Reliability versus reproducibility

International Nuclear Information System (INIS)

Lautzenheiser, C.E.

1976-01-01

Defect detection and reproducibility of results are two separate but closely related subjects. It is axiomatic that a defect must be detected from examination to examination or reproducibility of results is very poor. On the other hand, a defect can be detected on each of subsequent examinations for higher reliability and still have poor reproducibility of results

Validity and reproducibility of a Spanish dietary history.

Directory of Open Access Journals (Sweden)

Pilar Guallar-Castillón

Full Text Available To assess the validity and reproducibility of food and nutrient intake estimated with the electronic diet history of ENRICA (DH-E, which collects information on numerous aspects of the Spanish diet.The validity of food and nutrient intake was estimated using Pearson correlation coefficients between the DH-E and the mean of seven 24-hour recalls collected every 2 months over the previous year. The reproducibility was estimated using intraclass correlation coefficients between two DH-E made one year apart.The correlations coefficients between the DH-E and the mean of seven 24-hour recalls for the main food groups were cereals (r = 0.66, meat (r = 0.66, fish (r = 0.42, vegetables (r = 0.62 and fruits (r = 0.44. The mean correlation coefficient for all 15 food groups considered was 0.53. The correlations for macronutrients were: energy (r = 0.76, proteins (r= 0.58, lipids (r = 0.73, saturated fat (r = 0.73, monounsaturated fat (r = 0.59, polyunsaturated fat (r = 0.57, and carbohydrates (r = 0.66. The mean correlation coefficient for all 41 nutrients studied was 0.55. The intraclass correlation coefficient between the two DH-E was greater than 0.40 for most foods and nutrients.The DH-E shows good validity and reproducibility for estimating usual intake of foods and nutrients.

Effect of high image compression on the reproducibility of cardiac Sestamibi reporting

International Nuclear Information System (INIS)

Thomas, P.; Allen, L.; Beuzeville, S.

1999-01-01

Full text: Compression algorithms have been mooted to minimize storage space and transmission times of digital images. We assessed the impact of high-level lousy compression using JPEG and wavelet algorithms on image quality and reporting accuracy of cardiac Sestamibi studies. Twenty stress/rest Sestamibi cardiac perfusion studies were reconstructed into horizontal short, vertical long and horizontal long axis slices using conventional methods. Each of these six sets of slices were aligned for reporting and saved (uncompressed) as a bitmap. This bitmap was then compressed using JPEG compression, then decompressed and saved as a bitmap for later viewing. This process was repeated using the original bitmap and wavelet compression. Finally, a second copy of the original bitmap was made. All 80 bitmaps were randomly coded to ensure blind reporting. The bitmaps were read blinded and by consensus of 2 experienced nuclear medicine physicians using a 5-point scale and 25 cardiac segments. Subjective image quality was also reported using a 3-point scale. Samples of the compressed images were also subtracted from the original bitmap for visual comparison of differences. Results showed an average compression ratio of 23:1 for wavelet and 13:1 for JPEG. Image subtraction showed only very minor discordance between the original and compressed images. There was no significant difference in subjective quality between the compressed and uncompressed images. There was no significant difference in reporting reproducibility of the identical bitmap copy, the JPEG image and the wavelet image compared with the original bitmap. Use of the high compression algorithms described had no significant impact on reporting reproducibility and subjective image quality of cardiac Sestamibi perfusion studies

Evaluating the reproducibility of environmental radioactivity monitoring data through replicate sample analysis

International Nuclear Information System (INIS)

Lindeken, C.L.; White, J.H.; Silver, W.J.

1978-01-01

At the Lawrence Livermore Laboratory, about 10% of the sampling effort in the environmental monitoring program represents replicate sample collection. Replication of field samples was initiated as part of the quality assurance program for environmental monitoring to determine the reproducibility of environmental measurements. In the laboratory these replicates are processed along with routine samples. As all components of variance are included in analysis of such field samples, comparison of the analytical data from replicate analyses provides a basis for estimating the overall reproducibility of the measurements. The replication study indicates that the reproducibility of environmental radioactivity monitoring data is subject to considerably more variability than is indicated by the accompanying counting errors. The data are also compared with analyses of duplicate aliquots from a well mixed sample or with duplicate aliquots of samples with known radionuclide content. These comparisons show that most of the variability is associated with the collection and preparation of the sample rather than with the analytical procedures

The Need for Reproducibility

Energy Technology Data Exchange (ETDEWEB)

Robey, Robert W. [Los Alamos National Laboratory

2016-06-27

The purpose of this presentation is to consider issues of reproducibility, specifically it determines whether bitwise reproducible computation is possible, if computational research in DOE improves its publication process, and if reproducible results can be achieved apart from the peer review process?

Reproducibility of somatosensory spatial perceptual maps.

Science.gov (United States)

Steenbergen, Peter; Buitenweg, Jan R; Trojan, Jörg; Veltink, Peter H

2013-02-01

Various studies have shown subjects to mislocalize cutaneous stimuli in an idiosyncratic manner. Spatial properties of individual localization behavior can be represented in the form of perceptual maps. Individual differences in these maps may reflect properties of internal body representations, and perceptual maps may therefore be a useful method for studying these representations. For this to be the case, individual perceptual maps need to be reproducible, which has not yet been demonstrated. We assessed the reproducibility of localizations measured twice on subsequent days. Ten subjects participated in the experiments. Non-painful electrocutaneous stimuli were applied at seven sites on the lower arm. Subjects localized the stimuli on a photograph of their own arm, which was presented on a tablet screen overlaying the real arm. Reproducibility was assessed by calculating intraclass correlation coefficients (ICC) for the mean localizations of each electrode site and the slope and offset of regression models of the localizations, which represent scaling and displacement of perceptual maps relative to the stimulated sites. The ICCs of the mean localizations ranged from 0.68 to 0.93; the ICCs of the regression parameters were 0.88 for the intercept and 0.92 for the slope. These results indicate a high degree of reproducibility. We conclude that localization patterns of non-painful electrocutaneous stimuli on the arm are reproducible on subsequent days. Reproducibility is a necessary property of perceptual maps for these to reflect properties of a subject's internal body representations. Perceptual maps are therefore a promising method for studying body representations.

Quasi-particle and collective magnetism: Rotation, pairing and blocking in high-K isomers

International Nuclear Information System (INIS)

Stone, N.J.; Stone, J.R.; Walker, P.M.; Bingham, C.R.

2013-01-01

For the first time, a wide range of collective magnetic g-factors g R , obtained from a novel analysis of experimental data for multi-quasi-particle configurations in high-K isomers, is shown to exhibit a striking systematic variation with the relative number of proton and neutron quasi-particles, N p −N n . Using the principle of additivity, the quasi-particle contribution to magnetism in high-K isomers of Lu–Re, Z=71–75, has been estimated. Based on these estimates, band-structure branching ratio data are used to explore the behavior of the collective contribution as the number and proton/neutron nature (N p , N n ), of the quasi-particle excitations, change. Basic ideas of pairing, its quenching by quasi-particle excitation and the consequent changes to moment of inertia and collective magnetism are discussed. Existing model calculations do not reproduce the observed g R variation adequately. The paired superfluid system of nucleons in these nuclei, and their excitations, present properties of general physics interest. The new-found systematic behavior of g R in multi-quasi-particle excitations of this unique system, showing variation from close to zero for multi-neutron states to above 0.5 for multi-proton states, opens a fresh window on these effects and raises the important question of just which nucleons contribute to the ‘collective’ properties of these nuclei

Participant Nonnaiveté and the reproducibility of cognitive psychology

NARCIS (Netherlands)

R.A. Zwaan (Rolf); D. Pecher (Diane); G. Paolacci (Gabriele); S. Bouwmeester (Samantha); P.P.J.L. Verkoeijen (Peter); K. Dijkstra (Katinka); R. Zeelenberg (René)

2017-01-01

textabstractMany argue that there is a reproducibility crisis in psychology. We investigated nine well-known effects from the cognitive psychology literature—three each from the domains of perception/action, memory, and language, respectively—and found that they are highly reproducible. Not only can

High Collection Nonimaging Optics

Science.gov (United States)

Winston, Roland

1989-07-01

Nonimaging optics departs from the methods of traditional optical design to develop instead techniques for maximizing the collecting power of concentrating elements and systems. Designs which exceed the concentration attainable with focusing techniques by factors of four or more and approach the theoretical limit are possible (ideal concentrators). The methodology for designing high collection nonirnaging systems is described.

Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

Science.gov (United States)

Spjuth, Ola; Willighagen, Egon L; Guha, Rajarshi; Eklund, Martin; Wikberg, Jarl Es

2010-06-30

QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but

Towards interoperable and reproducible QSAR analyses: Exchange of datasets

Directory of Open Access Journals (Sweden)

Spjuth Ola

2010-06-01

Full Text Available Abstract Background QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. Results We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Conclusions Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join

Reproducibility of the chamber scarification test

DEFF Research Database (Denmark)

Andersen, Klaus Ejner

1996-01-01

The chamber scarification test is a predictive human skin irritation test developed to rank the irritation potential of products and ingredients meant for repeated use on normal and diseased skin. 12 products or ingredients can be tested simultaneously on the forearm skin of each volunteer....... The test combines with the procedure scratching of the skin at each test site and subsequent closed patch tests with the products, repeated daily for 3 days. The test is performed on groups of human volunteers: a skin irritant substance or products is included in each test as a positive control...... high reproducibility of the test. Further, intra-individual variation in skin reaction to the 2 control products in 26 volunteers, who participated 2x, is shown, which supports the conclusion that the chamber scarification test is a useful short-term human skin irritation test with high reproducibility....

Which potentials have to be surface peaked to reproduce large angle proton scattering at high energy?

International Nuclear Information System (INIS)

Raynal, J.

1990-01-01

Corrections to the usual form factors of the optical potential are studied with a view to getting a better fit for proton elastic scattering at large angles on 40 Ca at 497 and 800 MeV. When a real surface form factor is added to the central potential in the Schrodinger formalism, the experimental data are as well reproduced as in the standard Dirac formalism. Coupling to the strong 3 - collective state gives a better fit. The use of surface corrections to the imaginary Dirac potential also gives improved results. A slightly better fit is obtained by coupling to the 3 - state with, at the same time, a weakening of these corrections. Further corrections to the potential do not give significant improvements

Estimating the reproducibility of psychological science

NARCIS (Netherlands)

Anderson, Joanna E.; Aarts, Alexander A.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahník, Štěpán; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Brüning, Jovita; Calhoun-Sauls, Ann; Callahan, Shannon P.; Chagnon, Elizabeth; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Christopherson, Cody D.; Cillessen, Linda; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Conn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Alvarez, Leslie D Cramblet; Cremata, Ed; Crusius, Jan; DeCoster, Jamie; DeGaetano, Michelle A.; Penna, Nicolás Delia; Den Bezemer, Bobby; Deserno, Marie K.; Devitt, Olivia; Dewitte, Laura; Dobolyi, David G.; Dodson, Geneva T.; Donnellan, M. Brent; Donohue, Ryan; Dore, Rebecca A.; Dorrough, Angela; Dreber, Anna; Dugas, Michelle; Dunn, Elizabeth W.; Easey, Kayleigh; Eboigbe, Sylvia; Eggleston, Casey; Embley, Jo; Epskamp, Sacha; Errington, Timothy M.; Estel, Vivien; Farach, Frank J.; Feather, Jenelle; Fedor, Anna; Fernández-Castilla, Belén; Fiedler, Susann; Field, James G.; Fitneva, Stanka A.; Flagan, Taru; Forest, Amanda L.; Forsell, Eskil; Foster, Joshua D.; Frank, Michael C.; Frazier, Rebecca S.; Fuchs, Heather; Gable, Philip; Galak, Jeff; Galliani, Elisa Maria; Gampa, Anup; Garcia, Sara; Gazarian, Douglas; Gilbert, Elizabeth; Giner-Sorolla, Roger; Glöckner, Andreas; Goellner, Lars; Goh, Jin X.; Goldberg, Rebecca; Goodbourn, Patrick T.; Gordon-McKeon, Shauna; Gorges, Bryan; Gorges, Jessie; Goss, Justin; Graham, Jesse; Grange, James A.; Gray, Jeremy; Hartgerink, Chris; Hartshorne, Joshua; Hasselman, Fred; Hayes, Timothy; Heikensten, Emma; Henninger, Felix; Hodsoll, John; Holubar, Taylor; Hoogendoorn, Gea; Humphries, Denise J.; Hung, Cathy O Y; Immelman, Nathali; Irsik, Vanessa C.; Jahn, Georg; Jäkel, Frank; Jekel, Marc; Johannesson, Magnus; Johnson, Larissa G.; Johnson, David J.; Johnson, Kate M.; Johnston, William J.; Jonas, Kai; Joy-Gaba, Jennifer A.; Kappes, Heather Barry; Kelso, Kim; Kidwell, Mallory C.; Kim, Seung Kyung; Kirkhart, Matthew; Kleinberg, Bennett; Knežević, Goran; Kolorz, Franziska Maria; Kossakowski, Jolanda J.; Krause, Robert Wilhelm; Krijnen, Job; Kuhlmann, Tim; Kunkels, Yoram K.; Kyc, Megan M.; Lai, Calvin K.; Laique, Aamir; Lakens, Daniël|info:eu-repo/dai/nl/298811855; Lane, Kristin A.; Lassetter, Bethany; Lazarević, Ljiljana B.; Le Bel, Etienne P.; Lee, Key Jung; Lee, Minha; Lemm, Kristi; Levitan, Carmel A.; Lewis, Melissa; Lin, Lin; Lin, Stephanie; Lippold, Matthias; Loureiro, Darren; Luteijn, Ilse; MacKinnon, Sean; Mainard, Heather N.; Marigold, Denise C.; Martin, Daniel P.; Martinez, Tylar; Masicampo, E. J.; Matacotta, Josh; Mathur, Maya; May, Michael; Mechin, Nicole; Mehta, Pranjal; Meixner, Johannes; Melinger, Alissa; Miller, Jeremy K.; Miller, Mallorie; Moore, Katherine; Möschl, Marcus; Motyl, Matt; Müller, Stephanie M.; Munafo, Marcus; Neijenhuijs, Koen I.; Nervi, Taylor; Nicolas, Gandalf; Nilsonne, Gustav; Nosek, Brian A.; Nuijten, Michèle B.; Olsson, Catherine; Osborne, Colleen; Ostkamp, Lutz; Pavel, Misha; Penton-Voak, Ian S.; Perna, Olivia; Pernet, Cyril; Perugini, Marco; Pipitone, R. Nathan; Pitts, Michael; Plessow, Franziska; Prenoveau, Jason M.; Rahal, Rima Maria; Ratliff, Kate A.; Reinhard, David; Renkewitz, Frank; Ricker, Ashley A.; Rigney, Anastasia; Rivers, Andrew M.; Roebke, Mark; Rutchick, Abraham M.; Ryan, Robert S.; Sahin, Onur; Saide, Anondah; Sandstrom, Gillian M.; Santos, David; Saxe, Rebecca; Schlegelmilch, René; Schmidt, Kathleen; Scholz, Sabine; Seibel, Larissa; Selterman, Dylan Faulkner; Shaki, Samuel; Simpson, William B.; Sinclair, H. Colleen; Skorinko, Jeanine L M; Slowik, Agnieszka; Snyder, Joel S.; Soderberg, Courtney; Sonnleitner, Carina; Spencer, Nick; Spies, Jeffrey R.; Steegen, Sara; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B.; Talhelm, Thomas; Tapia, Megan; Te Dorsthorst, Anniek; Thomae, Manuela; Thomas, Sarah L.; Tio, Pia; Traets, Frits; Tsang, Steve; Tuerlinckx, Francis; Turchan, Paul; Valášek, Milan; Van't Veer, Anna E.; Van Aert, Robbie; Van Assen, Marcel|info:eu-repo/dai/nl/407629971; Van Bork, Riet; Van De Ven, Mathijs; Van Den Bergh, Don; Van Der Hulst, Marije; Van Dooren, Roel; Van Doorn, Johnny; Van Renswoude, Daan R.; Van Rijn, Hedderik; Vanpaemel, Wolf; Echeverría, Alejandro Vásquez; Vazquez, Melissa; Velez, Natalia; Vermue, Marieke; Verschoor, Mark; Vianello, Michelangelo; Voracek, Martin; Vuu, Gina; Wagenmakers, Eric Jan; Weerdmeester, Joanneke; Welsh, Ashlee; Westgate, Erin C.; Wissink, Joeri; Wood, Michael; Woods, Andy; Wright, Emily; Wu, Sining; Zeelenberg, Marcel; Zuni, Kellylynn

2015-01-01

Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available.

Magni Reproducibility Example

DEFF Research Database (Denmark)

2016-01-01

An example of how to use the magni.reproducibility package for storing metadata along with results from a computational experiment. The example is based on simulating the Mandelbrot set.......An example of how to use the magni.reproducibility package for storing metadata along with results from a computational experiment. The example is based on simulating the Mandelbrot set....

Highly reliable field electron emitters produced from reproducible damage-free carbon nanotube composite pastes with optimal inorganic fillers

Science.gov (United States)

Kim, Jae-Woo; Jeong, Jin-Woo; Kang, Jun-Tae; Choi, Sungyoul; Ahn, Seungjoon; Song, Yoon-Ho

2014-02-01

Highly reliable field electron emitters were developed using a formulation for reproducible damage-free carbon nanotube (CNT) composite pastes with optimal inorganic fillers and a ball-milling method. We carefully controlled the ball-milling sequence and time to avoid any damage to the CNTs, which incorporated fillers that were fully dispersed as paste constituents. The field electron emitters fabricated by printing the CNT pastes were found to exhibit almost perfect adhesion of the CNT emitters to the cathode, along with good uniformity and reproducibility. A high field enhancement factor of around 10 000 was achieved from the CNT field emitters developed. By selecting nano-sized metal alloys and oxides and using the same formulation sequence, we also developed reliable field emitters that could survive high-temperature post processing. These field emitters had high durability to post vacuum annealing at 950 °C, guaranteeing survival of the brazing process used in the sealing of field emission x-ray tubes. We evaluated the field emitters in a triode configuration in the harsh environment of a tiny vacuum-sealed vessel and observed very reliable operation for 30 h at a high current density of 350 mA cm-2. The CNT pastes and related field emitters that were developed could be usefully applied in reliable field emission devices.

Imaging of striatal dopamine transporters in rat brain with single pinhole SPECT and co-aligned MRI is highly reproducible

International Nuclear Information System (INIS)

Booij, Jan; Bruin, Kora de; Win, Maartje M.L. de; Lavini, Cristina Mphil; Heeten, Gerard J. den; Habraken, Jan

2003-01-01

A recently developed pinhole high-resolution SPECT system was used to measure striatal to non-specific binding ratios in rats (n = 9), after injection of the dopamine transporter ligand 123 I-FP-CIT, and to assess its test/retest reproducibility. For co-alignment purposes, the rat brain was imaged on a 1.5 Tesla clinical MRI scanner using a specially developed surface coil. The SPECT images showed clear striatal uptake. On the MR images, cerebral and extra-cerebral structures could be easily delineated. The mean striatal to non-specific [ 123 I]FP-CIT binding ratios of the test/retest studies were 1.7 ± 0.2 and 1.6 ± 0.2, respectively. The test/retest variability was approximately 9%. We conclude that the assessment of striatal [ 123 I]FP-CIT binding ratios in rats is highly reproducible

Tools for Reproducibility and Extensibility in Scientific Research

CERN Multimedia

CERN. Geneva

2018-01-01

Open inquiry through reproducing results is fundamental to the scientific process. Contemporary research relies on software engineering pipelines to collect, process, and analyze data. The open source projects within Project Jupyter facilitate these objectives by bringing software engineering within the context of scientific communication. We will highlight specific projects that are computational building blocks for scientific communication, starting with the Jupyter Notebook. We will also explore applications of projects that build off of the Notebook such as Binder, JupyterHub, and repo2docker. We will discuss how these projects can individually and jointly improve reproducibility in scientific communication. Finally, we will demonstrate applications of Jupyter software that allow researchers to build upon the code of other scientists, both to extend their work and the work of others.    There will be a follow-up demo session in the afternoon, hosted by iML. Details can be foun...

