by adjective-noun pairs such as slow car, and verb-noun pairs such as flying insects, which are under explored. Therefore, in this work we investigate the relation between audio content and both adjective-noun pairs and verb-noun pairs. Due to the lack of datasets with these kinds of annotations, we collected and processed the AudioPairBank corpus cons...

  20. Telomerase Repeated Amplification Protocol (TRAP).

    Science.gov (United States)

    Mender, Ilgen; Shay, Jerry W

    2015-11-20

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

  1. The paired-domination and the upper paired-domination numbers of graphs

    Directory of Open Access Journals (Sweden)

    Włodzimierz Ulatowski

    2015-01-01

    Full Text Available In this paper we continue the study of paired-domination in graphs. A paired-dominating set, abbreviated PDS, of a graph \\(G\\ with no isolated vertex is a dominating set of vertices whose induced subgraph has a perfect matching. The paired-domination number of \\(G\\, denoted by \\(\\gamma_{p}(G\\, is the minimum cardinality of a PDS of \\(G\\. The upper paired-domination number of \\(G\\, denoted by \\(\\Gamma_{p}(G\\, is the maximum cardinality of a minimal PDS of \\(G\\. Let \\(G\\ be a connected graph of order \\(n\\geq 3\\. Haynes and Slater in [Paired-domination in graphs, Networks 32 (1998, 199-206], showed that \\(\\gamma_{p}(G\\leq n-1\\ and they determine the extremal graphs \\(G\\ achieving this bound. In this paper we obtain analogous results for \\(\\Gamma_{p}(G\\. Dorbec, Henning and McCoy in [Upper total domination versus upper paired-domination, Questiones Mathematicae 30 (2007, 1-12] determine \\(\\Gamma_{p}(P_n\\, instead in this paper we determine \\(\\Gamma_{p}(C_n\\. Moreover, we describe some families of graphs \\(G\\ for which the equality \\(\\gamma_{p}(G=\\Gamma_{p}(G\\ holds.

  2. Collaboration in recall: do pairs of people cross-cue each other to produce new memories?

    Science.gov (United States)

    Meudell, P R; Hitch, G J; Boyle, M M

    1995-02-01

    When people collaborate over their recall of a shared experience, it might be expected that they could "cross-cue" each other so as to produce new memories not available to either member of the pair on their own. In a previous series of experiments (Meudell et al., 1992), we found that pairs of people always recalled more than one person, but we failed to show that social interaction facilitated performance so as to produce such "emergent" new memories. However, a phenomenon akin to cross-cuing was employed by Tulving and Pearlstone (1966) in their classic study of the availability and accessibility of memories; accordingly, in this study, we repeated Tulving and Pearlstone's work directly in a social context. So as to assess whether new memories emerged in collaborating pairs, a sequential design was employed. People learned categorized lists of words, and then all the subjects recalled the items strictly on their own. Subjects then recalled again in pairs (collaboratively) or once more on their own. The results showed that even when the opportunity for cross-cuing was directly manipulated through the provision of categorized lists, no additional new memories emerged in the collaborating groups. Possible mechanisms for the results are considered.

  3. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

    Directory of Open Access Journals (Sweden)

    Michael F Sloma

    2017-11-01

    Full Text Available Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package.

  4. Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.

    Science.gov (United States)

    Sloma, Michael F; Mathews, David H

    2017-11-01

    Prediction of RNA tertiary structure from sequence is an important problem, but generating accurate structure models for even short sequences remains difficult. Predictions of RNA tertiary structure tend to be least accurate in loop regions, where non-canonical pairs are important for determining the details of structure. Non-canonical pairs can be predicted using a knowledge-based model of structure that scores nucleotide cyclic motifs, or NCMs. In this work, a partition function algorithm is introduced that allows the estimation of base pairing probabilities for both canonical and non-canonical interactions. Pairs that are predicted to be probable are more likely to be found in the true structure than pairs of lower probability. Pair probability estimates can be further improved by predicting the structure conserved across multiple homologous sequences using the TurboFold algorithm. These pairing probabilities, used in concert with prior knowledge of the canonical secondary structure, allow accurate inference of non-canonical pairs, an important step towards accurate prediction of the full tertiary structure. Software to predict non-canonical base pairs and pairing probabilities is now provided as part of the RNAstructure software package.

  5. Umbilical cord Wharton's jelly repeated culture system: a new device and method for obtaining abundant mesenchymal stem cells for bone tissue engineering.

    Directory of Open Access Journals (Sweden)

    Zhengqi Chang

    Full Text Available To date, various types of cells for seeding regenerative scaffolds have been used for bone tissue engineering. Among seed cells, the mesenchymal stem cells derived from human umbilical cord Wharton's jelly (hUCMSCs represent a promising candidate and hold potential for bone tissue engineering due to the the lack of ethical controversies, accessibility, sourced by non-invasive procedures for donors, a reduced risk of contamination, osteogenic differentiation capacities, and higher immunomodulatory capacity. However, the current culture methods are somewhat complicated and inefficient and often fail to make the best use of the umbilical cord (UC tissues. Moreover, these culture processes cannot be performed on a large scale and under strict quality control. As a result, only a small quantity of cells can be harvested using the current culture methods. To solve these problems, we designed and evaluated an UC Wharton's jelly repeated culture device. Using this device, hUCMSCs were obtained from the repeated cultures and their quantities and biological characteristics were compared. We found that using our culture device, which retained all tissue blocks on the bottom of the dish, the total number of obtained cells increased 15-20 times, and the time required for the primary passage was reduced. Moreover, cells harvested from the repeated cultures exhibited no significant difference in their immunophenotype, potential for multilineage differentiation, or proliferative, osteoinductive capacities, and final osteogenesis. The application of the repeated culture frame (RCF not only made full use of the Wharton's jelly but also simplified and specified the culture process, and thus, the culture efficiency was significantly improved. In summary, abundant hUCMSCs of dependable quality can be acquired using the RCF.

  6. Safety of Repeated Yttrium-90 Radioembolization

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  7. Safety of Repeated Yttrium-90 Radioembolization

    Energy Technology Data Exchange (ETDEWEB)

    Lam, Marnix G. E. H.; Louie, John D. [Stanford University School of Medicine, Division of Interventional Radiology (United States); Iagaru, Andrei H.; Goris, Michael L. [Stanford University School of Medicine, Division of Nuclear Medicine (United States); Sze, Daniel Y., E-mail: dansze@stanford.edu [Stanford University School of Medicine, Division of Interventional Radiology (United States)

    2013-10-15

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

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

    International Nuclear Information System (INIS)

    Bagchi, Manjari

    2017-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Bagchi, Manjari, E-mail: manjari@imsc.res.in [The Institute of Mathematical Sciences (IMSc-HBNI), 4th Cross Road, CIT Campus, Taramani, Chennai 600113 (India)

    2017-04-01

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

  10. 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.

    2017-12-01

    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation (MLI) 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 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 Glenn Research Center (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 has been fabricated by Yetispace and tested by Florida State University, the repeatability between coupons has been shown to be +/- 15-25%. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  11. Enhancing the prediction of protein pairings between interacting families using orthology information

    Directory of Open Access Journals (Sweden)

    Pazos Florencio

    2008-01-01

    Full Text Available Abstract Background It has repeatedly been shown that interacting protein families tend to have similar phylogenetic trees. These similarities can be used to predicting the mapping between two families of interacting proteins (i.e. which proteins from one family interact with which members of the other. The correct mapping will be that which maximizes the similarity between the trees. The two families may eventually comprise orthologs and paralogs, if members of the two families are present in more than one organism. This fact can be exploited to restrict the possible mappings, simply by impeding links between proteins of different organisms. We present here an algorithm to predict the mapping between families of interacting proteins which is able to incorporate information regarding orthologues, or any other assignment of proteins to "classes" that may restrict possible mappings. Results For the first time in methods for predicting mappings, we have tested this new approach on a large number of interacting protein domains in order to statistically assess its performance. The method accurately predicts around 80% in the most favourable cases. We also analysed in detail the results of the method for a well defined case of interacting families, the sensor and kinase components of the Ntr-type two-component system, for which up to 98% of the pairings predicted by the method were correct. Conclusion Based on the well established relationship between tree similarity and interactions we developed a method for predicting the mapping between two interacting families using genomic information alone. The program is available through a web interface.

  12. Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs

    Directory of Open Access Journals (Sweden)

    Sadiye Peral Eyduran

    2016-01-01

    Full Text Available In this research, two well-recognized standard grape cultivars, Cabernet Sauvignon and Merlot, together with eight historical autochthonous grapevine cultivars from Eastern Anatolia in Turkey, were genetically characterized by using 12 pairs of simple sequence repeat (SSR primers in order to evaluate their genetic diversity and relatedness. All of the used SSR primers produced successful amplifications and revealed DNA polymorphisms, which were subsequently utilized to evaluate the genetic relatedness of the grapevine cultivars. Allele richness was implied by the identification of 69 alleles in 8 autochthonous cultivars with a mean value of 5.75 alleles per locus. The average expected heterozygosity and observed heterozygosity were found to be 0.749 and 0.739, respectively. Taking into account the generated alleles, the highest number was recorded in VVC2C3 and VVS2 loci (nine and eight alleles per locus, respectively, whereas the lowest number was recorded in VrZAG83 (three alleles per locus. Two main clusters were produced by using the unweighted pair-group method with arithmetic mean dendrogram constructed on the basis of the SSR data. Only Cabernet Sauvignon and Merlot cultivars were included in the first cluster. The second cluster involved the rest of the autochthonous cultivars. The results obtained during the study illustrated clearly that SSR markers have verified to be an effective tool for fingerprinting grapevine cultivars and carrying out grapevine biodiversity studies. The obtained data are also meaningful references for grapevine domestication.

  13. Deployment Repeatability

    Science.gov (United States)

    2016-04-01

    evaluating the deployment repeatability builds upon the testing or analysis of deployment kinematics (Chapter 6) and adds repetition. Introduction...material yield or failure during a test. For the purposes of this chapter, zero shift will refer to permanent changes in the structure, while reversible ...the content of other chapters in this book: Gravity Compensation (Chapter 4) and Deployment Kinematics and Dynamics (Chapter 6). Repeating the

  14. Pair- ${v}$ -SVR: A Novel and Efficient Pairing nu-Support Vector Regression Algorithm.

    Science.gov (United States)

    Hao, Pei-Yi

    This paper proposes a novel and efficient pairing nu-support vector regression (pair--SVR) algorithm that combines successfully the superior advantages of twin support vector regression (TSVR) and classical -SVR algorithms. In spirit of TSVR, the proposed pair--SVR solves two quadratic programming problems (QPPs) of smaller size rather than a single larger QPP, and thus has faster learning speed than classical -SVR. The significant advantage of our pair--SVR over TSVR is the improvement in the prediction speed and generalization ability by introducing the concepts of the insensitive zone and the regularization term that embodies the essence of statistical learning theory. Moreover, pair--SVR has additional advantage of using parameter for controlling the bounds on fractions of SVs and errors. Furthermore, the upper bound and lower bound functions of the regression model estimated by pair--SVR capture well the characteristics of data distributions, thus facilitating automatic estimation of the conditional mean and predictive variance simultaneously. This may be useful in many cases, especially when the noise is heteroscedastic and depends strongly on the input values. The experimental results validate the superiority of our pair--SVR in both training/prediction speed and generalization ability.This paper proposes a novel and efficient pairing nu-support vector regression (pair--SVR) algorithm that combines successfully the superior advantages of twin support vector regression (TSVR) and classical -SVR algorithms. In spirit of TSVR, the proposed pair--SVR solves two quadratic programming problems (QPPs) of smaller size rather than a single larger QPP, and thus has faster learning speed than classical -SVR. The significant advantage of our pair--SVR over TSVR is the improvement in the prediction speed and generalization ability by introducing the concepts of the insensitive zone and the regularization term that embodies the essence of statistical learning theory

  15. Paired methods to measure biofilm killing and removal: a case study with Penicillin G treatment of Staphylococcus aureus biofilm.

    Science.gov (United States)

    Ausbacher, D; Lorenz, L; Pitts, B; Stewart, P S; Goeres, D M

    2018-03-01

    Biofilms are microbial aggregates that show high tolerance to antibiotic treatments in vitro and in vivo. Killing and removal are both important in biofilm control, therefore methods that measure these two mechanisms were evaluated in a parallel experimental design. Kill was measured using the single tube method (ASTM method E2871) and removal was determined by video microscopy and image analysis using a new treatment flow cell. The advantage of the parallel test design is that both methods used biofilm covered coupons harvested from a CDC biofilm reactor, a well-established and standardized biofilm growth method. The control Staphylococcus aureus biofilms treated with growth medium increased by 0·6 logs during a 3-h contact time. Efficacy testing showed biofilms exposed to 400 μmol l -1 penicillin G decreased by only 0·3 logs. Interestingly, time-lapse confocal scanning laser microscopy revealed that penicillin G treatment dispersed the biofilm despite being an ineffective killing agent. In addition, no biofilm removal was detected when assays were performed in 96-well plates. These results illustrate that biofilm behaviour and impact of treatments can vary substantially when assayed by different methods. Measuring both killing and removal with well-characterized methods will be crucial for the discovery of new anti-biofilm strategies. Biofilms are tolerant to antimicrobial treatments and can lead to persistent infections. Finding new anti-biofilm strategies and understanding their mode-of-action is therefore of high importance. Historically, antimicrobial testing has focused on measuring the decrease in viability. While kill data are undeniably important, measuring biofilm disruption provides equally useful information. Starting with biofilm grown in the same reactor, we paired assessment of biofilm removal using a new treatment-flow-cell and real-time microscopy with kill data collected using the single tube method (ASTM E2871). Pairing these two methods

  16. A Novel Mechanism of High-Level, Broad-Spectrum Antibiotic Resistance Caused by a Single Base Pair Change in Neisseria gonorrhoeae

    Science.gov (United States)

    2011-09-20

    respect, Eisenstein and Sparling noted that a single base pair deletion in the inverted repeat in the mtrR promoter, a mutation which also confers high...Regulation of the MtrC-MtrD-MtrE efflux-pump system modulates the in vivo fitness of Neisseria gonorrhoeae. J. Infect. Dis. 196:1804 –1812. 21. Eisenstein BI

  17. Inferring relationships between pairs of individuals from locus heterozygosities

    Directory of Open Access Journals (Sweden)

    Spinetti Isabella

    2002-11-01

    Full Text Available Abstract Background The traditional exact method for inferring relationships between individuals from genetic data is not easily applicable in all situations that may be encountered in several fields of applied genetics. This study describes an approach that gives affordable results and is easily applicable; it is based on the probabilities that two individuals share 0, 1 or both alleles at a locus identical by state. Results We show that these probabilities (zi depend on locus heterozygosity (H, and are scarcely affected by variation of the distribution of allele frequencies. This allows us to obtain empirical curves relating zi's to H for a series of common relationships, so that the likelihood ratio of a pair of relationships between any two individuals, given their genotypes at a locus, is a function of a single parameter, H. Application to large samples of mother-child and full-sib pairs shows that the statistical power of this method to infer the correct relationship is not much lower than the exact method. Analysis of a large database of STR data proves that locus heterozygosity does not vary significantly among Caucasian populations, apart from special cases, so that the likelihood ratio of the more common relationships between pairs of individuals may be obtained by looking at tabulated zi values. Conclusions A simple method is provided, which may be used by any scientist with the help of a calculator or a spreadsheet to compute the likelihood ratios of common alternative relationships between pairs of individuals.

  18. 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 T 1 -weighted images (3D-T 1 WIs) 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.

  19. Report on Pairing-based Cryptography.

    Science.gov (United States)

    Moody, Dustin; Peralta, Rene; Perlner, Ray; Regenscheid, Andrew; Roginsky, Allen; Chen, Lily

    2015-01-01

    This report summarizes study results on pairing-based cryptography. The main purpose of the study is to form NIST's position on standardizing and recommending pairing-based cryptography schemes currently published in research literature and standardized in other standard bodies. The report reviews the mathematical background of pairings. This includes topics such as pairing-friendly elliptic curves and how to compute various pairings. It includes a brief introduction to existing identity-based encryption (IBE) schemes and other cryptographic schemes using pairing technology. The report provides a complete study of the current status of standard activities on pairing-based cryptographic schemes. It explores different application scenarios for pairing-based cryptography schemes. As an important aspect of adopting pairing-based schemes, the report also considers the challenges inherent in validation testing of cryptographic algorithms and modules. Based on the study, the report suggests an approach for including pairing-based cryptography schemes in the NIST cryptographic toolkit. The report also outlines several questions that will require further study if this approach is followed.

  20. Enhanced appetitive conditioning following repeated pretreatment with d-amphetamine.

    Science.gov (United States)

    Harmer, C J; Phillips, G D

    1998-07-01

    The behavioural response to psychomotor stimulants is augmented with repeated exposure to these drugs. Enhanced stimulated dopamine overflow within the nucleus accumbens and amygdala has been found to accompany this behavioural sensitization. In the present experiment, rats received 2 mg/kg d-amphetamine or 1 ml/kg physiological saline once per day for 5 days. Five days later, a behavioural assay confirmed that prior repeated d-amphetamine treatment markedly enhanced the locomotor activating effects of a d-amphetamine (0.5 mg/kg, i.p.) challenge. Training on a Pavlovian conditioning task began six days subsequently. In Stage 1, a stimulus (light or tone, S-) was presented negatively correlated with a sucrose reward. In Stage 2, presentation of the alternative counterbalanced stimulus (light or tone, S+) was paired with the availability of a 10% sucrose solution. There were no differences between the two groups in their response to the the S- stimulus. However, sensitized animals showed a selective enhancement in the acquisition of conditioned responding to S+, relative to vehicle-injected controls. No differences in behaviour were recorded during the prestimulus periods, nor during presentations of sucrose. Levels of activity within the operant chamber extraneous to alcove approach were also similar in both groups of animals. The conditioned instrumental efficacy of S+, relative to S- was assessed in Stage 3, in which stimulus availability was made contingent on a novel lever-pressing response. Both groups showed a similar preference for the S+ over the S- stimulus. Hence, rats sensitized by prior repeated d-amphetamine showed enhanced appetitive Pavlovian conditioning, without subsequent effect on conditioned reward efficacy. These data are discussed in light of possible changes in mesoamygdaloid dopamine functioning.

  1. Paired Pulse Basis Functions for the Method of Moments EFIE Solution of Electromagnetic Problems Involving Arbitrarily-shaped, Three-dimensional Dielectric Scatterers

    Science.gov (United States)

    MacKenzie, Anne I.; Rao, Sadasiva M.; Baginski, Michael E.

    2007-01-01

    A pair of basis functions is presented for the surface integral, method of moment solution of scattering by arbitrarily-shaped, three-dimensional dielectric bodies. Equivalent surface currents are represented by orthogonal unit pulse vectors in conjunction with triangular patch modeling. The electric field integral equation is employed with closed geometries for dielectric bodies; the method may also be applied to conductors. Radar cross section results are shown for dielectric bodies having canonical spherical, cylindrical, and cubic shapes. Pulse basis function results are compared to results by other methods.

  2. 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.

  3. Hybridized plasmon in an asymmetric cut-wire-pair structure

    Energy Technology Data Exchange (ETDEWEB)

    Tung, Nguyen Thanh [Vietnamese Military Academy of Science and Technology, Hanoi (Viet Nam); Hanyang University, Seoul (Korea, Republic of); Rhee, Joo Yull [Sungkyunkwan University, Suwon (Korea, Republic of); Park, Jin Woo; Lee, Young Pak [Hanyang University, Seoul (Korea, Republic of)

    2010-12-15

    In this report, we discuss an electromagnetic analog of the molecular-orbital theory for metamaterial structures. We show that the electromagnetic responses of a metamagnetic structure consisting of paired cut-wires can be well understood by using the plasmon-hybridization mechanism. The simulated transmission spectra of the asymmetric cut-wire-pair structure, which were obtained utilizing the transfer-matrix method, strongly support our suggestion.

  4. Lax Pairs for Discrete Integrable Equations via Darboux Transformations

    International Nuclear Information System (INIS)

    Cao Ce-Wen; Zhang Guang-Yao

    2012-01-01

    A method is developed to construct discrete Lax pairs using Darboux transformations. More kinds of Lax pairs are found for some newly appeared discrete integrable equations, including the H1, the special H3 and the Q1 models in the Adler—Bobenko—Suris list and the closely related discrete and semi-discrete pKdV, pMKdV, SG and Liouville equations. (general)

  5. Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

    Science.gov (United States)

    Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

    2014-04-08

    The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

  6. Analyzing Repeated Measures Marginal Models on Sample Surveys with Resampling Methods

    Directory of Open Access Journals (Sweden)

    James D. Knoke

    2005-12-01

    Full Text Available Packaged statistical software for analyzing categorical, repeated measures marginal models on sample survey data with binary covariates does not appear to be available. Consequently, this report describes a customized SAS program which accomplishes such an analysis on survey data with jackknifed replicate weights for which the primary sampling unit information has been suppressed for respondent confidentiality. First, the program employs the Macro Language and the Output Delivery System (ODS to estimate the means and covariances of indicator variables for the response variables, taking the design into account. Then, it uses PROC CATMOD and ODS, ignoring the survey design, to obtain the design matrix and hypothesis test specifications. Finally, it enters these results into another run of CATMOD, which performs automated direct input of the survey design specifications and accomplishes the appropriate analysis. This customized SAS program can be employed, with minor editing, to analyze general categorical, repeated measures marginal models on sample surveys with replicate weights. Finally, the results of our analysis accounting for the survey design are compared to the results of two alternate analyses of the same data. This comparison confirms that such alternate analyses, which do not properly account for the design, do not produce useful results.

  7. Unmatched Projector/Backprojector Pairs: Perturbation and Convergence Analysis

    DEFF Research Database (Denmark)

    Elfving, Tommy; Hansen, Per Christian

    2018-01-01

    methods in order to understand the role played by the nonmatch of the matrices. We also study the convergence properties of linear stationary iterations based on unmatched matrix pairs, leading to insight into the behavior of some important row-and column-oriented algebraic iterative methods. We conclude...

  8. Narrative exposure therapy for posttraumatic stress disorder associated with repeated interpersonal trauma in patients with severe mental illness: a mixed methods design

    Directory of Open Access Journals (Sweden)

    Maria W. Mauritz

    2016-09-01

    Full Text Available Background: In the Netherlands, most patients with severe mental illness (SMI receive flexible assertive community treatment (FACT provided by multidisciplinary community mental health teams. SMI patients with comorbid posttraumatic stress disorder (PTSD are sometimes offered evidence-based trauma-focused treatment like eye movement desensitization reprocessing or prolonged exposure. There is a large amount of evidence for the effectiveness of narrative exposure therapy (NET within various vulnerable patient groups with repeated interpersonal trauma. Some FACT-teams provide NET for patients with comorbid PTSD, which is promising, but has not been specifically studied in SMI patients. Objectives: The primary aim is to evaluate NET in SMI patients with comorbid PTSD associated with repeated interpersonal trauma to get insight into whether (1 PTSD and dissociative symptoms changes and (2 changes occur in the present SMI symptoms, care needs, quality of life, global functioning, and care consumption. The second aim is to gain insight into patients’ experiences with NET and to identify influencing factors on treatment results. Methods: This study will have a mixed methods convergent design consisting of quantitative repeated measures and qualitative semi-structured in-depth interviews based on Grounded Theory. The study population will include adult SMI outpatients (n=25 with comorbid PTSD and receiving NET. The quantitative study parameters will be existence and severity of PTSD, dissociative, and SMI symptoms; care needs; quality of life; global functioning; and care consumption. In a longitudinal analysis, outcomes will be analyzed using mixed models to estimate the difference in means between baseline and repeated measurements. The qualitative study parameters will be experiences with NET and perceived factors for success or failure. Integration of quantitative and qualitative results will be focused on interpreting how qualitative results

  9. PENINGKATAN KEMAMPUAN REPRESENTASI MATEMATIS MELALUI MODEL PEMBELAJARAN KOOPERATIF THINK PAIR SHARE

    Directory of Open Access Journals (Sweden)

    Yunni Arnidha

    2016-04-01

    Full Text Available This study aims to analyze the improvement of students’ mathematicalrepresentation achievement taught by cooperative learning think pair share andstudents’ mathematical representation achievement taught by conventional method.This study is quasi experimental with Pretest –Posttest Control Group Design. Thisstudy conducted at SMPN 3 Pringsewu. The population was all of the eight gradestudents at SMPN 3 Pringsewu, with the samples of this study consists of the VIII-2class as the experiment class and VIII-5 class as the control class. To obtain thedata, it used mathematical representation achievement test instrument. The dataanalysis was conducted to know the average difference between two samples usingt-test. The result showed the improvement of mathematical representationachievement taught by cooperative learning think pair share is better than thestudents taught by conventional learning method.Keywords: think pair share model, conventional learning method,Mathematical representation

  10. Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

    Science.gov (United States)

    Takezawa, Yusuke; Shionoya, Mitsuhiko

    2012-12-18

    With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional

  11. Density functional approach for pairing in finite size systems

    International Nuclear Information System (INIS)

    Hupin, G.

    2011-09-01

    The combination of functional theory where the energy is written as a functional of the density, and the configuration mixing method, provides an efficient description of nuclear ground and excited state properties. The specific pathologies that have been recently observed, show the lack of a clear underlying justification associated to the breaking and the restoration of symmetries within density functional theory. This thesis focuses on alternative treatments of pairing correlations in finite many body systems that consider the breaking and the restoration of the particle number conservation. The energy is written as a functional of a projected quasi-particle vacuum and can be linked to the one obtained within the configuration mixing framework. This approach has been applied to make the projection either before or after the application of the variational principle. It is more flexible than the usual configuration mixing method since it can handle more general effective interactions than the latter. The application to the Krypton isotopes shows the feasibility and the efficiency of the method to describe pairing near closed shell nuclei. Following a parallel path, a theory where the energy is written as a functional of the occupation number and natural orbitals is proposed. The new functional is benchmarked in an exactly solvable model, the pairing Hamiltonian. The efficiency and the applicability of the new theory have been tested for various pairing strengths, single particle energy spectra and numbers of particles. (author)

  12. Cooper Pairs in Insulators?

    International Nuclear Information System (INIS)

    Valles, James

    2008-01-01

    Nearly 50 years elapsed between the discovery of superconductivity and the emergence of the microscopic theory describing this zero resistance state. The explanation required a novel phase of matter in which conduction electrons joined in weakly bound pairs and condensed with other pairs into a single quantum state. Surprisingly, this Cooper pair formation has also been invoked to account for recently uncovered high-resistance or insulating phases of matter. To address this possibility, we have used nanotechnology to create an insulating system that we can probe directly for Cooper pairs. I will present the evidence that Cooper pairs exist and dominate the electrical transport in these insulators and I will discuss how these findings provide new insight into superconductor to insulator quantum phase transitions.