A PHYSICAL ACTIVITY QUESTIONNAIRE: REPRODUCIBILITY AND VALIDITY

Directory of Open Access Journals (Sweden)

Nicolas Barbosa

2007-12-01

Full Text Available This study evaluates the Quantification de L'Activite Physique en Altitude chez les Enfants (QAPACE supervised self-administered questionnaire reproducibility and validity on the estimation of the mean daily energy expenditure (DEE on Bogotá's schoolchildren. The comprehension was assessed on 324 students, whereas the reproducibility was studied on a different random sample of 162 who were exposed twice to it. Reproducibility was assessed using both the Bland-Altman plot and the intra-class correlation coefficient (ICC. The validity was studied in a sample of 18 girls and 18 boys randomly selected, which completed the test - re-test study. The DEE derived from the questionnaire was compared with the laboratory measurement results of the peak oxygen uptake (Peak VO2 from ergo-spirometry and Leger Test. The reproducibility ICC was 0.96 (95% C.I. 0.95-0.97; by age categories 8-10, 0.94 (0.89-0. 97; 11-13, 0.98 (0.96- 0.99; 14-16, 0.95 (0.91-0.98. The ICC between mean TEE as estimated by the questionnaire and the direct and indirect Peak VO2 was 0.76 (0.66 (p<0.01; by age categories, 8-10, 11-13, and 14-16 were 0.89 (0.87, 0.76 (0.78 and 0.88 (0.80 respectively. The QAPACE questionnaire is reproducible and valid for estimating PA and showed a high correlation with the Peak VO2 uptake

Systematic heterogenization for better reproducibility in animal experimentation.

Science.gov (United States)

Richter, S Helene

2017-08-31

The scientific literature is full of articles discussing poor reproducibility of findings from animal experiments as well as failures to translate results from preclinical animal studies to clinical trials in humans. Critics even go so far as to talk about a "reproducibility crisis" in the life sciences, a novel headword that increasingly finds its way into numerous high-impact journals. Viewed from a cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. So far, poor reproducibility and translational failures in animal experimentation have mostly been attributed to biased animal data, methodological pitfalls, current publication ethics and animal welfare constraints. More recently, the concept of standardization has also been identified as a potential source of these problems. By reducing within-experiment variation, rigorous standardization regimes limit the inference to the specific experimental conditions. In this way, however, individual phenotypic plasticity is largely neglected, resulting in statistically significant but possibly irrelevant findings that are not reproducible under slightly different conditions. By contrast, systematic heterogenization has been proposed as a concept to improve representativeness of study populations, contributing to improved external validity and hence improved reproducibility. While some first heterogenization studies are indeed very promising, it is still not clear how this approach can be transferred into practice in a logistically feasible and effective way. Thus, further research is needed to explore different heterogenization strategies as well as alternative routes toward better reproducibility in animal experimentation.

Assessing the reproducibility of high definition urethral pressure profilometry and its correlation with an air-charged system.

Science.gov (United States)

Klünder, Mario; Amend, Bastian; Sawodny, Oliver; Stenzl, Arnulf; Ederer, Michael; Kelp, Alexandra; Sievert, Karl-Dietrich; Feuer, Ronny

2017-06-01

Recently, a new urodynamic method for the assessment of stress urinary incontinence called high definition urethral pressure profilometry (HD-UPP) has been introduced. This method combines a novel microtip catheter with advanced signal processing to enable spatial data location and the reconstruction of a pressure image inside the urethra. In order to assess the reproducibility of HD-UPP data, we statistically evaluate HD-UPP datasets and compare them to data from a double balloon air-charged system. Both catheters are used on sedated female minipigs. Data from the microtip catheter are processed through a signal reconstruction algorithm, urodynamic features are extracted, and compared to the air-charged system. Reproducibility of HD-UPP data is assessed by statistically evaluating consecutive, intra-individual datasets. HD-UPP delivers results in agreement with previous comparisons of microtip and air-charged systems. The average deviation of two consecutive, intra-individual pressure images is very low at 7 cm H 2 O. HD-UPP provides physicians with detailed information on the pressure distribution inside the urethra. Through comparison with an air-charged catheter, it is shown that HD-UPP delivers results in agreement with previous studies on the comparison of microtip and air-charged catheters. It provides excellent reproducibility, as the difference between sequentially measured profiles from the same minipig is significantly lower than the one between profiles from different minipigs. © 2016 Wiley Periodicals, Inc.

Can cancer researchers accurately judge whether preclinical reports will reproduce?

Directory of Open Access Journals (Sweden)

Daniel Benjamin

2017-06-01

Full Text Available There is vigorous debate about the reproducibility of research findings in cancer biology. Whether scientists can accurately assess which experiments will reproduce original findings is important to determining the pace at which science self-corrects. We collected forecasts from basic and preclinical cancer researchers on the first 6 replication studies conducted by the Reproducibility Project: Cancer Biology (RP:CB to assess the accuracy of expert judgments on specific replication outcomes. On average, researchers forecasted a 75% probability of replicating the statistical significance and a 50% probability of replicating the effect size, yet none of these studies successfully replicated on either criterion (for the 5 studies with results reported. Accuracy was related to expertise: experts with higher h-indices were more accurate, whereas experts with more topic-specific expertise were less accurate. Our findings suggest that experts, especially those with specialized knowledge, were overconfident about the RP:CB replicating individual experiments within published reports; researcher optimism likely reflects a combination of overestimating the validity of original studies and underestimating the difficulties of repeating their methodologies.

Effect of Initial Conditions on Reproducibility of Scientific Research

Science.gov (United States)

Djulbegovic, Benjamin; Hozo, Iztok

2014-01-01

Background: It is estimated that about half of currently published research cannot be reproduced. Many reasons have been offered as explanations for failure to reproduce scientific research findings- from fraud to the issues related to design, conduct, analysis, or publishing scientific research. We also postulate a sensitive dependency on initial conditions by which small changes can result in the large differences in the research findings when attempted to be reproduced at later times. Methods: We employed a simple logistic regression equation to model the effect of covariates on the initial study findings. We then fed the input from the logistic equation into a logistic map function to model stability of the results in repeated experiments over time. We illustrate the approach by modeling effects of different factors on the choice of correct treatment. Results: We found that reproducibility of the study findings depended both on the initial values of all independent variables and the rate of change in the baseline conditions, the latter being more important. When the changes in the baseline conditions vary by about 3.5 to about 4 in between experiments, no research findings could be reproduced. However, when the rate of change between the experiments is ≤2.5 the results become highly predictable between the experiments. Conclusions: Many results cannot be reproduced because of the changes in the initial conditions between the experiments. Better control of the baseline conditions in-between the experiments may help improve reproducibility of scientific findings. PMID:25132705

Reproducibility in a multiprocessor system

Science.gov (United States)

Bellofatto, Ralph A; Chen, Dong; Coteus, Paul W; Eisley, Noel A; Gara, Alan; Gooding, Thomas M; Haring, Rudolf A; Heidelberger, Philip; Kopcsay, Gerard V; Liebsch, Thomas A; Ohmacht, Martin; Reed, Don D; Senger, Robert M; Steinmacher-Burow, Burkhard; Sugawara, Yutaka

2013-11-26

Fixing a problem is usually greatly aided if the problem is reproducible. To ensure reproducibility of a multiprocessor system, the following aspects are proposed; a deterministic system start state, a single system clock, phase alignment of clocks in the system, system-wide synchronization events, reproducible execution of system components, deterministic chip interfaces, zero-impact communication with the system, precise stop of the system and a scan of the system state.

SU-E-T-676: Reproducibility and Consistency of Two SunNuclear 3D Scanning Tanks

International Nuclear Information System (INIS)

Hessler, J; DiCostanzo, D; Grzetic, S; Ayan, A; Gupta, N; Woollard, J

2015-01-01

Purpose: To determine if two Sun Nuclear 3D Scanning (SNC 3DS) tanks collect reproducible and consistent data and test the precision of the SNC Dosimetry auto-setup. Methods: Percent depth doses (PDDs) and profiles were collected on two SNC 3DS tanks with a Varian TrueBeam linear accelerator. SNC Dosimetry auto-setup application was used with CC13 ionization chambers. After auto-setup, collimator light field was checked manually against the position of the chamber. Comparing measured data for repeated measurements with tank 1 allowed evaluation of SNC-3DS auto-setup and tank reproducibility. Comparing measured data between tanks 1 and 2 allowed evaluation of consistency between tanks. Results: Preliminary results showed reproducibility of depth of maximum dose (Dmax) of 0.38mm for a 10cmx10cm field and 0.67mm for 30cmx30cm on a single tank. PDD values at 5cm, 10cm, and 20cm depths were reproducible within 0.26%. Consistency of Dmax between tanks was 0.17mm for a 10cmx10cm field and 0.44mm for 30cmx30cm. PDD values at 5cm, 10cm, and 20cmwere consistent within 0.06%. Profiles showed reproducibility in field width within 0.4mm for a 10cmx10cm field and 0.7mm for a 30cmx30cm field. Profiles showed consistency in field width within 0.2mm for 10cmx10cm and 30cmx30cm field sizes. Penumbra width was reproducible and consistent to under 0.5mm except for 30cmx30cm field size at 30cm depth where the reproducibility was 2.2mm and the consistency was 2.6mm. Conclusion: In conclusion, the SNC 3DS tank shows good reproducibility in measured data. Since the tank to tank variation in measured data is within the uncertainty of repeated single tank measurements the tanks also perform consistently

Determinants, reproducibility, and seasonal variation of ergosterol levels in house dust.

Science.gov (United States)

Leppänen, H K; Nevalainen, A; Vepsäläinen, A; Roponen, M; Täubel, M; Laine, O; Rantakokko, P; von Mutius, E; Pekkanen, J; Hyvärinen, A

2014-06-01

This study aimed to clarify the determinants that affect the concentrations of ergosterol and viable fungi in house dust and to examine the seasonal variation and reproducibility of ergosterol concentrations indoors. In studying the determinants, dust samples from living room floors and vacuum cleaner dust bags were collected from 107 farming and 105 non-farming homes. Ergosterol levels were determined with gas chromatography-mass spectrometry,and the dust bag dust was cultivated for enumeration of fungal genera. Lifestyle and environmental factors, for example using of the fireplace, and visible mold observations in homes, explained 20–26% of the variation of fungal concentrations. For the reproducibility study, samples were collected from five urban homes in four different seasons. The reproducibility of ergosterol determinations within a sample was excellent (ICC = 89.8) for floor dust and moderate (ICC = 63.8) for dust bag dust, but poor when sampling the same home throughout a year (ICC = 31.3 and 12.6, respectively) due to large temporal variation in ergosterol concentrations. In conclusion, environmental characteristics only partially predicted the variation of fungal concentrations. Based on these studies, we recommend repeated sampling of dust over time if one seeks to adequately describe overall fungal levels and exposure in a home. This study shows that levels of ergosterol and viable fungi in house dust are related to visible mold observations. Only 20% of the variation in fungal levels can be explained with questionnaires, and therefore, environmental samples need to be taken in addition. Reproducibility of ergosterol determination was excellent for floor dust, and thus, ergosterol measurements from floor dust samples could be suitable for assessing the fungal load in building investigations. The temporal variation needs to be taken into account when describing the ergosterol concentration of urban homes.

Disposable Collection Kit for Rapid and Reliable Collection of Saliva

OpenAIRE

Yamaguchi, Masaki; Tezuka, Yuki; Takeda, Kazunori; Shetty, Vivek

2015-01-01

Objectives To describe and evaluate disposable saliva collection kit for rapid, reliable, and reproducible collection of saliva samples. Methods The saliva collection kit comprised of a saliva absorbent swab and an extractor unit was used to retrieve whole saliva samples from 10 subjects. The accuracy and precision of the extracted volumes (3, 10, and 30 ?l) were compared to similar volumes drawn from control samples obtained by passive drool. Additionally, the impact of kit collection method...

A high-speed data-collection system for large-unit-cell crystals using an imaging plate as a detector

International Nuclear Information System (INIS)

Sato, Mamoru; Yamamoto, Masaki; Imada, Katsumi; Katsube, Yukiteru; Tanaka, Nobuo; Higashi, Tsuneyuki

1992-01-01

A high-speed data-collection system for large-unit-cell crystals is presented, using the Fuji Imaging Plate as an X-ray detector and a rotating-anode generator as the X-ray source. It is an automatic data-acquisition system that requires almost no manual intervention. The quality of data collected on the system is discussed. Merging R values ranged from 0.04 to 0.05. Compared with a four-circle diffractometer, data reproducibility was better, isomorphous/anomalous Patterson maps were almost identical in quality and data from a small-molecule crystal, cytidine, were of almost the same quality. Protein structures were refinable using the data measured on the system, the final crystallographic R value of the 2.2 A 3-isopropylmalate dehydrogenase structure being 0.185 and that of the 1.88 A Flammulina veltipes agglutinin structure being 0.199. (orig.)

Contextual sensitivity in scientific reproducibility

Science.gov (United States)

Van Bavel, Jay J.; Mende-Siedlecki, Peter; Brady, William J.; Reinero, Diego A.

2016-01-01

In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher’s degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed “hidden moderators”) between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility. PMID:27217556

Contextual sensitivity in scientific reproducibility.

Science.gov (United States)

Van Bavel, Jay J; Mende-Siedlecki, Peter; Brady, William J; Reinero, Diego A

2016-06-07

In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.

ZIF-8 Membranes with Improved Reproducibility Fabricated from Sputter-Coated ZnO/Alumina Supports

KAUST Repository

Yu, Jian; Pan, Yichang; Wang, Chongqing; Lai, Zhiping

2015-01-01

for reproducible fabrication of high-quality membranes. In this study, high-quality ZIF-8 membranes were prepared through hydrothermal synthesis under the partial self-conversion of sputter-coated ZnO layer on porous α-alumina supports. The reproducibility

Standing Together for Reproducibility in Large-Scale Computing: Report on reproducibility@XSEDE

OpenAIRE

James, Doug; Wilkins-Diehr, Nancy; Stodden, Victoria; Colbry, Dirk; Rosales, Carlos; Fahey, Mark; Shi, Justin; Silva, Rafael F.; Lee, Kyo; Roskies, Ralph; Loewe, Laurence; Lindsey, Susan; Kooper, Rob; Barba, Lorena; Bailey, David

2014-01-01

This is the final report on reproducibility@xsede, a one-day workshop held in conjunction with XSEDE14, the annual conference of the Extreme Science and Engineering Discovery Environment (XSEDE). The workshop's discussion-oriented agenda focused on reproducibility in large-scale computational research. Two important themes capture the spirit of the workshop submissions and discussions: (1) organizational stakeholders, especially supercomputer centers, are in a unique position to promote, enab...

Theory of reproducing kernels and applications

CERN Document Server

Saitoh, Saburou

2016-01-01

This book provides a large extension of the general theory of reproducing kernels published by N. Aronszajn in 1950, with many concrete applications. In Chapter 1, many concrete reproducing kernels are first introduced with detailed information. Chapter 2 presents a general and global theory of reproducing kernels with basic applications in a self-contained way. Many fundamental operations among reproducing kernel Hilbert spaces are dealt with. Chapter 2 is the heart of this book. Chapter 3 is devoted to the Tikhonov regularization using the theory of reproducing kernels with applications to numerical and practical solutions of bounded linear operator equations. In Chapter 4, the numerical real inversion formulas of the Laplace transform are presented by applying the Tikhonov regularization, where the reproducing kernels play a key role in the results. Chapter 5 deals with ordinary differential equations; Chapter 6 includes many concrete results for various fundamental partial differential equations. In Chapt...

Paper-based microfluidic approach for surface-enhanced raman spectroscopy and highly reproducible detection of proteins beyond picomolar concentration.

Science.gov (United States)

Saha, Arindam; Jana, Nikhil R

2015-01-14

Although microfluidic approach is widely used in various point of care diagnostics, its implementation in surface enhanced Raman spectroscopy (SERS)-based detection is challenging. This is because SERS signal depends on plasmonic nanoparticle aggregation induced generation of stable electromagnetic hot spots and in currently available microfluidic platform this condition is difficult to adapt. Here we show that SERS can be adapted using simple paper based microfluidic system where both the plasmonic nanomaterials and analyte are used in mobile phase. This approach allows analyte induced controlled particle aggregation and electromagnetic hot spot generation inside the microfluidic channel with the resultant SERS signal, which is highly reproducible and sensitive. This approach has been used for reproducible detection of protein in the pico to femtomolar concentration. Presented approach is simple, rapid, and cost-effective, and requires low sample volume. Method can be extended for SERS-based detection of other biomolecules.

High-speed and high-fidelity system and method for collecting network traffic

Science.gov (United States)

Weigle, Eric H [Los Alamos, NM

2010-08-24

A system is provided for the high-speed and high-fidelity collection of network traffic. The system can collect traffic at gigabit-per-second (Gbps) speeds, scale to terabit-per-second (Tbps) speeds, and support additional functions such as real-time network intrusion detection. The present system uses a dedicated operating system for traffic collection to maximize efficiency, scalability, and performance. A scalable infrastructure and apparatus for the present system is provided by splitting the work performed on one host onto multiple hosts. The present system simultaneously addresses the issues of scalability, performance, cost, and adaptability with respect to network monitoring, collection, and other network tasks. In addition to high-speed and high-fidelity network collection, the present system provides a flexible infrastructure to perform virtually any function at high speeds such as real-time network intrusion detection and wide-area network emulation for research purposes.

SiGe epitaxial memory for neuromorphic computing with reproducible high performance based on engineered dislocations

Science.gov (United States)

Choi, Shinhyun; Tan, Scott H.; Li, Zefan; Kim, Yunjo; Choi, Chanyeol; Chen, Pai-Yu; Yeon, Hanwool; Yu, Shimeng; Kim, Jeehwan

2018-01-01

Although several types of architecture combining memory cells and transistors have been used to demonstrate artificial synaptic arrays, they usually present limited scalability and high power consumption. Transistor-free analog switching devices may overcome these limitations, yet the typical switching process they rely on—formation of filaments in an amorphous medium—is not easily controlled and hence hampers the spatial and temporal reproducibility of the performance. Here, we demonstrate analog resistive switching devices that possess desired characteristics for neuromorphic computing networks with minimal performance variations using a single-crystalline SiGe layer epitaxially grown on Si as a switching medium. Such epitaxial random access memories utilize threading dislocations in SiGe to confine metal filaments in a defined, one-dimensional channel. This confinement results in drastically enhanced switching uniformity and long retention/high endurance with a high analog on/off ratio. Simulations using the MNIST handwritten recognition data set prove that epitaxial random access memories can operate with an online learning accuracy of 95.1%.