  13. Drift wave in pair-ion plasma

    Indian Academy of Sciences (India)

    of charged particles in electromagnetic fields. The linear and nonlinear collective modes in electron-positron plasma have been investigated theoretically [3–6]. Recently, Oohara and Hatakeyama [7] have developed a novel method for generating a pair plasma con- sisting of only negative and positive ions with equal mass ...

  14. Semiclassical description of soliton-antisoliton pair production in particle collisions

    Energy Technology Data Exchange (ETDEWEB)

    Demidov, S.V.; Levkov, D.G. [Institute for Nuclear Research of the Russian Academy of Sciences,60th October Anniversary prospect 7a, Moscow 117312 (Russian Federation)

    2015-11-10

    We develop a consistent semiclassical method to calculate the probability of topological soliton-antisoliton pair production in collisions of elementary particles. In our method one adds an auxiliary external field pulling the soliton and antisoliton in the opposite directions. This transforms the original scattering process into a Schwinger pair creation of the solitons induced by the particle collision. One describes the Schwinger process semiclassically and recovers the original scattering probability in the limit of vanishing external field. We illustrate the method in (1+1)-dimensional scalar field model where the suppression exponents of soliton-antisoliton production in the multiparticle and two-particle collisions are computed numerically.

  15. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA).

    Science.gov (United States)

    Jensen, Ronald W; Rivest, Jason; Li, Wei; Vissa, Varalakshmi

    2011-07-15

    The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO, leprosy remains endemic in many countries with approximately 250,000 new cases each year. The entire M. leprae genome has been mapped and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites). Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci. Variable number tandem repeat (VNTR) analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA) has been used to study leprosy evolution and transmission in several countries including China, Malawi, the Philippines, and Brazil. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS). The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions. The PCR products may be subjected to agarose gel electrophoresis to verify the

  16. An automated method for the analysis of phenolic acids in plasma based on ion-pairing micro-extraction coupled on-line to gas chromatography/mass spectrometry with in-liner derivatisation

    NARCIS (Netherlands)

    Peters, S.; Kaal, E.; Horsting, I.; Janssen, H.-G.

    2012-01-01

    A new method is presented for the analysis of phenolic acids in plasma based on ion-pairing ‘Micro-extraction in packed sorbent’ (MEPS) coupled on-line to in-liner derivatisation-gas chromatography-mass spectrometry (GC-MS). The ion-pairing reagent served a dual purpose. It was used both to improve

  17. Repeated episodes of chronic intermittent ethanol promote insensitivity to devaluation of the reinforcing effect of ethanol.

    Science.gov (United States)

    Lopez, M F; Becker, H C; Chandler, L J

    2014-11-01

    Studies in animal models have shown that repeated episodes of alcohol dependence and withdrawal promote escalation of drinking that is presumably associated with alterations in the addiction neurocircuitry. Using a lithium chloride-ethanol pairing procedure to devalue the reinforcing properties of ethanol, the present study determined whether multiple cycles of chronic intermittent ethanol (CIE) exposure by vapor inhalation also alters the sensitivity of drinking behavior to the devaluation of ethanol's reinforcing effects. The effect of devaluation on operant ethanol self-administration and extinction was examined in mice prior to initiation of CIE (short drinking history) and after repeated cycles of CIE or air control exposure (long drinking history). Devaluation significantly attenuated the recovery of baseline ethanol self-administration when tested either prior to CIE or in the air-exposed controls that had experienced repeated bouts of drinking but no CIE. In contrast, in mice that had undergone repeated cycles of CIE exposure that promoted escalation of ethanol drinking, self-administration was completely resistant to the effect of devaluation. Devaluation had no effect on the time course of extinction training in either pre-CIE or post-CIE mice. Taken together, these results are consistent with the suggestion that repeated cycles of ethanol dependence and withdrawal produce escalation of ethanol self-administration that is associated with a change in sensitivity to devaluation of the reinforcing properties of ethanol. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Charge Aspects of Composite Pair Superconductivity

    Science.gov (United States)

    Flint, Rebecca

    2014-03-01

    Conventional Cooper pairs form from well-defined electronic quasiparticles, making the internal structure of the pair irrelevant. However, in the 115 family of superconductors, the heavy electrons are forming as they pair and the internal pair structure becomes as important as the pairing mechanism. Conventional spin fluctuation mediated pairing cannot capture the direct transition from incoherent local moments to heavy fermion superconductivity, but the formation of composite pairs favored by the two channel Kondo effect can. These composite pairs are local d-wave pairs formed by two conduction electrons in orthogonal Kondo channels screening the same local moment. Composite pairing shares the same symmetries as magnetically mediated pairing, however, only composite pairing necessarily involves a redistribution of charge within the unit cell originating from the internal pair structure, both as a monopole (valence change) and a quadrupole effect. This redistribution will onset sharply at the superconducting transition temperature. A smoking gun test for composite pairing is therefore a sharp signature at Tc - for example, a cusp in the Mossbauer isomer shift in NpPd5Al2 or in the NQR shift in (Ce,Pu)CoIn5.

  19. A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

    Science.gov (United States)

    Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

    2017-11-06

    Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

  20. Pairing correlations around scission

    International Nuclear Information System (INIS)

    Krappe, H.J.; Fadeev, S.

    2001-01-01

    To describe pairing correlations in a fissioning system one commonly projects the BCS wave function separately onto good particle numbers in each fragment in the exit channel, but only onto the total number of particles in the parent system. We propose to interpolate between these limiting situations by the generator-coordinate method with the particle-number difference between the nascent fragments as the generator coordinate. Model calculations are presented for the Hill-Wheeler-box potential with a δ-function diaphragm to mimic scission

  1. Repeat: a framework to assess empirical reproducibility in biomedical research

    Directory of Open Access Journals (Sweden)

    Leslie D. McIntosh

    2017-09-01

    Full Text Available Abstract Background The reproducibility of research is essential to rigorous science, yet significant concerns of the reliability and verifiability of biomedical research have been recently highlighted. Ongoing efforts across several domains of science and policy are working to clarify the fundamental characteristics of reproducibility and to enhance the transparency and accessibility of research. Methods The aim of the proceeding work is to develop an assessment tool operationalizing key concepts of research transparency in the biomedical domain, specifically for secondary biomedical data research using electronic health record data. The tool (RepeAT was developed through a multi-phase process that involved coding and extracting recommendations and practices for improving reproducibility from publications and reports across the biomedical and statistical sciences, field testing the instrument, and refining variables. Results RepeAT includes 119 unique variables grouped into five categories (research design and aim, database and data collection methods, data mining and data cleaning, data analysis, data sharing and documentation. Preliminary results in manually processing 40 scientific manuscripts indicate components of the proposed framework with strong inter-rater reliability, as well as directions for further research and refinement of RepeAT. Conclusions The use of RepeAT may allow the biomedical community to have a better understanding of the current practices of research transparency and accessibility among principal investigators. Common adoption of RepeAT may improve reporting of research practices and the availability of research outputs. Additionally, use of RepeAT will facilitate comparisons of research transparency and accessibility across domains and institutions.

  2. 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.

  3. Experimental Test of Data Analysis Methods from Staggered Pair X-ray Beam Position Monitors at Bending Magnet Beamlines

    Science.gov (United States)

    Buth, G.; Huttel, E.; Mangold, S.; Steininger, R.; Batchelor, D.; Doyle, S.; Simon, R.

    2013-03-01

    Different methods have been proposed to calculate the vertical position of the photon beam centroid from the four blade currents of staggered pair X-ray beam position monitors (XBPMs) at bending magnet beamlines since they emerged about 15 years ago. The original difference-over-sum method introduced by Peatman and Holldack is still widely used, even though it has been proven to be rather inaccurate at large beam displacements. By systematically generating bumps in the electron orbit of the ANKA storage ring and comparing synchronized data from electron BPMs and XBPM blade currents, we have been able to show that the log-ratio method by S. F. Lin, B.G. Sun et al. is superior (meaning the characteristic being closer to linear) to the ratio method, which in turn is superior to the difference over sum method. These findings are supported by simulations of the XBPM response to changes of the beam centroid. The heuristic basis for each of the methods is investigated. The implications on using XBPM readings for orbit correction are discussed

  4. A neural-network approach to the problem of photon-pair combinatorics

    International Nuclear Information System (INIS)

    Awes, T.C.

    1990-06-01

    A recursive neural-network algorithm is applied to the problem of correctly pairing photons from π 0 , η, and higher resonance decays in the presence of a large background of photons resulting from many simultaneous decays. The method uses the full information of the multi-photon final state to suppress the selection of false photon pairs which arise from the many combinatorial possibilities. The method is demonstrated for simulated photon events under semirealistic experimental conditions. 3 refs., 3 figs

  5. Repeated morphine treatment influences operant and spatial learning differentially

    Institute of Scientific and Technical Information of China (English)

    Mei-Na WANG; Zhi-Fang DONG; Jun CAO; Lin XU

    2006-01-01

    Objective To investigate whether repeated morphine exposure or prolonged withdrawal could influence operant and spatial learning differentially. Methods Animals were chronically treated with morphine or subjected to morphine withdrawal. Then, they were subjected to two kinds of learning: operant conditioning and spatial learning.Results The acquisition of both simple appetitive and cued operant learning was impaired after repeated morphine treatment. Withdrawal for 5 weeks alleviated the impairments. Single morphine exposure disrupted the retrieval of operant memory but had no effect on rats after 5-week withdrawal. Contrarily, neither chronic morphine exposure nor 5-week withdrawal influenced spatial learning task of the Morris water maze. Nevertheless, the retrieval of spatial memory was impaired by repeated morphine exposure but not by 5-week withdrawal. Conclusion These observations suggest that repeated morphine exposure can influence different types of learning at different aspects, implicating that the formation of opiate addiction may usurp memory mechanisms differentially.

  6. The Role of the Repeat in the Bear Feast in Traditional Khanty Culture

    Directory of Open Access Journals (Sweden)

    Anna A. Grinevich (Zorkoltseva

    2012-09-01

    Full Text Available This paper is devoted to a role of repeat in Khanty folklore. Songs of a bear feast have served as the source material for the research. The author traces the role of a repeat at different text levels: structure, lexical level, and plot. The repeat is proposed as a fundamental method of traditional Khanty arts.

  7. Detection of no-model input-output pairs in closed-loop systems.

    Science.gov (United States)

    Potts, Alain Segundo; Alvarado, Christiam Segundo Morales; Garcia, Claudio

    2017-11-01

    The detection of no-model input-output (IO) pairs is important because it can speed up the multivariable system identification process, since all the pairs with null transfer functions are previously discarded and it can also improve the identified model quality, thus improving the performance of model based controllers. In the available literature, the methods focus just on the open-loop case, since in this case there is not the effect of the controller forcing the main diagonal in the transfer matrix to one and all the other terms to zero. In this paper, a modification of a previous method able to detect no-model IO pairs in open-loop systems is presented, but adapted to perform this duty in closed-loop systems. Tests are performed by using the traditional methods and the proposed one to show its effectiveness. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

  8. Effective interionic pair potentials in liquid alkali metals

    International Nuclear Information System (INIS)

    Kumaravadivel, R.

    1984-06-01

    Information on the effective pair potential of liquid alkali metals is obtained from liquid structure factor data by the combination of two approximate methods in the theory of liquids. One method stems from treating the indirect ion-ion interaction in the optimised random phase approximation (ORPA) and the other uses the modified hypernetted chain (MHNC) equation. It is shown that, in the region of the main attractive well, the effective pair potential is bracketed by the results obtained from these two methods. The MHNC inversion scheme does not fare well in providing information on the potential in the region of interionic distance in the tail of the interionic potential. A cross-over from the hard-sphere bridge function to the mean spherical approximation (MSA) bridge function for the long range behaviour of the bridge term in the MHNC equation does not provide appreciable improvement. (author)

  9. Repeated extraction of DNA from FTA cards

    DEFF Research Database (Denmark)

    Stangegaard, Michael; Ferrero, Laura; Børsting, Claus

    2011-01-01

    Extraction of DNA using magnetic bead based techniques on automated DNA extraction instruments provides a fast, reliable and reproducible method for DNA extraction from various matrices. However, the yield of extracted DNA from FTA-cards is typically low. Here, we demonstrate that it is possible...... to repeatedly extract DNA from the processed FTA-disk. The method increases the yield from the nanogram range to the microgram range....

  10. A comparison of genetic map distance and linkage disequilibrium between 15 polymorphic dinucleotide repeat loci in two populations

    Energy Technology Data Exchange (ETDEWEB)

    Urbanek, M.; Goldman, D.; Long, J.C. [Lab. of Neurogenetics, Rockville, MD (United States)

    1994-09-01

    Linkage disequilibrium has recently been used to map the diastrophic dysplasia gene in a Finnish sample. One advantage of this method is that the large pedigrees required by some other methods are unnecessary. Another advantage is that linkage disequilibrium mapping capitalizes on the cumulative history of recombination events, rather than those occurring within the sampled individuals. A potential limitation of linkage disequilibrium mapping is that linkage equilibrium is likely to prevail in all but the most isolated populations, e.g., those which have recently experienced founder effects or severe population bottlenecks. In order to test the method`s generality, we examined patterns of linkage disequilibrium between pairs of loci within a known genetic map. Two populations were analyzed. The first population, Navajo Indians (N=45), is an isolate that experienced a severe bottleneck in the 1860`s. The second population, Maryland Caucasians (N=45), is cosmopolitan. We expected the Navajo sample to display more linkage disequilibrium than the Caucasian sample, and possibly that the Navajo disequilibrium pattern would reflect the genetic map. Linkage disequilibrium coefficients were estimated between pairs of alleles at different loci using maximum likelihood. The genetic isolate structure of Navajo Indians is confirmed by the DNA typings. Heterozygosity is lower than in the Caucasians, and fewer different alleles are observed. However, a relationship between genetic map distance and linkage disequilibrium could be discerned in neither the Navajo nor the Maryland samples. Slightly more linkage disequilibrium was observed in the Navajos, but both data sets were characterized by very low disequilibrium levels. We tentatively conclude that linkage disequilibrium mapping with dinucleotide repeats will only be useful with close linkage between markers and diseases, even in very isolated populations.

  11. Pseudoautosomal region in schizophrenia: linkage analysis of seven loci by sib-pair and lod-score methods.

    Science.gov (United States)

    d'Amato, T; Waksman, G; Martinez, M; Laurent, C; Gorwood, P; Campion, D; Jay, M; Petit, C; Savoye, C; Bastard, C

    1994-05-01

    In a previous study, we reported a nonrandom segregation between schizophrenia and the pseudoautosomal locus DXYS14 in a sample of 33 sibships. That study has been extended by the addition of 16 new sibships from 16 different families. Data from six other loci of the pseudoautosomal region and of the immediately adjacent part of the X specific region have also been analyzed. Two methods of linkage analysis were used: the affected sibling pair (ASP) method and the lod-score method. Lod-score analyses were performed on the basis of three different models--A, B, and C--all shown to be consistent with the epidemiological data on schizophrenia. No clear evidence for linkage was obtained with any of these models. However, whatever the genetic model and the disease classification, maximum lod scores were positive with most of the markers, with the highest scores generally being obtained for the DXYS14 locus. When the ASP method was used, the earlier finding of nonrandom segregation between schizophrenia and the DXYS14 locus was still supported in this larger data set, at an increased level of statistical significance. Findings of ASP analyses were not significant for the other loci. Thus, findings obtained from analyses using the ASP method, but not the lod-score method, were consistent with the pseudoautosomal hypothesis for schizophrenia.

  12. Top quark pair production beyond NNLO

    Energy Technology Data Exchange (ETDEWEB)

    Muselli, Claudio [TIF Lab, Dipartimento di Fisica, Università di Milano, and INFN - Sezione di Milano,Via Celoria 16, I-20133 Milano (Italy); Bonvini, Marco [Rudolf Peierls Centre for Theoretical Physics, University of Oxford,1 Keble Road, OX1 3NP, Oxford (United Kingdom); Forte, Stefano [TIF Lab, Dipartimento di Fisica, Università di Milano, and INFN - Sezione di Milano,Via Celoria 16, I-20133 Milano (Italy); Marzani, Simone [Center for Theoretical Physics, Massachusetts Institute of Technology,77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Ridolfi, Giovanni [Dipartimento di Fisica, Università di Genova and INFN - Sezione di Genova,Via Dodecaneso 33, I-16146 Genova (Italy)

    2015-08-17

    We construct an approximate expression for the total cross section for the production of a heavy quark-antiquark pair in hadronic collisions at next-to-next-to-next-to-leading order (N{sup 3}LO) in α{sub s}. We use a technique which exploits the analyticity of the Mellin space cross section, and the information on its singularity structure coming from large N (soft gluon, Sudakov) and small N (high energy, BFKL) all order resummations, previously introduced and used in the case of Higgs production. We validate our method by comparing to available exact results up to NNLO. We find that N{sup 3}LO corrections increase the predicted top pair cross section at the LHC by about 4% over the NNLO.

  13. Top quark pair production beyond NNLO

    International Nuclear Information System (INIS)

    Muselli, Claudio; Bonvini, Marco; Forte, Stefano; Marzani, Simone; Ridolfi, Giovanni

    2015-01-01

    We construct an approximate expression for the total cross section for the production of a heavy quark-antiquark pair in hadronic collisions at next-to-next-to-next-to-leading order (N 3 LO) in α s . We use a technique which exploits the analyticity of the Mellin space cross section, and the information on its singularity structure coming from large N (soft gluon, Sudakov) and small N (high energy, BFKL) all order resummations, previously introduced and used in the case of Higgs production. We validate our method by comparing to available exact results up to NNLO. We find that N 3 LO corrections increase the predicted top pair cross section at the LHC by about 4% over the NNLO.

  14. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

    Science.gov (United States)

    Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

    2016-01-07

    The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

  15. PENGARUH PELAKSANAAN MODEL PEMBELAJARAN KOOPERATIF TIPE THINK PAIR SHARE TERHADAP HASIL BELAJAR IPS SISWA

    Directory of Open Access Journals (Sweden)

    andi fathur asdar

    2016-08-01

    Full Text Available The objective of this research was to describe: 1 Teacher ability in the implementation of cooperative learning Think Pair Share, 2 Ttudent activities in the implementation of cooperative learning Think Pair Share, 3 Tearning result on IPS before and after the implementation of cooperative learning Think Pair Share, 4 learning result on IPS before and after learning process with lecture method, 5 to find out the influence of the implementation of cooperative learning Think Pair Share toward learning result on IPS. The method used was true experiment with pre-test post-test control group design. The population in the study are 4th grade student at SDN Sungguminasa II Somba Opu District Gowa Regency. Samples used are 40 student 20 student each from experiment and comparing group. chosen by simple random sampling. The data obtained from samples were analyzed with descritive and inferensial statistic. The result shows: 1 teacher ability in the implementation of cooperative learning Think Pair Share have increased, 2 student activities in the implementation of cooperative learning Think Pair Share, 3 student learning result who teached by cooperative learning Think Pair Share have increased, 4 student learning result who teached by lecture method have not increased, 5 the implementation of cooperative learning Think Pair Share is influencing toward learning result on IPS in 4th grade student at SDN Sungguminasa II Somba Opu District Gowa Regency.

  16. Predictive labeling with dependency pairs using SAT

    NARCIS (Netherlands)

    Koprowski, A.; Middeldorp, A.; Pfenning, F.

    2007-01-01

    This paper combines predictive labeling with dependency pairs and reports on its implementation. Our starting point is the method of proving termination of rewrite systems using semantic labeling with infinite models in combination with lexicographic path orders. We replace semantic labeling with

  17. Importance of interlayer pair tunneling: A variational perspective

    International Nuclear Information System (INIS)

    Medhi, Amal; Basu, Saurabh

    2011-01-01

    We study the effect of interlayer pair tunneling in a bilayer superconductor where each layer is described by a two dimensional t-J model and the two layers are connected by the Josephson pair tunneling term. We study this model using a grand canonical variational Monte Carlo (GVMC) method, for which we develop a new algorithm to perform Monte Carlo simulation of a system with fluctuating particle number. The variational wavefunction is taken to be the product of two Gutzwiller projected d-wave BCS wavefunctions with variable particle densities, one for each layer. We calculate the energy of the above state as a function of the d-wave superconducting gap parameter, Δ. We find that the interlayer pair tunneling energy, E perpendicular shows interesting variation with Δ. E perpendicular tends to enhance the optimal value of Δ, thereby the superconducting pairing. However the magnitude of the tunneling energy is found to be too small to have any appreciable effect on the physical properties. While the result is supported by early experiments and hence may appear known to the community, the current work presents a new approach to the problem and confirms the diminished role of interlayer pair tunneling by directly calculating its contribution to superconducting condensation energy.

  18. Study of the pair-interaction function in some normal metals; Etude de l'interaction de paire dans quelques metaux normaux

    Energy Technology Data Exchange (ETDEWEB)

    Pick, R [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1965-06-01

    The pair interaction function has been derived for the following metals: Li, Na, K, Al. It is obtained via a second order perturbation expansion of the wave functions of the conduction electrons using a self-consistent pseudo-potential. Exchange and correlations between those electrons have been ignored. Such an interaction is only valid at constant volume and depends on a single experimental parameter, namely the ionic volume. Its main features are a pronounced minimum in the vicinity of the nearest neighbours, especially marked in alkaline metals, and an asymptotic decrease of the form cos(2k{sub F}r)/r{sup 3}. This interaction gives the correct crystalline structure of these metals at 0 K as well as a good approximation of the phonon spectrum of an alkaline. The validity of the perturbation technique is discussed. We prove that the pair interaction function is correctly given to second order in the pseudo-potential despite the various approximations and errors involved by such a method. (author) [French] L'interaction de paire effective entre ions a ete calculee dans les metaux Li, Na, K et Al. Elle est obtenue par un developpement en serie de perturbation des fonctions d'onde des electrons de conduction. Le developpement est pousse au deuxieme ordre et utilise un pseudo-potentiel self-consistant. Les phenomenes d'echange et de correlations entre ces electrons ont ete negliges. L'interaction calculee n'a de sens qu'a volume constant. Elle depend d'un seul parametre experimental, le volume ionique. Elle se caracterise par un minimum prononce de l'energie de paire pour les proches voisins, surtout marque chez les alcalins. Elle decroit asymptotiquement en cos(2k{sub F}r)/r{sup 3}. Elle permet de predire la structure cristalline la plus stable a 0 K; elle donne le spectre de phonons des alcalins avec une assez bonne precision. Par ailleurs, la validite de la methode de perturbation du deuxieme ordre est discutee. On montre qu'elle donne correctement l

  19. A family of integrable differential–difference equations, its bi-Hamiltonian structure and binary nonlinearization of the Lax pairs and adjoint Lax pairs

    International Nuclear Information System (INIS)

    Xu Xixiang

    2012-01-01

    Highlights: ► We deduce a family of integrable differential–difference equations. ► We present a discrete Hamiltonian operator involving two arbitrary real parameters. ► We establish the bi-Hamiltonian structure for obtained integrable family. ► Liouvolle integrability of the obtained family is demonstrated. ► Every equation in obtained family is factored through the binary nonlinearization. - Abstract: A family of integrable differential–difference equations is derived by the method of Lax pairs. A discrete Hamiltonian operator involving two arbitrary real parameters is introduced. When the parameters are suitably selected, a pair of discrete Hamiltonian operators is presented. Bi-Hamiltonian structure of obtained family is established by discrete trace identity. Then, Liouville integrability for the obtained family is proved. Ultimately, through the binary nonlinearization of the Lax pairs and adjoint Lax pairs, every differential–difference equation in obtained family is factored by an integrable symplectic map and a finite-dimensional integrable system in Liouville sense.

  20. EFEKTIVITAS PENGGUNAAN METODE THINK PAIR SHARE DALAM PEMBELAJARAN EKONOMI POKOK BAHASAN PEMBENTUKAN HARGA PASAR DI SMP

    Directory of Open Access Journals (Sweden)

    Joko Widodo

    2011-06-01

    Full Text Available The result of teaching-learning by using Think Pair Share method can improve the students’ activities. It can be seen from the steps to apply the Think Pair Share method that focused on student-centre. Think pair share learning has a simple structure, as a basic of the development ‘cooperative class’ which can help the learning process actively for students, thus it can improve the students’ study result. Students actively can show their ability to discuss and share and express the answer of questions in front of the class. Teachers in teaching- learning process by using think pair share method acted as mediator, facilitator and motivator. It is different with conventional teaching-learning process which focused on teacher-center. Students were passive in teaching-learning process. Students tended to be bored if the teacher was lack to give motivation for students to pay attention to the teacher. Thus, the using of think pair share would be more effective if we see on how the students interaction in learning process. Teacher can vary think pair share with conventional method or other method to improve the students’ activities in learning process, therefore the students’ result study will be increased.   Keywords: Think-pair-share, the increase of result study.

  1. EFEKTIVITAS PENGGUNAAN METODE THINK PAIR SHARE DALAM PEMBELAJARAN EKONOMI POKOK BAHASAN PEMBENTUKAN HARGA PASAR DI SMP

    Directory of Open Access Journals (Sweden)

    Joko Widodo

    2007-06-01

    Full Text Available The result of teaching-learning by using Think Pair Share method can improve the students’ activities. It can be seen from the steps to apply the Think Pair Share method that focused on student-centre. Think pair share learning has a simple structure, as a basic of the development ‘cooperative class’ which can help the learning process actively for students, thus it can improve the students’ study result. Students actively can show their ability to discuss and share and express the answer of questions in front of the class. Teachers in teaching- learning process by using think pair share method acted as mediator, facilitator and motivator. It is different with conventional teaching-learning process which focused on teacher-center. Students were passive in teaching-learning process. Students tended to be bored if the teacher was lack to give motivation for students to pay attention to the teacher. Thus, the using of think pair share would be more effective if we see on how the students interaction in learning process. Teacher can vary think pair share with conventional method or other method to improve the students’ activities in learning process, therefore the students’ result study will be increased.   Keywords: Think-pair-share, the increase of result study.