Design Procedure and Fabrication of Reproducible Silicon Vernier Devices for High-Performance Refractive Index Sensing.

Science.gov (United States)

Troia, Benedetto; Khokhar, Ali Z; Nedeljkovic, Milos; Reynolds, Scott A; Hu, Youfang; Mashanovich, Goran Z; Passaro, Vittorio M N

2015-06-10

In this paper, we propose a generalized procedure for the design of integrated Vernier devices for high performance chemical and biochemical sensing. In particular, we demonstrate the accurate control of the most critical design and fabrication parameters of silicon-on-insulator cascade-coupled racetrack resonators operating in the second regime of the Vernier effect, around 1.55 μm. The experimental implementation of our design strategies has allowed a rigorous and reliable investigation of the influence of racetrack resonator and directional coupler dimensions as well as of waveguide process variability on the operation of Vernier devices. Figures of merit of our Vernier architectures have been measured experimentally, evidencing a high reproducibility and a very good agreement with the theoretical predictions, as also confirmed by relative errors even lower than 1%. Finally, a Vernier gain as high as 30.3, average insertion loss of 2.1 dB and extinction ratio up to 30 dB have been achieved.

Reproducing an extreme flood with uncertain post-event information

Directory of Open Access Journals (Sweden)

D. Fuentes-Andino

2017-07-01

Full Text Available Studies for the prevention and mitigation of floods require information on discharge and extent of inundation, commonly unavailable or uncertain, especially during extreme events. This study was initiated by the devastating flood in Tegucigalpa, the capital of Honduras, when Hurricane Mitch struck the city. In this study we hypothesized that it is possible to estimate, in a trustworthy way considering large data uncertainties, this extreme 1998 flood discharge and the extent of the inundations that followed from a combination of models and post-event measured data. Post-event data collected in 2000 and 2001 were used to estimate discharge peaks, times of peak, and high-water marks. These data were used in combination with rain data from two gauges to drive and constrain a combination of well-known modelling tools: TOPMODEL, Muskingum–Cunge–Todini routing, and the LISFLOOD-FP hydraulic model. Simulations were performed within the generalized likelihood uncertainty estimation (GLUE uncertainty-analysis framework. The model combination predicted peak discharge, times of peaks, and more than 90 % of the observed high-water marks within the uncertainty bounds of the evaluation data. This allowed an inundation likelihood map to be produced. Observed high-water marks could not be reproduced at a few locations on the floodplain. Identifications of these locations are useful to improve model set-up, model structure, or post-event data-estimation methods. Rainfall data were of central importance in simulating the times of peak and results would be improved by a better spatial assessment of rainfall, e.g. from radar data or a denser rain-gauge network. Our study demonstrated that it was possible, considering the uncertainty in the post-event data, to reasonably reproduce the extreme Mitch flood in Tegucigalpa in spite of no hydrometric gauging during the event. The method proposed here can be part of a Bayesian framework in which more events

ITK: Enabling Reproducible Research and Open Science

Directory of Open Access Journals (Sweden)

Matthew Michael McCormick

2014-02-01

Full Text Available Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature.Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification.This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

Reproducibility of scoring emphysema by HRCT

International Nuclear Information System (INIS)

Malinen, A.; Partanen, K.; Rytkoenen, H.; Vanninen, R.; Erkinjuntti-Pekkanen, R.

2002-01-01

Purpose: We evaluated the reproducibility of three visual scoring methods of emphysema and compared these methods with pulmonary function tests (VC, DLCO, FEV1 and FEV%) among farmer's lung patients and farmers. Material and Methods: Three radiologists examined high-resolution CT images of farmer's lung patients and their matched controls (n=70) for chronic interstitial lung diseases. Intraobserver reproducibility and interobserver variability were assessed for three methods: severity, Sanders' (extent) and Sakai. Pulmonary function tests as spirometry and diffusing capacity were measured. Results: Intraobserver -values for all three methods were good (0.51-0.74). Interobserver varied from 0.35 to 0.72. The Sanders' and the severity methods correlated strongly with pulmonary function tests, especially DLCO and FEV1. Conclusion: The Sanders' method proved to be reliable in evaluating emphysema, in terms of good consistency of interpretation and good correlation with pulmonary function tests

Reproducibility principles, problems, practices, and prospects

CERN Document Server

Maasen, Sabine

2016-01-01

Featuring peer-reviewed contributions from noted experts in their fields of research, Reproducibility: Principles, Problems, Practices, and Prospects presents state-of-the-art approaches to reproducibility, the gold standard sound science, from multi- and interdisciplinary perspectives. Including comprehensive coverage for implementing and reflecting the norm of reproducibility in various pertinent fields of research, the book focuses on how the reproducibility of results is applied, how it may be limited, and how such limitations can be understood or even controlled in the natural sciences, computational sciences, life sciences, social sciences, and studies of science and technology. The book presents many chapters devoted to a variety of methods and techniques, as well as their epistemic and ontological underpinnings, which have been developed to safeguard reproducible research and curtail deficits and failures. The book also investigates the political, historical, and social practices that underlie repro...

Validation of a method for accurate and highly reproducible quantification of brain dopamine transporter SPECT studies

DEFF Research Database (Denmark)

Jensen, Peter S; Ziebell, Morten; Skouboe, Glenna

2011-01-01

In nuclear medicine brain imaging, it is important to delineate regions of interest (ROIs) so that the outcome is both accurate and reproducible. The purpose of this study was to validate a new time-saving algorithm (DATquan) for accurate and reproducible quantification of the striatal dopamine t...... transporter (DAT) with appropriate radioligands and SPECT and without the need for structural brain scanning....

Collective space of high-rise housing complex

Directory of Open Access Journals (Sweden)

Bakaeva Tatyana

2018-01-01

Full Text Available The article considers the problems of support of citizens a comfortable living environment in the conditions of the limited territory of the megalopolis, the typological principles of formation of space-planning structure high-rise residence complexes with public space. The collective space for residents of high-rise housing estates on the example of international experience of design and construction is in detail considered. The collective space and the area of the standard apartment are analysed on comfort classes: a social - complex Pinnacle @ Duxton, a business - Monde Condos and an elite - Hamilton Scotts. Interdependence the area of the standard flat and the total area of housing collective space, in addiction on the comfort level, is revealed. In the conditions of high-density urban development, the collective space allows to form the comfortable environment for accommodation. The recommendations for achievement of integrity and improvement of quality of the city environment are made. The convenient collective space makes a contribution to civil policy, it creates the socializing sense of interaction of residents, coagulates social effect.

Collective space of high-rise housing complex

Science.gov (United States)

Bakaeva, Tatyana

2018-03-01

The article considers the problems of support of citizens a comfortable living environment in the conditions of the limited territory of the megalopolis, the typological principles of formation of space-planning structure high-rise residence complexes with public space. The collective space for residents of high-rise housing estates on the example of international experience of design and construction is in detail considered. The collective space and the area of the standard apartment are analysed on comfort classes: a social - complex Pinnacle @ Duxton, a business - Monde Condos and an elite - Hamilton Scotts. Interdependence the area of the standard flat and the total area of housing collective space, in addiction on the comfort level, is revealed. In the conditions of high-density urban development, the collective space allows to form the comfortable environment for accommodation. The recommendations for achievement of integrity and improvement of quality of the city environment are made. The convenient collective space makes a contribution to civil policy, it creates the socializing sense of interaction of residents, coagulates social effect.

Enriched reproducing kernel particle method for fractional advection-diffusion equation

Science.gov (United States)

Ying, Yuping; Lian, Yanping; Tang, Shaoqiang; Liu, Wing Kam

2018-06-01

The reproducing kernel particle method (RKPM) has been efficiently applied to problems with large deformations, high gradients and high modal density. In this paper, it is extended to solve a nonlocal problem modeled by a fractional advection-diffusion equation (FADE), which exhibits a boundary layer with low regularity. We formulate this method on a moving least-square approach. Via the enrichment of fractional-order power functions to the traditional integer-order basis for RKPM, leading terms of the solution to the FADE can be exactly reproduced, which guarantees a good approximation to the boundary layer. Numerical tests are performed to verify the proposed approach.

Reproducibility of scoring emphysema by HRCT

Energy Technology Data Exchange (ETDEWEB)

Malinen, A.; Partanen, K.; Rytkoenen, H.; Vanninen, R. [Kuopio Univ. Hospital (Finland). Dept. of Clinical Radiology; Erkinjuntti-Pekkanen, R. [Kuopio Univ. Hospital (Finland). Dept. of Pulmonary Diseases

2002-04-01

Purpose: We evaluated the reproducibility of three visual scoring methods of emphysema and compared these methods with pulmonary function tests (VC, DLCO, FEV1 and FEV%) among farmer's lung patients and farmers. Material and Methods: Three radiologists examined high-resolution CT images of farmer's lung patients and their matched controls (n=70) for chronic interstitial lung diseases. Intraobserver reproducibility and interobserver variability were assessed for three methods: severity, Sanders' (extent) and Sakai. Pulmonary function tests as spirometry and diffusing capacity were measured. Results: Intraobserver -values for all three methods were good (0.51-0.74). Interobserver varied from 0.35 to 0.72. The Sanders' and the severity methods correlated strongly with pulmonary function tests, especially DLCO and FEV1. Conclusion: The Sanders' method proved to be reliable in evaluating emphysema, in terms of good consistency of interpretation and good correlation with pulmonary function tests.

Reproducibility of coronary atherosclerotic plaque characteristics in populations with low, intermediate, and high prevalence of coronary artery disease by multidetector computer tomography

DEFF Research Database (Denmark)

de Knegt, Martina C; Linde, Jesper J; Fuchs, Andreas

2016-01-01

To evaluate the interobserver agreement of visual coronary plaque characteristics by 320-slice multidetector computed tomography (MDCT) in three populations with low, intermediate and high CAD prevalence and to identify determinants for the reproducible assessment of these plaque characteristics...

Testing Reproducibility in Earth Sciences

Science.gov (United States)

Church, M. A.; Dudill, A. R.; Frey, P.; Venditti, J. G.

2017-12-01

Reproducibility represents how closely the results of independent tests agree when undertaken using the same materials but different conditions of measurement, such as operator, equipment or laboratory. The concept of reproducibility is fundamental to the scientific method as it prevents the persistence of incorrect or biased results. Yet currently the production of scientific knowledge emphasizes rapid publication of previously unreported findings, a culture that has emerged from pressures related to hiring, publication criteria and funding requirements. Awareness and critique of the disconnect between how scientific research should be undertaken, and how it actually is conducted, has been prominent in biomedicine for over a decade, with the fields of economics and psychology more recently joining the conversation. The purpose of this presentation is to stimulate the conversation in earth sciences where, despite implicit evidence in widely accepted classifications, formal testing of reproducibility is rare.As a formal test of reproducibility, two sets of experiments were undertaken with the same experimental procedure, at the same scale, but in different laboratories. Using narrow, steep flumes and spherical glass beads, grain size sorting was examined by introducing fine sediment of varying size and quantity into a mobile coarse bed. The general setup was identical, including flume width and slope; however, there were some variations in the materials, construction and lab environment. Comparison of the results includes examination of the infiltration profiles, sediment mobility and transport characteristics. The physical phenomena were qualitatively reproduced but not quantitatively replicated. Reproduction of results encourages more robust research and reporting, and facilitates exploration of possible variations in data in various specific contexts. Following the lead of other fields, testing of reproducibility can be incentivized through changes to journal

Highly reproducible and reliable metal/graphene contact by ultraviolet-ozone treatment

Energy Technology Data Exchange (ETDEWEB)

Li, Wei [Key Laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics, Peking University, Beijing 100871 (China); Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Hacker, Christina A.; Cheng, Guangjun; Hight Walker, A. R.; Richter, Curt A.; Gundlach, David J., E-mail: david.gundlach@nist.gov, E-mail: liangxl@pku.edu.cn [Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Liang, Yiran; Tian, Boyuan; Liang, Xuelei, E-mail: david.gundlach@nist.gov, E-mail: liangxl@pku.edu.cn; Peng, Lianmao [Key Laboratory for the Physics and Chemistry of Nanodevices and Department of Electronics, Peking University, Beijing 100871 (China)

2014-03-21

Resist residue from the device fabrication process is a significant source of contamination at the metal/graphene contact interface. Ultraviolet Ozone (UVO) treatment is proven here, by X-ray photoelectron spectroscopy and Raman measurement, to be an effective way of cleaning the metal/graphene interface. Electrical measurements of devices that were fabricated by using UVO treatment of the metal/graphene contact region show that stable and reproducible low resistance metal/graphene contacts are obtained and the electrical properties of the graphene channel remain unaffected.

Highly reproducible and reliable metal/graphene contact by ultraviolet-ozone treatment

International Nuclear Information System (INIS)

Li, Wei; Hacker, Christina A.; Cheng, Guangjun; Hight Walker, A. R.; Richter, Curt A.; Gundlach, David J.; Liang, Yiran; Tian, Boyuan; Liang, Xuelei; Peng, Lianmao

2014-01-01

Resist residue from the device fabrication process is a significant source of contamination at the metal/graphene contact interface. Ultraviolet Ozone (UVO) treatment is proven here, by X-ray photoelectron spectroscopy and Raman measurement, to be an effective way of cleaning the metal/graphene interface. Electrical measurements of devices that were fabricated by using UVO treatment of the metal/graphene contact region show that stable and reproducible low resistance metal/graphene contacts are obtained and the electrical properties of the graphene channel remain unaffected

Using prediction markets to estimate the reproducibility of scientific research

Science.gov (United States)

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A.; Johannesson, Magnus

2015-01-01

Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants’ individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a “statistically significant” finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications. PMID:26553988

Using prediction markets to estimate the reproducibility of scientific research.

Science.gov (United States)

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus

2015-12-15

Concerns about a lack of reproducibility of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants' individual forecasts. This shows that prediction markets are a promising tool for assessing the reproducibility of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a "statistically significant" finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.

Reproducibility of clinical research in critical care: a scoping review.

Science.gov (United States)

Niven, Daniel J; McCormick, T Jared; Straus, Sharon E; Hemmelgarn, Brenda R; Jeffs, Lianne; Barnes, Tavish R M; Stelfox, Henry T

2018-02-21

The ability to reproduce experiments is a defining principle of science. Reproducibility of clinical research has received relatively little scientific attention. However, it is important as it may inform clinical practice, research agendas, and the design of future studies. We used scoping review methods to examine reproducibility within a cohort of randomized trials examining clinical critical care research and published in the top general medical and critical care journals. To identify relevant clinical practices, we searched the New England Journal of Medicine, The Lancet, and JAMA for randomized trials published up to April 2016. To identify a comprehensive set of studies for these practices, included articles informed secondary searches within other high-impact medical and specialty journals. We included late-phase randomized controlled trials examining therapeutic clinical practices in adults admitted to general medical-surgical or specialty intensive care units (ICUs). Included articles were classified using a reproducibility framework. An original study was the first to evaluate a clinical practice. A reproduction attempt re-evaluated that practice in a new set of participants. Overall, 158 practices were examined in 275 included articles. A reproduction attempt was identified for 66 practices (42%, 95% CI 33-50%). Original studies reported larger effects than reproduction attempts (primary endpoint, risk difference 16.0%, 95% CI 11.6-20.5% vs. 8.4%, 95% CI 6.0-10.8%, P = 0.003). More than half of clinical practices with a reproduction attempt demonstrated effects that were inconsistent with the original study (56%, 95% CI 42-68%), among which a large number were reported to be efficacious in the original study and to lack efficacy in the reproduction attempt (34%, 95% CI 19-52%). Two practices reported to be efficacious in the original study were found to be harmful in the reproduction attempt. A minority of critical care practices with research published

SU-C-201-03: Ionization Chamber Collection Efficiency in Pulsed Radiation Fields of High Pulse Dose

Energy Technology Data Exchange (ETDEWEB)

Gotz, M; Karsch, L [Oncoray - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden (Germany); Pawelke, J [Oncoray - National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universitaet Dresden, Helmholtz-Zentrum Dresden - Rossendorf, Dresden (Germany); Helmholtz-Zentrum Dresden - Rossendorf, Dresden (Germany)

2016-06-15

Purpose: To investigate the reduction of collection efficiency of ionization chambers (IC) by volume recombination and its correction in pulsed fields of very high pulse dose. Methods: Measurements of the collection efficiency of a plane-parallel advanced Markus IC (PTW 34045, 1mm electrode spacing, 300V nominal voltage) were obtained for collection voltages of 100V and 300V by irradiation with a pulsed electron beam (20MeV) of varied pulse dose up to approximately 600mGy (0.8nC liberated charge). A reference measurement was performed with a Faraday cup behind the chamber. It was calibrated for the liberated charge in the IC by a linear fit of IC measurement to reference measurement at low pulse doses. The results were compared to the commonly used two voltage approximation (TVA) and to established theories for volume recombination, with and without considering a fraction of free electrons. In addition, an equation system describing the charge transport and reactions in the chamber was solved numerically. Results: At 100V collection voltage and moderate pulse doses the established theories accurately predict the observed collection efficiency, but at extreme pulse doses a fraction of free electrons needs to be considered. At 300V the observed collection efficiency deviates distinctly from that predicted by any of the established theories, even at low pulse doses. However, the numeric solution of the equation system is able to reproduce the measured collection efficiency across the entire dose range of both voltages with a single set of parameters. Conclusion: At high electric fields (3000V/cm here) the existing theoretical descriptions of collection efficiency, including the TVA, are inadequate to predict pulse dose dependency. Even at low pulse doses they might underestimate collection efficiency. The presented, more accurate numeric solution, which considers additional effects like electric shielding by the charges, might provide a valuable tool for future

SU-C-201-03: Ionization Chamber Collection Efficiency in Pulsed Radiation Fields of High Pulse Dose

International Nuclear Information System (INIS)

Gotz, M; Karsch, L; Pawelke, J

2016-01-01

Purpose: To investigate the reduction of collection efficiency of ionization chambers (IC) by volume recombination and its correction in pulsed fields of very high pulse dose. Methods: Measurements of the collection efficiency of a plane-parallel advanced Markus IC (PTW 34045, 1mm electrode spacing, 300V nominal voltage) were obtained for collection voltages of 100V and 300V by irradiation with a pulsed electron beam (20MeV) of varied pulse dose up to approximately 600mGy (0.8nC liberated charge). A reference measurement was performed with a Faraday cup behind the chamber. It was calibrated for the liberated charge in the IC by a linear fit of IC measurement to reference measurement at low pulse doses. The results were compared to the commonly used two voltage approximation (TVA) and to established theories for volume recombination, with and without considering a fraction of free electrons. In addition, an equation system describing the charge transport and reactions in the chamber was solved numerically. Results: At 100V collection voltage and moderate pulse doses the established theories accurately predict the observed collection efficiency, but at extreme pulse doses a fraction of free electrons needs to be considered. At 300V the observed collection efficiency deviates distinctly from that predicted by any of the established theories, even at low pulse doses. However, the numeric solution of the equation system is able to reproduce the measured collection efficiency across the entire dose range of both voltages with a single set of parameters. Conclusion: At high electric fields (3000V/cm here) the existing theoretical descriptions of collection efficiency, including the TVA, are inadequate to predict pulse dose dependency. Even at low pulse doses they might underestimate collection efficiency. The presented, more accurate numeric solution, which considers additional effects like electric shielding by the charges, might provide a valuable tool for future

A refined, rapid and reproducible high resolution melt (HRM-based method suitable for quantification of global LINE-1 repetitive element methylation

Directory of Open Access Journals (Sweden)

Tse M Yat

2011-12-01

Full Text Available Abstract Background The methylation of DNA is recognized as a key mechanism in the regulation of genomic stability and evidence for its role in the development of cancer is accumulating. LINE-1 methylation status represents a surrogate measure of genome-wide methylation. Findings Using high resolution melt (HRM curve analysis technology, we have established an in-tube assay that is linear (r > 0.9986 with a high amplification efficiency (90-105%, capable of discriminating between partcipant samples with small differences in methylation, and suitable for quantifying a wide range of LINE-1 methylation levels (0-100%--including the biologically relevant range of 50-90% expected in human DNA. We have optimized this procedure to perform using 2 μg of starting DNA and 2 ng of bisulfite-converted DNA for each PCR reaction. Intra- and inter-assay coefficients of variation were 1.44% and 0.49%, respectively, supporting the high reproducibility and precision of this approach. Conclusions In summary, this is a completely linear, quantitative HRM PCR method developed for the measurement of LINE-1 methylation. This cost-efficient, refined and reproducible assay can be performed using minimal amounts of starting DNA. These features make our assay suitable for high throughput analysis of multiple samples from large population-based studies.

Reproducibility of gene expression across generations of Affymetrix microarrays

Directory of Open Access Journals (Sweden)

Haslett Judith N

2003-06-01

Full Text Available Abstract Background The development of large-scale gene expression profiling technologies is rapidly changing the norms of biological investigation. But the rapid pace of change itself presents challenges. Commercial microarrays are regularly modified to incorporate new genes and improved target sequences. Although the ability to compare datasets across generations is crucial for any long-term research project, to date no means to allow such comparisons have been developed. In this study the reproducibility of gene expression levels across two generations of Affymetrix GeneChips® (HuGeneFL and HG-U95A was measured. Results Correlation coefficients were computed for gene expression values across chip generations based on different measures of similarity. Comparing the absolute calls assigned to the individual probe sets across the generations found them to be largely unchanged. Conclusion We show that experimental replicates are highly reproducible, but that reproducibility across generations depends on the degree of similarity of the probe sets and the expression level of the corresponding transcript.

Madagascar: open-source software project for multidimensional data analysis and reproducible computational experiments

Directory of Open Access Journals (Sweden)

Sergey Fomel

2013-11-01

Full Text Available The Madagascar software package is designed for analysis of large-scale multidimensional data, such as those occurring in exploration geophysics. Madagascar provides a framework for reproducible research. By “reproducible research” we refer to the discipline of attaching software codes and data to computational results reported in publications. The package contains a collection of (a computational modules, (b data-processing scripts, and (c research papers. Madagascar is distributed on SourceForge under a GPL v2 license https://sourceforge.net/projects/rsf/. By October 2013, more than 70 people from different organizations around the world have contributed to the project, with increasing year-to-year activity. The Madagascar website is http://www.ahay.org/.

LHC Orbit Correction Reproducibility and Related Machine Protection

CERN Document Server

Baer, T; Schmidt, R; Wenninger, J

2012-01-01

The Large Hadron Collider (LHC) has an unprecedented nominal stored beam energy of up to 362 MJ per beam. In order to ensure an adequate machine protection by the collimation system, a high reproducibility of the beam position at collimators and special elements like the final focus quadrupoles is essential. This is realized by a combination of manual orbit corrections, feed forward and real time feedback. In order to protect the LHC against inconsistent orbit corrections, which could put the machine in a vulnerable state, a novel software-based interlock system for orbit corrector currents was developed. In this paper, the principle of the new interlock system is described and the reproducibility of the LHC orbit correction is discussed against the background of this system.

Reproducing Epidemiologic Research and Ensuring Transparency.

Science.gov (United States)

Coughlin, Steven S

2017-08-15

Measures for ensuring that epidemiologic studies are reproducible include making data sets and software available to other researchers so they can verify published findings, conduct alternative analyses of the data, and check for statistical errors or programming errors. Recent developments related to the reproducibility and transparency of epidemiologic studies include the creation of a global platform for sharing data from clinical trials and the anticipated future extension of the global platform to non-clinical trial data. Government agencies and departments such as the US Department of Veterans Affairs Cooperative Studies Program have also enhanced their data repositories and data sharing resources. The Institute of Medicine and the International Committee of Medical Journal Editors released guidance on sharing clinical trial data. The US National Institutes of Health has updated their data-sharing policies. In this issue of the Journal, Shepherd et al. (Am J Epidemiol. 2017;186:387-392) outline a pragmatic approach for reproducible research with sensitive data for studies for which data cannot be shared because of legal or ethical restrictions. Their proposed quasi-reproducible approach facilitates the dissemination of statistical methods and codes to independent researchers. Both reproducibility and quasi-reproducibility can increase transparency for critical evaluation, further dissemination of study methods, and expedite the exchange of ideas among researchers. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A novel highly reproducible and lethal nonhuman primate model for orthopox virus infection.

Directory of Open Access Journals (Sweden)

Marit Kramski

Full Text Available The intentional re-introduction of Variola virus (VARV, the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV and Monkeypox virus (MPXV cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus.A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1-3 days after onset of symptoms, even when very low infectious viral doses of 5x10(2 pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed.We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID(50 (minimal monkey infectious dose 50% of 8.3x10(2 pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis.

Reproducibility of Psychological Experiments as a Problem of Post-Nonclassical Science

Directory of Open Access Journals (Sweden)

Vachkov I.V.,

2016-04-01

Full Text Available A fundamental project on reproducibility carried out in the USA by Brian Nosek in 2015 (the Reproducibility Project revealed a serious methodological problem in psychology: the issue of replication of psycho- logical experiments. Reproducibility has been traditionally perceived as one of the basic principles of the scientific method. However, methodological analysis of the modern post-nonclassical stage in the development of science suggests that this might be a bit too uncompromising as applied to psychology. It seems that the very criteria of scientific research need to be reconsidered with regard to the specifics of post-nonclassical science, and, as the authors put it, as a result, reproducibility might lose its key status or even be excluded at all. The reviewed problem and the proposed ways of coping with it are of high importance to research and practice in psychology as they define the strategies for organizing, conducting and evaluating experimental research.

Enacting the International/Reproducing Eurocentrism

Directory of Open Access Journals (Sweden)

Zeynep Gülşah Çapan

Full Text Available Abstract This article focuses on the way in which Eurocentric conceptualisations of the ‘international’ are reproduced in different geopolitical contexts. Even though the Eurocentrism of International Relations has received growing attention, it has predominantly been concerned with unearthing the Eurocentrism of the ‘centre’, overlooking its varied manifestations in other geopolitical contexts. The article seeks to contribute to discussions about Eurocentrism by examining how different conceptualisations of the international are at work at a particular moment, and how these conceptualisations continue to reproduce Eurocentrism. It will focus on the way in which Eurocentric designations of spatial and temporal hierarchies were reproduced in the context of Turkey through a reading of how the ‘Gezi Park protests’ of 2013 and ‘Turkey’ itself were written into the story of the international.

Reproducibility and geometric accuracy of the fixster system during hypofractionated stereotactic radiotherapy

International Nuclear Information System (INIS)

Lindvall, Peter; Bergström, Per; Löfroth, Per-Olov; Henriksson, Roger; Bergenheim, A Tommy

2008-01-01

Hypofractionated radiotherapy has been used for the treatment of AVMs and brain metastases. Hypofractionation necessitates the use of a relocatable stereotactic frame that has to be applied on several occasions. The stereotactic frame needs to have a high degree of reproducibility, and patient positioning is crucial to achieve a high accuracy of the treatment. In this study we have, by radiological means, evaluated the reproducibility of the isocenter in consecutive treatment sessions using the Fixster frame. Deviations in the X, Y and Z-axis were measured in 10 patients treated with hypofractionated radiotherapy. The mean deviation in the X-axis was 0.4 mm (range -2.1 – 2.1, median 0.7 mm) and in the Y-axis -0.3 mm (range -1.4 – 0.7, median -0.2 mm). The mean deviation in the Z-axis was -0.6 (range -1.4 – 1.4, median 0.0 mm). There is a high degree of reproducibility of the isocenter during successive treatment sessions with HCSRT using the Fixster frame for stereotactic targeting. The high reducibility enables a safe treatment using hypofractionated stereotactic radiotherapy

Reproducibility of the sella turcica landmark in three dimensions using a sella turcica-specific reference system

International Nuclear Information System (INIS)

Pittayapat, Pisha; Jacobs, Reinhilde; Odri, Guillaume A.; De Faria Vasconcelos, Karla; Willems, Guy; Olszewski, Raphael

2015-01-01

This study was performed to assess the reproducibility of identifying the sella turcica landmark in a three-dimensional (3D) model by using a new sella-specific landmark reference system. Thirty-two cone-beam computed tomographic scans (3D Accuitomo 170, J. Morita, Kyoto, Japan) were retrospectively collected. The 3D data were exported into the Digital Imaging and Communications in Medicine standard and then imported into the Maxilim software (Medicim NV, Sint-Niklaas, Belgium) to create 3D surface models. Five observers identified four osseous landmarks in order to create the reference frame and then identified two sella landmarks. The x, y, and z coordinates of each landmark were exported. The observations were repeated after four weeks. Statistical analysis was performed using the multiple paired t-test with Bonferroni correction (intraobserver precision: p<0.005, interobserver precision: p<0.0011). The intraobserver mean precision of all landmarks was <1 mm. Significant differences were found when comparing the intraobserver precision of each observer (p<0.005). For the sella landmarks, the intraobserver mean precision ranged from 0.43±0.34 mm to 0.51±0.46 mm. The intraobserver reproducibility was generally good. The overall interobserver mean precision was <1 mm. Significant differences between each pair of observers for all anatomical landmarks were found (p<0.0011). The interobserver reproducibility of sella landmarks was good, with >50% precision in locating the landmark within 1 mm. A newly developed reference system offers high precision and reproducibility for sella turcica identification in a 3D model without being based on two-dimensional images derived from 3D data.

Reproducibility of the sella turcica landmark in three dimensions using a sella turcica-specific reference system

Energy Technology Data Exchange (ETDEWEB)

Pittayapat, Pisha; Jacobs, Reinhilde [University Hospitals Leuven, University of Leuven, Leuven (Belgium); Odri, Guillaume A. [Service de Chirurgie Orthopedique et Traumatologique, Centre Hospitalier Regional d' Orleans, Orleans Cedex2 (France); De Faria Vasconcelos, Karla [Dept. of Oral Diagnosis, Division of Oral Radiology, Piracicaba Dental School, University of Campinas, Sao Paulo (Brazil); Willems, Guy [Dept. of Oral Health Sciences, Orthodontics, KU Leuven and Dentistry, University Hospitals Leuven, University of Leuven, Leuven (Belgium); Olszewski, Raphael [Dept. of Oral and Maxillofacial Surgery, Cliniques Universitaires Saint Luc, Universite Catholique de Louvain, Brussels (Belgium)

2015-03-15

This study was performed to assess the reproducibility of identifying the sella turcica landmark in a three-dimensional (3D) model by using a new sella-specific landmark reference system. Thirty-two cone-beam computed tomographic scans (3D Accuitomo 170, J. Morita, Kyoto, Japan) were retrospectively collected. The 3D data were exported into the Digital Imaging and Communications in Medicine standard and then imported into the Maxilim software (Medicim NV, Sint-Niklaas, Belgium) to create 3D surface models. Five observers identified four osseous landmarks in order to create the reference frame and then identified two sella landmarks. The x, y, and z coordinates of each landmark were exported. The observations were repeated after four weeks. Statistical analysis was performed using the multiple paired t-test with Bonferroni correction (intraobserver precision: p<0.005, interobserver precision: p<0.0011). The intraobserver mean precision of all landmarks was <1 mm. Significant differences were found when comparing the intraobserver precision of each observer (p<0.005). For the sella landmarks, the intraobserver mean precision ranged from 0.43±0.34 mm to 0.51±0.46 mm. The intraobserver reproducibility was generally good. The overall interobserver mean precision was <1 mm. Significant differences between each pair of observers for all anatomical landmarks were found (p<0.0011). The interobserver reproducibility of sella landmarks was good, with >50% precision in locating the landmark within 1 mm. A newly developed reference system offers high precision and reproducibility for sella turcica identification in a 3D model without being based on two-dimensional images derived from 3D data.

A discrete particle model reproducing collective dynamics of a bee swarm.

Science.gov (United States)

Bernardi, Sara; Colombi, Annachiara; Scianna, Marco

2018-02-01

In this article, we present a microscopic discrete mathematical model describing collective dynamics of a bee swarm. More specifically, each bee is set to move according to individual strategies and social interactions, the former involving the desire to reach a target destination, the latter accounting for repulsive/attractive stimuli and for alignment processes. The insects tend in fact to remain sufficiently close to the rest of the population, while avoiding collisions, and they are able to track and synchronize their movement to the flight of a given set of neighbors within their visual field. The resulting collective behavior of the bee cloud therefore emerges from non-local short/long-range interactions. Differently from similar approaches present in the literature, we here test different alignment mechanisms (i.e., based either on an Euclidean or on a topological neighborhood metric), which have an impact also on the other social components characterizing insect behavior. A series of numerical realizations then shows the phenomenology of the swarm (in terms of pattern configuration, collective productive movement, and flight synchronization) in different regions of the space of free model parameters (i.e., strength of attractive/repulsive forces, extension of the interaction regions). In this respect, constraints in the possible variations of such coefficients are here given both by reasonable empirical observations and by analytical results on some stability characteristics of the defined pairwise interaction kernels, which have to assure a realistic crystalline configuration of the swarm. An analysis of the effect of unconscious random fluctuations of bee dynamics is also provided. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reproducible fabrication of stable small nano Pt with high activity for sensor applications

International Nuclear Information System (INIS)

Ye Pingping; Guo Xiaoyu; Liu Guiting; Chen Huifen; Pan Yuxia; Wen Ying; Yang Haifeng

2013-01-01

Pt nanoparticles with an average size of 2–3 nm in diameter were reproducibly synthesized by reduction of H 2 PtCl 6 solution containing inositol hexaphosphate (IP 6 ) as the stabilizing agent. Single crystals with Pt(111) faces of the resulting cubic nanoparticles were revealed by the electron diffraction pattern. The PtNPs–IP 6 nanoparticles were used to modify an electrode as a nonenzymatic sensor for H 2 O 2 detection, exhibiting a fast response and high sensitivity. A low detection limit of 2.0 × 10 −7 M (S/N = 3) with two linear ranges between 2.4 × 10 −7 and 1.3 × 10 −3 M (R 2 = 0.9987) and between 1.3 × 10 −3 and 1.3 × 10 −2 M (R 2 = 0.9980) was achieved. The attractive electrochemical performance of PtNPs–IP 6 enables it to be employed as a promising material for the development of Pt-based analytical systems and other applications. (paper)

Cervical vertebrae maturation method morphologic criteria: poor reproducibility.

Science.gov (United States)

Nestman, Trenton S; Marshall, Steven D; Qian, Fang; Holton, Nathan; Franciscus, Robert G; Southard, Thomas E

2011-08-01

The cervical vertebrae maturation (CVM) method has been advocated as a predictor of peak mandibular growth. A careful review of the literature showed potential methodologic errors that might influence the high reported reproducibility of the CVM method, and we recently established that the reproducibility of the CVM method was poor when these potential errors were eliminated. The purpose of this study was to further investigate the reproducibility of the individual vertebral patterns. In other words, the purpose was to determine which of the individual CVM vertebral patterns could be classified reliably and which could not. Ten practicing orthodontists, trained in the CVM method, evaluated the morphology of cervical vertebrae C2 through C4 from 30 cephalometric radiographs using questions based on the CVM method. The Fleiss kappa statistic was used to assess interobserver agreement when evaluating each cervical vertebrae morphology question for each subject. The Kendall coefficient of concordance was used to assess the level of interobserver agreement when determining a "derived CVM stage" for each subject. Interobserver agreement was high for assessment of the lower borders of C2, C3, and C4 that were either flat or curved in the CVM method, but interobserver agreement was low for assessment of the vertebral bodies of C3 and C4 when they were either trapezoidal, rectangular horizontal, square, or rectangular vertical; this led to the overall poor reproducibility of the CVM method. These findings were reflected in the Fleiss kappa statistic. Furthermore, nearly 30% of the time, individual morphologic criteria could not be combined to generate a final CVM stage because of incompatible responses to the 5 questions. Intraobserver agreement in this study was only 62%, on average, when the inconclusive stagings were excluded as disagreements. Intraobserver agreement was worse (44%) when the inconclusive stagings were included as disagreements. For the group of subjects

Intra-and interobserver reproducibility of shear wave elastography for evaluation of the breast lesions

International Nuclear Information System (INIS)

Hong, Min Ji; Kim, Hak Hee

2017-01-01

To evaluate reproducibility of shear wave elastography (SWE) for breast lesions within and between observers and compare the reproducibility of SWE features. For intraobserver reproducibility, 225 masses with 208 patients were included; and two consecutive SWE images were acquired by each observer. For interobserver reproducibility, SWE images of the same mass were obtained by another observer before surgery in 40 patients. Intraclass correlation coefficients (ICC) were used to determine intra- and interobserver reproducibility. Intraobserver reliability for mean elasticity (Emean) and maximum elasticity (Emax) were excellent (ICC = 0.803, 0.799). ICC for SWE ratio and minimum elasticity (Emin) were fair to good (ICC = 0.703, 0.539). Emean showed excellent ICC regardless of histopathologic type and tumor size. Emax, SWE ratio and Emin represented excellent or fair to good reproducibility based on histopathologic type and tumor size. In interobserver study, ICC for Emean, Emax and SWE ratio were excellent. Emean, Emax and SWE ratio represented excellent ICC irrespective of histopathologic type. ICC for Emean was excellent regardless of tumor size. SWE ratio and Emax showed fair to good interobserver reproducibility based on tumor size. Emin represented poor interobserver reliability. Emean in SWE was highly reproducible within and between observers

Intra-and interobserver reproducibility of shear wave elastography for evaluation of the breast lesions

Energy Technology Data Exchange (ETDEWEB)

Hong, Min Ji [Dept. of Radiology, Gil Hospital, Gachon University of Medicine and Science, Incheon (Korea, Republic of); Kim, Hak Hee [Dept. of Radiology, and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

2017-03-15

To evaluate reproducibility of shear wave elastography (SWE) for breast lesions within and between observers and compare the reproducibility of SWE features. For intraobserver reproducibility, 225 masses with 208 patients were included; and two consecutive SWE images were acquired by each observer. For interobserver reproducibility, SWE images of the same mass were obtained by another observer before surgery in 40 patients. Intraclass correlation coefficients (ICC) were used to determine intra- and interobserver reproducibility. Intraobserver reliability for mean elasticity (Emean) and maximum elasticity (Emax) were excellent (ICC = 0.803, 0.799). ICC for SWE ratio and minimum elasticity (Emin) were fair to good (ICC = 0.703, 0.539). Emean showed excellent ICC regardless of histopathologic type and tumor size. Emax, SWE ratio and Emin represented excellent or fair to good reproducibility based on histopathologic type and tumor size. In interobserver study, ICC for Emean, Emax and SWE ratio were excellent. Emean, Emax and SWE ratio represented excellent ICC irrespective of histopathologic type. ICC for Emean was excellent regardless of tumor size. SWE ratio and Emax showed fair to good interobserver reproducibility based on tumor size. Emin represented poor interobserver reliability. Emean in SWE was highly reproducible within and between observers.