  2. Kappa statistic for clustered matched-pair data.

    Science.gov (United States)

    Yang, Zhao; Zhou, Ming

    2014-07-10

    Kappa statistic is widely used to assess the agreement between two procedures in the independent matched-pair data. For matched-pair data collected in clusters, on the basis of the delta method and sampling techniques, we propose a nonparametric variance estimator for the kappa statistic without within-cluster correlation structure or distributional assumptions. The results of an extensive Monte Carlo simulation study demonstrate that the proposed kappa statistic provides consistent estimation and the proposed variance estimator behaves reasonably well for at least a moderately large number of clusters (e.g., K ≥50). Compared with the variance estimator ignoring dependence within a cluster, the proposed variance estimator performs better in maintaining the nominal coverage probability when the intra-cluster correlation is fair (ρ ≥0.3), with more pronounced improvement when ρ is further increased. To illustrate the practical application of the proposed estimator, we analyze two real data examples of clustered matched-pair data. Copyright © 2014 John Wiley & Sons, Ltd.

  3. Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

    Science.gov (United States)

    Schnall-Levin, Michael; Rissland, Olivia S.; Johnston, Wendy K.; Perrimon, Norbert; Bartel, David P.; Berger, Bonnie

    2011-01-01

    MicroRNAs (miRNAs) regulate numerous biological processes by base-pairing with target messenger RNAs (mRNAs), primarily through sites in 3′ untranslated regions (UTRs), to direct the repression of these targets. Although miRNAs have sometimes been observed to target genes through sites in open reading frames (ORFs), large-scale studies have shown such targeting to be generally less effective than 3′ UTR targeting. Here, we show that several miRNAs each target significant groups of genes through multiple sites within their coding regions. This ORF targeting, which mediates both predictable and effective repression, arises from highly repeated sequences containing miRNA target sites. We show that such sequence repeats largely arise through evolutionary duplications and occur particularly frequently within families of paralogous C2H2 zinc-finger genes, suggesting the potential for their coordinated regulation. Examples of ORFs targeted by miR-181 include both the well-known tumor suppressor RB1 and RBAK, encoding a C2H2 zinc-finger protein and transcriptional binding partner of RB1. Our results indicate a function for repeat-rich coding sequences in mediating post-transcriptional regulation and reveal circumstances in which miRNA-mediated repression through ORF sites can be reliably predicted. PMID:21685129

  4. Numerical studies of pair creation in counterpropagating laser fields

    Energy Technology Data Exchange (ETDEWEB)

    Ruf, Matthias

    2009-05-27

    Pair creation from vacuum induced by electromagnetic fields is probably one of the most intriguing phenomena in physics. If the fields are sufficiently strong, the QED vacuum become unstable. Due to the remarkable progress in laser technology during recent years an experimental investigation of pair creation by pure laser light is coming into reach. The focus of this thesis is on pair creation in counterpropagating laser beams. The pair creation probability is calculated employing the numerically obtained solutions of the Dirac equation. This numerical ansatz has the capability of calculating the momentum distribution of the created pairs in a single propagation, for pure time dependent field configurations. Furthermore, it allows to take the magnetic component of the laser fields into account, which is usually neglected. The latter strongly affects the creation process at high laser frequency. The involved numerical calculations are rather time consuming, therefore the second project of this thesis was to develop a highly efficient code for solving relativistic quantum mechanical problems. This is accomplished by adopting the split-operator method to the Klein-Gordon equation. Here the possibility arises to use parallel computing. However the corresponding spin-statistics becomes crucial in the case of pair creation, demonstrated in several examples. (orig.)

  5. Numerical studies of pair creation in counterpropagating laser fields

    International Nuclear Information System (INIS)

    Ruf, Matthias

    2009-01-01

    Pair creation from vacuum induced by electromagnetic fields is probably one of the most intriguing phenomena in physics. If the fields are sufficiently strong, the QED vacuum become unstable. Due to the remarkable progress in laser technology during recent years an experimental investigation of pair creation by pure laser light is coming into reach. The focus of this thesis is on pair creation in counterpropagating laser beams. The pair creation probability is calculated employing the numerically obtained solutions of the Dirac equation. This numerical ansatz has the capability of calculating the momentum distribution of the created pairs in a single propagation, for pure time dependent field configurations. Furthermore, it allows to take the magnetic component of the laser fields into account, which is usually neglected. The latter strongly affects the creation process at high laser frequency. The involved numerical calculations are rather time consuming, therefore the second project of this thesis was to develop a highly efficient code for solving relativistic quantum mechanical problems. This is accomplished by adopting the split-operator method to the Klein-Gordon equation. Here the possibility arises to use parallel computing. However the corresponding spin-statistics becomes crucial in the case of pair creation, demonstrated in several examples. (orig.)

  6. Molecular Characterization of Respiratory Syncytial Virus in Children with Repeated Infections with Subgroup B in the Philippines.

    Science.gov (United States)

    Okamoto, Michiko; Dapat, Clyde P; Sandagon, Ann Marie D; Batangan-Nacion, Leilanie P; Lirio, Irene C; Tamaki, Raita; Saito, Mayuko; Saito-Obata, Mariko; Lupisan, Socorro P; Oshitani, Hitoshi

    2018-05-02

    Human respiratory syncytial virus (RSV) is the leading cause of severe acute respiratory infection in infants and young children, which is characterized by repeated infections. However, the role of amino acid substitutions in repeated infections remains unclear. Hence, this study aimed to elucidate the genetic characteristics of RSV in children with repeated infections using molecular analyses of F and G genes. We conducted a cohort study for children younger than 5 years in the Philippines. We collected nasopharyngeal swabs from children with acute respiratory symptoms and compared F and G sequences between prior and subsequent RSV infections. We examined 1,802 children from May 2014 to January 2016 and collected 3,471 samples. Repeated infections were observed in 25 children, including 4 with homologous RSV-B reinfections. Viruses from the 4 pairs of homologous reinfections had amino acid substitutions in the G protein mostly at O-glycosylation sites, whereas changes in the F protein were identified at antigenic sites V (L173S) and θ (Q209K), considered essential epitopes for the prefusion conformation of the F protein. Amino acid substitutions in G and F proteins of RSV-B might have led to antigenic changes, potentially contributing to homologous reinfections observed in this study.

  7. Secondary partitioning isotope effects on solvolytic ion pair intermediates

    International Nuclear Information System (INIS)

    Abbey, K.J.

    1976-01-01

    The thermal decomposition of N-benzhydryl N-nitrosobenzamide (BNB) has been shown to produce an ion pair which either forms ester or reacts with the solvent. In ethanol, the fraction of ester produced, R, was much smaller than R values obtained from solvolysis or from the diphenyldiazomethane (DDM)-benzoic acid reaction, which was suggested to yield the same ion pair as solvolysis. This difference led to the conclusion that the ionic species for the nitrosamide decomposition is a nitrogen-separated ion pair. This study was initiated on the assumption that BNB led to solvolytic ion pairs, but that both the intimate and solvent-separated ion pairs were produced directly from the nitrosamide. The use of α-tritiated BNB for the study of partitioning isotope effects (PIE's) in this system led to activity ratios much lower than expected from other reported work. Results of studies of ''special'' salt effect were not consistent for all situations, but the results do suggest that the assumption that BNB leads to solvolytic ion pairs is probably valid. The investigation of the more stable p-methoxybenzhydryl benzoate system proved to be highly productive. The ester fraction produced, R, responded dramatically to the addition of common-ion as well as ''special'' salts. The functional relationship of R on salt concentration could be explained in terms of Winstein's solvolytic scheme where the intimate ion pair, the solvent-separated ion pair, and the dissociated ion were important. Tritium-labelled compounds were used for PIE studies on 3 different compounds, and three different methods of reaction are proposed

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

    Science.gov (United States)

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

    2014-02-01

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

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    The Gd 5 Ge 2 Si 2 alloy and the off-stoichiometric Ni 50 Mn 35 In 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 5 Ge 2 Si 2 and Ni 50 Mn 35 In 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

  10. Pair potentials in liquid metals

    International Nuclear Information System (INIS)

    Faber, T.E.

    1980-01-01

    The argument which justifies the use of a pair potential to describe the structure-dependent term in the energy of liquid metals is briefly reviewed. Because there is an additional term in the energy which depends upon volume rather than structure, and because the pair potential itself is volume-dependent, the relationship between pair potential and observable properties such as pressure, bulk modulus and pair distribution function is more complicated for liquid metals than it is for molecular liquids. Perhaps for this reason, the agreement between pair potentials inferred from observable properties and pair potentials calculated by means of pseudo-potential theory is still far from complete. The pair potential concept is applicable only to simple liquid metals, in which the electron-ion interaction is weak. No attempt is made to discuss liquid transition and rare-earth metals, which are not simple in this sense. (author)

  11. 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.

  12. Vital Signs: Repeat Births Among Teens — United States, 2007–2010

    OpenAIRE

    Gavin, Lorrie; Warner, Lee; O’Neil, Mary Elizabeth; Duong, Linh M.; Marshall, Cassondra; Hastings, Philip A.; Harrison, Ayanna T.; Barfield, Wanda

    2013-01-01

    Background Teen childbearing has potential negative health, economic, and social consequences for mother and child. Repeat teen childbearing further constrains the mother’s education and employment possibilities. Rates of preterm and low birth weight are higher in teens with a repeat birth, compared with first births. Methods To assess patterns of repeat childbearing and postpartum contraceptive use among teens, CDC analyzed natality data from the National Vital Statistics System (NVSS) and t...

  13. Repeat Gamma Knife Radiosurgery for Trigeminal Neuralgia

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  14. Repeat Gamma Knife Radiosurgery for Trigeminal Neuralgia

    Energy Technology Data Exchange (ETDEWEB)

    Aubuchon, Adam C., E-mail: acaubuchon@gmail.com [Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC (United States); Chan, Michael D. [Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC (United States); Lovato, James F. [Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, NC (United States); Balamucki, Christopher J. [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Ellis, Thomas L.; Tatter, Stephen B. [Department of Neurosurgery, Wake Forest University School of Medicine, Winston-Salem, NC (United States); McMullen, Kevin P.; Munley, Michael T.; Deguzman, Allan F.; Ekstrand, Kenneth E.; Bourland, J. Daniel; Shaw, Edward G. [Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC (United States)

    2011-11-15

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

  15. 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

  16. Pairing correlations in nuclei

    International Nuclear Information System (INIS)

    Baba, C.V.K.

    1988-01-01

    There are many similarities between the properties of nucleons in nuclei and electrons in metals. In addition to the properties explainable in terms of independent particle motion, there are many important co-operative effects suggesting correlated motion. Pairing correlation which leads to superconductivity in metals and several important properties in nuclei , is an exmple of such correlations. An attempt has been made to review the effects of pairing correlations in nuclei. Recent indications of reduction in pairing correlations at high angular momenta is discussed. A comparision between pairing correlations in the cases of nuclei and electrons in metals is attempted. (author). 20 refs., 10 figs

  17. μ- and tau-pair production from relativistic heavy-ion collisions

    International Nuclear Information System (INIS)

    Bottcher, C.; Strayer, M.R.

    1986-01-01

    The question is addressed of μ- and tau-pair production from the motional Coulomb fields available at the new relativistic heavy-ion accelerators. A semiclassical field theory is developed which is appropriate for families of leptons which are coupled electromagnetically. The field equations are mapped on to a lattice of collocation points using basis spline methods, and techniques for solving the resulting lattice equations are outlined. The properties of the transverse electromagnetic field near the heavy-ion beam are examined and physical arguments are given as to the feasibility of pair creation under a variety of circumstances. Using the Dirac-Hartree equations developed in part one, we shall dynamically evolve the vacuum, using the appropriate fields, and compute μ-pair and tau-pair production cross sections. 16 refs., 10 figs

  18. Prediction of regulatory gene pairs using dynamic time warping and gene ontology.

    Science.gov (United States)

    Yang, Andy C; Hsu, Hui-Huang; Lu, Ming-Da; Tseng, Vincent S; Shih, Timothy K

    2014-01-01

    Selecting informative genes is the most important task for data analysis on microarray gene expression data. In this work, we aim at identifying regulatory gene pairs from microarray gene expression data. However, microarray data often contain multiple missing expression values. Missing value imputation is thus needed before further processing for regulatory gene pairs becomes possible. We develop a novel approach to first impute missing values in microarray time series data by combining k-Nearest Neighbour (KNN), Dynamic Time Warping (DTW) and Gene Ontology (GO). After missing values are imputed, we then perform gene regulation prediction based on our proposed DTW-GO distance measurement of gene pairs. Experimental results show that our approach is more accurate when compared with existing missing value imputation methods on real microarray data sets. Furthermore, our approach can also discover more regulatory gene pairs that are known in the literature than other methods.

  19. Intermittent pair-housing, pair relationship qualities, and HPA activity in adult female rhesus macaques.

    Science.gov (United States)

    Hannibal, Darcy L; Cassidy, Lauren C; Vandeleest, Jessica; Semple, Stuart; Barnard, Allison; Chun, Katie; Winkler, Sasha; McCowan, Brenda

    2018-05-02

    Laboratory rhesus macaques are often housed in pairs and may be temporarily or permanently separated for research, health, or management reasons. While both long-term social separations and introductions can stimulate a stress response that impacts inflammation and immune function, the effects of short-term overnight separations and whether qualities of the pair relationship mediate these effects are unknown. In this study, we investigated the effects of overnight separations on the urinary cortisol concentration of 20 differentially paired adult female rhesus macaques (Macaca mulatta) at the California National Primate Research Center. These females were initially kept in either continuous (no overnight separation) or intermittent (with overnight separation) pair-housing and then switched to the alternate pair-housing condition part way through the study. Each study subject was observed for 5 weeks, during which we collected measures of affiliative, aggressive, anxious, abnormal, and activity-state behaviors in both pair-housing conditions. Additionally, up to three urine samples were collected from each subject per week and assayed for urinary free cortisol and creatinine. Lastly, the behavioral observer scored each pair on four relationship quality attributes ("Anxious," "Tense," "Well-meshed," and "Friendly") using a seven-point scale. Data were analyzed using a generalized linear model with gamma distribution and an information theoretic approach to determine the best model set. An interaction between the intermittent pairing condition and tense pair adjective rating was in the top three models of the best model set. Dominance and rates of affiliation were also important for explaining urinary cortisol variation. Our results suggest that to prevent significant changes in HPA-axis activation in rhesus macaque females, which could have unintended effects on research outcomes, pairs with "Tense" relationships and overnight separations preventing tactile contact

  20. A method for conversion of Hounsfield number to electron density and prediction of macroscopic pair production cross-sections

    International Nuclear Information System (INIS)

    Knoeoes, T.; Nilsson, M.; Ahlgren, L.

    1986-01-01

    A method for the determination of electron density using a narrow beam attenuation geometry is described. The method does not require that the elemental composition of the phantom materials is known. The Hounsfield numbers for the phantom materials used were determined using five different CT scanners. A relationship between Hounsfield number and electron density can thus be established, which is of considerable value in radiation therapy treatment planning procedures. Measurements of the ratio coherent/incoherent scattering of low energy photons in a certain geometry has proven valuable for determination of atomic number, which in its turn can be used for estimation of macroscopic pair production coefficients for high energy photons. The combination of knowledge of electron density with methods for determination of processes, dependent on atomic number, can form a base for adequate composition of phantom materials for purposes of testing dose calculation algorithms for photons and electrons. (orig.)

  1. A NEW METHOD TO DIRECTLY MEASURE THE JEANS SCALE OF THE INTERGALACTIC MEDIUM USING CLOSE QUASAR PAIRS

    International Nuclear Information System (INIS)

    Rorai, Alberto; Hennawi, Joseph F.; White, Martin

    2013-01-01

    only 20 close quasar pair spectra can pinpoint the Jeans scale to ≅ 5% precision, independent of the amplitude T 0 and slope γ of the temperature-density relation of the IGM T=T 0 (ρ/ ρ-bar ) γ-1 . This exquisite sensitivity arises because even long-wavelength one-dimensional Fourier modes ∼10 Mpc, i.e., two orders of magnitude larger than the Jeans scale, are nevertheless dominated by projected small-scale three-dimensional (3D) power. Hence phase angle differences between all modes of quasar pair spectra actually probe the shape of the 3D power spectrum on scales comparable to the pair separation. We show that this new method for measuring the Jeans scale is unbiased and is insensitive to a battery of systematics that typically plague Lyα forest measurements, such as continuum fitting errors, imprecise knowledge of the noise level and/or spectral resolution, and metal-line absorption

  2. A NEW METHOD TO DIRECTLY MEASURE THE JEANS SCALE OF THE INTERGALACTIC MEDIUM USING CLOSE QUASAR PAIRS

    Energy Technology Data Exchange (ETDEWEB)

    Rorai, Alberto; Hennawi, Joseph F. [Max-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg (Germany); White, Martin [Department of Astronomy, University of California at Berkeley, 601 Campbell Hall, Berkeley, CA 94720-3411 (United States)

    2013-10-01

    only 20 close quasar pair spectra can pinpoint the Jeans scale to ≅ 5% precision, independent of the amplitude T{sub 0} and slope γ of the temperature-density relation of the IGM T=T{sub 0}(ρ/ ρ-bar ){sup γ-1}. This exquisite sensitivity arises because even long-wavelength one-dimensional Fourier modes ∼10 Mpc, i.e., two orders of magnitude larger than the Jeans scale, are nevertheless dominated by projected small-scale three-dimensional (3D) power. Hence phase angle differences between all modes of quasar pair spectra actually probe the shape of the 3D power spectrum on scales comparable to the pair separation. We show that this new method for measuring the Jeans scale is unbiased and is insensitive to a battery of systematics that typically plague Lyα forest measurements, such as continuum fitting errors, imprecise knowledge of the noise level and/or spectral resolution, and metal-line absorption.

  3. Rapid-rate paired associative stimulation over the primary somatosensory cortex.

    Directory of Open Access Journals (Sweden)

    Philemon Tsang

    Full Text Available Rapid-rate paired associative stimulation (rPAS involves repeat pairing of peripheral nerve stimulation and Transcranial magnetic stimulation (TMS pulses at a 5 Hz frequency. RPAS over primary motor cortex (M1 operates with spike-timing dependent plasticity such that increases in corticospinal excitability occur when the nerve and TMS pulse temporally coincide in cortex. The present study investigates the effects of rPAS over primary somatosensory cortex (SI which has not been performed to date. In a series of experiments, rPAS was delivered over SI and M1 at varying timing intervals between the nerve and TMS pulse based on the latency of the N20 somatosensory evoked potential (SEP component within each participant (intervals for SI-rPAS: N20, N20-2.5 ms, N20 + 2.5 ms, intervals for M1-rPAS: N20, N20+5 ms. Changes in SI physiology were measured via SEPs (N20, P25, N20-P25 and SEP paired-pulse inhibition, and changes in M1 physiology were measured with motor evoked potentials and short-latency afferent inhibition. Measures were obtained before rPAS and at 5, 25 and 45 minutes following stimulation. Results indicate that paired-pulse inhibition and short-latency afferent inhibition were reduced only when the SI-rPAS nerve-TMS timing interval was set to N20-2.5 ms. SI-rPAS over SI also led to remote effects on motor physiology over a wider range of nerve-TMS intervals (N20-2.5 ms - N20+2.5 ms during which motor evoked potentials were increased. M1-rPAS increased motor evoked potentials and reduced short-latency afferent inhibition as previously reported. These data provide evidence that, similar to M1, rPAS over SI is spike-timing dependent and is capable of exerting changes in SI and M1 physiology.

  4. PENERAPAN MODEL PEMBELAJARAN THINK PAIR SHARE DALAM MENINGKATKAN HASIL BELAJAR

    Directory of Open Access Journals (Sweden)

    Pramita Dewi Harjayanti

    2012-06-01

    Full Text Available Penelitian ini bertujuan� untuk mengetahui apakah ada peningkatan hasil pada kompetensi dasar memelihara peralatan kantor, setelah dilakukan penelitian tindakan kelas dengan model pembelajaran think pair share. Subyek penelitian ini adalah siswa kelas X AP SMK YPPM Boja. Hasil penelitian setelah dilakukan tindakan hasil belajar siswa pada post test meningkat hingga mencapai ketuntasan klasikal 66,67% dengan rata-rata nilai 72,45. Kemudian pada siklus II ketuntasan klasikal mengalami peningkatan menjadi 83,33% dengan nilai rata-rata siswa 77,45 sehingga peningkatan dari siklus I ke siklus II sebesar 16,67%. Pembelajaran dengan model pembelajaran think pair share mendapat respon baik dari siswa pada siklus I sebesar 77,5% meningkat menjadi 90% pada siklus II. Berdasarkan hasil penelitian disimpulkan bahwa ada peningkatan hasil belajar siswa kelas X AP SMK YPPM Boja pada kompetensi dasar memelihara peralatan kantor dengan model pembelajaran think pair share. This study aims to determine whether there is an increase in learning outcomes of administration on the subject of adjusting entries, having done research with the collaboration of a class action use method of think pair share. Subyek think this study is the students' high school grade� X AP SMK YPPM Boja. The results obtained student learning outcomes through before the action reaches 66,67% classical completeness with the average value 0f 72,45 in once siklus. After the students' actions in second siklus on the post test increased to 83,33% with the classical completeness the average value of 77,45. Resulting in an increase of 16,67%. Collaborative learning with the method of think pair share received good response from students with average percentage of responses 77,5% in first siklus and increased to 90% in second siklus. Based on the results of the study concluded that there was an increase in students' social studies class X AP on the subject of an adjusting entry through with the

  5. Development of a REBCO HTS magnet for Maglev - repeated bending tests of HTS pancake coils -

    Science.gov (United States)

    Sugino, Motohikoa; Mizuno, Katsutoshi; Tanaka, Minoru; Ogata, Masafumi

    2018-01-01

    In the past study, two manufacturing methods were developed that can manufacture pancake coils by using REBCO coated conductors. It was confirmed that the conductors have no electric degradation that caused by the manufacturing method. The durability evaluation tests of the pancake coils were conducted as the final evaluation of the coil manufacturing method in this study. The repeated bending deformation was applied to manufactured pancake coils in the tests. As the results of these tests, it was confirmed that the pancake coils that were manufactured by two methods had the durability for the repeated bending deformation and the coils maintained the appropriate mechanical performance and electric performance. We adopted the fusion bonding method as the coil manufacturing method of the HTS magnet Furthermore, using the prototype pancake coil that was manufactured by the fusion bonding method as a test sample, the repeated bending test under the exited condition was conducted. Thus it was confirmed that the coil manufactured by the fusion bonding method has no degradation of the electricity performance and the mechanical properties even if the repeated bending deformation was applied under the exited condition.

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

    Science.gov (United States)

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

    2014-01-01

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

  7. The separation of [32P]inositol phosphates by ion-pair chromatography: Optimization of the method and biological applications

    International Nuclear Information System (INIS)

    Sulpice, J.C.; Gascard, P.; Journet, E.; Rendu, F.; Renard, D.; Poggioli, J.; Giraud, F.

    1989-01-01

    We have developed an ion-pair reverse-phase HPLC method to measure inositol phosphates in 32 P-labeled cells. The different chromatographic parameters were analyzed to optimize the resolution of the 32 P-labeled metabolites. Analysis of inositol phosphates in biological samples was improved by a single charcoal pretreatment which eliminated interfering nucleotides without removing inositol phosphates. The kinetics of production of inositol phosphates in calcium-activated erythrocytes, vasopressin-stimulated hepatocytes, and thrombin-activated platelets were analyzed. Original data on the activation of phosphoinositide phospholipase C were obtained in intact erythrocytes by direct measurement of inositol (1,4,5)P3. Data from agonist-stimulated hepatocytes and platelets were consistent with those from previous studies. In conclusion, this technique offers many advantages over the methodologies currently employed involving anion-exchange chromatography and [ 3 H]inositol labeling: (i) 32 P labeling is less expensive and more efficient than 3 H labeling and can be used with all types of cells without permeabilization treatments and (ii) ion-pair HPLC gives good resolution of inositol phosphates from nucleotides with shorter retention times, and long reequilibration periods are not required

  8. Effect of Repeated Freeze-Thaw Cycles on Beef Quality and Safety

    Science.gov (United States)

    Rahman, Mohammad Hafizur; Hossain, Mohammad Mujaffar; Rahman, Syed Mohammad Ehsanur; Hashem, Mohammad Abul

    2014-01-01

    The objectives of this study were to know the effect of repeated freeze-thaw cycles of beef on the sensory, physicochemical quality and microbiological assessment. The effects of three successive freeze-thaw cycles on beef forelimb were investigated comparing with unfrozen fresh beef for 75 d by keeping at −20±1℃. The freeze-thaw cycles were subjected to three thawing methods and carried out to know the best one. As the number of freeze-thaw cycles increased color and odor declined significantly before cook within the cycles and tenderness, overall acceptability also declined among the cycles after cook by thawing methods. The thawing loss increased and dripping loss decreased significantly (pcycles and then decreased. Cooking loss increased in cycle 1 and 3, but decreased in cycle 2. pH decreased significantly (pcycles. Moreover, drip loss, cooking loss and WHC were affected (pcycles. 2-Thiobarbituric acid (TBARS) value increased (pcycles and among the cycles by thawing methods. Total viable bacteria, total coliform and total yeast-mould count decreased significantly (pcycles in comparison to the initial count in repeated freeze-thaw cycles. As a result, repeated freeze-thaw cycles affected the sensory, physicochemical and microbiological qua- lity of beef, causing the deterioration of beef quality, but improved the microbiological quality. Although repeated freeze-thaw cycles did not affect much on beef quality and safety but it may be concluded that repeated freeze and thaw should be minimized in terms of beef color for commercial value and WHC and tenderness/juiciness for eating quality. PMID:26761286

  9. Pair potentials and structure factors of liquid alkali metals

    International Nuclear Information System (INIS)

    Kumaravadivel, R.; Tosi, M.P.