Reproducibility of surface roughness in reaming

DEFF Research Database (Denmark)

Müller, Pavel; De Chiffre, Leonardo

An investigation on the reproducibility of surface roughness in reaming was performed to document the applicability of this approach for testing cutting fluids. Austenitic stainless steel was used as a workpiece material and HSS reamers as cutting tools. Reproducibility of the results was evaluat...

Reproducibility of abdominal fat assessment by ultrasound and computed tomography.

Science.gov (United States)

Mauad, Fernando Marum; Chagas-Neto, Francisco Abaeté; Benedeti, Augusto César Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge

2017-01-01

To test the accuracy and reproducibility of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good reproducibility.

Fabrication of reproducible, integration-compatible hybrid molecular/si electronics.

Science.gov (United States)

Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet

2014-12-29

Reproducible molecular junctions can be integrated within standard CMOS technology. Metal-molecule-semiconductor junctions are fabricated by direct Si-C binding of hexadecane or methyl-styrene onto oxide-free H-Si(111) surfaces, with the lateral size of the junctions defined by an etched SiO2 well and with evaporated Pb as the top contact. The current density, J, is highly reproducible with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. Reproducibility over such a large range indicates that transport is truly across the molecules and does not result from artifacts like edge effects or defects in the molecular monolayer. Device fabrication is tested for two n-Si doping levels. With highly doped Si, transport is dominated by tunneling and reveals sharp conductance onsets at room temperature. Using the temperature dependence of current across medium-doped n-Si, the molecular tunneling barrier can be separated from the Si-Schottky one, which is a 0.47 eV, in agreement with the molecular-modified surface dipole and quite different from the bare Si-H junction. This indicates that Pb evaporation does not cause significant chemical changes to the molecules. The ability to manufacture reliable devices constitutes important progress toward possible future hybrid Si-based molecular electronics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inexperienced clinicians can extract pathoanatomic information from MRI narrative reports with high reproducability for use in research/quality assurance

DEFF Research Database (Denmark)

Kent, Peter; Briggs, Andrew M; Albert, Hanne Birgit

2011-01-01

Background Although reproducibility in reading MRI images amongst radiologists and clinicians has been studied previously, no studies have examined the reproducibility of inexperienced clinicians in extracting pathoanatomic information from magnetic resonance imaging (MRI) narrative reports and t...

Development, validation and reproducibility of a food frequency questionnaire to measure flavonoid intake in older Australian adults.

Science.gov (United States)

Kent, Katherine; Charlton, Karen E

2018-02-01

To develop and assess the validity and reproducibility of a food frequency questionnaire (FFQ) to measure total flavonoid intake, and individual flavonoid subclasses, in older adults. Retrospective analysis of flavonoid intake in older adults informed the development of a FFQ to measure flavonoid intake and determine the flavonoid subclasses consumed (anthocyanins, flavan-3-ols, flavones, flavonols and flavanones). Older adults (n = 42, mean age 75.3 ± 8.6 years) attended two interviews 1 month apart where anthropometrics (height and weight), blood pressure (BP), demographic data and a 93-item self-administered FFQ were collected. A 4-day food record (FR) was randomly administered between the two interview dates, and each food item was assigned a flavonoid and flavonoid subclass content using the United States Department of Agriculture flavonoid database. The criterion validity and reproducibility of the FFQ was assessed against a 4-day FR using the Wilcoxon signed-rank sum test, Spearman's correlation coefficient (r), Bland-Altman Plots and Cohen's kappa. Total flavonoid intake was determined (median intake FFQ = 919.3 mg/day, FR = 781.4 mg/day). Tests of validity indicated that the FFQ consistently overestimated total flavonoid intake compared with the 4-day FR. There was a significant difference in estimates between the FFQ and the 4-day FR for total flavonoid intake (Wilcoxon signed-rank sum P tests of validity indicated greater discrepancy compared with 4-day FR. The FFQ showed high reproducibility for estimating total flavonoid intake (FFQ1vsFFQ2: Wilcoxon signed-rank sum test, P > 0.05; Spearman's r 0.91, P tests of reproducibility between FFQ1 and FFQ2 showed similarly high reproducibility. The developed FFQ appears suitable for satisfactorily ranking individuals according to total flavonoid intake. The FFQ shows limitations for estimating absolute total flavonoid intake and intake of flavonoid subclasses in comparison to a 4-day FR in terms of

Reproducibility in the Field: Transparency, Version Control and Collaboration on the Project Panormos Survey

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Strupler Néhémie

2017-11-01

Full Text Available Archaeological fieldwork is rarely considered reproducible in the sense of the ideal scientific method because of its destructive nature. But new digital technology now offers field practitioners a set of tools that can at least increase the transparency of the data-collection process as well as bring other benefits of an Open Science approach to archaeology. This article shares our perspectives, choices and experiences of piloting a set of tools (namely: ODK, Git, GitLab CE and R which can address reproducibility of fieldwork in the form of an intensive survey project in western Turkey, and highlights the potential consequences of Open Science approaches for archaeology as a whole.

Reproducibility of central lumbar vertebral BMD

International Nuclear Information System (INIS)

Chan, F.; Pocock, N.; Griffiths, M.; Majerovic, Y.; Freund, J.

1997-01-01

Full text: Lumbar vertebral bone mineral density (BMD) using dual X-ray absorptiometry (DXA) has generally been calculated from a region of interest which includes the entire vertebral body. Although this region excludes part of the transverse processes, it does include the outer cortical shell of the vertebra. Recent software has been devised to calculate BMD in a central vertebral region of interest which excludes the outer cortical envelope. Theoretically this area may be more sensitive to detecting osteoporosis which affects trabecular bone to a greater extent than cortical bone. Apart from the sensitivity of BMD estimation, the reproducibility of any measurement is important owing to the slow rate of change of bone mass. We have evaluated the reproducibility of this new vertebral region of interest in 23 women who had duplicate lumbar spine DXA scans performed on the same day. The patients were repositioned between each measurement. Central vertebral analysis was performed for L2-L4 and the reproducibility of area, bone mineral content (BMC) and BMD calculated as the coefficient of variation; these values were compared with those from conventional analysis. Thus we have shown that the reproducibility of the central BMD is comparable to the conventional analysis which is essential if this technique is to provide any additional clinical data. The reasons for the decrease in reproducibility of the area and hence BMC requires further investigation

Reproducibility of brain ADC histograms

International Nuclear Information System (INIS)

Steens, S.C.A.; Buchem, M.A. van; Admiraal-Behloul, F.; Schaap, J.A.; Hoogenraad, F.G.C.; Wheeler-Kingshott, C.A.M.; Tofts, P.S.; Cessie, S. le

2004-01-01

The aim of this study was to assess the effect of differences in acquisition technique on whole-brain apparent diffusion coefficient (ADC) histogram parameters, as well as to assess scan-rescan reproducibility. Diffusion-weighted imaging (DWI) was performed in 7 healthy subjects with b-values 0-800, 0-1000, and 0-1500 s/mm 2 and fluid-attenuated inversion recovery (FLAIR) DWI with b-values 0-1000 s/mm 2 . All sequences were repeated with and without repositioning. The peak location, peak height, and mean ADC of the ADC histograms and mean ADC of a region of interest (ROI) in the white matter were compared using paired-sample t tests. Scan-rescan reproducibility was assessed using paired-sample t tests, and repeatability coefficients were reported. With increasing maximum b-values, ADC histograms shifted to lower values, with an increase in peak height (p<0.01). With FLAIR DWI, the ADC histogram shifted to lower values with a significantly higher, narrower peak (p<0.01), although the ROI mean ADC showed no significant differences. For scan-rescan reproducibility, no significant differences were observed. Different DWI pulse sequences give rise to different ADC histograms. With a given pulse sequence, however, ADC histogram analysis is a robust and reproducible technique. Using FLAIR DWI, the partial-voluming effect of cerebrospinal fluid, and thus its confounding effect on histogram analyses, can be reduced

Repeatability and interobserver reproducibility of Artemis-2 high-frequency ultrasound in determination of human corneal thickness

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Ogbuehi KC

2012-05-01

Full Text Available Kelechi C Ogbuehi, Uchechukwu L OsuagwuOutpatient Clinic, Department of Optometry, King Saud University, Riyadh, Kingdom of Saudi ArabiaBackground: The purpose of this study was to assess the repeatability and limits of agreement of corneal thickness values measured by a high-frequency ultrasound (Artemis-2, hand-held ultrasound pachymeter (DGH-500 and a specular microscope (SP-3000P.Methods: Central corneal thickness (CCT was analyzed in this prospective randomized study that included 32 patients (18 men and 14 women aged 21–24 years. Measurements were obtained in two sessions, one week apart, by two examiners with three devices in a randomized order. Nine measurements were taken (three with each device on one randomly selected eye of each patient in each measurement session. The coefficient of repeatability and interobserver reproducibility for the values of each method were calculated. The limits of agreement between techniques were also evaluated.Results: There were no significant differences in CCT values between sessions for each of the three devices (P > 0.05. The repeatability coefficients for the Artemis-2 (±8 µm/±9 µm were superior to those of the SP-3000P (±9 µm/±11 µm and DGH 500 (±12 µm/±12 µm in session 1/session 2 respectively, while the interobserver reproducibility index (differences between session 1 and session 2 was superior for the SP-3000P (±17 µm with respect to DHG-500 (±29 µm and the Artemis-2 (±31 µm. In session 1 and session 2, the limits of agreement between the techniques were 35 µm to -31 µm and 34 to -20 µm, respectively, for DGH-500 versus Artemis-2, 73 µm to 3 µm and 60 µm to 9 µm for Artemis-2 versus SP-3000P, and 58 µm to 22 µm and 72 µm to 10 µm for DGH-500 versus SP-3000P comparisons. The DGH-500 and Artemis-2 gave similar values (P > 0.05 in both sessions, but both (Artemis-2 and DGH-500 values were significantly greater than that of the SP-3000P (P < 0.05 in both sessions

Reproducibility of airway luminal size in asthma measured by HRCT.

Science.gov (United States)

Brown, Robert H; Henderson, Robert J; Sugar, Elizabeth A; Holbrook, Janet T; Wise, Robert A

2017-10-01

Brown RH, Henderson RJ, Sugar EA, Holbrook JT, Wise RA, on behalf of the American Lung Association Airways Clinical Research Centers. Reproducibility of airway luminal size in asthma measured by HRCT. J Appl Physiol 123: 876-883, 2017. First published July 13, 2017; doi:10.1152/japplphysiol.00307.2017.-High-resolution CT (HRCT) is a well-established imaging technology used to measure lung and airway morphology in vivo. However, there is a surprising lack of studies examining HRCT reproducibility. The CPAP Trial was a multicenter, randomized, three-parallel-arm, sham-controlled 12-wk clinical trial to assess the use of a nocturnal continuous positive airway pressure (CPAP) device on airway reactivity to methacholine. The lack of a treatment effect of CPAP on clinical or HRCT measures provided an opportunity for the current analysis. We assessed the reproducibility of HRCT imaging over 12 wk. Intraclass correlation coefficients (ICCs) were calculated for individual airway segments, individual lung lobes, both lungs, and air trapping. The ICC [95% confidence interval (CI)] for airway luminal size at total lung capacity ranged from 0.95 (0.91, 0.97) to 0.47 (0.27, 0.69). The ICC (95% CI) for airway luminal size at functional residual capacity ranged from 0.91 (0.85, 0.95) to 0.32 (0.11, 0.65). The ICC measurements for airway distensibility index and wall thickness were lower, ranging from poor (0.08) to moderate (0.63) agreement. The ICC for air trapping at functional residual capacity was 0.89 (0.81, 0.94) and varied only modestly by lobe from 0.76 (0.61, 0.87) to 0.95 (0.92, 0.97). In stable well-controlled asthmatic subjects, it is possible to reproducibly image unstimulated airway luminal areas over time, by region, and by size at total lung capacity throughout the lungs. Therefore, any changes in luminal size on repeat CT imaging are more likely due to changes in disease state and less likely due to normal variability. NEW & NOTEWORTHY There is a surprising lack

Reproducibility in Research: Systems, Infrastructure, Culture

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Tom Crick

2017-11-01

Full Text Available The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around the ability to implement (and exploit novel algorithms and models. Taking a new approach from the literature and applying it to a new codebase frequently requires local knowledge missing from the published manuscripts and transient project websites. Alongside this issue, benchmarking, and the lack of open, transparent and fair benchmark sets present another barrier to the verification and validation of claimed results. In this paper, we outline several recommendations to address these issues, driven by specific examples from a range of scientific domains. Based on these recommendations, we propose a high-level prototype open automated platform for scientific software development which effectively abstracts specific dependencies from the individual researcher and their workstation, allowing easy sharing and reproduction of results. This new e-infrastructure for reproducible computational science offers the potential to incentivise a culture change and drive the adoption of new techniques to improve the quality and efficiency – and thus reproducibility – of scientific exploration.

Reproducibility of abdominal fat assessment by ultrasound and computed tomography

Energy Technology Data Exchange (ETDEWEB)

Mauad, Fernando Marum; Chagas-Neto, Francisco Abaete; Benedeti, Augusto Cesar Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge, E-mail: fernando@fatesa.edu.br [Faculdade de Tecnologia em Saude (FATESA), Ribeirao Preto, SP (Brazil); Universidade de Fortaleza (UNIFOR), Fortaleza, CE (Brazil). Departmento de Radiologia; Universidade de Sao Paulo (FMRP/USP), Ribeirao Preto, SP (Brazil). Faculdade de Medicina. Departmento de Medicina Clinica; Universidade de Sao Paulo (FFCLRP/USP), Ribeirao Preto, SP (Brazil). Faculdade de Filosofia, Ciencias e Letras; Hospital Mae de Deus, Porto Alegre, RS (Brazil)

2017-05-15

Objective: To test the accuracy and reproducibility of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Materials and Methods: Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Results: Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. Conclusion: In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good reproducibility. (author)

Evaluation of the Repeatability and the Reproducibility of AL-Scan Measurements Obtained by Residents

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Mehmet Kola

2014-01-01

Full Text Available Purpose. To assess the repeatability and reproducibility of ocular biometry and intraocular lens (IOL power measurements obtained by ophthalmology residents using an AL-Scan device, a novel optical biometer. Methods. Two ophthalmology residents were instructed regarding the AL-Scan device. Both performed ocular biometry and IOL power measurements using AL-Scan, three times on each of 128 eyes, independently of one another. Corneal keratometry readings, horizontal iris width, central corneal thickness, anterior chamber depth, pupil size, and axial length values measured by both residents were recorded together with IOL power values calculated on the basis of four different IOL calculation formulas (SRK/T, Holladay, and HofferQ. Repeatability and reproducibility of the measurements obtained were analyzed using the intraclass correlation coefficient (ICC. Results. Repeatability (ICC, 0.872-0.999 for resident 1 versus 0.905-0.999 for resident 2 and reproducibility (ICC, 0.916-0.999 were high for all biometric measurements. Repeatability (ICC, 0.981-0.983 for resident 1 versus 0.995-0.996 for resident 2 and reproducibility were also high for all IOL power measurements (ICC, 0.996 for all. Conclusions. The AL-Scan device exhibits good repeatability and reproducibility in all biometric measurements and IOL power calculations, independent of the operator concerned.

Examination of reproducibility in microbiological degredation experiments

DEFF Research Database (Denmark)

Sommer, Helle Mølgaard; Spliid, Henrik; Holst, Helle

1998-01-01

Experimental data indicate that certain microbiological degradation experiments have a limited reproducibility. Nine identical batch experiments were carried out on 3 different days to examine reproducibility. A pure culture, isolated from soil, grew with toluene as the only carbon and energy...... source. Toluene was degraded under aerobic conditions at a constant temperature of 28 degreesC. The experiments were modelled by a Monod model - extended to meet the air/liquid system, and the parameter values were estimated using a statistical nonlinear estimation procedure. Model reduction analysis...... resulted in a simpler model without the biomass decay term. In order to test for model reduction and reproducibility of parameter estimates, a likelihood ratio test was employed. The limited reproducibility for these experiments implied that all 9 batch experiments could not be described by the same set...

Reproducibility and differentiation of cervical arteriopathies using in vivo high-resolution black-blood MRI at 3 T

International Nuclear Information System (INIS)

Schwarz, Florian; Strobl, Frederik F.; Cyran, Clemens C.; Helck, Andreas D.; Hartmann, Martin; Schindler, Andreas; Reiser, Maximilian F.; Saam, Tobias; Nikolaou, Konstantin

2016-01-01

The aims of the present study are to evaluate the potential of high-resolution black-blood MRI (hr-bb-cMRI) to differentiate common cervical arteriopathies and to evaluate interobserver reproducibility. Forty-three consecutive patients with distinct cervical arteriopathies were examined with cervical hr-bb-cMRI at 3.0 Te with fat-saturated pre- and post-contrast T1w, T2w, and TOF images using dedicated carotid surface coils at our institution. Twenty-three patients had atherosclerotic disease, causing significant stenosis in 12 patients while 11 patients had moderate stenosis. Eight patients presented with cervical vasculitis, and five patients had arterial dissection. Furthermore, seven control subjects with no evidence of carotid disease were included. Two experienced readers blinded to all clinical information reviewed all MR images and classified both carotid and vertebral arteries as affected either by atherosclerosis, dissection, vasculitis, or no disease. Finally, a consensus reading was performed. On a per-vessel level, test performance parameters (sensitivity, specificity, positive predictive value, negative predictive value) were 95, 97.7, 92.9, and 98.5 % for atherosclerotic disease; 91, 100, 100, and 98.7 % for vasculitis; and 100, 100, 100, and 100 % for dissection, respectively. On a per-patient level, performance parameters were 95.7, 85.7, 97.2, and 85.7 % for the diagnosis of atherosclerosis and 100, 100, 100, and 100 % for the diagnosis of dissection and of vasculitis, respectively. Accuracy rates were all above 95 % for all entities. There was a high agreement between observers both in a per-vessel (κ = 0.83) and in a per-patient analysis (κ = 0.82). This study demonstrates that hr-bb-cMRI is able to non-invasively differentiate between the most common cervical arteriopathies with an excellent interreader reproducibility. (orig.)

Reproducibility and differentiation of cervical arteriopathies using in vivo high-resolution black-blood MRI at 3 T

Energy Technology Data Exchange (ETDEWEB)

Schwarz, Florian; Strobl, Frederik F.; Cyran, Clemens C.; Helck, Andreas D.; Hartmann, Martin; Schindler, Andreas; Reiser, Maximilian F.; Saam, Tobias [Ludwig-Maximilians-University Hospital Munich, Institute for Clinical Radiology, Munich (Germany); Nikolaou, Konstantin [Ludwig-Maximilians-University Hospital Munich, Institute for Clinical Radiology, Munich (Germany); Eberhard-Karls-University Tuebingen, Diagnostic and Interventional Radiology, Tuebingen (Germany)

2016-06-15

The aims of the present study are to evaluate the potential of high-resolution black-blood MRI (hr-bb-cMRI) to differentiate common cervical arteriopathies and to evaluate interobserver reproducibility. Forty-three consecutive patients with distinct cervical arteriopathies were examined with cervical hr-bb-cMRI at 3.0 Te with fat-saturated pre- and post-contrast T1w, T2w, and TOF images using dedicated carotid surface coils at our institution. Twenty-three patients had atherosclerotic disease, causing significant stenosis in 12 patients while 11 patients had moderate stenosis. Eight patients presented with cervical vasculitis, and five patients had arterial dissection. Furthermore, seven control subjects with no evidence of carotid disease were included. Two experienced readers blinded to all clinical information reviewed all MR images and classified both carotid and vertebral arteries as affected either by atherosclerosis, dissection, vasculitis, or no disease. Finally, a consensus reading was performed. On a per-vessel level, test performance parameters (sensitivity, specificity, positive predictive value, negative predictive value) were 95, 97.7, 92.9, and 98.5 % for atherosclerotic disease; 91, 100, 100, and 98.7 % for vasculitis; and 100, 100, 100, and 100 % for dissection, respectively. On a per-patient level, performance parameters were 95.7, 85.7, 97.2, and 85.7 % for the diagnosis of atherosclerosis and 100, 100, 100, and 100 % for the diagnosis of dissection and of vasculitis, respectively. Accuracy rates were all above 95 % for all entities. There was a high agreement between observers both in a per-vessel (κ = 0.83) and in a per-patient analysis (κ = 0.82). This study demonstrates that hr-bb-cMRI is able to non-invasively differentiate between the most common cervical arteriopathies with an excellent interreader reproducibility. (orig.)

Guidelines for Reproducibly Building and Simulating Systems Biology Models.

Science.gov (United States)

Medley, J Kyle; Goldberg, Arthur P; Karr, Jonathan R

2016-10-01

Reproducibility is the cornerstone of the scientific method. However, currently, many systems biology models cannot easily be reproduced. This paper presents methods that address this problem. We analyzed the recent Mycoplasma genitalium whole-cell (WC) model to determine the requirements for reproducible modeling. We determined that reproducible modeling requires both repeatable model building and repeatable simulation. New standards and simulation software tools are needed to enhance and verify the reproducibility of modeling. New standards are needed to explicitly document every data source and assumption, and new deterministic parallel simulation tools are needed to quickly simulate large, complex models. We anticipate that these new standards and software will enable researchers to reproducibly build and simulate more complex models, including WC models.

Reproducibility of small animal cine and scar cardiac magnetic resonance imaging using a clinical 3.0 tesla system

International Nuclear Information System (INIS)

Manka, Robert; Jahnke, Cosima; Hucko, Thomas; Dietrich, Thore; Gebker, Rolf; Schnackenburg, Bernhard; Graf, Kristof; Paetsch, Ingo

2013-01-01

To evaluate the inter-study, inter-reader and intra-reader reproducibility of cardiac cine and scar imaging in rats using a clinical 3.0 Tesla magnetic resonance (MR) system. Thirty-three adult rats (Sprague–Dawley) were imaged 24 hours after surgical occlusion of the left anterior descending coronary artery using a 3.0 Tesla clinical MR scanner (Philips Healthcare, Best, The Netherlands) equipped with a dedicated 70 mm solenoid receive-only coil. Left-ventricular (LV) volumes, mass, ejection fraction and amount of myocardial scar tissue were measured. Intra-and inter-observer reproducibility was assessed in all animals. In addition, repeat MR exams were performed in 6 randomly chosen rats within 24 hours to assess inter-study reproducibility. The MR imaging protocol was successfully completed in 32 (97%) animals. Bland-Altman analysis demonstrated high intra-reader reproducibility (mean bias%: LV end-diastolic volume (LVEDV), -1.7%; LV end-systolic volume (LVESV), -2.2%; LV ejection fraction (LVEF), 1.0%; LV mass, -2.7%; and scar mass, -1.2%) and high inter-reader reproducibility (mean bias%: LVEDV, 3.3%; LVESV, 6.2%; LVEF, -4.8%; LV mass, -1.9%; and scar mass, -1.8%). In addition, a high inter-study reproducibility was found (mean bias%: LVEDV, 0.1%; LVESV, -1.8%; LVEF, 1.0%; LV mass, -4.6%; and scar mass, -6.2%). Cardiac MR imaging of rats yielded highly reproducible measurements of cardiac volumes/function and myocardial infarct size on a clinical 3.0 Tesla MR scanner system. Consequently, more widely available high field clinical MR scanners can be employed for small animal imaging of the heart e.g. when aiming at serial assessments during therapeutic intervention studies

Banff initiative for quality assurance in transplantation (BIFQUIT): reproducibility of C4d immunohistochemistry in kidney allografts.

Science.gov (United States)

Mengel, M; Chan, S; Climenhaga, J; Kushner, Y B; Regele, H; Colvin, R B; Randhawa, P

2013-05-01

Detection of C4d is crucial for diagnosing antibody-mediated-rejection. We conducted a multicenter trial to assess the reproducibility for C4d immunohistochemistry on paraffin tissue. Unstained slides from a tissue microarray (TMA) comprising 44 kidney allograft specimens representing a full analytical spectrum for C4d were distributed to 73 institutions. Participants stained TMA slides using local protocols and evaluated their slides following the Banff C4d schema. Local staining details and evaluation scores were collected online. Stained slides were returned for centralized panel re-evaluation. Kappa statistics were used to determine reproducibility. Poor interinstitutional reproducibility was observed (kappa 0.17), which was equally due to limitations in interobserver (kappa 0.44) and interlaboratory reproducibility (kappa 0.46). Depending on the cut-off, reproducibility could be improved by omitting C4d grading and only considering ± calls. Heat-induced epitope recovery (pH 6-7, 20-30 min, citrate buffer) with polyclonal antibody incubation (40 min) appeared as best practice. The BIFQUIT trial results indicated that C4d staining on paraffin sections varies considerably between laboratories. Refinement of the current Banff C4d scoring schema and harmonization of tissue processing and staining protocols is necessary to achieve acceptable reproducibility. © Copyright 2013 The American Society of Transplantation and the American Society of Transplant Surgeons.

Acquisition of reproducible transmission near-infrared (NIR) spectra of solid samples with inconsistent shapes by irradiation with isotropically diffused radiation using polytetrafluoroethylene (PTFE) beads.

Science.gov (United States)

Lee, Jinah; Duy, Pham Khac; Yoon, Jihye; Chung, Hoeil

2014-06-21

A bead-incorporated transmission scheme (BITS) has been demonstrated for collecting reproducible transmission near-infrared (NIR) spectra of samples with inconsistent shapes. Isotropically diffused NIR radiation was applied around a sample and the surrounding radiation was allowed to interact homogeneously with the sample for transmission measurement. Samples were packed in 1.40 mm polytetrafluoroethylene (PTFE) beads, ideal diffusers without NIR absorption, and then transmission spectra were collected by illuminating the sample-containing beads using NIR radiation. When collimated radiation was directly applied, a small portion of the non-fully diffused radiation (NFDR) propagated through the void space of the packing and eventually degraded the reproducibility. Pre-diffused radiation was introduced by placing an additional PTFE disk in front of the packing to diminish NFDR, which produced more reproducible spectral features. The proposed scheme was evaluated by analyzing two different solid samples: density determination for individual polyethylene (PE) pellets and identification of mining locality for tourmalines. Because spectral collection was reproducible, the use of the spectrum acquired from one PE pellet was sufficient to accurately determine the density of nine other pellets with different shapes. The differentiation of tourmalines, which are even more dissimilar in appearance, according to their mining locality was also feasible with the help of the scheme.

Repeat: a framework to assess empirical reproducibility in biomedical research

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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.

Serous tubal intraepithelial carcinoma: diagnostic reproducibility and its implications.

Science.gov (United States)

Carlson, Joseph W; Jarboe, Elke A; Kindelberger, David; Nucci, Marisa R; Hirsch, Michelle S; Crum, Christopher P

2010-07-01

Serous tubal intraepithelial carcinoma (STIC) is detected in between 5% and 7% of women undergoing risk-reduction salpingooophorectomy for mutations in the BRCA1 or 2 genes (BRCA+), and seems to play a role in the pathogenesis of many ovarian and "primary peritoneal" serous carcinomas. The recognition of STIC is germane to the management of BRCA+ women; however, the diagnostic reproducibility of STIC is unknown. Twenty-one cases were selected and classified as STIC or benign, using both hematoxylin and eosin and immunohistochemical stains for p53 and MIB-1. Digital images of 30 hematoxylin and eosin-stained STICs (n=14) or benign tubal epithelium (n=16) were photographed and randomized for blind digital review in a Powerpoint format by 6 experienced gynecologic pathologists and 6 pathology trainees. A generalized kappa statistic for multiple raters was calculated for all groups. For all reviewers, the kappa was 0.333, indicating poor reproducibility; kappa was 0.453 for the experienced gynecologic pathologists (fair-to-good reproducibility), and kappa=0.253 for the pathology residents (poor reproducibility). In the experienced group, 3 of 14 STICs were diagnosed by all 6 reviewers, and 9 of 14 by a majority of the reviewers. These results show that interobserver concordance in the recognition of STIC in high-quality digital images is at best fair-to-good for even experienced gynecologic pathologists, and a proportion cannot be consistently identified even among experienced observers. In view of these findings, a diagnosis of STIC should be corroborated by a second pathologist, if feasible.

Genotypic variability enhances the reproducibility of an ecological study.

Science.gov (United States)

Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron M; Blouin, Manuel; Scheu, Stefan; Freschet, Grégoire T; Rose, Laura; Barot, Sebastien; Cesarz, Simone; Eisenhauer, Nico; Girin, Thomas; Assandri, Davide; Bonkowski, Michael; Buchmann, Nina; Butenschoen, Olaf; Devidal, Sebastien; Gleixner, Gerd; Gessler, Arthur; Gigon, Agnès; Greiner, Anna; Grignani, Carlo; Hansart, Amandine; Kayler, Zachary; Lange, Markus; Lata, Jean-Christophe; Le Galliard, Jean-François; Lukac, Martin; Mannerheim, Neringa; Müller, Marina E H; Pando, Anne; Rotter, Paula; Scherer-Lorenzen, Michael; Seyhun, Rahme; Urban-Mead, Katherine; Weigelt, Alexandra; Zavattaro, Laura; Roy, Jacques

2018-02-01

Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

The Economics of Reproducibility in Preclinical Research.

Directory of Open Access Journals (Sweden)

Leonard P Freedman

2015-06-01

Full Text Available Low reproducibility rates within life science research undermine cumulative knowledge production and contribute to both delays and costs of therapeutic drug development. An analysis of past studies indicates that the cumulative (total prevalence of irreproducible preclinical research exceeds 50%, resulting in approximately US$28,000,000,000 (US$28B/year spent on preclinical research that is not reproducible-in the United States alone. We outline a framework for solutions and a plan for long-term improvements in reproducibility rates that will help to accelerate the discovery of life-saving therapies and cures.

Does systematic variation improve the reproducibility of animal experiments?

NARCIS (Netherlands)

Jonker, R.M.; Guenther, A.; Engqvist, L.; Schmoll, T.

2013-01-01

Reproducibility of results is a fundamental tenet of science. In this journal, Richter et al.1 tested whether systematic variation in experimental conditions (heterogenization) affects the reproducibility of results. Comparing this approach with the current standard of ensuring reproducibility

Empirical evaluation of cross-site reproducibility in radiomic features for characterizing prostate MRI

Science.gov (United States)

Chirra, Prathyush; Leo, Patrick; Yim, Michael; Bloch, B. Nicolas; Rastinehad, Ardeshir R.; Purysko, Andrei; Rosen, Mark; Madabhushi, Anant; Viswanath, Satish

2018-02-01

The recent advent of radiomics has enabled the development of prognostic and predictive tools which use routine imaging, but a key question that still remains is how reproducible these features may be across multiple sites and scanners. This is especially relevant in the context of MRI data, where signal intensity values lack tissue specific, quantitative meaning, as well as being dependent on acquisition parameters (magnetic field strength, image resolution, type of receiver coil). In this paper we present the first empirical study of the reproducibility of 5 different radiomic feature families in a multi-site setting; specifically, for characterizing prostate MRI appearance. Our cohort comprised 147 patient T2w MRI datasets from 4 different sites, all of which were first pre-processed to correct acquisition-related for artifacts such as bias field, differing voxel resolutions, as well as intensity drift (non-standardness). 406 3D voxel wise radiomic features were extracted and evaluated in a cross-site setting to determine how reproducible they were within a relatively homogeneous non-tumor tissue region; using 2 different measures of reproducibility: Multivariate Coefficient of Variation and Instability Score. Our results demonstrated that Haralick features were most reproducible between all 4 sites. By comparison, Laws features were among the least reproducible between sites, as well as performing highly variably across their entire parameter space. Similarly, the Gabor feature family demonstrated good cross-site reproducibility, but for certain parameter combinations alone. These trends indicate that despite extensive pre-processing, only a subset of radiomic features and associated parameters may be reproducible enough for use within radiomics-based machine learning classifier schemes.

Reproducible segmentation of white matter hyperintensities using a new statistical definition.

Science.gov (United States)

Damangir, Soheil; Westman, Eric; Simmons, Andrew; Vrenken, Hugo; Wahlund, Lars-Olof; Spulber, Gabriela

2017-06-01

We present a method based on a proposed statistical definition of white matter hyperintensities (WMH), which can work with any combination of conventional magnetic resonance (MR) sequences without depending on manually delineated samples. T1-weighted, T2-weighted, FLAIR, and PD sequences acquired at 1.5 Tesla from 119 subjects from the Kings Health Partners-Dementia Case Register (healthy controls, mild cognitive impairment, Alzheimer's disease) were used. The segmentation was performed using a proposed definition for WMH based on the one-tailed Kolmogorov-Smirnov test. The presented method was verified, given all possible combinations of input sequences, against manual segmentations and a high similarity (Dice 0.85-0.91) was observed. Comparing segmentations with different input sequences to one another also yielded a high similarity (Dice 0.83-0.94) that exceeded intra-rater similarity (Dice 0.75-0.91). We compared the results with those of other available methods and showed that the segmentation based on the proposed definition has better accuracy and reproducibility in the test dataset used. Overall, the presented definition is shown to produce accurate results with higher reproducibility than manual delineation. This approach can be an alternative to other manual or automatic methods not only because of its accuracy, but also due to its good reproducibility.

Reproducibility and validity of the Shanghai Men's Health Study physical activity questionnaire.

Science.gov (United States)

Jurj, Adriana L; Wen, Wanqing; Xiang, Yong-Bing; Matthews, Charles E; Liu, Dake; Zheng, Wei; Shu, Xiao-Ou

2007-05-15

Reproducibility and validity of the physical activity questionnaire (PAQ) used in the Shanghai Men's Health Study (2003-2006, People's Republic of China) was evaluated in a random sample of 196 participants aged 40-74 years. Participants completed a PAQ at baseline and again 1 year later, 12 monthly 7-day physical activity recalls, and four quarterly 1-week physical activity logs. Reproducibility was evaluated by using the two PAQs and validity by comparing the PAQs with 1-year averages of the two criterion measures: 7-day physical activity recall and physical activity log. The PAQ had moderate to high reproducibility for measuring adult exercise participation (kappa = 0.60) and energy expenditure (r(s) = 0.68), nonexercise activities (correlation coefficients = 0.42-0.68), and total daily energy expenditure (r(s) = 0.68, kappa(quartiles) = 0.47). Correlations between the PAQ and criterion measures of adult exercise were 0.45 (7-day physical activity recall) and 0.51 (physical activity log) for the first PAQ and 0.62 (7-day physical activity recall) and 0.71 (physical activity log) for the second PAQ. Correlations between PAQ nonexercise activities and the physical activity log and 7-day physical activity recall were 0.31-0.86. Correlations for total energy expenditure were high (0.62-0.77). Results indicate that the Shanghai Men's Health Study PAQ has reasonable reproducibility and validity for classifying men by their level of exercise and nonexercise activities in this cohort.

Characteristics of crosstalk in the reproduced output of a newly developed multi-channel MR head

International Nuclear Information System (INIS)

Machida, K.; Hayashi, N.; Yoneda, Y.; Numazawa, J.; Kohro, M.; Tanabe, T.

2001-01-01

We prepared the multi-channel magnetoresistive head with a simple structural design and it has the advantages of high-density recording and ultra-high transfer rate. Characteristics of crosstalk in the reproduced output of our head have been estimated by a micromagnetic calculation using the Landau-Lifshitz-Gilbert (LLG) equation, while the specimen head was fabricated and evaluated. As a result, by applying a magnetic field of 40 Oe only between adjacent channels, the crosstalk was much decreased without reducing the reproduced output

Exploring the Coming Repositories of Reproducible Experiments: Challenges and Opportunities

DEFF Research Database (Denmark)

Freire, Juliana; Bonnet, Philippe; Shasha, Dennis

2011-01-01

Computational reproducibility efforts in many communities will soon give rise to validated software and data repositories of high quality. A scientist in a field may want to query the components of such repositories to build new software workflows, perhaps after adding the scientist’s own algorithms...

Learning Reproducibility with a Yearly Networking Contest

KAUST Repository

Canini, Marco

2017-08-10

Better reproducibility of networking research results is currently a major goal that the academic community is striving towards. This position paper makes the case that improving the extent and pervasiveness of reproducible research can be greatly fostered by organizing a yearly international contest. We argue that holding a contest undertaken by a plurality of students will have benefits that are two-fold. First, it will promote hands-on learning of skills that are helpful in producing artifacts at the replicable-research level. Second, it will advance the best practices regarding environments, testbeds, and tools that will aid the tasks of reproducibility evaluation committees by and large.

Thou Shalt Be Reproducible! A Technology Perspective

Directory of Open Access Journals (Sweden)

Patrick Mair

2016-07-01

Full Text Available This article elaborates on reproducibility in psychology from a technological viewpoint. Modernopen source computational environments are shown and explained that foster reproducibilitythroughout the whole research life cycle, and to which emerging psychology researchers shouldbe sensitized, are shown and explained. First, data archiving platforms that make datasets publiclyavailable are presented. Second, R is advocated as the data-analytic lingua franca in psychologyfor achieving reproducible statistical analysis. Third, dynamic report generation environments forwriting reproducible manuscripts that integrate text, data analysis, and statistical outputs such asfigures and tables in a single document are described. Supplementary materials are provided inorder to get the reader started with these technologies.

Reproducible research in palaeomagnetism

Science.gov (United States)

Lurcock, Pontus; Florindo, Fabio

2015-04-01

The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined

High-resolution 3D coronary vessel wall imaging with near 100% respiratory efficiency using epicardial fat tracking: reproducibility and comparison with standard methods.

Science.gov (United States)

Scott, Andrew D; Keegan, Jennifer; Firmin, David N

2011-01-01

To quantitatively assess the performance and reproducibility of 3D spiral coronary artery wall imaging with beat-to-beat respiratory-motion-correction (B2B-RMC) compared to navigator gated 2D spiral and turbo-spin-echo (TSE) acquisitions. High-resolution (0.7 × 0.7 mm) cross-sectional right coronary wall acquisitions were performed in 10 subjects using four techniques (B2B-RMC 3D spiral with alternate (2RR) and single (1RR) R-wave gating, navigator-gated 2D spiral (2RR) and navigator-gated 2D TSE (2RR)) on two occasions. Wall thickness measurements were compared with repeated measures analysis of variance (ANOVA). Reproducibility was assessed with the intraclass correlation coefficient (ICC). In all, 91% (73/80) of acquisitions were successful (failures: four TSE, two 3D spiral (1RR) and one 3D spiral (2RR)). Respiratory efficiency of the B2B-RMC was less variable and substantially higher than for navigator gating (99.6 ± 1.2% vs. 39.0 ± 7.5%, P B2B-RMC permits coronary vessel wall assessment over multiple thin contiguous slices in a clinically feasible duration. Excellent reproducibility of the technique potentially enables studies of disease progression/regression. Copyright © 2010 Wiley-Liss, Inc.