    1984-03-01

    Measured structure factors of liquid alkali metals are examined in the framework of screened-pair-potentials theory. Information on the main attractive well in the effective pair potential is obtained from the structural data by an approximate method stemming from an optimized random phase treatment of the indirect ion-ion attraction. The results are compared with a variety of theoretical pair potentials in the cases of sodium and potassium, after a test of the method against computer simulation data on a model for rubidium. Results for the other alkali metals are also given and discussed. The small-angle scattering region is then examined in considerable detail, with special attention to the possibility of a linear term in a series expansion of the structure factor at very small momentum transfer. Although sensitivity to both the bare electron-ion coupling and the local field factor in the screening function is demonstrated and analyzed, no linear term of the magnitude reported in recent X-ray diffraction experiments is found in the present theoretical framework. (author)

  10. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers

    Science.gov (United States)

    Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

    2016-01-01

    Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies. PMID:26960153

  11. Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers.

    Science.gov (United States)

    Li, Hui; Li, Defang; Chen, Anguo; Tang, Huijuan; Li, Jianjun; Huang, Siqi

    2016-01-01

    Kenaf (Hibiscus cannabinus L.) is an economically important natural fiber crop grown worldwide. However, only 20 expressed tag sequences (ESTs) for kenaf are available in public databases. The aim of this study was to develop large-scale simple sequence repeat (SSR) markers to lay a solid foundation for the construction of genetic linkage maps and marker-assisted breeding in kenaf. We used Illumina paired-end sequencing technology to generate new EST-simple sequences and MISA software to mine SSR markers. We identified 71,318 unigenes with an average length of 1143 nt and annotated these unigenes using four different protein databases. Overall, 9324 complementary pairs were designated as EST-SSR markers, and their quality was validated using 100 randomly selected SSR markers. In total, 72 primer pairs reproducibly amplified target amplicons, and 61 of these primer pairs detected significant polymorphism among 28 kenaf accessions. Thus, in this study, we have developed large-scale SSR markers for kenaf, and this new resource will facilitate construction of genetic linkage maps, investigation of fiber growth and development in kenaf, and also be of value to novel gene discovery and functional genomic studies.

  12. Cross section measurement of the bottom-quark-pair associated top-quark-pair production in the semi-leptonic channel with the CMS experiment

    Energy Technology Data Exchange (ETDEWEB)

    Heidemann, Fabian; Erdmann, Martin; Fischer, Robert [III. Physikalisches Institut A, RWTH Aachen University (Germany)

    2016-07-01

    We present a cross section measurement of the top-quark-pair-production with two bottom quarks which is the dominant background process to top-quark-pair associated Higgs Boson production. The semi-leptonic channel of top-quark decays is used due to its combination of a relatively large branching ratio and small QCD contamination. The analysis method relies on Standard Model Monte Carlo simulations of all relevant physics processes. Template distributions are created with Boosted Decision Tree classifiers on the simulated data. Subsequently, the composition of these templates is fitted to the data distribution to obtain the signal strength relative to the Standard Model prediction. A Bayesian interference method is used to perform the fit, in which systematic uncertainties are incorporated as nuisance parameters.

  13. Inferring repeat-protein energetics from evolutionary information.

    Directory of Open Access Journals (Sweden)

    Rocío Espada

    2017-06-01

    Full Text Available Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences. Still, many natural proteins that fold into the same structural topology show different stabilization energies, and these are often related to their physiological behavior. We propose a description for the energetic variation given by sequence modifications in repeat proteins, systems for which the overall problem is simplified by their inherent symmetry. We explicitly account for single amino acid and pair-wise interactions and treat higher order correlations with a single term. We show that the resulting evolutionary field can be interpreted with structural detail. We trace the variations in the energetic scores of natural proteins and relate them to their experimental characterization. The resulting energetic evolutionary field allows the prediction of the folding free energy change for several mutants, and can be used to generate synthetic sequences that are statistically indistinguishable from the natural counterparts.

  14. Schwinger pair creation of Kaluza-Klein particles: Pair creation without tunneling

    International Nuclear Information System (INIS)

    Friedmann, Tamar; Verlinde, Herman

    2005-01-01

    We study Schwinger pair creation of charged Kaluza-Klein (KK) particles from a static KK electric field. We find that the gravitational backreaction of the electric field on the geometry--which is incorporated via the electric KK-Melvin solution--prevents the electrostatic potential from overcoming the rest mass of the KK particles, thus impeding the tunneling mechanism which is often thought of as responsible for the pair creation. However, we find that pair creation still occurs with a finite rate formally similar to the classic Schwinger result, but via an apparently different mechanism, involving a combination of the Unruh effect and vacuum polarization due to the E-field

  15. 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.

  16. Energy relaxation and separation of a hot electron-hole pair in organic aggregates from a time-dependent wavepacket diffusion method

    International Nuclear Information System (INIS)

    Han, Lu; Liang, WanZhen; Zhao, Yi; Zhong, Xinxin

    2014-01-01

    The time-dependent wavepacket diffusive method [X. Zhong and Y. Zhao, J. Chem. Phys. 138, 014111 (2013)] is extended to investigate the energy relaxation and separation of a hot electron-hole pair in organic aggregates with incorporation of Coulomb interaction and electron-phonon coupling. The pair initial condition generated by laser pulse is represented by a Gaussian wavepacket with a central momentum. The results reveal that the hot electron energy relaxation is very well described by two rate processes with the fast rate much larger than the slow one, consistent with experimental observations, and an efficient electron-hole separation is accomplished accompanying the fast energy relaxation. Furthermore, although the extra energy indeed helps the separation by overcoming the Coulomb interaction, the width of initial wavepacket is much sensitive to the separation efficiency and the narrower wavepacket generates the more separated charges. This behavior may be useful to understand the experimental controversy of the hot carrier effect on charge separation

  17. Pair production from nuclear collisions and cosmic ray transport

    International Nuclear Information System (INIS)

    Norbury, John W

    2006-01-01

    Modern cosmic ray transport codes, that are capable of use for a variety of applications, need to include all significant atomic, nuclear and particle reactions at a variety of energies. Lepton pair production from nucleus-nucleus collisions has not been included in transport codes to date. Using the methods of Baur, Bertulani and Baron, the present report provides estimates of electron-positron pair production cross sections for nuclei and energies relevant to cosmic ray transport. It is shown that the cross sections are large compared to other typical processes such as single neutron removal due to strong or electromagnetic interactions. Therefore, lepton pair production may need to be included in some transport code applications involving MeV electrons. (brief report)

  18. Calculations of energy levels and electromagnetic properties for tellurium pair isotopes, by unified method

    International Nuclear Information System (INIS)

    Teixeira, R.R.P.

    1988-01-01

    Calculations with the Unified Model (vibrator coupled to two particles), of the energy levels and the eletromagnetic properties have been performed and compared with the twelve pair isotopes from tellurium with A between 112 and 134. The results were analysed using as particles interaction: pairing and SDI (Surface Delta Interaction). The SDI and 3 fonons collective states were used in the fittings, and a syntematic comparison between the theoretical and experimental results was made. The dependence of the results with the model parameters was determined, through large variation sof them. Calculations using 4 fonons have been made, and the importance of the introduced variations in the results was discussed. Calculations have been made in the VAX Computer of the Pelletron at IFUSP. (author) [pt

  19. Predicting co-complexed protein pairs using genomic and proteomic data integration

    Directory of Open Access Journals (Sweden)

    King Oliver D

    2004-04-01

    Full Text Available Abstract Background Identifying all protein-protein interactions in an organism is a major objective of proteomics. A related goal is to know which protein pairs are present in the same protein complex. High-throughput methods such as yeast two-hybrid (Y2H and affinity purification coupled with mass spectrometry (APMS have been used to detect interacting proteins on a genomic scale. However, both Y2H and APMS methods have substantial false-positive rates. Aside from high-throughput interaction screens, other gene- or protein-pair characteristics may also be informative of physical interaction. Therefore it is desirable to integrate multiple datasets and utilize their different predictive value for more accurate prediction of co-complexed relationship. Results Using a supervised machine learning approach – probabilistic decision tree, we integrated high-throughput protein interaction datasets and other gene- and protein-pair characteristics to predict co-complexed pairs (CCP of proteins. Our predictions proved more sensitive and specific than predictions based on Y2H or APMS methods alone or in combination. Among the top predictions not annotated as CCPs in our reference set (obtained from the MIPS complex catalogue, a significant fraction was found to physically interact according to a separate database (YPD, Yeast Proteome Database, and the remaining predictions may potentially represent unknown CCPs. Conclusions We demonstrated that the probabilistic decision tree approach can be successfully used to predict co-complexed protein (CCP pairs from other characteristics. Our top-scoring CCP predictions provide testable hypotheses for experimental validation.

  20. Excited cooper pairs

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Arrietea, M. G.; Solis, M. A.; De Llano, M. [Universidad Nacional Autonoma de Mexico, Mexico, D.F (Mexico)

    2001-02-01

    Excited cooper pairs formed in a many-fermion system are those with nonzero total center-of mass momentum (CMM). They are normally neglected in the standard Bardeen-Cooper-Schrieffer (BCS) theory of superconductivity for being too few compared with zero CMM pairs. However, a Bose-Einstein condensation picture requires both zero and nonzero CMM pairs. Assuming a BCS model interaction between fermions we determine the populations for all CMM values of Cooper pairs by actually calculating the number of nonzero-CMM pairs relative to that of zero-CMM ones in both 2D and 3D. Although this ratio decreases rapidly with CMM, the number of Cooper pairs for any specific CMM less than the maximum (or breakup of the pair) momentum turns out to be typically larger than about 95% of those with zero-CMM at zero temperature T. Even at T {approx}100 K this fraction en 2D is still as large as about 70% for typical quasi-2D cuprate superconductor parameters. [Spanish] Los pares de cooper excitados formados en un sistema de muchos electrones, son aquellos con momentos de centro de masa (CMM) diferente de cero. Normalmente estos no son tomados en cuenta en la teoria estandar de la superconductividad de Bardeen-Cooper-Schrieffer (BCS) al suponer que su numero es muy pequeno comparados con los pares de centro de masa igual a cero. Sin embargo, un esquema de condensacion Bose-Einstein requiere de ambos pares, con CMM cero y diferente de cero. Asumiendo una interaccion modelo BCS entre los fermiones, determinamos la poblacion de pares cooper con cada uno de todos los posibles valores del CMM calculando el numero de pares con momentos de centro de masa diferente de cero relativo a los pares de CMM igual a cero, en 2D y 3D. Aunque esta razon decrece rapidamente con el CMM, el numero de pares de cooper para cualquier CMM especifico menor que el momento maximo (o rompimiento de par) es tipicamente mas grande que el 95% de aquellos con CMM cero. Aun a T {approx}100 K esta fraccion en 2D es

  1. 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.

  2. Spatial cluster detection for repeatedly measured outcomes while accounting for residential history.

    Science.gov (United States)

    Cook, Andrea J; Gold, Diane R; Li, Yi

    2009-10-01

    Spatial cluster detection has become an important methodology in quantifying the effect of hazardous exposures. Previous methods have focused on cross-sectional outcomes that are binary or continuous. There are virtually no spatial cluster detection methods proposed for longitudinal outcomes. This paper proposes a new spatial cluster detection method for repeated outcomes using cumulative geographic residuals. A major advantage of this method is its ability to readily incorporate information on study participants relocation, which most cluster detection statistics cannot. Application of these methods will be illustrated by the Home Allergens and Asthma prospective cohort study analyzing the relationship between environmental exposures and repeated measured outcome, occurrence of wheeze in the last 6 months, while taking into account mobile locations.

  3. Adatom pair distribution up to half coverage: O-Pd(100)

    OpenAIRE

    Kappus, Wolfgang

    2017-01-01

    Using substrate mediated elastic interactions fitted previously to first principles (FP) calculations, adatom pair distributions are derived for O-Pd(100) evaluating a statistical BGY based integral equation. The evaluation method utilizes the superposition approximation, a temperature scaling scheme, and for one variant the particle-hole symmetry of a pair interaction lattice gas Hamiltonian. The elastic Hamiltonian is taken from a previous 3 parameter analytical model. The resulting adatom ...

  4. Mesoscopic pairing without superconductivity

    Science.gov (United States)

    Hofmann, Johannes

    2017-12-01

    We discuss pairing signatures in mesoscopic nanowires with a variable attractive pairing interaction. Depending on the wire length, density, and interaction strength, these systems realize a simultaneous bulk-to-mesoscopic and BCS-BEC crossover, which we describe in terms of the parity parameter that quantifies the odd-even energy difference and generalizes the bulk Cooper pair binding energy to mesoscopic systems. We show that the parity parameter can be extracted from recent measurements of conductance oscillations in SrTiO3 nanowires by Cheng et al. [Nature (London) 521, 196 (2015), 10.1038/nature14398], where it marks the critical magnetic field that separates pair and single-particle currents. Our results place the experiment in the fluctuation-dominated mesoscopic regime on the BCS side of the crossover.

  5. How Many Alternatives Can Be Ranked? A Comparison of the Paired Comparison and Ranking Methods.

    Science.gov (United States)

    Ock, Minsu; Yi, Nari; Ahn, Jeonghoon; Jo, Min-Woo

    2016-01-01

    To determine the feasibility of converting ranking data into paired comparison (PC) data and suggest the number of alternatives that can be ranked by comparing a PC and a ranking method. Using a total of 222 health states, a household survey was conducted in a sample of 300 individuals from the general population. Each respondent performed a PC 15 times and a ranking method 6 times (two attempts of ranking three, four, and five health states, respectively). The health states of the PC and the ranking method were constructed to overlap each other. We converted the ranked data into PC data and examined the consistency of the response rate. Applying probit regression, we obtained the predicted probability of each method. Pearson correlation coefficients were determined between the predicted probabilities of those methods. The mean absolute error was also assessed between the observed and the predicted values. The overall consistency of the response rate was 82.8%. The Pearson correlation coefficients were 0.789, 0.852, and 0.893 for ranking three, four, and five health states, respectively. The lowest mean absolute error was 0.082 (95% confidence interval [CI] 0.074-0.090) in ranking five health states, followed by 0.123 (95% CI 0.111-0.135) in ranking four health states and 0.126 (95% CI 0.113-0.138) in ranking three health states. After empirically examining the consistency of the response rate between a PC and a ranking method, we suggest that using five alternatives in the ranking method may be superior to using three or four alternatives. Copyright © 2016 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

  6. Evaluating Effectiveness of Pair Programming as a Teaching Tool in Programming Courses

    Science.gov (United States)

    Faja, Silvana

    2014-01-01

    This study investigates the effectiveness of pair programming on student learning and satisfaction in introductory programming courses. Pair programming, used in the industry as a practice of an agile development method, can be adopted in classroom settings to encourage peer learning, increase students' social skills, and enhance student…

  7. Distributed Pair Programming Using Collaboration Scripts: An Educational System and Initial Results

    Science.gov (United States)

    Tsompanoudi, Despina; Satratzemi, Maya; Xinogalos, Stelios

    2015-01-01

    Since pair programming appeared in the literature as an effective method of teaching computer programming, many systems were developed to cover the application of pair programming over distance. Today's systems serve personal, professional and educational purposes allowing distributed teams to work together on the same programming project. The…

  8. Using Dictionary Pair Learning for Seizure Detection.

    Science.gov (United States)

    Ma, Xin; Yu, Nana; Zhou, Weidong

    2018-02-13

    Automatic seizure detection is extremely important in the monitoring and diagnosis of epilepsy. The paper presents a novel method based on dictionary pair learning (DPL) for seizure detection in the long-term intracranial electroencephalogram (EEG) recordings. First, for the EEG data, wavelet filtering and differential filtering are applied, and the kernel function is performed to make the signal linearly separable. In DPL, the synthesis dictionary and analysis dictionary are learned jointly from original training samples with alternating minimization method, and sparse coefficients are obtained by using of linear projection instead of costly [Formula: see text]-norm or [Formula: see text]-norm optimization. At last, the reconstructed residuals associated with seizure and nonseizure sub-dictionary pairs are calculated as the decision values, and the postprocessing is performed for improving the recognition rate and reducing the false detection rate of the system. A total of 530[Formula: see text]h from 20 patients with 81 seizures were used to evaluate the system. Our proposed method has achieved an average segment-based sensitivity of 93.39%, specificity of 98.51%, and event-based sensitivity of 96.36% with false detection rate of 0.236/h.

  9. Three-dimensional x-ray stereometry from paired coplanar images: a progress report.

    Science.gov (United States)

    Baumrind, S; Moffitt, F H; Curry, S

    1983-10-01

    More than fifty years ago, Broadbent reported the development of a three-dimensional cephalometric method which complexed information from pairs of x-ray images oriented in two planes at right angles to each other. Empirical problems have prevented the routine clinical use of this "biplanar" method, notwithstanding its obvious conceptual brilliance. The present article reports on recent work toward the development of an alternative method of three-dimensional cephalometry in which the two images of each x-ray pair are positioned in the same plane rather than being at right angles to each other. It is believed that this "coplanar" method avoids many of the technical problems that have limited the use of the Broadbent method.

  10. 78 FR 65594 - Vehicular Repeaters

    Science.gov (United States)

    2013-11-01

    ... coordinators estimate the effect on coordination fees? Does the supposed benefit that mobile repeater stations... allow the licensing and operation of vehicular repeater systems and other mobile repeaters by public... email: [email protected] or phone: 202-418- 0530 or TTY: 202-418-0432. For detailed instructions for...

  11. PandA : pairings and arithmetic

    NARCIS (Netherlands)

    Chuengsatiansup, C.; Naehrig, M.; Ribarski, P.; Schwabe, P.; Cao, Z.; Zhang, F.

    2014-01-01

    This paper introduces PandA, a software framework for Pairings and Arithmetic. It is designed to bring together advances in the efficient computation of cryptographic pairings and the development and implementation of pairing-based protocols. The intention behind the PandA framework is to give

  12. Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes.

    OpenAIRE

    Kegler-Ebo, D M; Docktor, C M; DiMaio, D

    1994-01-01

    We describe codon cassette mutagenesis, a simple method of mutagenesis that uses universal mutagenic cassettes to deposit single codons at specific sites in double-stranded DNA. A target molecule is first constructed that contains a blunt, double-strand break at the site targeted for mutagenesis. A double-stranded mutagenic codon cassette is then inserted at the target site. Each mutagenic codon cassette contains a three base pair direct terminal repeat and two head-to-head recognition sequen...

  13. Tevatron serial data repeater system

    International Nuclear Information System (INIS)

    Ducar, R.J.

    1981-01-01

    A ten megabit per second serial data repeater system has been developed for the 6.28km Tevatron accelerator. The repeaters are positioned at each of the thirty service buildings and accommodate control and abort system communications as well as distribution of the Tevatron time and energy clocks. The repeaters are transparent to the particular protocol of the transmissions. Serial data are encoded locally as unipolar two volt signals employing the self-clocking Manchester Bi-Phase code. The repeaters modulate the local signals to low-power bursts of 50 MHz rf carrier for the 260m transmission between service buildings. The repeaters also demodulate the transmission and restructure the data for local utilization. The employment of frequency discrimination techniques yields high immunity to the characteristic noise spectrum

  14. Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey

    Directory of Open Access Journals (Sweden)

    Varala Kranthi

    2007-05-01

    Full Text Available Abstract Background Extensive computational and database tools are available to mine genomic and genetic databases for model organisms, but little genomic data is available for many species of ecological or agricultural significance, especially those with large genomes. Genome surveys using conventional sequencing techniques are powerful, particularly for detecting sequences present in many copies per genome. However these methods are time-consuming and have potential drawbacks. High throughput 454 sequencing provides an alternative method by which much information can be gained quickly and cheaply from high-coverage surveys of genomic DNA. Results We sequenced 78 million base-pairs of randomly sheared soybean DNA which passed our quality criteria. Computational analysis of the survey sequences provided global information on the abundant repetitive sequences in soybean. The sequence was used to determine the copy number across regions of large genomic clones or contigs and discover higher-order structures within satellite repeats. We have created an annotated, online database of sequences present in multiple copies in the soybean genome. The low bias of pyrosequencing against repeat sequences is demonstrated by the overall composition of the survey data, which matches well with past estimates of repetitive DNA content obtained by DNA re-association kinetics (Cot analysis. Conclusion This approach provides a potential aid to conventional or shotgun genome assembly, by allowing rapid assessment of copy number in any clone or clone-end sequence. In addition, we show that partial sequencing can provide access to partial protein-coding sequences.

  15. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  16. Repeat Customer Success in Extension

    Science.gov (United States)

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

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

  17. Influence of isovector pairing and particle-number projection effects on spectroscopic factors for one-pair like-particle transfer reactions in proton-rich even-even nuclei

    Science.gov (United States)

    Benbouzid, Y.; Allal, N. H.; Fellah, M.; Oudih, M. R.

    2018-04-01

    Isovector neutron-proton (np) pairing and particle-number fluctuation effects on the spectroscopic factors (SF) corresponding to one-pair like-particle transfer reactions in proton-rich even-even nuclei are studied. With this aim, expressions of the SF corresponding to two-neutron stripping and two-proton pick-up reactions, which take into account the isovector np pairing effect, are established within the generalized BCS approach, using a schematic definition proposed by Chasman. Expressions of the same SF which strictly conserve the particle number are also established within the Sharp-BCS (SBCS) discrete projection method. In both cases, it is shown that these expressions generalize those obtained when only the pairing between like particles is considered. First, the formalism is tested within the Richardson schematic model. Second, it is applied to study even-even proton-rich nuclei using the single-particle energies of a Woods-Saxon mean-field. In both cases, it is shown that the np pairing effect and the particle-number projection effect on the SF values are important, particularly in N = Z nuclei, and must then be taken into account.

  18. Does Dry Eye Affect Repeatability of Corneal Topography Measurements?

    Directory of Open Access Journals (Sweden)

    Aysun Şanal Doğan

    2018-04-01

    Full Text Available Objectives: The purpose of this study was to assess the repeatability of corneal topography measurements in dry eye patients and healthy controls. Materials and Methods: Participants underwent consecutive corneal topography measurements (Sirius; Costruzione Strumenti Oftalmici, Florence, Italy. Two images with acquisition quality higher than 90% were accepted. The following parameters were evaluated: minimum and central corneal thickness, aqueous depth, apex curvature, anterior chamber volume, horizontal anterior chamber diameter, iridocorneal angle, cornea volume, and average simulated keratometry. Repeatability was assessed by calculating intra-class correlation coefficient. Results: Thirty-three patients with dry eye syndrome and 40 healthy controls were enrolled to the study. The groups were similar in terms of age (39 [18-65] vs. 30.5 [18-65] years, p=0.198 and gender (M/F: 4/29 vs. 8/32, p=0.366. Intra-class correlation coefficients among all topography parameters within both groups showed excellent repeatability (>0.90. Conclusion: The anterior segment measurements provided by the Sirius corneal topography system were highly repeatable for dry eye patients and are sufficiently reliable for clinical practice and research.

  19. Repfinder: Finding approximately repeated scene elements for image editing

    KAUST Repository

    Cheng, Ming-Ming

    2010-07-26

    Repeated elements are ubiquitous and abundant in both manmade and natural scenes. Editing such images while preserving the repetitions and their relations is nontrivial due to overlap, missing parts, deformation across instances, illumination variation, etc. Manually enforcing such relations is laborious and error-prone. We propose a novel framework where user scribbles are used to guide detection and extraction of such repeated elements. Our detection process, which is based on a novel boundary band method, robustly extracts the repetitions along with their deformations. The algorithm only considers the shape of the elements, and ignores similarity based on color, texture, etc. We then use topological sorting to establish a partial depth ordering of overlapping repeated instances. Missing parts on occluded instances are completed using information from other instances. The extracted repeated instances can then be seamlessly edited and manipulated for a variety of high level tasks that are otherwise difficult to perform. We demonstrate the versatility of our framework on a large set of inputs of varying complexity, showing applications to image rearrangement, edit transfer, deformation propagation, and instance replacement. © 2010 ACM.

  20. Repeat migration and disappointment.

    Science.gov (United States)

    Grant, E K; Vanderkamp, J

    1986-01-01

    This article investigates the determinants of repeat migration among the 44 regions of Canada, using information from a large micro-database which spans the period 1968 to 1971. The explanation of repeat migration probabilities is a difficult task, and this attempt is only partly successful. May of the explanatory variables are not significant, and the overall explanatory power of the equations is not high. In the area of personal characteristics, the variables related to age, sex, and marital status are generally significant and with expected signs. The distance variable has a strongly positive effect on onward move probabilities. Variables related to prior migration experience have an important impact that differs between return and onward probabilities. In particular, the occurrence of prior moves has a striking effect on the probability of onward migration. The variable representing disappointment, or relative success of the initial move, plays a significant role in explaining repeat migration probabilities. The disappointment variable represents the ratio of actural versus expected wage income in the year after the initial move, and its effect on both repeat migration probabilities is always negative and almost always highly significant. The repeat probabilities diminish after a year's stay in the destination region, but disappointment in the most recent year still has a bearing on the delayed repeat probabilities. While the quantitative impact of the disappointment variable is not large, it is difficult to draw comparisons since similar estimates are not available elsewhere.

  1. The elimination of singularities in pair correlation functions of a multicomponent liquid system

    International Nuclear Information System (INIS)

    Vasil'jev, O.M.; Chalij, O.V.

    2004-01-01

    In this paper we propose a method that allows to find nonsingular expressions for pair correlation functions of a multicomponent liquid system. The nature of the method deals with using integral and differential Ornstein-Zernike equations for finding asymptotic expressions for pair correlation functions and their subsequent precision. The obtained results are analyzed taking into account their possible applicability for studying the correlative behaviour of multicomponent liquid systems

  2. Filipino au pairs on the move

    DEFF Research Database (Denmark)

    Dalgas, Karina Märcher

    2016-01-01

    Most Filipina au pairs in Denmark send remittances back home, and for many, au pairing forms part of longer-term migration trajectories. This article explores how Filipina au pairs try to carve out a future for themselves abroad. It shows that they navigate within tight webs of financial interdep......Most Filipina au pairs in Denmark send remittances back home, and for many, au pairing forms part of longer-term migration trajectories. This article explores how Filipina au pairs try to carve out a future for themselves abroad. It shows that they navigate within tight webs of financial...