Reproducibility and relative validity of food group intake in a food frequency questionnaire developed for Nepalese diet.

Science.gov (United States)

Shrestha, Archana; Koju, Rajendra Prasad; Beresford, Shirley A A; Chan, Kwun Chuen Gary; Connell, Frederik A; Karmacharya, Biraj Man; Shrestha, Pramita; Fitzpatrick, Annette L

2017-08-01

We developed a food frequency questionnaire (FFQ) designed to measure the dietary practices of adult Nepalese. The present study examined the validity and reproducibility of the FFQ. To evaluate the reproducibility of the FFQ, 116 subjects completed two 115-item FFQ across a four-month interval. Six 24-h dietary recalls were collected (1 each month) to assess the validity of the FFQ. Seven major food groups and 23 subgroups were clustered from the FFQ based on macronutrient composition. Spearman correlation coefficients evaluating reproducibility for all food groups were greater than 0.5, with the exceptions of oil. The correlations varied from 0.41 (oil) to 0.81 (vegetables). All crude spearman coefficients for validity were greater than 0.5 except for dairy products, pizzas/pastas and sausage/burgers. The FFQ was found to be reliable and valid for ranking the intake of food groups for Nepalese dietary intake.

Reproducibility of subgingival bacterial samples from patients with peri-implant mucositis

DEFF Research Database (Denmark)

Hallström, Hadar; Persson, G Rutger; Strömberg, Ulf

2015-01-01

collected with paper points and analyzed using the checkerboard DNA-DNA hybridization technique. Whole genomic probes of 74 preselected bacterial species were used. Based on the bacterial scores, Cohen's kappa coefficient was used to calculate the inter-annotator agreement for categorical data......OBJECTIVE: The aim of the present study was to investigate the reproducibility of bacterial enumeration from subsequent subgingival samples collected from patients with peri-implant mucositis. MATERIAL AND METHODS: Duplicate microbial samples from 222 unique implant sites in 45 adult subjects were....... The percentage agreement was considered as "good" when the two samples showed the same score or differed by 1 to the power of 10. RESULTS: Moderate to fair kappa values were displayed for all bacterial species in the test panel (range 0.21-0.58). There were no significant differences between Gram...

Reproducibility of ultrasonic testing

International Nuclear Information System (INIS)

Lecomte, J.-C.; Thomas, Andre; Launay, J.-P.; Martin, Pierre

The reproducibility of amplitude quotations for both artificial and natural reflectors was studied for several combinations of instrument/search unit, all being of the same type. This study shows that in industrial inspection if a range of standardized equipment is used, a margin of error of about 6 decibels has to be taken into account (confidence interval of 95%). This margin is about 4 to 5 dB for natural or artificial defects located in the central area and about 6 to 7 dB for artificial defects located on the back surface. This lack of reproducibility seems to be attributable first to the search unit and then to the instrument and operator. These results were confirmed by analysis of calibration data obtained from 250 tests performed by 25 operators under shop conditions. The margin of error was higher than the 6 dB obtained in the study [fr

Highly sensitive, reproducible and stable SERS substrate based on reduced graphene oxide/silver nanoparticles coated weighing paper

Energy Technology Data Exchange (ETDEWEB)

Xiao, Guina, E-mail: xiaoguina@shnu.edu.cn; Li, Yunxiang; Shi, Wangzhou; Shen, Leo; Chen, Qi; Huang, Lei, E-mail: leihuang@shnu.edu.cn

2017-05-15

Highlights: • We developed a paper-based SERS substrate by gravure and inkjet printing methods. • The S-RGO/AgNPs comoposite structure had higher SERS activity than the pure AgNPs. • The Raman enhancement factor of S-RGO/AgNPs substrate was calculated to be 10{sup 9}. • The paper-based substrate exhibited good reproducibility and long-term stability. - Abstract: Paper-based surface-enhanced Raman scattering (SERS) substrates receive a great deal of attention due to low cost and high flexibility. Herein, we developed an efficient SERS substrate by gravure printing of sulfonated reduced graphene-oxide (S-RGO) thin film and inkjet printing of silver nanoparticles (AgNPs) on weighing paper successively. Malachite green (MG) and rhodamine 6G (R6G) were chosen as probe molecules to evaluate the enhanced performance of the fabricated SERS-active substrates. It was found that the S-RGO/AgNPs composite structure possessed higher enhancement ability than the pure AgNPs. The Raman enhancement factor of S-RGO/AgNPs was calculated to be as large as 10{sup 9}. The minimum detection limit for MG and R6G was down to 10{sup −7} M with good linear responses (R{sup 2} = 0.9996, 0.9983) range from 10{sup −4} M to 10{sup −7} M. In addition, the S-RGO/AgNPs exhibited good uniformity with a relative standard deviation (RSD) of 7.90% measured by 572 points, excellent reproducibility with RSD smaller than 3.36%, and long-term stability with RSD less than 7.19%.

On the solutions of electrohydrodynamic flow with fractional differential equations by reproducing kernel method

Directory of Open Access Journals (Sweden)

Akgül Ali

2016-01-01

Full Text Available In this manuscript we investigate electrodynamic flow. For several values of the intimate parameters we proved that the approximate solution depends on a reproducing kernel model. Obtained results prove that the reproducing kernel method (RKM is very effective. We obtain good results without any transformation or discretization. Numerical experiments on test examples show that our proposed schemes are of high accuracy and strongly support the theoretical results.

High Reproducibility of ELISPOT Counts from Nine Different Laboratories

Directory of Open Access Journals (Sweden)

Srividya Sundararaman

2015-01-01

Full Text Available The primary goal of immune monitoring with ELISPOT is to measure the number of T cells, specific for any antigen, accurately and reproducibly between different laboratories. In ELISPOT assays, antigen-specific T cells secrete cytokines, forming spots of different sizes on a membrane with variable background intensities. Due to the subjective nature of judging maximal and minimal spot sizes, different investigators come up with different numbers. This study aims to determine whether statistics-based, automated size-gating can harmonize the number of spot counts calculated between different laboratories. We plated PBMC at four different concentrations, 24 replicates each, in an IFN-γ ELISPOT assay with HCMV pp65 antigen. The ELISPOT plate, and an image file of the plate was counted in nine different laboratories using ImmunoSpot® Analyzers by (A Basic Count™ relying on subjective counting parameters set by the respective investigators and (B SmartCount™, an automated counting protocol by the ImmunoSpot® Software that uses statistics-based spot size auto-gating with spot intensity auto-thresholding. The average coefficient of variation (CV for the mean values between independent laboratories was 26.7% when counting with Basic Count™, and 6.7% when counting with SmartCount™. Our data indicates that SmartCount™ allows harmonization of counting ELISPOT results between different laboratories and investigators.

Hexamethylenetetramine-mediated growth of grain-boundary-passivation CH3NH3PbI3 for highly reproducible and stable perovskite solar cells

Science.gov (United States)

Zheng, Yan-Zhen; Li, Xi-Tao; Zhao, Er-Fei; Lv, Xin-Ding; Meng, Fan-Li; Peng, Chao; Lai, Xue-Sen; Huang, Meilan; Cao, Guozhong; Tao, Xia; Chen, Jian-Feng

2018-02-01

Simultaneously achieving the long-term device stability and reproducibility has proven challenging in perovskite solar cells because solution-processing produced perovskite film with grain boundary is sensitive to moisture. Herein, we develop a hexamethylenetetramine (HMTA)-mediated one-step solution-processing deposition strategy that leads to the formation of high-purity and grain-boundary-passivation CH3NH3PbI3 film and thereby advances cell optoelectronic performance. Through morphological and structural characterizations and theoretical calculations, we demonstrate that HMTA fully occupies the moisture-exposed surface to build a bridge across grain boundary and coordinates with Pb ions to inhibit the formation of detrimental PbI2. Such HMTA-mediated grown CH3NH3PbI3 films achieves a decent augmentation of power conversion efficiency (PCE) from 12.70% to 17.87%. A full coverage of PbI2-free CH3NH3PbI3 surface on ZnO also boosts the device's stability and reproducibility.

Preserve specimens for reproducibility

Czech Academy of Sciences Publication Activity Database

Krell, F.-T.; Klimeš, Petr; Rocha, L. A.; Fikáček, M.; Miller, S. E.

2016-01-01

Roč. 539, č. 7628 (2016), s. 168 ISSN 0028-0836 Institutional support: RVO:60077344 Keywords : reproducibility * specimen * biodiversity Subject RIV: EH - Ecology, Behaviour Impact factor: 40.137, year: 2016 http://www.nature.com/nature/journal/v539/n7628/full/539168b.html

A multiparametric automatic method to monitor long-term reproducibility in digital mammography: results from a regional screening programme.

Science.gov (United States)

Gennaro, G; Ballaminut, A; Contento, G

2017-09-01

This study aims to illustrate a multiparametric automatic method for monitoring long-term reproducibility of digital mammography systems, and its application on a large scale. Twenty-five digital mammography systems employed within a regional screening programme were controlled weekly using the same type of phantom, whose images were analysed by an automatic software tool. To assess system reproducibility levels, 15 image quality indices (IQIs) were extracted and compared with the corresponding indices previously determined by a baseline procedure. The coefficients of variation (COVs) of the IQIs were used to assess the overall variability. A total of 2553 phantom images were collected from the 25 digital mammography systems from March 2013 to December 2014. Most of the systems showed excellent image quality reproducibility over the surveillance interval, with mean variability below 5%. Variability of each IQI was 5%, with the exception of one index associated with the smallest phantom objects (0.25 mm), which was below 10%. The method applied for reproducibility tests-multi-detail phantoms, cloud automatic software tool to measure multiple image quality indices and statistical process control-was proven to be effective and applicable on a large scale and to any type of digital mammography system. • Reproducibility of mammography image quality should be monitored by appropriate quality controls. • Use of automatic software tools allows image quality evaluation by multiple indices. • System reproducibility can be assessed comparing current index value with baseline data. • Overall system reproducibility of modern digital mammography systems is excellent. • The method proposed and applied is cost-effective and easily scalable.

Reproducibility of 201Tl myocardial imaging

International Nuclear Information System (INIS)

McLaughlin, P.R.; Martin, R.P.; Doherty, P.; Daspit, S.; Goris, M.; Haskell, W.; Lewis, S.; Kriss, J.P.; Harrison, D.C.

1977-01-01

Seventy-six thallium-201 myocardial perfusion studies were performed on twenty-five patients to assess their reproducibility and the effect of varying the level of exercise on the results of imaging. Each patient had a thallium-201 study at rest. Fourteen patients had studies on two occasions at maximum exercise, and twelve patients had studies both at light and at maximum exercise. Of 70 segments in the 14 patients assessed on each of two maximum exercise tests, 64 (91 percent) were reproducible. Only 53 percent (16/30) of the ischemic defects present at maximum exercise were seen in the light exercise study in the 12 patients assessed at two levels of exercise. Correlation of perfusion defects with arteriographically proven significant coronary stenosis was good for the left anterior descending and right coronary arteries, but not as good for circumflex artery disease. Thallium-201 myocardial imaging at maximum exercise is reproducible within acceptable limits, but careful attention to exercise technique is essential for valid comparative studies

Undefined cellulase formulations hinder scientific reproducibility.

Science.gov (United States)

Himmel, Michael E; Abbas, Charles A; Baker, John O; Bayer, Edward A; Bomble, Yannick J; Brunecky, Roman; Chen, Xiaowen; Felby, Claus; Jeoh, Tina; Kumar, Rajeev; McCleary, Barry V; Pletschke, Brett I; Tucker, Melvin P; Wyman, Charles E; Decker, Stephen R

2017-01-01

In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparations may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.

On the origin of reproducible sequential activity in neural circuits

Science.gov (United States)

Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.

2004-12-01

Robustness and reproducibility of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of reproducible transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and reproducible sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.

The Harm Done to Reproducibility by the Culture of Null Hypothesis Significance Testing.

Science.gov (United States)

Lash, Timothy L

2017-09-15

In the last few years, stakeholders in the scientific community have raised alarms about a perceived lack of reproducibility of scientific results. In reaction, guidelines for journals have been promulgated and grant applicants have been asked to address the rigor and reproducibility of their proposed projects. Neither solution addresses a primary culprit, which is the culture of null hypothesis significance testing that dominates statistical analysis and inference. In an innovative research enterprise, selection of results for further evaluation based on null hypothesis significance testing is doomed to yield a low proportion of reproducible results and a high proportion of effects that are initially overestimated. In addition, the culture of null hypothesis significance testing discourages quantitative adjustments to account for systematic errors and quantitative incorporation of prior information. These strategies would otherwise improve reproducibility and have not been previously proposed in the widely cited literature on this topic. Without discarding the culture of null hypothesis significance testing and implementing these alternative methods for statistical analysis and inference, all other strategies for improving reproducibility will yield marginal gains at best. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Inter-Scan Reproducibility of Carotid Plaque Volume Measurements by 3-D Ultrasound

DEFF Research Database (Denmark)

Sandholt, Benjamin V; Collet-Billon, Antoine; Entrekin, Robert

2018-01-01

(PPV) measure centered on MPT. Total plaque volume (TPV), PPV from a 10-mm segment and MPT were measured using dedicated semi-automated software on 38 plaques from 26 patients. Inter-scan reproducibility was assessed using the t-test, Bland-Altman plots and Pearson's correlation coefficient....... There was a mean difference of 0.01 mm in MPT (limits of agreement: -0.45 to 0.42 mm, Pearson's correlation coefficient: 0.96). Both volume measurements exhibited high reproducibility, with PPV being superior (limits of agreement: -35.3 mm3to 33.5 mm3, Pearson's correlation coefficient: 0.96) to TPV (limits...... of agreement: -88.2 to 61.5 mm3, Pearson's correlation coefficient: 0.91). The good reproducibility revealed by the present results encourages future studies on establishing plaque quantification as part of cardiovascular risk assessment and for follow-up of disease progression over time....

Reproducible statistical analysis with multiple languages

DEFF Research Database (Denmark)

Lenth, Russell; Højsgaard, Søren

2011-01-01

This paper describes the system for making reproducible statistical analyses. differs from other systems for reproducible analysis in several ways. The two main differences are: (1) Several statistics programs can be in used in the same document. (2) Documents can be prepared using OpenOffice or ......Office or \\LaTeX. The main part of this paper is an example showing how to use and together in an OpenOffice text document. The paper also contains some practical considerations on the use of literate programming in statistics....

Towards Reproducibility in Computational Hydrology

Science.gov (United States)

Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

2017-04-01

Reproducibility is a foundational principle in scientific research. The ability to independently re-run an experiment helps to verify the legitimacy of individual findings, and evolve (or reject) hypotheses and models of how environmental systems function, and move them from specific circumstances to more general theory. Yet in computational hydrology (and in environmental science more widely) the code and data that produces published results are not regularly made available, and even if they are made available, there remains a multitude of generally unreported choices that an individual scientist may have made that impact the study result. This situation strongly inhibits the ability of our community to reproduce and verify previous findings, as all the information and boundary conditions required to set up a computational experiment simply cannot be reported in an article's text alone. In Hutton et al 2016 [1], we argue that a cultural change is required in the computational hydrological community, in order to advance and make more robust the process of knowledge creation and hypothesis testing. We need to adopt common standards and infrastructures to: (1) make code readable and re-useable; (2) create well-documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; (3) make code and workflows available, easy to find, and easy to interpret, using code and code metadata repositories. To create change we argue for improved graduate training in these areas. In this talk we reflect on our progress in achieving reproducible, open science in computational hydrology, which are relevant to the broader computational geoscience community. In particular, we draw on our experience in the Switch-On (EU funded) virtual water science laboratory (http://www.switch-on-vwsl.eu/participate/), which is an open platform for collaboration in hydrological experiments (e.g. [2]). While we use computational hydrology as

Reproducibility of Computer-Aided Detection Marks in Digital Mammography

International Nuclear Information System (INIS)

Kim, Seung Ja; Moon, Woo Kyung; Cho, Nariya; Kim, Sun Mi; Im, Jung Gi; Cha, Joo Hee

2007-01-01

To evaluate the performance and reproducibility of a computeraided detection (CAD) system in mediolateral oblique (MLO) digital mammograms taken serially, without release of breast compression. A CAD system was applied preoperatively to the fulfilled digital mammograms of two MLO views taken without release of breast compression in 82 patients (age range: 33 83 years; mean age: 49 years) with previously diagnosed breast cancers. The total number of visible lesion components in 82 patients was 101: 66 masses and 35 microcalcifications. We analyzed the sensitivity and reproducibility of the CAD marks. The sensitivity of the CAD system for first MLO views was 71% (47/66) for masses and 80% (28/35) for microcalcifications. The sensitivity of the CAD system for second MLO views was 68% (45/66) for masses and 17% (6/35) for microcalcifications. In 84 ipsilateral serial MLO image sets (two patients had bilateral cancers), identical images, regardless of the existence of CAD marks, were obtained for 35% (29/84) and identical images with CAD marks were obtained for 29% (23/78). Identical images, regardless of the existence of CAD marks, for contralateral MLO images were 65% (52/80) and identical images with CAD marks were obtained for 28% (11/39). The reproducibility of CAD marks for the true positive masses in serial MLO views was 84% (42/50) and that for the true positive microcalcifications was 0% (0/34). The CAD system in digital mammograms showed a high sensitivity for detecting masses and microcalcifications. However, reproducibility of microcalcification marks was very low in MLO views taken serially without release of breast compression. Minute positional change and patient movement can alter the images and result in a significant effect on the algorithm utilized by the CAD for detecting microcalcifications

A reproducible brain tumour model established from human glioblastoma biopsies

International Nuclear Information System (INIS)

Wang, Jian; Chekenya, Martha; Bjerkvig, Rolf; Enger, Per Ø; Miletic, Hrvoje; Sakariassen, Per Ø; Huszthy, Peter C; Jacobsen, Hege; Brekkå, Narve; Li, Xingang; Zhao, Peng; Mørk, Sverre

2009-01-01

Establishing clinically relevant animal models of glioblastoma multiforme (GBM) remains a challenge, and many commonly used cell line-based models do not recapitulate the invasive growth patterns of patient GBMs. Previously, we have reported the formation of highly invasive tumour xenografts in nude rats from human GBMs. However, implementing tumour models based on primary tissue requires that these models can be sufficiently standardised with consistently high take rates. In this work, we collected data on growth kinetics from a material of 29 biopsies xenografted in nude rats, and characterised this model with an emphasis on neuropathological and radiological features. The tumour take rate for xenografted GBM biopsies were 96% and remained close to 100% at subsequent passages in vivo, whereas only one of four lower grade tumours engrafted. Average time from transplantation to the onset of symptoms was 125 days ± 11.5 SEM. Histologically, the primary xenografts recapitulated the invasive features of the parent tumours while endothelial cell proliferations and necrosis were mostly absent. After 4-5 in vivo passages, the tumours became more vascular with necrotic areas, but also appeared more circumscribed. MRI typically revealed changes related to tumour growth, several months prior to the onset of symptoms. In vivo passaging of patient GBM biopsies produced tumours representative of the patient tumours, with high take rates and a reproducible disease course. The model provides combinations of angiogenic and invasive phenotypes and represents a good alternative to in vitro propagated cell lines for dissecting mechanisms of brain tumour progression

A reproducible brain tumour model established from human glioblastoma biopsies

Directory of Open Access Journals (Sweden)

Li Xingang

2009-12-01

Full Text Available Abstract Background Establishing clinically relevant animal models of glioblastoma multiforme (GBM remains a challenge, and many commonly used cell line-based models do not recapitulate the invasive growth patterns of patient GBMs. Previously, we have reported the formation of highly invasive tumour xenografts in nude rats from human GBMs. However, implementing tumour models based on primary tissue requires that these models can be sufficiently standardised with consistently high take rates. Methods In this work, we collected data on growth kinetics from a material of 29 biopsies xenografted in nude rats, and characterised this model with an emphasis on neuropathological and radiological features. Results The tumour take rate for xenografted GBM biopsies were 96% and remained close to 100% at subsequent passages in vivo, whereas only one of four lower grade tumours engrafted. Average time from transplantation to the onset of symptoms was 125 days ± 11.5 SEM. Histologically, the primary xenografts recapitulated the invasive features of the parent tumours while endothelial cell proliferations and necrosis were mostly absent. After 4-5 in vivo passages, the tumours became more vascular with necrotic areas, but also appeared more circumscribed. MRI typically revealed changes related to tumour growth, several months prior to the onset of symptoms. Conclusions In vivo passaging of patient GBM biopsies produced tumours representative of the patient tumours, with high take rates and a reproducible disease course. The model provides combinations of angiogenic and invasive phenotypes and represents a good alternative to in vitro propagated cell lines for dissecting mechanisms of brain tumour progression.