  3. Quantum repeated games revisited

    International Nuclear Information System (INIS)

    Frąckiewicz, Piotr

    2012-01-01

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

  4. Repeatability and number of growing seasons for the selection of custard apple progenies

    Directory of Open Access Journals (Sweden)

    Julio César Do Vale

    2011-01-01

    Full Text Available This study aimed to estimate the repeatability coefficient and determine the minimum number of samplesrequired for effective selection for yield of custard apple. Twenty progenies were evaluated in randomized blocks, fivereplications and four plants per plot. The fruits were collected, counted and weighed every two days of the year. Estimates ofthe repeatability coefficients were obtained by the methods of analysis of variance - ANOVA and principal components - PC.The estimates from the repeatability analysis of biennial data are higher than those based on individual years. The estimatesof the PC method were accurate even in the first harvest, unlike ANOVA. Four biennia were sufficient to ensure effectiveprogeny selection of custard apple.

  5. Orbitally limited pair-density-wave phase of multilayer superconductors

    Science.gov (United States)

    Möckli, David; Yanase, Youichi; Sigrist, Manfred

    2018-04-01

    We investigate the magnetic field dependence of an ideal superconducting vortex lattice in the parity-mixed pair-density-wave phase of multilayer superconductors within a circular cell Ginzburg-Landau approach. In multilayer systems, due to local inversion symmetry breaking, a Rashba spin-orbit coupling is induced at the outer layers. This combined with a perpendicular paramagnetic (Pauli) limiting magnetic field stabilizes a staggered layer dependent pair-density-wave phase in the superconducting singlet channel. The high-field pair-density-wave phase is separated from the low-field BCS phase by a first-order phase transition. The motivating guiding question in this paper is: What is the minimal necessary Maki parameter αM for the appearance of the pair-density-wave phase of a superconducting trilayer system? To address this problem we generalize the circular cell method for the regular flux-line lattice of a type-II superconductor to include paramagnetic depairing effects. Then, we apply the model to the trilayer system, where each of the layers are characterized by Ginzburg-Landau parameter κ0 and a Maki parameter αM. We find that when the spin-orbit Rashba interaction compares to the superconducting condensation energy, the orbitally limited pair-density-wave phase stabilizes for Maki parameters αM>10 .

  6. A Novel Approach for Collaborative Pair Programming

    Science.gov (United States)

    Goel, Sanjay; Kathuria, Vanshi

    2010-01-01

    The majority of an engineer's time in the software industry is spent working with other programmers. Agile methods of software development like eXtreme Programming strongly rely upon practices like daily meetings and pair programming. Hence, the need to learn the skill of working collaboratively is of primary importance for software developers.…

  7. Optimized paired-sgRNA/Cas9 cloning and expression cassette triggers high-efficiency multiplex genome editing in kiwifruit.

    Science.gov (United States)

    Wang, Zupeng; Wang, Shuaibin; Li, Dawei; Zhang, Qiong; Li, Li; Zhong, Caihong; Liu, Yifei; Huang, Hongwen

    2018-01-13

    Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing. In this study, we developed a new cloning strategy for generating paired-sgRNA/Cas9 vectors containing four sgRNAs targeting the kiwifruit phytoene desaturase gene (AcPDS). Comparing to the previous method of paired-sgRNA cloning, our strategy only requires the synthesis of two gRNA-containing primers which largely reduces the cost. We further compared efficiencies of paired-sgRNA/Cas9 vectors containing different sgRNA expression devices, including both the polycistronic tRNA-sgRNA cassette (PTG) and the traditional CRISPR expression cassette. We found the mutagenesis frequency of the PTG/Cas9 system was 10-fold higher than that of the CRISPR/Cas9 system, coinciding with the relative expressions of sgRNAs in two different expression cassettes. In particular, we identified large chromosomal fragment deletions induced by the paired-sgRNAs of the PTG/Cas9 system. Finally, as expected, we found both systems can successfully induce the albino phenotype of kiwifruit plantlets regenerated from the G418-resistance callus lines. We conclude that the PTG/Cas9 system is a more powerful system than the traditional CRISPR/Cas9 system for kiwifruit genome editing, which provides valuable clues for optimizing CRISPR/Cas9 editing system in other plants. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons

  8. Rapid ion-pair liquid chromatographic method for the determination of fenbendazole marker residue in fermented dairy products.

    Science.gov (United States)

    Vousdouka, Venetia I; Papapanagiotou, Elias P; Angelidis, Apostolos S; Fletouris, Dimitrios J

    2017-04-15

    A simple, rapid and sensitive liquid chromatographic method that allows for the quantitative determination of fenbendazole residues in fermented dairy products is described. Samples were extracted with a mixture of acetonitrile-phosphoric acid and the extracts were defatted with hexane to be further partitioned into ethyl acetate. The organic layer was evaporated to dryness and the residue was reconstituted in mobile phase. Separation of fenbendazole and its sulphoxide, sulphone, and p-hydroxylated metabolites was carried out isocratically with a mobile phase containing both positively and negatively charged pairing ions. Overall recoveries ranged from 79.8 to 88.8%, while precision data, based on within and between days variations, suggested an overall relative standard deviation of 6.3-11.0%. The detection and quantification limits were lower than 9 and 21μg/kg, respectively. The method has been successfully applied to quantitate fenbendazole residues in Feta cheese and yoghurt made from spiked and incurred ovine milk. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Collective neutrino-pair emission due to Cooper pairing of protons in superconducting neutron stars

    International Nuclear Information System (INIS)

    Leinson, L.B.

    2001-01-01

    The neutrino emission due to formation and breaking of Cooper pairs of protons in superconducting cores of neutron stars is considered with taking into account the electromagnetic coupling of protons to ambient electrons. It is shown that collective response of electrons to the proton quantum transition contributes coherently to the complete interaction with a neutrino field and enhances the neutrino-pair production. Our calculation shows that the contribution of the vector weak current to the ννbar emissivity of protons is much larger than that calculated by different authors without taking into account the plasma effects. Partial contribution of the pairing protons to the total neutrino radiation from the neutron star core is very sensitive to the critical temperatures for the proton and neutron pairing. We show domains of these parameters where the neutrino radiation, caused by a singlet-state pairing of protons is dominating

  10. On summary measure analysis of linear trend repeated measures data: performance comparison with two competing methods.

    Science.gov (United States)

    Vossoughi, Mehrdad; Ayatollahi, S M T; Towhidi, Mina; Ketabchi, Farzaneh

    2012-03-22

    The summary measure approach (SMA) is sometimes the only applicable tool for the analysis of repeated measurements in medical research, especially when the number of measurements is relatively large. This study aimed to describe techniques based on summary measures for the analysis of linear trend repeated measures data and then to compare performances of SMA, linear mixed model (LMM), and unstructured multivariate approach (UMA). Practical guidelines based on the least squares regression slope and mean of response over time for each subject were provided to test time, group, and interaction effects. Through Monte Carlo simulation studies, the efficacy of SMA vs. LMM and traditional UMA, under different types of covariance structures, was illustrated. All the methods were also employed to analyze two real data examples. Based on the simulation and example results, it was found that the SMA completely dominated the traditional UMA and performed convincingly close to the best-fitting LMM in testing all the effects. However, the LMM was not often robust and led to non-sensible results when the covariance structure for errors was misspecified. The results emphasized discarding the UMA which often yielded extremely conservative inferences as to such data. It was shown that summary measure is a simple, safe and powerful approach in which the loss of efficiency compared to the best-fitting LMM was generally negligible. The SMA is recommended as the first choice to reliably analyze the linear trend data with a moderate to large number of measurements and/or small to moderate sample sizes.

  11. Equations-of-motion treatment of pairing correlations: Seniority-one states

    International Nuclear Information System (INIS)

    Andreozzi, F.; Covello, A.; Gargano, A.; Porrino, A.

    1988-01-01

    In prior work we have developed an equations-of-motion method for treating seniority-one states in pairing-force theory. Here we present a new and simpler version of that method. Some numerical applications to Sn isotopes show its considerable practical value

  12. QSO Pairs across Active Galaxies

    Indian Academy of Sciences (India)

    2016-01-27

    Jan 27, 2016 ... Several QSO pairs have been reported and their redshifts determined, where the two objects in each pair are located across an active galaxy. The usually accepted explanation of such occurrences is that the pair is ejected from the parent galaxy. Currently interpreted redshifted spectra for both the QSOs ...

  13. A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs.

    Directory of Open Access Journals (Sweden)

    Izabella Baranowska Körberg

    Full Text Available The white spotting locus (S in dogs is colocalized with the MITF (microphtalmia-associated transcription factor gene. The phenotypic effects of the four S alleles range from solid colour (S to extreme white spotting (s(w. We have investigated four candidate mutations associated with the s(w allele, a SINE insertion, a SNP at a conserved site and a simple repeat polymorphism all associated with the MITF-M promoter as well as a 12 base pair deletion in exon 1B. The variants associated with white spotting at all four loci were also found among wolves and we conclude that none of these could be a sole causal mutation, at least not for extreme white spotting. We propose that the three canine white spotting alleles are not caused by three independent mutations but represent haplotype effects due to different combinations of causal polymorphisms. The simple repeat polymorphism showed extensive diversity both in dogs and wolves, and allele-sharing was common between wolves and white spotted dogs but was non-existent between solid and spotted dogs as well as between wolves and solid dogs. This finding was unexpected as Solid is assumed to be the wild-type allele. The data indicate that the simple repeat polymorphism has been a target for selection during dog domestication and breed formation. We also evaluated the significance of the three MITF-M associated polymorphisms with a Luciferase assay, and found conclusive evidence that the simple repeat polymorphism affects promoter activity. Three alleles associated with white spotting gave consistently lower promoter activity compared with the allele associated with solid colour. We propose that the simple repeat polymorphism affects cooperativity between transcription factors binding on either flanking sides of the repeat. Thus, both genetic and functional evidence show that the simple repeat polymorphism is a key regulator of white spotting in dogs.

  14. About long range pairing correlations in the Hubbard U-t-t' models

    International Nuclear Information System (INIS)

    Moreo, A.

    1991-01-01

    Using a quantum Monte Carlo method the authors measured pair correlation functions with different symmetries as a function of the filling, U/t and t'/t for the Hubbard and U-t-t' models. For the first time the Monte Carlo results are presented for U/t larger than the bandwidth 8t, away from half-filling. D-wave and extended S-wave pairing correlations are enhanced. D-wave pairing is stronger at half-filling but this behavior is reversed when the filling decreases. However, none of the eight pairing correlations that were studied increases as a function of lattice size, which makes the existence of long range superconducting order unlikely. (author). 10 refs.; 5 figs

  15. Chromosome-specific DNA Repeat Probes

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-03-16

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

  16. Think Pair Share: A Teaching Learning Strategy to Enhance Students' Critical Thinking

    Science.gov (United States)

    Kaddoura, Mahmoud

    2013-01-01

    This study investigated the change in critical thinking (CT) skills of baccalaureate nursing students who were educated using a Think-Pair-Share (TPS) or an equivalent Non-Think-Pair-Share (Non-TPS) teaching method. Critical thinking has been an essential outcome of nursing students to prepare them to provide effective and safe quality care for…

  17. Resistance of human spermatozoa to cryoinjury in repeated cycles of thaw-refreezing

    Directory of Open Access Journals (Sweden)

    Sidney Verza Jr.

    2009-10-01

    Full Text Available Objective: To study the resistance of human spermatozoa to cryoinjury in repeated cycles of thaw-refreezing by using the fast liquid nitrogen vapor method. Material and Methods: Semen specimens were obtained from sixteen normal and oligozoospermic individuals who required disposal at the sperm bank. Five of them had testicular cancer. Specimens were thawed and an aliquot was removed for analysis. The remaining specimens were refrozen without removing the cryomedia. Repeated freeze-thaw cycles were performed until no motile sperm were observed. Sperm motility, number of motile spermatozoa and viability were determined after thawing. Resistance to cryoinjury was compared between groups and also after each refreezing cycle within groups. Results: Motile spermatozoa were recovered after five and two refreeze-thawing cycles in normozoospermic and oligozoospermic specimens, respectively. There were no significant differences in the recovery of motile spermatozoa between thaws within each group of normal and oligozoospermic specimens, but percentage motility and total number of motile spermatozoa were significantly lower in the oligozoospermic one. Specimens from men with cancer were exposed to six refreeze-thawing cycles. Although recovery of motile spermatozoa was significantly impaired after each thawing, there were no significant differences in the recovery of motile sperm between thaws in cancer and non-cancer groups. Conclusions: Human spermatozoa resist repeated cryopreservation using the fast liquid nitrogen vapor method. Normozoospermic specimens withstand refreezing for an average two cycles longer than oligozoospermic ones. Specimens from cancer patients seem to resist repeated cryoinjury similarly to non-cancer counterparts. Resistance to repeated cryoinjury was related to the initial semen quality.

  18. 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

  19. Measuring top-quark polarization in top-pair + missing-energy events.

    Science.gov (United States)

    Berger, Edmond L; Cao, Qing-Hong; Yu, Jiang-Hao; Zhang, Hao

    2012-10-12

    The polarization of a top quark can be sensitive to new physics beyond the standard model. Since the charged lepton from top-quark decay is maximally correlated with the top-quark spin, it is common to measure the polarization from the distribution in the angle between the charged lepton and the top-quark directions. We propose a novel method based on the charged lepton energy fraction and illustrate the method with a detailed simulation of top-quark pairs produced in supersymmetric top squark pair production. We show that the lepton energy ratio distribution that we define is very sensitive to the top-quark polarization but insensitive to the precise measurement of the top-quark energy.

  20. Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

    KAUST Repository

    Auzinger, Winfried; Hofstä tter, Harald; Ketcheson, David I.; Koch, Othmar

    2016-01-01

    We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

  1. Practical splitting methods for the adaptive integration of nonlinear evolution equations. Part I: Construction of optimized schemes and pairs of schemes

    KAUST Repository

    Auzinger, Winfried

    2016-07-28

    We present a number of new contributions to the topic of constructing efficient higher-order splitting methods for the numerical integration of evolution equations. Particular schemes are constructed via setup and solution of polynomial systems for the splitting coefficients. To this end we use and modify a recent approach for generating these systems for a large class of splittings. In particular, various types of pairs of schemes intended for use in adaptive integrators are constructed.

  2. Repeatability and comparison of clinical techniques for anterior chamber angle assessment.

    Science.gov (United States)

    Campbell, Peter; Redmond, Tony; Agarwal, Rishi; Marshall, Lewis R; Evans, Bruce J W

    2015-03-01

    To assess the repeatability of gonioscopy, van Herick method and anterior segment Optical Coherence Tomography (AS-OCT) and determine the agreement between these techniques within a community optometry setting. Gonioscopy, van Herick method and AS-OCT imaging were performed by an optometrist on two occasions, 1 month apart, on 80 subjects aged over 40 years recruited from community optometry practices. Anterior segment images were captured with a spectral domain OCT (Topcon 3D OCT-2000; wavelength 840 nm) set to the Anterior Segment (AS) mode. Eyes were graded as open or occludable for each method. AS-OCT images from both visits were graded by a second optometrist masked to the gonioscopy and van Herick method results, and the visit on which the images were acquired. Cohen's kappa (κ) was used to describe the intra-observer repeatability. Likelihood ratios, sensitivity and specificity of van Herick method and AS-OCT were calculated, using gonioscopy as the reference standard. Measurements were obtained from 80 eyes of 80 subjects. In four cases, AS-OCT images were un-gradable due to difficulty in locating the scleral spur. The repeatability of gonioscopy was fair κ = 0.29, while that of the van Herick method (κ = 0.54) and AS-OCT (κ = 0.47) were somewhat better. The van Herick method showed good sensitivity (visit 1: 75%, visit 2: 69%) and high specificity (visit 1: 88%, visit 2: 96%). The sensitivity of AS-OCT was fair (visit 1: 46%, visit 2: 25%), but specificity was high (visit 1: 87%. visit 2: 89%). Intra-observer repeatability was better for van Herick method and for AS-OCT than for gonioscopy, despite the latter being considered the gold standard method. The van Herick method appeared to be more sensitive than AS-OCT when identifying eyes at risk of angle closure. A standalone anterior segment OCT with a longer wavelength laser could afford better visualisation of the angle, and might therefore be expected to enable the examiner to make more

  3. Reproducibility and repeatability of a new computerized software for sagittal spinopelvic and scoliosis curvature radiologic measurements: Keops(®).

    Science.gov (United States)

    Maillot, C; Ferrero, E; Fort, D; Heyberger, C; Le Huec, J-C

    2015-07-01

    The purpose of this study was to evaluate the inter- and intra-observer variability of the computerized radiologic measurements using Keops(®) and to determine the bias between the software and the standard paper measurement. Four individuals measured all frontal and sagittal variables on the 30 X-rays randomly selected on two occasions (test and retest conditions). The Bland-Altman plot was used to determine the degree of agreement between the measurement on paper X-ray and the measurement using Keops(®) for all reviewers and for the two measures; the intraclass correlation coefficient (ICC) was calculated for each pair of analyses to assess interobserver reproducibility among the four reviewers for the same patient using either paper X-ray or Keops(®) measurement and finally, concordance correlation coefficient (rc) was calculated to assess intraobserver repeatability among the same reviewer for one patient between the two measure using the same method (paper or Keops(®)). The mean difference calculated between the two methods was minimal at -0, 4° ± 3.41° [-7.1; 6.4] for frontal measurement and 0.1° ± 3.52° [-6.7; 6.8] for sagittal measurement. Keops(®) has a better interobserver reproducibility than paper measurement for determination of the sagittal pelvic parameter (ICC = 0.9960 vs. 0.9931; p = 0.0001). It has a better intraobserver repeatability than paper for determination of Cobbs angle (rc = 0.9872 vs. 0.9808; p rc = 0.9981 vs. 0.9953; p plane and that the use of this software can be recommended for clinical application. Diagnostic, level III.

  4. Analysis and optimization of kinematic pair force in control rod drive mechanism

    International Nuclear Information System (INIS)

    Sun Zhenguo; Liu Sen; Ran Xiaobing; Dai Changnian; Li Yuezhong

    2015-01-01

    Function expressions of kinematic pair force with latch dimensions, friction coefficient, link angle and external load was obtained by theoretical analysis, and the expression was verified by the motion analysis software. Key parameters of kinematic pair were confirmed, and their effect trends with force of parts were obtained. They show that the available method of kinematic pair optimization is increasing the space of latch holes. Using the motion analysis software, the forces of parts before and after optimization was compared. The result shows that the forces of parts were improved after the optimization. (authors)

  5. Electron-positron pair production in ultrastrong laser fields

    Directory of Open Access Journals (Sweden)

    Bai Song Xie

    2017-09-01

    Full Text Available Electron–positron pair production due to the decay of vacuum in ultrastrong laser fields is an interesting topic which is revived recently because of the rapid development of current laser technology. The theoretical and numerical research progress of this challenging topic is reviewed. Many new findings are presented by different approaches such as the worldline instantons, the S-matrix theory, the kinetic method by solving the quantum Vlasov equation or/and the real-time Dirac–Heisenberg–Wigner formalism, the computational quantum field theory by solving the Dirac equation and so on. In particular, the effects of electric field polarizations on pair production are unveiled with different patterns of created momentum spectra. The effects of polarizations on the number density of created particles and the nonperturbative signatures of multiphoton process are also presented. The competitive interplay between the multiphoton process and nonperturbation process plays a key role in these new findings. These newly discovered phenomena are valuable to deepen the understanding of pair production in complex fields and even have an implication to the study of strong-field ionization. More recent studies on the pair production in complex fields as well as beyond laser fields are briefly presented in the view point of perspective future.

  6. Ion pairing in ionic liquids

    International Nuclear Information System (INIS)

    Kirchner, Barbara; Malberg, Friedrich; Firaha, Dzmitry S; Hollóczki, Oldamur

    2015-01-01

    In the present article we briefly review the extensive discussion in literature about the presence or absence of ion pair-like aggregates in ionic liquids. While some experimental studies point towards the presence of neutral subunits in ionic liquids, many other experiments cannot confirm or even contradict their existence. Ion pairs can be detected directly in the gas phase, but no direct method is available to observe such association behavior in the liquid, and the corresponding indirect experimental proofs are based on such assumptions as unity charges at the ions. However, we have shown by calculating ionic liquid clusters of different sizes that assuming unity charges for ILs is erroneous, because a substantial charge transfer is taking place between the ionic liquid ions that reduce their total charge. Considering these effects might establish a bridge between the contradicting experimental results on this matter. Beside these results, according to molecular dynamics simulations the lifetimes of ion–ion contacts and their joint motions are far too short to verify the existence of neutral units in these materials. (topical review)

  7. Some advances in pairing theory

    International Nuclear Information System (INIS)

    Rowe, D.J.

    2001-01-01

    Two advances are reviewed in the application of pairing-force theory in the nuclear shell model. The first exploits a discovery that a wide range of two-nucleon interactions conserve seniority as a good quantum number. As a consequence, the eigenstates of a Hamiltonian with such an interaction belong to irreducible representations of a compact unitary-symplectic group. This makes it possible to extend the simply-solvable models with J=0 pairing forces to a much richer set of models and still obtain states uniquely classified by their seniority and angular momentum quantum numbers. Moreover, many of the low-lying energy levels of such models can be obtained algebraically; in technical terms, the models are in some cases completely solvable and in other cases partially solvable by algebraic methods. The second advance exploits the discovery that, in a coherent state representation, states of good nucleon number can be projected analytically from BCS vacuum and excited quasiparticle states. This makes it possible to perform calculations in a number-projected BCS basis without losing much of the advantage of working of the quasiparticle scheme. (Author)

  8. Calculation of nuclear moment of inertia with proper treatment of pairing interaction

    International Nuclear Information System (INIS)

    Tazaki, S.; Ando, Y.; Hasegawa, M.

    1997-01-01

    An attempt to calculate nuclear moments of inertia treating the pairing interaction exactly is reported. As usual, hamiltonian is composed of the Nilsson's singleparticle energies and the pairing interaction, but the eigenstates and the eigenvalues are calculated exactly in a realistic, sufficiently large model space. The method of calculating the moment of inertia is presented. (author)

  9. Limitations in small artisanal gold mining addressed by educational components paired with alternative mining methods.

    Science.gov (United States)

    Zolnikov, Tara R

    2012-03-01

    Current solutions continue to be inadequate in addressing the longstanding, worldwide problem of mercury emissions from small artisanal gold mining. Mercury, an inexpensive and easily accessible heavy metal, is used in the process of extracting gold from ore. Mercury emissions disperse, affecting human populations by causing adverse health effects and environmental and social ramifications. Many developing nations have sizable gold ore deposits, making small artisanal gold mining a major source of employment in the world. Poverty drives vulnerable, rural populations into gold mining because of social and economic instabilities. Educational programs responding to this environmental hazard have been implemented in the past, but have had low positive results due to lack of governmental support and little economic incentive. Educational and enforced intervention programs must be developed in conjunction with governmental agencies in order to successfully eliminate this ongoing problem. Industry leaders offered hopeful suggestions, but revealed limitations when trying to develop encompassing solutions to halt mercury emissions. This research highlights potential options that have been attempted in the past and suggests alternative solutions to improve upon these methods. Some methods include buyer impact recognition, risk assessment proposals exposing a cost-benefit analysis and toxicokinetic modeling, public health awareness campaigns, and the education of miners, healthcare workers, and locals within hazardous areas of mercury exposure. These methods, paired with the implementation of alternative mining techniques, propose a substantial reduction of mercury emissions. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Affine pairings on ARM

    NARCIS (Netherlands)

    Acar, T.; Lauter, K.; Naehrig, M.; Shumow, D.

    2011-01-01

    Pairings on elliptic curves are being used in an increasing number of cryptographic applications on many different devices and platforms, but few performance numbers for cryptographic pairings have been reported on embedded and mobile devices. In this paper we give performance numbers for affine and

  11. Solutions of nuclear pairing

    International Nuclear Information System (INIS)

    Balantekin, A. B.; Pehlivan, Y.

    2007-01-01

    We give the exact solution of orbit dependent nuclear pairing problem between two nondegenerate energy levels using the Bethe ansatz technique. Our solution reduces to previously solved cases in the appropriate limits including Richardson's treatment of reduced pairing in terms of rational Gaudin algebra operators

  12. Relativistic mean field theory for deformed nuclei with pairing correlations

    International Nuclear Information System (INIS)

    Geng, Lisheng; Toki, Hiroshi; Sugimoto, Satoru; Meng, Jie

    2003-01-01

    We develop a relativistic mean field (RMF) description of deformed nuclei with pairing correlations in the BCS approximation. The treatment of the pairing correlations for nuclei whose Fermi surfaces are close to the threshold of unbound states needs special attention. With this in mind, we use a delta function interaction for the pairing interaction to pick up those states whose wave functions are concentrated in the nuclear region and employ the standard BCS approximation for the single-particle states obtained from the BMF theory with deformation. We apply the RMF + BCS method to the Zr isotopes and obtain a good description of the binding energies and the nuclear radii of nuclei from the proton drip line to the neutron drip line. (author)

  13. Virialization in N-body models of the expanding universe. I. Isolated pairs

    International Nuclear Information System (INIS)

    Evrard, A.E.; Yahil, A.; and Institute of Astronomy, University of Cambridge)

    1985-01-01

    The degree of virialization of isolated pairs of galaxies is investigated in the N-body simulations of Efstathiou and Eastwood for open (Ω 0 = 0.1) and critical (Ω 0 = 1.0) universes, utilizing the three-dimensional information available for both position and velocity. Roughly half of the particles in the models form isolated pairs whose dynamics is dominated by their own two-body force. Three-quarters or more of these pairs are bound, and this ensemble of bound isolated pairs is found to yield excellent mass estimates upon application of the virial theorem. Contamination from unbound pairs introduces error factors smaller than 2 in mass estimates, and these errors can be corrected by simple methods. Oribts of bound pairs are highly eccentric, but this does not lead to serious selection effects in orbital phases, since these are uniformly distributed. The relative velocity of these pairs of mass points shows a Keplerian falloff with separation, contrary to observational evidence for real galaxies. All the above results are independent of the value of Ω 0 , but may be sensitive to initial conditions and the point-mass nature of the particles

  14. A multi-segment foot model based on anatomically registered technical coordinate systems: method repeatability and sensitivity in pediatric planovalgus feet.

    Science.gov (United States)

    Saraswat, Prabhav; MacWilliams, Bruce A; Davis, Roy B; D'Astous, Jacques L

    2013-01-01

    Several multisegment foot models have been proposed and some have been used to study foot pathologies. These models have been tested and validated on typically developed populations; however application of such models to feet with significant deformities presents an additional set of challenges. For the first time, in this study, a multisegment foot model is tested for repeatability in a population of children with symptomatic abnormal feet. The results from this population are compared to the same metrics collected from an age matched (8-14 years) typically developing population. The modified Shriners Hospitals for Children, Greenville (mSHCG) foot model was applied to ten typically developing children and eleven children with planovalgus feet by two clinicians. Five subjects in each group were retested by both clinicians after 4-6 weeks. Both intra-clinician and inter-clinician repeatability were evaluated using static and dynamic measures. A plaster mold method was used to quantify variability arising from marker placement error. Dynamic variability was measured by examining trial differences from the same subjects when multiple clinicians carried out the data collection multiple times. For hindfoot and forefoot angles, static and dynamic variability in both groups was found to be less than 4° and 6° respectively. The mSHCG model strategy of minimal reliance on anatomical markers for dynamic measures and inherent flexibility enabled by separate anatomical and technical coordinate systems resulted in a model equally repeatable in typically developing and planovalgus populations. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Quantifying inbreeding avoidance through extra-pair reproduction.

    Science.gov (United States)

    Reid, Jane M; Arcese, Peter; Keller, Lukas F; Germain, Ryan R; Duthie, A Bradley; Losdat, Sylvain; Wolak, Matthew E; Nietlisbach, Pirmin

    2015-01-01

    Extra-pair reproduction is widely hypothesized to allow females to avoid inbreeding with related socially paired males. Consequently, numerous field studies have tested the key predictions that extra-pair offspring are less inbred than females' alternative within-pair offspring, and that the probability of extra-pair reproduction increases with a female's relatedness to her socially paired male. However, such studies rarely measure inbreeding or relatedness sufficiently precisely to detect subtle effects, or consider biases stemming from failure to observe inbred offspring that die during early development. Analyses of multigenerational song sparrow (Melospiza melodia) pedigree data showed that most females had opportunity to increase or decrease the coefficient of inbreeding of their offspring through extra-pair reproduction with neighboring males. In practice, observed extra-pair offspring had lower inbreeding coefficients than females' within-pair offspring on average, while the probability of extra-pair reproduction increased substantially with the coefficient of kinship between a female and her socially paired male. However, simulations showed that such effects could simply reflect bias stemming from inbreeding depression in early offspring survival. The null hypothesis that extra-pair reproduction is random with respect to kinship therefore cannot be definitively rejected in song sparrows, and existing general evidence that females avoid inbreeding through extra-pair reproduction requires reevaluation given such biases. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  16. Ion-pair chromatography of nucleic acid derivatives

    International Nuclear Information System (INIS)

    Perrone, P.A.; Brown, P.R.

    1985-01-01

    Little work has been done on the ion-pair chromatography of nucleic acid constituents, although there is a great potential for the use of this technique in the field. Since the classic work in 1949, nucleotides, as well as nucleosides and bases, have been separated by ion-exchange chromatography. However, ion exchange is a difficult mode and most researchers prefer the use of reversed-phase whenever possible. Although reversed-phase is now the method of choice, ionic compounds like nucleotides and some of the more polar bases are not adequately retained by many systems of this type. In addition, it is difficult to analyze simultaneously members of all three classes of nucleic acid compounds (bases, nucleosides, and nucleotides) using a reversed-phase system, even with gradient elution. Ion pairing can be a useful technique because, theoretically, the separation of nonionic bases and nucleosides along with the ionic nucleotides can be achieved. Additionally, each group of compounds may be separated isocratically. In this chapter, they will discuss ion-pair chromatography as applied to nucleic acid constituents. The current theories, advantages and disadvantages, a limited number of applications, and potential for future work are presented

  17. Pair correlation of super-deformed rotation band

    International Nuclear Information System (INIS)

    Shimizu, Yoshio

    1989-01-01

    The effect of pair correlation, one of the most important residual interactions associated with the super-deformed rotation band, is discussed in terms of the characteristics of the rotation band (its effect on the moment of inertia in particular), and the tunneling into an normal deformed state in relation to its effect on the angular momentum dependence of the potential energy plane as a function of the deformation. The characteristics of the rotation band is discussed in terms of the kinematic and dynamic momenta of inertia. It is shown that the pair correlation in a super-deformed rotation band acts to decrease the former and increase the latter momentum mainly due to dynamic pair correlation. A theoretical approach that takes this effect into account can provide results that are consistent with measured momenta, although large differences can occur in some cases. Major conflicts include a large measured kinetic momentum of inertia compared to the theoretical value, and the absence of the abnormality (shape increase) generally seen in low-spin experiments. The former seems likely to be associated with the method of measuring the angular momentum. (N.K.)

  18. Frustrated Lewis pairs-assisted reduction of carbonyl compounds

    DEFF Research Database (Denmark)

    Marek, Ales; Pedersen, Martin Holst Friborg

    2015-01-01

    An alternative and robust method for the reduction of carbonyl groups by frustrated Lewis pairs (FLPs) is reported in this paper. With its very mild reaction conditions, good to excellent yields, absolute regioselectivity and the non-metallic character of the reagent, it provides an excellent too...

  19. Secure pairing with biometrics

    NARCIS (Netherlands)

    Buhan, I.R.; Boom, B.J.; Doumen, J.M.; Hartel, Pieter H.; Veldhuis, Raymond N.J.

    Secure pairing enables two devices that share no prior context with each other to agree upon a security association, which they can use to protect their subsequent communication. Secure pairing offers guarantees of the association partner identity and it should be resistant to eavesdropping and to a

  20. A number-projected model with generalized pairing interaction in application to rotating nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Satula, W. [Warsaw Univ. (Poland)]|[Joint Institute for Heavy Ion Research, Oak Ridge, TN (United States)]|[Univ. of Tennessee, Knoxville, TN (United States)]|[Royal Institute of Technology, Stockholm (Sweden); Wyss, R. [Royal Institute of Technology, Stockholm (Sweden)

    1996-12-31

    A cranked mean-field model that takes into account both T=1 and T=0 pairing interactions is presented. The like-particle pairing interaction is described by means of a standard seniority force. The neutron-proton channel includes simultaneously correlations among particles moving in time reversed orbits (T=1) and identical orbits (T=0). The coupling between different pairing channels and nuclear rotation is taken into account selfconsistently. Approximate number-projection is included by means of the Lipkin-Nogami method. The transitions between different pairing phases are discussed as a function of neutron/proton excess, T{sub z}, and rotational frequency, {Dirac_h}{omega}.

  1. 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...... to sphericity assumptions, use of F tests and the Greenhouse-Geisser and Huynh-Feldt adjustments to compensate for deviations from sphericity. During a recent implementation of such methods in the R language, the general structure of such transformations was reconsidered, leading to a flexible specification...

  2. Property (RD) for Hecke Pairs

    International Nuclear Information System (INIS)

    Shirbisheh, Vahid

    2012-01-01

    As the first step towards developing noncommutative geometry over Hecke C ∗ -algebras, we study property (RD) (Rapid Decay) for Hecke pairs. When the subgroup H in a Hecke pair (G, H) is finite, we show that the Hecke pair (G, H) has (RD) if and only if G has (RD). This provides us with a family of examples of Hecke pairs with property (RD). We also adapt Paul Jolissant’s works in Jolissaint (J K-Theory 2:723–735, 1989; Trans Amer Math Soc 317(1):167–196, 1990) to the setting of Hecke C ∗ -algebras and show that when a Hecke pair (G, H) has property (RD), the algebra of rapidly decreasing functions on the set of double cosets is closed under holomorphic functional calculus of the associated (reduced) Hecke C ∗ -algebra. Hence they have the same K 0 -groups.

  3. Investigations into nuclear pairing

    International Nuclear Information System (INIS)

    Clark, R.M.

    2006-01-01

    This paper is divided in two main sections focusing on different aspects of collective nuclear behavior. In the first section, solutions are considered for the collective pairing Hamiltonian. In particular, an approximate solution at the critical point of the pairing transition from harmonic vibration (normal nuclear behavior) to deformed rotation (superconducting behavior) in gauge space is found by analytic solution of the Hamiltonian. The eigenvalues are expressed in terms of the zeros of Bessel functions of integer order. The results are compared to the pairing bands based on the Pb isotopes. The second section focuses on the experimental search for the Giant Pairing Vibration (GPV) in nuclei. After briefly describing the origin of the GPV, and the reasons that the state has remained unidentified, a novel idea for populating this state is presented. A recent experiment has been performed using the LIBERACE+STARS detector system at the 88-Inch Cyclotron of LBNL to test the idea. (Author)

  4. The effect of sensory-nutrient congruency on food intake after repeated exposure: do texture and/or energy density matter?

    Science.gov (United States)

    Hogenkamp, P S

    2014-09-01

    Sensory properties guide the amount that people eat. In particular, food texture plays an important role in a food's 'expected satiation', which in turn affects the food-related decision making process. One hypothesis is that incongruent pairing of a textural cue with a post-ingestive outcome compromises this process, leading to poor energy compensation. Several studies examined the effect of both energy density and sensory characteristics (i.e. increased creaminess and thickness) on expectations, subjective appetite and food intake. To add to this literature, a re-analysis of data assessed whether the effect of sensory-nutrient pairings on energy intake compensation persisted after repeated exposure to a food. In this cross-over design, 27 participants consumed two preloads with 'congruent' (low-energy/liquid; high-energy/semi-solid) and two preloads with 'incongruent' (low-energy/semi-solid; high-energy/liquid) texture-nutrient combinations for nine subsequent meals, during which ad libitum intake was measured. Intake at first exposure did not differ between the low-energy (280±150kcal) and high-energy preloads (292±183kcal) in the incongruent conditions. By contrast, it was greater after the low-energy (332±203kcal) than after the high-energy (236±132kcal) preload in the congruent conditions (energy∗incongruent/congruent, p=0.04). Post-exposure, this pattern changed: intake depended on the energy density of the preloads in all conditions, and was greater after low-energy preloads (day∗energy∗incongruent/congruent-interaction for breakfast: p=0.02). Thus, manipulating the sensory properties of a food influenced energy compensation and meal size, but only at initial exposure. Repeated exposure 'corrected' the initial lack of compensation observed in conditions with incongruent sensory-nutrient pairings. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Electron-positron pair creation from vacuum induced by variable electric field

    International Nuclear Information System (INIS)

    Marinov, M.S.; Popov, V.S.

    1977-01-01

    Problem is considered of spontaneous creation of electron-positron pairs from the vacuum induced by external electric field, that is homogeneous and depends on time in an arbitrary way. The Heisenberg equations of motion are obtained for the creation-annihilation operators. The solution is a linear canonical transformation. The problem is reduced to a set of differential equations for the second-order matrices determining this transformation. A consequence of the CP symmetry of the Dirac equation with an external electric field is that the e + e - pair is created from the vacuum in a state with total spin 1. The case when the variating electric field conserves its direction, is considered in more detail. In this case the equations are much simplified and may be reduced to the Riccati equation or to problem of oscillator with variable frequency, so the problem is equivalent to the one-dimensional quantal problem of a barrier penetration. Two approximate methods to calculate the pair creation probabilities are discussed: the quasiclassical approach and the antidiabatical method, applicable for sharp variations of the external field. Numerical estimates are obtained for the number of e + e - pairs produced by the field E(t) = E cos ωt. Group-theoretical aspects of the problem are also considered. (author)

  6. Fostering repeat donations in Ghana.

    Science.gov (United States)

    Owusu-Ofori, S; Asenso-Mensah, K; Boateng, P; Sarkodie, F; Allain, J-P

    2010-01-01

    Most African countries are challenged in recruiting and retaining voluntary blood donors by cost and other complexities and in establishing and implementing national blood policies. The availability of replacement donors who are a cheaper source of blood has not enhanced repeat voluntary donor initiatives. An overview of activities for recruiting and retaining voluntary blood donors was carried out. Donor records from mobile sessions were reviewed from 2002 to 2008. A total of 71,701 blood donations; 45,515 (63.5%) being voluntary donations with 11,680 (25%) repeat donations were collected during the study period. Donations from schools and colleges contributed a steady 60% of total voluntary whilst radio station blood drives increased contribution from 10 to 27%. Though Muslim population is less than 20%, blood collection was above the 30-donation cost-effectiveness threshold with a repeat donation trend reaching 60%. In contrast Christian worshippers provided donations. Repeat donation trends amongst school donors and radio blood drives were 20% and 70% respectively. Repeat donations rates have been variable amongst different blood donor groups in Kumasi, Ghana. The impact of community leaders in propagating altruism cannot be overemphasized. Programs aiming at motivating replacement donors to be repeat donors should be developed and assessed. Copyright 2009 The International Association for Biologicals. All rights reserved.

  7. Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

    Science.gov (United States)

    Ayesh, Basim M

    2017-01-01

    Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

  8. Abortion trends from 1996 to 2011 in Estonia: special emphasis on repeat abortion

    Science.gov (United States)

    2014-01-01

    Background The study aimed to describe the overall and age-specific trends of induced abortions from 1996 to 2011 with an emphasis on socio-demographic characteristics and contraceptive use of women having had repeat abortions in Estonia. Methods Data were retrieved from the Estonian Medical Birth and Abortion Registry and Statistics Estonia. Total induced abortion numbers, rates, ratios and age-specific rates are presented for 1996–2011. The percentage change in the number of repeat abortions within selected socio-demographic subgroups, contraception use and distribution of induced abortions among Estonians and non-Estonians for the first, second, third, fourth and subsequent abortions were calculated for the periods 1996–2003 and 2004–2011. Results Observed trends over the 16-year study period indicated a considerable decline in induced abortions with a reduction in abortion rate of 57.1%, which was mainly attributed to younger cohorts. The percentage of women undergoing repeat abortions fell steadily from 63.8% during 1996–2003 to 58.0% during 2004–2011. The percentage of women undergoing repeat abortions significantly decreased over the 16 years within all selected socio-demographic subgroups except among women with low educational attainment and students. Within each time period, a greater percentage of non-Estonians than Estonians underwent repeat abortions and obtained third and subsequent abortions. Most women did not use any contraceptive method prior to their first or subsequent abortion. Conclusion A high percentage of women obtaining repeat abortions reflects a high historical abortion rate. If current trends continue, a rapid decline in repeat abortions may be predicted. To decrease the burden of sexual ill health, routine contraceptive counselling, as standard care in the abortion process, should be seriously addressed with an emphasis on those groups - non-Estonians, women with lower educational attainment, students and women with children

  9. Instability of vortex pair leapfrogging

    DEFF Research Database (Denmark)

    Tophøj, Laust; Aref, Hassan

    2013-01-01

    Leapfrogging is a periodic solution of the four-vortex problem with two positive and two negative point vortices all of the same absolute circulation arranged as co-axial vortex pairs. The set of co-axial motions can be parameterized by the ratio 0 vortex pair sizes at the time when one...... pair passes through the other. Leapfrogging occurs for α > σ2, where is the silver ratio. The motion is known in full analytical detail since the 1877 thesis of Gröbli and a well known 1894 paper by Love. Acheson ["Instability of vortex leapfrogging," Eur. J. Phys.21, 269-273 (2000...... pairs fly off to infinity, and a "walkabout" mode, where the vortices depart from leapfrogging but still remain within a finite distance of one another. We show numerically that this transition is more gradual, a result that we relate to earlier investigations of chaotic scattering of vortex pairs [L...

  10. Pairing induced superconductivity in holography

    Science.gov (United States)

    Bagrov, Andrey; Meszena, Balazs; Schalm, Koenraad

    2014-09-01

    We study pairing induced superconductivity in large N strongly coupled systems at finite density using holography. In the weakly coupled dual gravitational theory the mechanism is conventional BCS theory. An IR hard wall cut-off is included to ensure that we can controllably address the dynamics of a single confined Fermi surface. We address in detail the interplay between the scalar order parameter field and fermion pairing. Adding an explicitly dynamical scalar operator with the same quantum numbers as the fermion-pair, the theory experiences a BCS/BEC crossover controlled by the relative scaling dimensions. We find the novel result that this BCS/BEC crossover exposes resonances in the canonical expectation value of the scalar operator. This occurs not only when the scaling dimension is degenerate with the Cooper pair, but also with that of higher derivative paired operators. We speculate that a proper definition of the order parameter which takes mixing with these operators into account stays finite nevertheless.

  11. Molecular identification and characterization of clustered regularly interspaced short palindromic repeats (CRISPRs) in a urease-positive thermophilic Campylobacter sp. (UPTC).

    Science.gov (United States)

    Tasaki, E; Hirayama, J; Tazumi, A; Hayashi, K; Hara, Y; Ueno, H; Moore, J E; Millar, B C; Matsuda, M

    2012-02-01

    Novel clustered regularly-interspaced short palindromic repeats (CRISPRs) locus [7,500 base pairs (bp) in length] occurred in the urease-positive thermophilic Campylobacter (UPTC) Japanese isolate, CF89-12. The 7,500 bp gene loci consisted of the 5'-methylaminomethyl-2-thiouridylate methyltransferase gene, putative (P) CRISPR associated (p-Cas), putative open reading frames, Cas1 and Cas2, leader sequence region (146 bp), 12 CRISPRs consensus sequence repeats (each 36 bp) separated by a non-repetitive unique spacer region of similar length (26-31 bp) and the phosphatidyl glycerophosphatase A gene. When the CRISPRs loci in the UPTC CF89-12 and five C. jejuni isolates were compared with one another, these six isolates contained p-Cas, Cas1 and Cas2 within the loci. Four to 12 CRISPRs consensus sequence repeats separated by a non-repetitive unique spacer region occurred in six isolates and the nucleotide sequences of those repeats gave approximately 92-100% similarity with each other. However, no sequence similarity occurred in the unique spacer regions among these isolates. The putative σ(70) transcriptional promoter and the hypothetical ρ-independent terminator structures for the CRISPRs and Cas were detected. No in vivo transcription of p-Cas, Cas1 and Cas2 was confirmed in the UPTC cells.

  12. Beverage Intake Assessment Questionnaire: Relative Validity and Repeatability in a Spanish Population with Metabolic Syndrome from the PREDIMED-PLUS Study

    Science.gov (United States)

    Ferreira-Pêgo, Cíntia; Nissensohn, Mariela; Kavouras, Stavros A.; Babio, Nancy; Serra-Majem, Lluís; Martín Águila, Adys; Mauromoustakos, Andy; Álvarez Pérez, Jacqueline; Salas-Salvadó, Jordi

    2016-01-01

    We assess the repeatability and relative validity of a Spanish beverage intake questionnaire for assessing water intake from beverages. The present analysis was performed within the framework of the PREDIMED-PLUS trial. The study participants were adults (aged 55–75) with a BMI ≥27 and <40 kg/m2, and at least three components of Metabolic Syndrome (MetS). A trained dietitian completed the questionnaire. Participants provided 24-h urine samples, and the volume and urine osmolality were recorded. The repeatability of the baseline measurement at 6 and 1 year was examined by paired Student’s t-test comparisons. A total of 160 participants were included in the analysis. The Bland–Altman analysis showed relatively good agreement between total daily fluid intake assessed using the fluid-specific questionnaire, and urine osmolality and 24-h volume with parameter estimates of −0.65 and 0.22, respectively (R2 = 0.20; p < 0.001). In the repeatability test, no significant differences were found between neither type of beverage nor total daily fluid intake at 6 months and 1-year assessment, compared to baseline. The proposed fluid-specific assessment questionnaire designed to assess the consumption of water and other beverages in Spanish adult individuals was found to be relatively valid with good repeatability. PMID:27483318

  13. Top quark pair production at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Baernreuther, Peter

    2012-06-28

    One of the most interesting and manifold processes in the Standard Model of elementary particle physics is the top quark pair production. It enabled the discovery of the top quark at the Tevatron in 1995 and the determination of many of its properties. By means of a precise measurement and calculation of the cross section of top quark pair production it is possible to extract the top quark mass. Improvements in the gluon parton distribution functions (important for the Higgs boson production) or improvements in the prediction of the Higgs mass are also closely linked with the top quark pair production. Furthermore, the production process plays an important role in the discovery of new physics. On the one hand the top quark pair decays form the largest part of the background in many BSM models, on the other hand BSM physics can be detected directly in the decay process by investigating the charge symmetry or the invariant mass spectrum. At the LHC it will be possible for the first time to produce a large amount of top quarks; thereby the statistical errors of the observables will be strongly reduced. The enormous increase in the production rate has two reasons. On the one hand, the acceleration energy of the LHC (14 TeV and 7 TeV) is significantly greater than that of the Tevatron (1.96 Tev). This leads to an increase of the cross section by a factor of 100 ({proportional_to}7.3 pb at the Tevatron to {proportional_to}800 pb at 14 TeV LHC). On the other hand, the luminosity of the LHC outperforms the Tevatron by a factor of 10-100. The reduced experimental errors for the observables demand an improvement of the theoretical error. The experimental accuracy of the LHC and the great relevance of the process led to an intensive activity of different research groups in order to improve the calculation of the cross section of top quark pair production. This work presents for the first time a complete numerical result for the full NNLO correction for the top quark pair

  14. Top quark pair production at the LHC

    International Nuclear Information System (INIS)

    Baernreuther, Peter

    2012-01-01

    One of the most interesting and manifold processes in the Standard Model of elementary particle physics is the top quark pair production. It enabled the discovery of the top quark at the Tevatron in 1995 and the determination of many of its properties. By means of a precise measurement and calculation of the cross section of top quark pair production it is possible to extract the top quark mass. Improvements in the gluon parton distribution functions (important for the Higgs boson production) or improvements in the prediction of the Higgs mass are also closely linked with the top quark pair production. Furthermore, the production process plays an important role in the discovery of new physics. On the one hand the top quark pair decays form the largest part of the background in many BSM models, on the other hand BSM physics can be detected directly in the decay process by investigating the charge symmetry or the invariant mass spectrum. At the LHC it will be possible for the first time to produce a large amount of top quarks; thereby the statistical errors of the observables will be strongly reduced. The enormous increase in the production rate has two reasons. On the one hand, the acceleration energy of the LHC (14 TeV and 7 TeV) is significantly greater than that of the Tevatron (1.96 Tev). This leads to an increase of the cross section by a factor of 100 (∝7.3 pb at the Tevatron to ∝800 pb at 14 TeV LHC). On the other hand, the luminosity of the LHC outperforms the Tevatron by a factor of 10-100. The reduced experimental errors for the observables demand an improvement of the theoretical error. The experimental accuracy of the LHC and the great relevance of the process led to an intensive activity of different research groups in order to improve the calculation of the cross section of top quark pair production. This work presents for the first time a complete numerical result for the full NNLO correction for the top quark pair production in quark anti

  15. Strong quasi-particle tunneling study in the paired quantum Hall states

    OpenAIRE

    Nomura, Kentaro; Yoshioka, Daijiro

    2001-01-01

    The quasi-particle tunneling phenomena in the paired fractional quantum Hall states are studied. A single point-contact system is first considered. Because of relevancy of the quasi-particle tunneling term, the strong tunneling regime should be investigated. Using the instanton method it is shown that the strong quasi-particle tunneling regime is described as the weak electron tunneling regime effectively. Expanding to the network model the paired quantum Hall liquid to insulator transition i...

  16. Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.

    Science.gov (United States)

    Nishimasu, Rieko; Komori, Hirofumi; Higuchi, Yoshiki; Nishimasu, Hiroshi; Hiroaki, Hidekazu

    2010-10-21

    Doa1/Ufd3 is involved in ubiquitin (Ub)-dependent cellular processes in Saccharomyces cerevisiae, and consists of WD40, PFU, and PUL domains. Previous studies showed that the PFU and PUL domains interact with Ub and Hse1, and Cdc48, respectively. However, their detailed functional interactions with Doa1 remained elusive. We report the crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å resolution. The conserved surface of the PFU domain may be involved in binding to Ub and Hse1. Unexpectedly, the PUL domain consists of an Armadillo (ARM)-like repeat structure. The positively charged concave surface of the PUL domain may bind to the negatively charged C-terminal region of Cdc48. A structural comparison of Doa1 with Ufd2 revealed that they share a similar ARM-like repeat, supporting a model in which Doa1 and Ufd2 compete for Cdc48 binding and may dictate the fate of ubiquitinated proteins in the proteasome pathway.

  17. [Paired kidneys in transplant].

    Science.gov (United States)

    Regueiro López, Juan C; Leva Vallejo, Manuel; Prieto Castro, Rafael; Anglada Curado, Francisco; Vela Jiménez, Francisco; Ruiz García, Jesús

    2009-02-01

    Many factors affect the graft and patient survival on the renal transplant outcome. These factors depend so much of the recipient and donor. We accomplished a study trying to circumvent factors that depend on the donor. We checked the paired kidneys originating of a same donor cadaver. We examined the risk factors in the evolution and follow-up in 278 couples of kidney transplant. We describe their differences, significance, the graft and patient survival, their functionality in 3 and 5 years and the risk factors implicated in their function. We study immunogenic and no immunogenic variables, trying to explain the inferior results in the grafts that are established secondly. We regroup the paired kidneys in those that they did not show paired initial function within the same couple. The results yield a discreet deterioration in the graft and patient survival for second group establish, superior creatinina concentration, without obtaining statistical significance. The Cox regression study establishes the early rejection (inferior to three months) and DR incompatibility values like risk factors. This model of paired kidneys would be able to get close to best-suited form for risk factors analysis in kidney transplant from cadaver donors, if more patients examine themselves in the same way. The paired kidneys originating from the same donor do not show the same function in spite of sharing the same conditions of the donor and perioperative management.

  18. Dual origin of pairing in nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Idini, A. [University of Jyvaskyla, Department of Physics (Finland); Potel, G. [Michigan State University, National Superconducting Cyclotron Laboratory (United States); Barranco, F. [Escuela Superior de Ingenieros, Universidad de Sevilla, Departamento de Fìsica Aplicada III (Spain); Vigezzi, E., E-mail: enrico.vigezzi@mi.infn.it [INFN Sezione di Milano (Italy); Broglia, R. A. [Università di Milano, Dipartimento di Fisica (Italy)

    2016-11-15

    The pairing correlations of the nucleus {sup 120}Sn are calculated by solving the Nambu–Gor’kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairing interaction. The first is the strong {sup 1}S{sub 0} short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- (v{sub p}{sup bare}) and long-range (v{sub p}{sup ind}) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.

  19. Dual origin of pairing in nuclei

    Science.gov (United States)

    Idini, A.; Potel, G.; Barranco, F.; Vigezzi, E.; Broglia, R. A.

    2016-11-01

    The pairing correlations of the nucleus 120Sn are calculated by solving the Nambu-Gor'kov equations, including medium polarization effects resulting from the interweaving of quasiparticles, spin and density vibrations, taking into account, within the framework of nuclear field theory (NFT), processes leading to self-energy and vertex corrections and to the induced pairing interaction. From these results one can not only demonstrate the inevitability of the dual origin of pairing in nuclei, but also extract information which can be used at profit to quantitatively disentangle the contributions to the pairing gap Δ arising from the bare and from the induced pairing interaction. The first is the strong 1 S 0 short-range NN potential resulting from meson exchange between nucleons moving in time reversal states within an energy range of hundreds of MeV from the Fermi energy. The second results from the exchange of vibrational modes between nucleons moving within few MeV from the Fermi energy. Short- ( v p bare) and long-range ( v p ind) pairing interactions contribute essentially equally to nuclear Cooper pair stability. That is to the breaking of gauge invariance in open-shell superfluid nuclei and thus to the order parameter, namely to the ground state expectation value of the pair creation operator. In other words, to the emergent property of generalized rigidity in gauge space, and associated rotational bands and Cooper pair tunneling between members of these bands.

  20. Aberrant approach-avoidance conflict resolution following repeated cocaine pre-exposure.

    Science.gov (United States)

    Nguyen, David; Schumacher, Anett; Erb, Suzanne; Ito, Rutsuko

    2015-10-01

    Addiction is characterized by persistence to seek drug reinforcement despite negative consequences. Drug-induced aberrations in approach and avoidance processing likely facilitate the sustenance of addiction pathology. Currently, the effects of repeated drug exposure on the resolution of conflicting approach and avoidance motivational signals have yet to be thoroughly investigated. The present study sought to investigate the effects of cocaine pre-exposure on conflict resolution using novel approach-avoidance paradigms. We used a novel mixed-valence conditioning paradigm to condition cocaine-pre-exposed rats to associate visuo-tactile cues with either the delivery of sucrose reward or shock punishment in the arms in which the cues were presented. Following training, exploration of an arm containing a superimposition of the cues was assessed as a measure of conflict resolution behavior. We also used a mixed-valence runway paradigm wherein cocaine-pre-exposed rats traversed an alleyway toward a goal compartment to receive a pairing of sucrose reward and shock punishment. Latency to enter the goal compartment across trials was taken as a measure of motivational conflict. Our results reveal that cocaine pre-exposure attenuated learning for the aversive cue association in our conditioning paradigm and enhanced preference for mixed-valence stimuli in both paradigms. Repeated cocaine pre-exposure allows appetitive approach motivations to gain greater influence over behavioral output in the context of motivational conflict, due to aberrant positive and negative incentive motivational processing.

  1. Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    Science.gov (United States)

    Moriya, Yuki; Yamada, Takuji; Okuda, Shujiro; Nakagawa, Zenichi; Kotera, Masaaki; Tokimatsu, Toshiaki; Kanehisa, Minoru; Goto, Susumu

    2016-03-28

    Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies that estimate the number of candidate enzyme genes, these studies required some additional information aside from the structures of metabolites such as gene expression and order in the genome. In this study, we developed a novel method to identify a candidate enzyme gene of a reaction using the chemical structures of the substrate-product pair (reactant pair). The proposed method is based on a search for similar reactant pairs in a reference database and offers ortholog groups that possibly mediate the given reaction. We applied the proposed method to two experimentally validated reactions. As a result, we confirmed that the histidine transaminase was correctly identified. Although our method could not directly identify the asparagine oxo-acid transaminase, we successfully found the paralog gene most similar to the correct enzyme gene. We also applied our method to infer candidate enzyme genes in the mesaconate pathway. The advantage of our method lies in the prediction of possible genes for orphan enzyme reactions where any associated gene sequences are not determined yet. We believe that this approach will facilitate experimental identification of genes for orphan enzymes.

  2. Shell-model calculations with a basis that contains correlated pairs

    International Nuclear Information System (INIS)

    Boisson, J.P.; Silvestre-Brac, B.A.; Liotta, R.J.

    1979-01-01

    A method to solve the shell-model equations within a basis that contains correlated pairs of particles is presented. The method is illustrated for the three-identical-particle system. Applications in nuclei around 208 Pb are given and comparisons with both experimental data and other calculations are carried out. (Auth.)

  3. New de-embedding structures for extracting the electrical parameters of a through-silicon-via pair

    International Nuclear Information System (INIS)

    Zhou Jing; Wan Lixi; Li Jun; Wang Huijuan; Dai Fengwei; Cao Liqiang; Yu Daquan; Guidotti, Daniel

    2013-01-01

    Two innovative de-embedding methods are proposed for extracting an electrical model for a through-silicon-via (TSV) pair consisting of a ground-signal (GS) structure. In addition, based on microwave network theory, a new solution scheme is developed for dealing with multiple solutions of the transfer matrix during the process of de-embedding. A unique solution is determined based on the amplitude and the phase characteristic of S parameters. In the first de-embedding method, a typical “π“ type model of the TSV pair is developed, which illustrates the need to allow for frequency dependence in the equivalent TSV pair Spice model. This de-embedding method is shown to be effective for extracting the electrical properties of the TSVs. The feasibility of a second de-embedding method is also investigated. (semiconductor integrated circuits)

  4. KEEFEKTIFAN THINK-PAIR-SHARE UNTUK MENINGKATKAN PEMAHAMAN MAHASISWA MENGENAI KONSEP DASAR HUBUNGAN MASYARAKAT

    Directory of Open Access Journals (Sweden)

    Nina Oktarina

    2016-01-01

    Full Text Available Intention of research this is to improve quality of study of public relations, to increase the spirit of learning student, to uplift skill teacher in developing model and study media and to increase the achievement learn student. This research is research of class action which is consisted of three cycle. Result of research show achievement learn natural student of improvement in each its cycle. learn student of before applying of method Think-Pair-Share 0%, after applying of method Think-Pair-Share, learn from student after conducted by a final test is 76,67%. Enthusiasm, livelines and student cooperation in course of study of 1-4 result is good ( 3,39. Perception result hit skill teacher in study management by using method Think-Pair-Share with 1-4 showing good result with rate from cycle 1, cycle 2, and cycle 3 is 3,38. The score represent rate from entire/all aspect perceived at three

  5. Interesting features of nonlinear shock equations in dissipative pair-ion-electron plasmas

    International Nuclear Information System (INIS)

    Masood, W.; Rizvi, H.

    2011-01-01

    Two dimensional nonlinear electrostatic waves are studied in unmagnetized, dissipative pair-ion-electron plasmas in the presence of weak transverse perturbation. The dissipation in the system is taken into account by incorporating the kinematic viscosity of both positive and negative ions. In the linear case, a biquadratic dispersion relation is obtained, which yields the fast and slow modes in a pair-ion-electron plasma. It is shown that the limiting cases of electron-ion and pair-ion can be retrieved from the general biquadratic dispersion relation, and the differences in the characters of the waves propagating in both the cases are also highlighted. Using the small amplitude approximation method, the nonlinear Kadomtsev Petviashvili Burgers as well as Burgers-Kadomtsev Petviashvili equations are derived and their applicability for pair-ion-electron plasma is explained in detail. The present study may have relevance to understand the formation of two dimensional electrostatic shocks in laboratory produced pair-ion-electron plasmas.

  6. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  7. The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China

    Directory of Open Access Journals (Sweden)

    Yang Li

    2018-04-01

    Full Text Available This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%. By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP, and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%. By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.

  8. A counter-rotating vortex pair in inviscid fluid

    Science.gov (United States)

    Habibah, Ummu; Fukumoto, Yasuhide

    2017-12-01

    We study the motion of a counter-rotating vortex pair with the circulations ±Γ move in incompressible fluid. The assumption is made that the core is very thin, that is the core radius σ is much smaller than the vortex radius d such that ɛ = σ/d ≪ 1. With this condition, the method of matched asymptotic expansion is employed. The solutions of the Navier-Stokes equations and the Biot-Savart law, regarding the inner and outer solutions respectively, are constructed in the form of a small parameter. An asymptotic expansion of the Biot-Savart law near the vortex core provides with the matching condition for an asymptotic expansion for limiting the Navier-Stokes equations for large radius r. The general formula of an anti-parallel vortex pair is established. At leading order O(ɛ0), we apply the special case in inviscid fluid, the Rankine vortex, a circular vortex of uniform vorticity. Furthermore at leading order O(ɛ5) we show the traveling speed of a vortex pair.

  9. Singlet-paired coupled cluster theory for open shells

    Science.gov (United States)

    Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

    2016-06-01

    Restricted single-reference coupled cluster theory truncated to single and double excitations accurately describes weakly correlated systems, but often breaks down in the presence of static or strong correlation. Good coupled cluster energies in the presence of degeneracies can be obtained by using a symmetry-broken reference, such as unrestricted Hartree-Fock, but at the cost of good quantum numbers. A large body of work has shown that modifying the coupled cluster ansatz allows for the treatment of strong correlation within a single-reference, symmetry-adapted framework. The recently introduced singlet-paired coupled cluster doubles (CCD0) method is one such model, which recovers correct behavior for strong correlation without requiring symmetry breaking in the reference. Here, we extend singlet-paired coupled cluster for application to open shells via restricted open-shell singlet-paired coupled cluster singles and doubles (ROCCSD0). The ROCCSD0 approach retains the benefits of standard coupled cluster theory and recovers correct behavior for strongly correlated, open-shell systems using a spin-preserving ROHF reference.

  10. Singlet-paired coupled cluster theory for open shells

    International Nuclear Information System (INIS)

    Gomez, John A.; Henderson, Thomas M.; Scuseria, Gustavo E.

    2016-01-01

    Restricted single-reference coupled cluster theory truncated to single and double excitations accurately describes weakly correlated systems, but often breaks down in the presence of static or strong correlation. Good coupled cluster energies in the presence of degeneracies can be obtained by using a symmetry-broken reference, such as unrestricted Hartree-Fock, but at the cost of good quantum numbers. A large body of work has shown that modifying the coupled cluster ansatz allows for the treatment of strong correlation within a single-reference, symmetry-adapted framework. The recently introduced singlet-paired coupled cluster doubles (CCD0) method is one such model, which recovers correct behavior for strong correlation without requiring symmetry breaking in the reference. Here, we extend singlet-paired coupled cluster for application to open shells via restricted open-shell singlet-paired coupled cluster singles and doubles (ROCCSD0). The ROCCSD0 approach retains the benefits of standard coupled cluster theory and recovers correct behavior for strongly correlated, open-shell systems using a spin-preserving ROHF reference.

  11. Molecular Characterization of Cultivated Bromeliad Accessions with Inter-Simple Sequence Repeat (ISSR Markers

    Directory of Open Access Journals (Sweden)

    Yongming Yu

    2012-05-01

    Full Text Available Bromeliads are of great economic importance in flower production; however little information is available with respect to genetic characterization of cultivated bromeliads thus far. In the present study, a selection of cultivated bromeliads was characterized via inter-simple sequence repeat (ISSR markers with an emphasis on genetic diversity and population structure. Twelve ISSR primers produced 342 bands, of which 287 (~84% were polymorphic, with polymorphic bands per primer ranging from 17 to 34. The Jaccard’s similarity ranged from 0.08 to 0.89 and averaged ~0.30 for the investigated bromeliads. The Bayesian-based approach, together with the un-weighted paired group method with arithmetic average (UPGMA-based clustering and the principal coordinate analysis (PCoA, distinctly grouped the bromeliads from Neoregelia, Guzmania, and Vriesea into three separately clusters, well corresponding with their botanical classifications; whereas the bromeliads of Aechmea other than the recently selected hybrids were not well assigned to a cluster. Additionally, ISSR marker was proven efficient for the identification of hybrids and bud sports of cultivated bromeliads. The findings achieved herein will further our knowledge about the genetic variability within cultivated bromeliads and therefore facilitate breeding for new varieties of cultivated bromeliads in future as well.

  12. Topological characteristics of helical repeat proteins

    NARCIS (Netherlands)

    Groves, M R; Barford, D

    The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

  13. Evaluation of genetic diversity in rice using simple sequence repeats ...

    African Journals Online (AJOL)

    The genetic diversity of 64 rice genotypes using 20 SSR primers on chromosome number 7-12 was investigated. DNA was extracted by modified cetyl trimethyl ammonium bromide (CTAB) method. The banding pattern was recorded in the form of 0-1 data sheet which was analyzed using unweighted pair group method with ...

  14. EFEKTIVITAS PENGGUNAAN METODE THINK PAIR SHARE DALAM PEMBELAJARAN EKONOMI POKOK BAHASAN PEMBENTUKAN HARGA PASAR DI SMP

    OpenAIRE

    Joko Widodo

    2007-01-01

    The result of teaching-learning by using Think Pair Share method can improve the students’ activities. It can be seen from the steps to apply the Think Pair Share method that focused on student-centre. Think pair share learning has a simple structure, as a basic of the development ‘cooperative class’ which can help the learning process actively for students, thus it can improve the students’ study result. Students actively can show their ability to discuss and share and express the an...

  15. Efektivitas Penggunaan Metode Think Pair Share Dalam Pembelajaran Ekonomi Pokok Bahasan Pembentukan Harga Pasar Di SMP

    OpenAIRE

    Widodo, Joko

    2007-01-01

    The result of teaching-learning by using Think Pair Share method can improve the students’ activities. It can be seen from the steps to apply the Think Pair Share method that focused on student-centre. Think pair share learning has a simple structure, as a basic of the development ‘cooperative class’ which can help the learning process actively for students, thus it can improve the students’ study result. Students actively can show their ability to discuss and share and express the an...

  16. Comparative study of the requantization of the time-dependent mean field for the dynamics of nuclear pairing

    Science.gov (United States)

    Ni, Fang; Nakatsukasa, Takashi

    2018-04-01

    To describe quantal collective phenomena, it is useful to requantize the time-dependent mean-field dynamics. We study the time-dependent Hartree-Fock-Bogoliubov (TDHFB) theory for the two-level pairing Hamiltonian, and compare results of different quantization methods. The one constructing microscopic wave functions, using the TDHFB trajectories fulfilling the Einstein-Brillouin-Keller quantization condition, turns out to be the most accurate. The method is based on the stationary-phase approximation to the path integral. We also examine the performance of the collective model which assumes that the pairing gap parameter is the collective coordinate. The applicability of the collective model is limited for the nuclear pairing with a small number of single-particle levels, because the pairing gap parameter represents only a half of the pairing collective space.

  17. Development of a Method to Compensate for Signal Quality Variations in Repeated Auditory Event-Related Potential Recordings

    Science.gov (United States)

    Paukkunen, Antti K. O.; Leminen, Miika M.; Sepponen, Raimo

    2010-01-01

    Reliable measurements are mandatory in clinically relevant auditory event-related potential (AERP)-based tools and applications. The comparability of the results gets worse as a result of variations in the remaining measurement error. A potential method is studied that allows optimization of the length of the recording session according to the concurrent quality of the recorded data. In this way, the sufficiency of the trials can be better guaranteed, which enables control of the remaining measurement error. The suggested method is based on monitoring the signal-to-noise ratio (SNR) and remaining measurement error which are compared to predefined threshold values. The SNR test is well defined, but the criterion for the measurement error test still requires further empirical testing in practice. According to the results, the reproducibility of average AERPs in repeated experiments is improved in comparison to a case where the number of recorded trials is constant. The test-retest reliability is not significantly changed on average but the between-subject variation in the value is reduced by 33–35%. The optimization of the number of trials also prevents excessive recordings which might be of practical interest especially in the clinical context. The efficiency of the method may be further increased by implementing online tools that improve data consistency. PMID:20407635

  18. Unmatched Projector/Backprojector Pairs: Perturbation and Convergence Analysis

    DEFF Research Database (Denmark)

    Elfving, Tommy; Hansen, Per Christian

    2018-01-01

    are not each other's transpose. Surprisingly, the influence of such errors in algebraic iterative reconstruction methods has received little attention in the literature. The goal of this paper is to perform a rigorous first-order perturbation analysis of the minimization problems underlying the algebraic...... methods in order to understand the role played by the nonmatch of the matrices. We also study the convergence properties of linear stationary iterations based on unmatched matrix pairs, leading to insight into the behavior of some important row-and column-oriented algebraic iterative methods. We conclude...

  19. Neutron pair and proton pair transfer reactions between identical cores in the sulfur region

    International Nuclear Information System (INIS)

    Mermaz, M.C.

    1995-12-01

    Optical model and exact finite range distorted-wave Born approximation analyses were performed on neutron pair exchange between identical cores for 32 S and 34 S nuclei and on proton pair exchange between identical cores for 30 Si and 32 S. The extracted spectroscopic factors were compared with theoretical ones deduced from Hartree-Fock calculations on these pair of nuclei. The enhancement of the experimental cross sections with respect to the theoretical ones strongly suggests evidence for a nuclear Josephson effect. (author). 15 refs., 5 figs., 3 tabs

  20. Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis.

    Science.gov (United States)

    Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo

    2013-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.

  1. Probing Amorphous Components in High Temperature TE Materials by in situ Total Scattering and the Pair Distribution Function (PDF) Method

    DEFF Research Database (Denmark)

    Reardon, Hazel; Iversen, Bo Brummerstedt; Blichfeld, Anders Bank

    -I clathrate Ba8Ga16Ge30. This suggests that local structure reorientations in the cage are likely to be the root cause of the degradation of the structure. This deepens our understanding of disordered clathrates, and provides evidence that the PDF technique is an effective method for probing local structure.......e., by measuring both the Bragg and diffuse scattering from a sample. This method has rarely been exploited by the non-oxide thermoelectrics community. , , Treating total scattering data by the Pair Distribution Function method is a logical approach to understanding defects, disorder and amorphous components...... to heating cycles, then we are closer to distinguishing how we may generate materials that do not undergo specific structure reorientation processes, and/or how we may mitigate them before they occur. Here, we will present a total scattering and PDF study that probes the local structure of the Type...

  2. Dispersion analysis of the Pn -Pn-1DG mixed finite element pair for atmospheric modelling

    Science.gov (United States)

    Melvin, Thomas

    2018-02-01

    Mixed finite element methods provide a generalisation of staggered grid finite difference methods with a framework to extend the method to high orders. The ability to generate a high order method is appealing for applications on the kind of quasi-uniform grids that are popular for atmospheric modelling, so that the method retains an acceptable level of accuracy even around special points in the grid. The dispersion properties of such schemes are important to study as they provide insight into the numerical adjustment to imbalance that is an important component in atmospheric modelling. This paper extends the recent analysis of the P2 - P1DG pair, that is a quadratic continuous and linear discontinuous finite element pair, to higher polynomial orders and also spectral element type pairs. In common with the previously studied element pair, and also with other schemes such as the spectral element and discontinuous Galerkin methods, increasing the polynomial order is found to provide a more accurate dispersion relation for the well resolved part of the spectrum but at the cost of a number of unphysical spectral gaps. The effects of these spectral gaps are investigated and shown to have a varying impact depending upon the width of the gap. Finally, the tensor product nature of the finite element spaces is exploited to extend the dispersion analysis into two-dimensions.

  3. Dynamical pairing correlations in rotating nuclei

    International Nuclear Information System (INIS)

    Szymanski, Z.

    1985-01-01

    When the atomic nucleus rotates fast enough the static pair correlations may be destroyed. In this situation the pair-vibrations become an important manifestation of the short-range attractive pairing force. The influence of this effect on nuclear properties at high spin is discussed. (orig.)

  4. Pair creation at large inherent angles

    International Nuclear Information System (INIS)

    Chen, P.; Tauchi, T.; Schroeder, D.V.

    1992-01-01

    In the next-generation linear colliders, the low-energy e + e - pairs created during the collision of high-energy e + e - beams would cause potential deleterious background problems to the detectors. At low collider energies, the pairs are made essentially by the incoherent process, where the pair is created by the interaction of beamstrahlung photons on the individual particles in the oncoming beam. This problem was first identified by Zolotarev, et al. At energies where the beamstrahlung parameter Υ lies approximately in the range 0.6 approx-lt Υ approx-lt 100, pair creation from the beamstrahlung photons is dominated by a coherent process, first noted by Chen. The seriousness of this pair creation problem lies in the transverse momenta that the pair particles carry when leaving the interaction point (IP) with large angles. Since the central issue is the transverse momentum for particles with large angles, the authors notice that there is another source for it. Namely, when the pair particles are created at low energies, the intrinsic angles of these pairs when produced may already be large. In this paper they reinvestigate the problem, following essentially the same equivalent photon approach, but with changes in specific details including the virtual photon spectrum. In addition, various assumptions are made more explicit. The formulas derived are then applied to the collider parameters designed by Palmer

  5. 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.

  6. Determining the reaction in kinematic pairs of certain mechanisms using a digital computer

    Energy Technology Data Exchange (ETDEWEB)

    Chifchieva, V N

    1980-01-01

    In Dorr classifiers, walking excavators, conveyors, sieves and other mechanisms, one finds a triad with a sliding pair. An algorithm is proposed for determining reactions in the kinematic connections of a triad with one, two or three sliding pairs. The algorithm is suitable for use in digital computers. It is based on the transfer function method, and has several advantages over the technnique of determining reactions in kinematic pairs of V. Zinovyev. A concrete example is given of calculating reactions in the connections of a crank and lever mechanism of a walking excavator.

  7. Radical-pair based avian magnetoreception

    Science.gov (United States)

    Procopio, Maria; Ritz, Thorsten

    2014-03-01

    Behavioural experiments suggest that migratory birds possess a magnetic compass sensor able to detect the direction of the geomagnetic. One hypothesis for the basis of this remarkable sensory ability is that the coherent quantum spin dynamics of photoinduced radical pair reactions transduces directional magnetic information from the geomagnetic field into changes of reaction yields, possibly involving the photoreceptor cryptochrome in the birds retina. The suggested radical-pair based avian magnetoreception has attracted attention in the field of quantum biology as an example of a biological sensor which might exploit quantum coherences for its biological function. Investigations on such a spin-based sensor have focussed on uncovering the design features for the design of a biomimetic magnetic field sensor. We study the effects of slow fluctuations in the nuclear spin environment on the directional signal. We quantitatively evaluate the robustness of signals under fluctuations on a timescale longer than the lifetime of a radical pair, utilizing two models of radical pairs. Our results suggest design principles for building a radical-pair based compass sensor that is both robust and highly directional sensitive.

  8. Repeat Stereotactic Radiosurgery for Acoustic Neuromas

    International Nuclear Information System (INIS)

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

    2010-01-01

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

  9. 32 species validation of a new Illumina paired-end approach for the development of microsatellites.

    Directory of Open Access Journals (Sweden)

    Stacey L Lance

    Full Text Available Development and optimization of novel species-specific microsatellites, or simple sequence repeats (SSRs remains an important step for studies in ecology, evolution, and behavior. Numerous approaches exist for identifying new SSRs that vary widely in terms of both time and cost investments. A recent approach of using paired-end Illumina sequence data in conjunction with the bioinformatics pipeline, PAL_FINDER, has the potential to substantially reduce the cost and labor investment while also improving efficiency. However, it does not appear that the approach has been widely adopted, perhaps due to concerns over its broad applicability across taxa. Therefore, to validate the utility of the approach we developed SSRs for 32 species representing 30 families, 25 orders, 11 classes, and six phyla and optimized SSRs for 13 of the species. Overall the IPE method worked extremely well and we identified 1000s of SSRs for all species (mean = 128,485, with 17% of loci being potentially amplifiable loci, and 25% of these met our most stringent criteria designed to that avoid SSRs associated with repetitive elements. Approximately 61% of screened primers yielded strong amplification of a single locus.

  10. Type I-E CRISPR-Cas Systems Discriminate Target from Non-Target DNA through Base Pairing-Independent PAM Recognition

    Science.gov (United States)

    Datsenko, Kirill A.; Jackson, Ryan N.; Wiedenheft, Blake; Severinov, Konstantin; Brouns, Stan J. J.

    2013-01-01

    Discriminating self and non-self is a universal requirement of immune systems. Adaptive immune systems in prokaryotes are centered around repetitive loci called CRISPRs (clustered regularly interspaced short palindromic repeat), into which invader DNA fragments are incorporated. CRISPR transcripts are processed into small RNAs that guide CRISPR-associated (Cas) proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not complementary DNA sequences (i.e., self-sequences) located in the host's own CRISPR locus. Previous work on the Type III-A CRISPR system from Staphylococcus epidermidis has demonstrated that a portion of the CRISPR RNA-guide sequence is involved in self versus non-self discrimination. This self-avoidance mechanism relies on sensing base pairing between the RNA-guide and sequences flanking the target DNA. To determine if the RNA-guide participates in self versus non-self discrimination in the Type I-E system from Escherichia coli we altered base pairing potential between the RNA-guide and the flanks of DNA targets. Here we demonstrate that Type I-E systems discriminate self from non-self through a base pairing-independent mechanism that strictly relies on the recognition of four unchangeable PAM sequences. In addition, this work reveals that the first base pair between the guide RNA and the PAM nucleotide immediately flanking the target sequence can be disrupted without affecting the interference phenotype. Remarkably, this indicates that base pairing at this position is not involved in foreign DNA recognition. Results in this paper reveal that the Type I-E mechanism of avoiding self sequences and preventing autoimmunity is fundamentally different from that employed by Type III-A systems. We propose the exclusive targeting of PAM-flanked sequences to be termed a target versus non-target discrimination mechanism. PMID:24039596

  11. DFT study on metal-mediated uracil base pair complexes

    Directory of Open Access Journals (Sweden)

    Ayhan Üngördü

    2017-11-01

    Full Text Available The most stable of metal-mediated uracil base pair complexes were determined. Method was used density functional theory, B3LYP. The calculations of systems containing C, H, N, O were described by 6-311++G(d,p and cc-PVTZ basis sets and LANL2DZ and SDD basis sets was used for transition metals. Then Egap values of complexes were calculated and the electrical conductivity of the complexes for single nanowires was studied by band theory. Metal-mediated uracil base pair complexes which will be used as conductive wires in nanotechnology were predicted. In nanoworld, this study is expected to show a way for practical applications.

  12. Protective Effect of Extract of Folium Ginkgo on Repeated Cerebral Ischemia-Reperfusion Injury

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective: To study the protective effect of extract of Folium Ginkgo (FGE) on repeated cerebral ischemia-reperfusion injury. Methods: The model in waking mice induced by repeated cerebral ischemia-reperfusion were used in the experiment to observe the effect of FGE on behavior, oxygen free radical metabolism and prostaglandin E2 (PGE2) content by step-through experiment, diving stand and colorimetric method. Results: FGE could obviously improve the learning ability and memory of model animals, and could lower obviously the content of malonyldialdehyde, nitric oxide and PGE2, restore the lowered activity of superoxide dismutase and catalase in cerebral tissue. Conclusion: FGE has highly protective effect against repeated ischemia-reperfusion injury, the mechanism might be related with its action on anti-lipid oxidatin, improve the activity of antioxidase and inhibit the producing of PGE2.

  13. Tyrosine Kinase Ligand-Receptor Pair Prediction by Using Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Masayuki Yarimizu

    2015-01-01

    Full Text Available Receptor tyrosine kinases are essential proteins involved in cellular differentiation and proliferation in vivo and are heavily involved in allergic diseases, diabetes, and onset/proliferation of cancerous cells. Identifying the interacting partner of this protein, a growth factor ligand, will provide a deeper understanding of cellular proliferation/differentiation and other cell processes. In this study, we developed a method for predicting tyrosine kinase ligand-receptor pairs from their amino acid sequences. We collected tyrosine kinase ligand-receptor pairs from the Database of Interacting Proteins (DIP and UniProtKB, filtered them by removing sequence redundancy, and used them as a dataset for machine learning and assessment of predictive performance. Our prediction method is based on support vector machines (SVMs, and we evaluated several input features suitable for tyrosine kinase for machine learning and compared and analyzed the results. Using sequence pattern information and domain information extracted from sequences as input features, we obtained 0.996 of the area under the receiver operating characteristic curve. This accuracy is higher than that obtained from general protein-protein interaction pair predictions.

  14. Heteroditopic receptors for ion-pair recognition.

    Science.gov (United States)

    McConnell, Anna J; Beer, Paul D

    2012-05-21

    Ion-pair recognition is a new field of research emerging from cation and anion coordination chemistry. Specific types of heteroditopic receptor designs for ion pairs and the complexity of ion-pair binding are discussed to illustrate key concepts such as cooperativity. The importance of this area of research is reflected by the wide variety of potential applications of ion-pair receptors, including applications as membrane transport and salt solubilization agents and sensors. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Assessing Intimacy: The Pair Inventory.

    Science.gov (United States)

    Schaefer, Mark T.; Olson, David H.

    1981-01-01

    Personal Assessment of Intimacy in Relationships (PAIR) provides systematic information in five types of intimacy: emotional, social, sexual, intellectual and recreational. PAIR can be used with couples in marital therapy and enrichment groups. (Author)

  16. Computational studies of a cut-wire pair and combined metamaterials

    International Nuclear Information System (INIS)

    Nguyen, Thanh Tung; Lievens, Peter; Lee, Young Pak; Vu, Dinh Lam

    2011-01-01

    The transfer-matrix method and finite-integration simulations show how the transmission properties of combined metamaterials, which consist of metallic cut-wire pairs and continuous wires, are affected by geometric parameters. The corresponding effective permittivity and permeability are retrieved from the complex scattering parameters using the standard retrieval procedure. The electromagnetic properties of the cut-wire pair as well as the left-handed behavior of the combined structure are understood by the effective medium theory. In addition, the dimensional dependence of transmission properties, the shapes of cut-wire pairs and continuous wire, and the impact of dielectric spacer are both examined. Finally, by expanding the results of previous research (Koschny et al 2003 Phys. Rev. Lett. 93 016608), we generalize the transmission picture of combined structures in terms of the correlation between electric and magnetic responses. (review)

  17. Ion-pairing reversed-phased chromatography/mass spectrometry of heparin

    DEFF Research Database (Denmark)

    Henriksen, Jens; Roepstorff, Peter; Ringborg, Lene H.

    2006-01-01

    not well characterised. In order to further characterise such mixtures, two on-line ion-pairing reverse-phased chromatography electrospray ionisation (ESI) mass spectrometry methods have been developed. One of the systems allows the determination of more than 200 components in a medium molecular weight...

  18. Quantum entanglement and phase transition in a two-dimensional photon-photon pair model

    International Nuclear Information System (INIS)

    Zhang Jianjun; Yuan Jianhui; Zhang Junpei; Cheng Ze

    2013-01-01

    We propose a two-dimensional model consisting of photons and photon pairs. In the model, the mixed gas of photons and photon pairs is formally equivalent to a two-dimensional system of massive bosons with non-vanishing chemical potential, which implies the existence of two possible condensate phases. Using the variational method, we discuss the quantum phase transition of the mixed gas and obtain the critical coupling line analytically. Moreover, we also find that the phase transition of the photon gas can be interpreted as enhanced second harmonic generation. We then discuss the entanglement between photons and photon pairs. Additionally, we also illustrate how the entanglement between photons and photon pairs can be associated with the phase transition of the system.

  19. Repeating Marx

    DEFF Research Database (Denmark)

    Fuchs, Christian; Monticelli, Lara

    2018-01-01

    This introduction sets out the context of the special issue “Karl Marx @ 200: Debating Capitalism & Perspectives for the Future of Radical Theory”, which was published on the occasion of Marx’s bicentenary on 5 May 2018. First, we give a brief overview of contemporary capitalism’s development...... and its crises. Second, we argue that it is important to repeat Marx today. Third, we reflect on lessons learned from 200 years of struggles for alternatives to capitalism. Fourth, we give an overview of the contributions in this special issue. Taken together, the contributions in this special issue show...... that Marx’s theory and politics remain key inspirations for understanding exploitation and domination in 21st-century society and for struggles that aim to overcome these phenomena and establishing a just and fair society. We need to repeat Marx today....

  20. Accuracy of repeated kidney size estimation by ultrasonography and urography in children

    International Nuclear Information System (INIS)

    Hederstroem, E.; Forsberg, L.

    1985-01-01

    The accuracy of repeated sonographic and urographic kidney length measurements in kidney size evaluation was investigated in 80 children 0 to 14 years of age, mean age 4.5 years. At sonography 250 kidney lengths were compared. A difference of 0 to 1.0 cm in repeated length measurement was considered to be good accuracy and 94 per cent of right and 96 per cent of left kidney length were found within this interval-a better result than for urography with 76 per cent of repeated right kidney and 79 per cent of kidney lengths within the same interval (94 lengths). Both methods display a variation of kidney lengths which may lead to under- and overestimation of kidney size and growth. The investigation thus indicates good accuracy for repeated sonographic kidney size assessment which should be repeated often enough to estabilish a growth chart displaying the trend rather than rely too much on single measurements. Sonography can be highly recommended as a convenient and harmless alternative to urography. (orig.)

  1. Separation of seven arsenic species by ion-pair and ion-exchange high performance liquid chromatography

    DEFF Research Database (Denmark)

    Larsen, Erik Huusfeldt; Hansen, Sven Hedegaard

    1992-01-01

    Arsenite, arsenate, monomethylarsonate, dimethylarsinate, arsenobetaine, arsenocholine and the tetramethylarsonium ion were subjected to ion-exchange and ion-pair reversed phase HPLC. The ion exchange method was superior in selectivity and time of analysis for the arsenic anions. The ammonium ions...... used for the ion-pair method only resulted in separation of some of the anionic arsenic compounds. Flame atomic absorption spectrometry was used for on-line arsenic-specific detection....

  2. Modeling and evaluating repeatability and reproducibility of ordinal classifications

    NARCIS (Netherlands)

    de Mast, J.; van Wieringen, W.N.

    2010-01-01

    This paper argues that currently available methods for the assessment of the repeatability and reproducibility of ordinal classifications are not satisfactory. The paper aims to study whether we can modify a class of models from Item Response Theory, well established for the study of the reliability

  3. Prediction of plant promoters based on hexamers and random triplet pair analysis

    Directory of Open Access Journals (Sweden)

    Noman Nasimul

    2011-06-01

    Full Text Available Abstract Background With an increasing number of plant genome sequences, it has become important to develop a robust computational method for detecting plant promoters. Although a wide variety of programs are currently available, prediction accuracy of these still requires further improvement. The limitations of these methods can be addressed by selecting appropriate features for distinguishing promoters and non-promoters. Methods In this study, we proposed two feature selection approaches based on hexamer sequences: the Frequency Distribution Analyzed Feature Selection Algorithm (FDAFSA and the Random Triplet Pair Feature Selecting Genetic Algorithm (RTPFSGA. In FDAFSA, adjacent triplet-pairs (hexamer sequences were selected based on the difference in the frequency of hexamers between promoters and non-promoters. In RTPFSGA, random triplet-pairs (RTPs were selected by exploiting a genetic algorithm that distinguishes frequencies of non-adjacent triplet pairs between promoters and non-promoters. Then, a support vector machine (SVM, a nonlinear machine-learning algorithm, was used to classify promoters and non-promoters by combining these two feature selection approaches. We referred to this novel algorithm as PromoBot. Results Promoter sequences were collected from the PlantProm database. Non-promoter sequences were collected from plant mRNA, rRNA, and tRNA of PlantGDB and plant miRNA of miRBase. Then, in order to validate the proposed algorithm, we applied a 5-fold cross validation test. Training data sets were used to select features based on FDAFSA and RTPFSGA, and these features were used to train the SVM. We achieved 89% sensitivity and 86% specificity. Conclusions We compared our PromoBot algorithm to five other algorithms. It was found that the sensitivity and specificity of PromoBot performed well (or even better with the algorithms tested. These results show that the two proposed feature selection methods based on hexamer frequencies

  4. Effect of fatigue on force production and force application technique during repeated sprints.

    Science.gov (United States)

    Morin, Jean-Benoit; Samozino, Pierre; Edouard, Pascal; Tomazin, Katja

    2011-10-13

    We investigated the changes in the technical ability of force application/orientation against the ground vs. the physical capability of total force production after a multiple-set repeated sprints series. Twelve male physical education students familiar with sprint running performed four sets of five 6-s sprints (24s of passive rest between sprints, 3min between sets). Sprints were performed from a standing start on an instrumented treadmill, allowing the computation of vertical (F(V)), net horizontal (F(H)) and total (F(Tot)) ground reaction forces for each step. Furthermore, the ratio of forces was calculated as RF=F(H)F(Tot)(-1), and the index of force application technique (D(RF)) representing the decrement in RF with increase in speed was computed as the slope of the linear RF-speed relationship. Changes between pre- (first two sprints) and post-fatigue (last two sprints) were tested using paired t-tests. Performance decreased significantly (e.g. top speed decreased by 15.7±5.4%; Pmultiple-set repeated sprint series, both the total force production capability and the technical ability to apply force effectively against the ground are altered, the latter to a larger extent than the former. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. Quantized vortex pair production in 4He films as a boundary-layer problem

    International Nuclear Information System (INIS)

    McCauley, J.L. Jr.

    1979-01-01

    The author shows that the idea of a boundary layer for discrete vortices arises naturally from the equation of motion for the probability distribution of an interacting vortex pair. In contrast with classical hydrodynamics, this boundary layer is of statistical origin, and the method leads to a scaling law for the exact dissociation rate of a bound vortex pair. (Auth.)

  6. Appraising into the Sun: Six-State Solar Home Paired-Sale Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence Berkeley National Laboratory

    2015-11-12

    Although residential solar photovoltaic (PV) installations have proliferated, PV systems on some U.S. homes still receive no value during an appraisal because comparable home sales are lacking. To value residential PV, some previous studies have employed paired-sales appraisal methods to analyze small PV home samples in depth, while others have used statistical methods to analyze large samples. Our first-of-its-kind study connects the two approaches. It uses appraisal methods to evaluate sales price premiums for owned PV systems on single-unit detached houses that were also evaluated in a large statistical study. Independent appraisers evaluated 43 recent home sales pairs in six states: California, Oregon, Florida, Maryland, North Carolina, and Pennsylvania. We compare these results with contributory-value estimates—based on income (using the PV Value® tool), gross cost, and net cost—as well as hedonic modeling results from the recent statistical study. The results provide strong, appraisal-based evidence of PV premiums in all states. More importantly, the results support the use of cost- and incomebased PV premium estimates when paired-sales analysis is impossible. PV premiums from the paired-sales analysis are most similar to net PV cost estimates. PV Value® income results generally track the appraised premiums, although conservatively. The appraised premiums are in agreement with the hedonic modeling results as well, which bolsters the suitability of both approaches for estimating PV home premiums. Therefore, these results will benefit valuation professionals and mortgage lenders who increasingly are encountering homes equipped with PV and need to understand the factors that can both contribute to and detract from market value.

  7. Quantitative Analysis of Tenofovir by Titrimetric, Extractive Ion-pair ...

    African Journals Online (AJOL)

    Methods: Tenofovir disoproxil forms a complex of 1:1 molar ratio with fumaric acid that was employed in its aqueous titration with sodium hydroxide. Non-aqueous titration was also employed for its determination. Extractive ion-pair spectrophotometric technique using methyl orange was similarly employed to evaluate ...

  8. 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...

  9. HOW SOFT GAMMA REPEATERS MIGHT MAKE FAST RADIO BURSTS

    Energy Technology Data Exchange (ETDEWEB)

    Katz, J. I., E-mail: katz@wuphys.wustl.edu [Department of Physics and McDonnell Center for the Space Sciences, Washington University, St. Louis, Mo. 63130 (United States)

    2016-08-01

    There are several phenomenological similarities between soft gamma repeaters (SGRs) and fast radio bursts (FRBs), including duty factors, timescales, and repetition. The sudden release of magnetic energy in a neutron star magnetosphere, as in popular models of SGRs, can meet the energy requirements of FRBs, but requires both the presence of magnetospheric plasma, in order for dissipation to occur in a transparent region, and a mechanism for releasing much of that energy quickly. FRB sources and SGRs are distinguished by long-lived (up to thousands of years) current-carrying coronal arches remaining from the formation of the young neutron star, and their decay ends the phase of SGR/AXP/FRB activity even though “magnetar” fields may persist. Runaway increases in resistance when the current density exceeds a threshold, releases magnetostatic energy in a sudden burst, and produces high brightness GHz emission of FRB by a coherent process. SGRs are produced when released energy thermalizes as an equlibrium pair plasma. The failures of some alternative FRB models and the non-detection of SGR 1806-20 at radio frequencies are discussed in the appendices.

  10. HOW SOFT GAMMA REPEATERS MIGHT MAKE FAST RADIO BURSTS

    International Nuclear Information System (INIS)

    Katz, J. I.

    2016-01-01

    There are several phenomenological similarities between soft gamma repeaters (SGRs) and fast radio bursts (FRBs), including duty factors, timescales, and repetition. The sudden release of magnetic energy in a neutron star magnetosphere, as in popular models of SGRs, can meet the energy requirements of FRBs, but requires both the presence of magnetospheric plasma, in order for dissipation to occur in a transparent region, and a mechanism for releasing much of that energy quickly. FRB sources and SGRs are distinguished by long-lived (up to thousands of years) current-carrying coronal arches remaining from the formation of the young neutron star, and their decay ends the phase of SGR/AXP/FRB activity even though “magnetar” fields may persist. Runaway increases in resistance when the current density exceeds a threshold, releases magnetostatic energy in a sudden burst, and produces high brightness GHz emission of FRB by a coherent process. SGRs are produced when released energy thermalizes as an equlibrium pair plasma. The failures of some alternative FRB models and the non-detection of SGR 1806-20 at radio frequencies are discussed in the appendices.

  11. Interplay between I308 and Y310 residues in the third repeat of microtubule-binding domain is essential for tau filament formation.

    Science.gov (United States)

    Naruto, Keiko; Minoura, Katsuhiko; Okuda, Ryouhei; Taniguchi, Taizo; In, Yasuko; Ishida, Toshimasa; Tomoo, Koji

    2010-10-08

    Investigation of the mechanism of tau polymerization is indispensable for finding inhibitory conditions or identifying compounds preventing the formation of paired helical filament or oligomers. Tau contains a microtubule-binding domain consisting of three or four repeats in its C-terminal half. It has been considered that the key event in tau polymerization is the formation of a β-sheet structure arising from a short hexapeptide (306)VQIVYK(311) in the third repeat of tau. In this paper, we report for the first time that the C-H⋯π interaction between Ile308 and Tyr310 is the elemental structural scaffold essential for forming a dry "steric zipper" structure in tau amyloid fibrils. Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  12. Uncertainty evaluation for three-dimensional scanning electron microscope reconstructions based on the stereo-pair technique

    DEFF Research Database (Denmark)

    Carli, Lorenzo; Genta, G; Cantatore, Angela

    2011-01-01

    3D-SEM is a method, based on the stereophotogrammetry technique, which obtains three-dimensional topographic reconstructions starting typically from two SEM images, called the stereo-pair. In this work, a theoretical uncertainty evaluation of the stereo-pair technique, according to GUM (Guide to ...

  13. Evaluation of New Methodology for Health Hazard Assessment of Repeated Shock in Military Tactical Ground Vehicles

    National Research Council Canada - National Science Library

    Alem, Nabih; Hiltz, Ernest; Breaux-Sims, Arlene; Bumgardner, Bradley

    2004-01-01

    .... The research culminated with the development of a new HHA method for repeated jolt that is tailored for TGVs but is valid for most vehicles where the seated occupant is exposed to repeated (multiple) low-level shocks (jolt...

  14. RELAXATION OF BLAZAR-INDUCED PAIR BEAMS IN COSMIC VOIDS

    Energy Technology Data Exchange (ETDEWEB)

    Miniati, Francesco [Physics Department, Wolfgang-Pauli-Strasse 27, ETH-Zuerich, CH-8093 Zuerich (Switzerland); Elyiv, Andrii, E-mail: fm@phys.ethz.ch [Institut d' Astrophysique et de Geophysique, Universite de Liege, B-4000 Liege (Belgium)

    2013-06-10

    The stability properties of a low-density ultrarelativistic pair beam produced in the intergalactic medium (IGM) by multi-TeV gamma-ray photons from blazars are analyzed. The problem is relevant for probes of magnetic field in cosmic voids through gamma-ray observations. In addition, dissipation of such beams could considerably affect the thermal history of the IGM and structure formation. We use a Monte Carlo method to quantify the properties of the blazar-induced electromagnetic shower, in particular the bulk Lorentz factor and the angular spread of the pair beam generated by the shower, as a function of distance from the blazar itself. We then use linear and nonlinear kinetic theory to study the stability of the pair beam against the growth of electrostatic plasma waves, employing the Monte Carlo results for our quantitative estimates. We find that the fastest growing mode, like any perturbation mode with even a very modest component perpendicular to the beam direction, cannot be described in the reactive regime. Due to the effect of nonlinear Landau damping, which suppresses the growth of plasma oscillations, the beam relaxation timescale is found to be significantly longer than the inverse Compton loss time. Finally, density inhomogeneities associated with cosmic structure induce loss of resonance between the beam particles and plasma oscillations, strongly inhibiting their growth. We conclude that relativistic pair beams produced by blazars in the IGM are stable on timescales that are long compared with the electromagnetic cascades. There appears to be little or no effect of pair beams on the IGM.

  15. Statistical methods for conducting agreement (comparison of clinical tests) and precision (repeatability or reproducibility) studies in optometry and ophthalmology.

    Science.gov (United States)

    McAlinden, Colm; Khadka, Jyoti; Pesudovs, Konrad

    2011-07-01

    The ever-expanding choice of ocular metrology and imaging equipment has driven research into the validity of their measurements. Consequently, studies of the agreement between two instruments or clinical tests have proliferated in the ophthalmic literature. It is important that researchers apply the appropriate statistical tests in agreement studies. Correlation coefficients are hazardous and should be avoided. The 'limits of agreement' method originally proposed by Altman and Bland in 1983 is the statistical procedure of choice. Its step-by-step use and practical considerations in relation to optometry and ophthalmology are detailed in addition to sample size considerations and statistical approaches to precision (repeatability or reproducibility) estimates. Ophthalmic & Physiological Optics © 2011 The College of Optometrists.

  16. Repeated treatments of drooling with botulinum toxin B in neurology

    DEFF Research Database (Denmark)

    Møller, Eigild; Daugaard, Dorthe; Holm, Ole

    2015-01-01

    OBJECTIVES: To investigate efficacy, saliva flow, and composition in repeated BoNT-B treatments of drooling. MATERIALS AND METHODS: Seventeen neurological patients (median 66 years), referred for treatment of drooling participated in this observational study. Median total doses of 4000 units...

  17. Dependence of the paired motor unit analysis on motor unit discharge characteristics in the human tibialis anterior muscle

    Science.gov (United States)

    Stephenson, Jennifer L.; Maluf, Katrina S.

    2011-01-01

    The paired motor unit analysis provides in vivo estimates of the magnitude of persistent inward currents (PIC) in human motoneurons by quantifying changes in the firing rate (ΔF) of an earlier recruited (reference) motor unit at the time of recruitment and derecruitment of a later recruited (test) motor unit. This study assessed the variability of ΔF estimates, and quantified the dependence of ΔF on the discharge characteristics of the motor units selected for analysis. ΔF was calculated for 158 pairs of motor units recorded from nine healthy individuals during repeated submaximal contractions of the tibialis anterior muscle. The mean (SD) ΔF was 3.7 (2.5) pps (range −4.2 to 8.9 pps). The median absolute difference in ΔF for the same motor unit pair across trials was 1.8 pps, and the minimal detectable change in ΔF required to exceed measurement error was 4.8 pps. ΔF was positively related to the amount of discharge rate modulation in the reference motor unit (r2=0.335; Precruitment of the reference and test motor units (r2=0.229, Pmotor unit activity (r2=0.110, Precruitment threshold of the test motor unit (r2=0.237, Pmotor unit analysis. PMID:21459110

  18. Automatic coronary artery calcium scoring in cardiac CT angiography using paired convolutional neural networks.

    Science.gov (United States)

    Wolterink, Jelmer M; Leiner, Tim; de Vos, Bob D; van Hamersvelt, Robbert W; Viergever, Max A; Išgum, Ivana

    2016-12-01

    The amount of coronary artery calcification (CAC) is a strong and independent predictor of cardiovascular events. CAC is clinically quantified in cardiac calcium scoring CT (CSCT), but it has been shown that cardiac CT angiography (CCTA) may also be used for this purpose. We present a method for automatic CAC quantification in CCTA. This method uses supervised learning to directly identify and quantify CAC without a need for coronary artery extraction commonly used in existing methods. The study included cardiac CT exams of 250 patients for whom both a CCTA and a CSCT scan were available. To restrict the volume-of-interest for analysis, a bounding box around the heart is automatically determined. The bounding box detection algorithm employs a combination of three ConvNets, where each detects the heart in a different orthogonal plane (axial, sagittal, coronal). These ConvNets were trained using 50 cardiac CT exams. In the remaining 200 exams, a reference standard for CAC was defined in CSCT and CCTA. Out of these, 100 CCTA scans were used for training, and the remaining 100 for evaluation of a voxel classification method for CAC identification. The method uses ConvPairs, pairs of convolutional neural networks (ConvNets). The first ConvNet in a pair identifies voxels likely to be CAC, thereby discarding the majority of non-CAC-like voxels such as lung and fatty tissue. The identified CAC-like voxels are further classified by the second ConvNet in the pair, which distinguishes between CAC and CAC-like negatives. Given the different task of each ConvNet, they share their architecture, but not their weights. Input patches are either 2.5D or 3D. The ConvNets are purely convolutional, i.e. no pooling layers are present and fully connected layers are implemented as convolutions, thereby allowing efficient voxel classification. The performance of individual 2.5D and 3D ConvPairs with input sizes of 15 and 25 voxels, as well as the performance of ensembles of these ConvPairs

  19. Overcoming the rate-distance limit of quantum key distribution without quantum repeaters.

    Science.gov (United States)

    Lucamarini, M; Yuan, Z L; Dynes, J F; Shields, A J

    2018-05-01

    Quantum key distribution (QKD) 1,2 allows two distant parties to share encryption keys with security based on physical laws. Experimentally, QKD has been implemented via optical means, achieving key rates of 1.26 megabits per second over 50 kilometres of standard optical fibre 3 and of 1.16 bits per hour over 404 kilometres of ultralow-loss fibre in a measurement-device-independent configuration 4 . Increasing the bit rate and range of QKD is a formidable, but important, challenge. A related target, which is currently considered to be unfeasible without quantum repeaters 5-7 , is overcoming the fundamental rate-distance limit of QKD 8 . This limit defines the maximum possible secret key rate that two parties can distil at a given distance using QKD and is quantified by the secret-key capacity of the quantum channel 9 that connects the parties. Here we introduce an alternative scheme for QKD whereby pairs of phase-randomized optical fields are first generated at two distant locations and then combined at a central measuring station. Fields imparted with the same random phase are 'twins' and can be used to distil a quantum key. The key rate of this twin-field QKD exhibits the same dependence on distance as does a quantum repeater, scaling with the square-root of the channel transmittance, irrespective of who (malicious or otherwise) is in control of the measuring station. However, unlike schemes that involve quantum repeaters, ours is feasible with current technology and presents manageable levels of noise even on 550 kilometres of standard optical fibre. This scheme is a promising step towards overcoming the rate-distance limit of QKD and greatly extending the range of secure quantum communications.

  20. Isovector pairing effect on the particle-number projection two-proton separation energy

    Energy Technology Data Exchange (ETDEWEB)

    Mokhtari, Djamila; Kerrouchi, Slimane [Laboratoire de Physique Theorique, Faculte de Physique, Algiers (Algeria); Fellah, Mohamed; Allal, Nassima-Hosni [Laboratoire de Physique Theorique, Faculte de Physique, Algiers (Algeria); Centre de Recherche Nucleaire d' Alger, Comena, Algiers (Algeria)

    2009-07-01

    The two-proton separation energy is studied by performing a particle-number projection with and without inclusion of the isovector neutron-proton (np) pairing correlations. It is numerically evaluated for even-even rare-earth nuclei such that the np pairing parameter is non-zero. It is shown that the two-proton separation energy values calculated using the two approaches join, for almost all the considered elements, for the highest values of (N-Z). However, the results including the np pairing correlations are closest to the experimental data when available. Moreover, the two methods lead to the same prediction of the two-proton drip-line position, except for the Dysprosium and the Tungsten.