High-resolution morphological and biochemical imaging of articular cartilage of the ankle joint at 3.0 T using a new dedicated phased array coil: in vivo reproducibility study

International Nuclear Information System (INIS)

Welsch, Goetz H.; Trattnig, Siegfried; Mamisch, Tallal C.; Weber, Michael; Horger, Wilhelm; Bohndorf, Klaus

2008-01-01

The objective of this study was to evaluate the feasibility and reproducibility of high-resolution magnetic resonance imaging (MRI) and quantitative T2 mapping of the talocrural cartilage within a clinically applicable scan time using a new dedicated ankle coil and high-field MRI. Ten healthy volunteers (mean age 32.4 years) underwent MRI of the ankle. As morphological sequences, proton density fat-suppressed turbo spin echo (PD-FS-TSE), as a reference, was compared with 3D true fast imaging with steady-state precession (TrueFISP). Furthermore, biochemical quantitative T2 imaging was prepared using a multi-echo spin-echo T2 approach. Data analysis was performed three times each by three different observers on sagittal slices, planned on the isotropic 3D-TrueFISP; as a morphological parameter, cartilage thickness was assessed and for T2 relaxation times, region-of-interest (ROI) evaluation was done. Reproducibility was determined as a coefficient of variation (CV) for each volunteer; averaged as root mean square (RMSA) given as a percentage; statistical evaluation was done using analysis of variance. Cartilage thickness of the talocrural joint showed significantly higher values for the 3D-TrueFISP (ranging from 1.07 to 1.14 mm) compared with the PD-FS-TSE (ranging from 0.74 to 0.99 mm); however, both morphological sequences showed comparable good results with RMSA of 7.1 to 8.5%. Regarding quantitative T2 mapping, measurements showed T2 relaxation times of about 54 ms with an excellent reproducibility (RMSA) ranging from 3.2 to 4.7%. In our study the assessment of cartilage thickness and T2 relaxation times could be performed with high reproducibility in a clinically realizable scan time, demonstrating new possibilities for further investigations into patient groups. (orig.)

Reproducibility of a reaming test

DEFF Research Database (Denmark)

Pilny, Lukas; Müller, Pavel; De Chiffre, Leonardo

2012-01-01

The reproducibility of a reaming test was analysed to document its applicability as a performance test for cutting fluids. Reaming tests were carried out on a drilling machine using HSS reamers. Workpiece material was an austenitic stainless steel, machined using 4.75 m∙min-1 cutting speed and 0......). Process reproducibility was assessed as the ability of different operators to ensure a consistent rating of individual lubricants. Absolute average values as well as experimental standard deviations of the evaluation parameters were calculated, and uncertainty budgeting was performed. Results document...... a built-up edge occurrence hindering a robust evaluation of cutting fluid performance, if the data evaluation is based on surface finish only. Measurements of hole geometry provide documentation to recognize systematic error distorting the performance test....

Reproducibility of a reaming test

DEFF Research Database (Denmark)

Pilny, Lukas; Müller, Pavel; De Chiffre, Leonardo

2014-01-01

The reproducibility of a reaming test was analysed to document its applicability as a performance test for cutting fluids. Reaming tests were carried out on a drilling machine using HSS reamers. Workpiece material was an austenitic stainless steel, machined using 4.75 m•min−1 cutting speed and 0......). Process reproducibility was assessed as the ability of different operators to ensure a consistent rating of individual lubricants. Absolute average values as well as experimental standard deviations of the evaluation parameters were calculated, and uncertainty budgeting was performed. Results document...... a built–up edge occurrence hindering a robust evaluation of cutting fluid performance, if the data evaluation is based on surface finish only. Measurements of hole geometry provide documentation to recognise systematic error distorting the performance test....

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE

Science.gov (United States)

Cohen, K. Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E.

2018-01-01

There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication—an average of once a day per library. PMID:29568821

Assessment of precision and reproducibility of a new myograph

Directory of Open Access Journals (Sweden)

Piepenbrock Siegfried

2007-12-01

Full Text Available Abstract Background The physiological characteristics of muscle activity and the assessment of muscle strength represent important diagnostic information. There are many devices that measure muscle force in humans, but some require voluntary contractions, which are difficult to assess in weak or unconscious patients who are unable to complete a full range of voluntary force assessment tasks. Other devices, which obtain standard muscle contractions by electric stimulations, do not have the technology required to induce and measure reproducible valid contractions at the optimum muscle length. Methods In our study we used a newly developed diagnostic device which measures accurately the reproducibility and time-changed-variability of the muscle force in an individual muscle. A total of 500 in-vivo measurements of supra-maximal isometric single twitch contractions were carried out on the musculus adductor pollicis of 5 test subjects over 10 sessions, with ten repetitions per session. The same protocol was performed on 405 test subjects with two repetitions each to determine a reference-interval on healthy subjects. Results Using our test setting, we found a high reproducibility of the muscle contractions of each test subject. The precision of the measurements performed with our device was 98.74%. Only two consecutive measurements are needed in order to assess a real, representative individual value of muscle force. The mean value of the force of contraction was 9.51 N and the 95% reference interval was 4.77–14.25 N. Conclusion The new myograph is a highly reliable measuring device with which the adductor pollicis can be investigated at the optimum length. It has the potential to become a reliable and valid tool for diagnostic in the clinical setting and for monitoring neuromuscular diseases.

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

Science.gov (United States)

Beccuti, Marco; Cordero, Francesca; Arigoni, Maddalena; Panero, Riccardo; Amparore, Elvio G; Donatelli, Susanna; Calogero, Raffaele A

2018-03-01

Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with/without scripting experience. Docker container images, docker4seq package and the GUI are available at http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html. beccuti@di.unito.it. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Language-Agnostic Reproducible Data Analysis Using Literate Programming.

Science.gov (United States)

Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

2016-01-01

A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

Identification and reproducibility of dietary patterns in a Danish cohort: the Inter99 study.

Science.gov (United States)

Lau, Cathrine; Glümer, Charlotte; Toft, Ulla; Tetens, Inge; Carstensen, Bendix; Jørgensen, Torben; Borch-Johnsen, Knut

2008-05-01

We aimed to identify dietary patterns in a Danish adult population and assess the reproducibility of the dietary patterns identified. Baseline data of 3,372 women and 3,191 men (30-60 years old) from the population-based survey Inter99 was used. Food intake, assessed by a FFQ, was aggregated into thirty-four separate food groups. Dietary patterns were identified by principal component analysis. Confirmatory factor analysis and Bland Altman plots were used to assess the reproducibility of the dietary patterns identified. The Bland Altman plots were used as an alternative and new method. Two factors were retained for both women and men, which accounted for 15.1-17.4 % of the total variation. The 'Traditional' pattern was characterised by high loadings ( > or = 0.40) on paté or high-fat meat for sandwiches, mayonnaise salads, red meat, potatoes, butter and lard, low-fat fish, low-fat meat for sandwiches, and sauces. The 'Modern' pattern was characterised by high loadings on vegetables, fruit, mixed vegetable dishes, vegetable oil and vinegar dressing, poultry, and pasta, rice and wheat kernels. Small differences were observed between patterns identified for women and men. The root mean square error approximation from the confirmatory factor analysis was 0.08. The variation observed from the Bland Altman plots of factors from explorative v. confirmative analyses and explorative analyses from two sub-samples was between 18.8 and 47.7 %. Pearson's correlation was >0.89 (P < 0.0001). The reproducibility was better for women than for men. We conclude that the 'Traditional' and 'Modern' dietary patterns identified were reproducible.

Reproducibility of data-driven dietary patterns in two groups of adult Spanish women from different studies.

Science.gov (United States)

Castelló, Adela; Lope, Virginia; Vioque, Jesús; Santamariña, Carmen; Pedraz-Pingarrón, Carmen; Abad, Soledad; Ederra, Maria; Salas-Trejo, Dolores; Vidal, Carmen; Sánchez-Contador, Carmen; Aragonés, Nuria; Pérez-Gómez, Beatriz; Pollán, Marina

2016-08-01

The objective of the present study was to assess the reproducibility of data-driven dietary patterns in different samples extracted from similar populations. Dietary patterns were extracted by applying principal component analyses to the dietary information collected from a sample of 3550 women recruited from seven screening centres belonging to the Spanish breast cancer (BC) screening network (Determinants of Mammographic Density in Spain (DDM-Spain) study). The resulting patterns were compared with three dietary patterns obtained from a previous Spanish case-control study on female BC (Epidemiological study of the Spanish group for breast cancer research (GEICAM: grupo Español de investigación en cáncer de mama)) using the dietary intake data of 973 healthy participants. The level of agreement between patterns was determined using both the congruence coefficient (CC) between the pattern loadings (considering patterns with a CC≥0·85 as fairly similar) and the linear correlation between patterns scores (considering as fairly similar those patterns with a statistically significant correlation). The conclusions reached with both methods were compared. This is the first study exploring the reproducibility of data-driven patterns from two studies and the first using the CC to determine pattern similarity. We were able to reproduce the EpiGEICAM Western pattern in the DDM-Spain sample (CC=0·90). However, the reproducibility of the Prudent (CC=0·76) and Mediterranean (CC=0·77) patterns was not as good. The linear correlation between pattern scores was statistically significant in all cases, highlighting its arbitrariness for determining pattern similarity. We conclude that the reproducibility of widely prevalent dietary patterns is better than the reproducibility of more population-specific patterns. More methodological studies are needed to establish an objective measurement and threshold to determine pattern similarity.

Beyond Bundles - Reproducible Software Environments with GNU Guix

CERN Multimedia

CERN. Geneva; Wurmus, Ricardo

2018-01-01

Building reproducible data analysis pipelines and numerical experiments is a key challenge for reproducible science, in which tools to reproduce software environments play a critical role. The advent of “container-based” deployment tools such as Docker and Singularity has made it easier to replicate software environments. These tools are very much about bundling the bits of software binaries in a convenient way, not so much about describing how software is composed. Science is not just about replicating, though—it demands the ability to inspect and to experiment. In this talk we will present GNU Guix, a software management toolkit. Guix departs from container-based solutions in that it enables declarative composition of software environments. It is comparable to “package managers” like apt or yum, but with a significant difference: Guix provides accurate provenance tracking of build artifacts, and bit-reproducible software. We will illustrate the many ways in which Guix can improve how software en...

A Changing Number of Alternative States in the Boreal Biome: Reproducibility Risks of Replacing Remote Sensing Products.

Science.gov (United States)

Xu, Chi; Holmgren, Milena; Van Nes, Egbert H; Hirota, Marina; Chapin, F Stuart; Scheffer, Marten

2015-01-01

Publicly available remote sensing products have boosted science in many ways. The openness of these data sources suggests high reproducibility. However, as we show here, results may be specific to versions of the data products that can become unavailable as new versions are posted. We focus on remotely-sensed tree cover. Recent studies have used this public resource to detect multi-modality in tree cover in the tropical and boreal biomes. Such patterns suggest alternative stable states separated by critical tipping points. This has important implications for the potential response of these ecosystems to global climate change. For the boreal region, four distinct ecosystem states (i.e., treeless, sparse and dense woodland, and boreal forest) were previously identified by using the Collection 3 data of MODIS Vegetation Continuous Fields (VCF). Since then, the MODIS VCF product has been updated to Collection 5; and a Landsat VCF product of global tree cover at a fine spatial resolution of 30 meters has been developed. Here we compare these different remote-sensing products of tree cover to show that identification of alternative stable states in the boreal biome partly depends on the data source used. The updated MODIS data and the newer Landsat data consistently demonstrate three distinct modes around similar tree-cover values. Our analysis suggests that the boreal region has three modes: one sparsely vegetated state (treeless), one distinct 'savanna-like' state and one forest state, which could be alternative stable states. Our analysis illustrates that qualitative outcomes of studies may change fundamentally as new versions of remote sensing products are used. Scientific reproducibility thus requires that old versions remain publicly available.

The Reproducibility of Nuclear Morphometric Measurements in Invasive Breast Carcinoma

Directory of Open Access Journals (Sweden)

Pauliina Kronqvist

1997-01-01

Full Text Available The intraobserver and interobserver reproducibility of computerized nuclear morphometry was determined in repeated measurements of 212 samples of invasive breast cancer. The influence of biological variation and the selection of the measurement area was also tested. Morphometrically determined mean nuclear profile area (Pearson’s r 0.89, grading efficiency (GE 0.95 and standard deviation (SD of nuclear profile area (Pearson’s r 0.84, GE 0.89 showed high reproducibility. In this respect, nuclear morphometry equals with other established methods of quantitative pathology and exceeds the results of subjective grading of nuclear atypia in invasive breast cancer. A training period of eight days was sufficient to produce clear improvement in consistency of nuclear morphometry results. By estimating the sources of variation it could be shown that the variation associated with the measurement procedure itself is small. Instead, sample associated variation is responsible for the majority of variation in the measurements (82.9% in mean nuclear profile area and 65.9% in SD of nuclear profile area. This study points out that when standardized methods are applied computerized morphometry is a reproducible and reliable method of assessing nuclear atypia in invasive breast cancer. For further improvement special emphasize should be put on sampling rules of selecting the microscope fields and measurement areas.

[Natural head position's reproducibility on photographs].

Science.gov (United States)

Eddo, Marie-Line; El Hayeck, Émilie; Hoyeck, Maha; Khoury, Élie; Ghoubril, Joseph

2017-12-01

The purpose of this study is to evaluate the reproducibility of natural head position with time on profile photographs. Our sample is composed of 96 students (20-30 years old) at the department of dentistry of Saint Joseph University in Beirut. Two profile photographs were taken in natural head position about a week apart. No significant differences were found between T0 and T1 (E = 1.065°). Many studies confirmed this reproducibility with time. Natural head position can be adopted as an orientation for profile photographs in orthodontics. © EDP Sciences, SFODF, 2017.

Audiovisual biofeedback improves diaphragm motion reproducibility in MRI

Science.gov (United States)

Kim, Taeho; Pollock, Sean; Lee, Danny; O’Brien, Ricky; Keall, Paul

2012-01-01

Purpose: In lung radiotherapy, variations in cycle-to-cycle breathing results in four-dimensional computed tomography imaging artifacts, leading to inaccurate beam coverage and tumor targeting. In previous studies, the effect of audiovisual (AV) biofeedback on the external respiratory signal reproducibility has been investigated but the internal anatomy motion has not been fully studied. The aim of this study is to test the hypothesis that AV biofeedback improves diaphragm motion reproducibility of internal anatomy using magnetic resonance imaging (MRI). Methods: To test the hypothesis 15 healthy human subjects were enrolled in an ethics-approved AV biofeedback study consisting of two imaging sessions spaced ∼1 week apart. Within each session MR images were acquired under free breathing and AV biofeedback conditions. The respiratory signal to the AV biofeedback system utilized optical monitoring of an external marker placed on the abdomen. Synchronously, serial thoracic 2D MR images were obtained to measure the diaphragm motion using a fast gradient-recalled-echo MR pulse sequence in both coronal and sagittal planes. The improvement in the diaphragm motion reproducibility using the AV biofeedback system was quantified by comparing cycle-to-cycle variability in displacement, respiratory period, and baseline drift. Additionally, the variation in improvement between the two sessions was also quantified. Results: The average root mean square error (RMSE) of diaphragm cycle-to-cycle displacement was reduced from 2.6 mm with free breathing to 1.6 mm (38% reduction) with the implementation of AV biofeedback (p-value biofeedback (p-value biofeedback (p-value = 0.012). The diaphragm motion reproducibility improvements with AV biofeedback were consistent with the abdominal motion reproducibility that was observed from the external marker motion variation. Conclusions: This study was the first to investigate the potential of AV biofeedback to improve the motion

Short- and long-term reproducibility of radioisotopic examination of gastric emptying

Energy Technology Data Exchange (ETDEWEB)

Jonderko, K. (Silesian School of Medicine, Katowice (Poland). Dept. of Gastroenterology)

1990-01-01

Reproducibility of gastric emptying (GE) of a radiolabelled solid meal was assessed. The short-term reproducibility was evaluated on the basis of 12 paired GE examinations performed 1-3 days apart. Twelve paired GE examinations taken 3-8 months apart enabled long-term reproducibility assessment. Reproducibility of GE parameters was expressed in terms of the coefficient of variation, CV. No significant between-day variation of solid GE was found either regarding the short-term or the long-term reproducibility. Although slightly higher CV values characterized the long-term reproducibility of the GE parameters considered, the variations of the differences between repeated GE examinations did not differ significantly between short- and long-term GE reproducibility. The results obtained justify the use of radioisotopic GE measurement for the assessment of early and late results of pharmacologic or surgical management. (author).

ReproPhylo: An Environment for Reproducible Phylogenomics.

Directory of Open Access Journals (Sweden)

Amir Szitenberg

2015-09-01

Full Text Available The reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This 'single file' approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. This file, along with a Git repository, are the primary reproducibility outputs of the program. In addition, ReproPhylo produces an extensive human-readable report and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 Python module and is easily installed as a Docker image or a WinPython self-sufficient package, with a Jupyter Notebook GUI, or as a slimmer version in a Galaxy distribution.

Reproducibility in Computational Neuroscience Models and Simulations

Science.gov (United States)

McDougal, Robert A.; Bulanova, Anna S.; Lytton, William W.

2016-01-01

Objective Like all scientific research, computational neuroscience research must be reproducible. Big data science, including simulation research, cannot depend exclusively on journal articles as the method to provide the sharing and transparency required for reproducibility. Methods Ensuring model reproducibility requires the use of multiple standard software practices and tools, including version control, strong commenting and documentation, and code modularity. Results Building on these standard practices, model sharing sites and tools have been developed that fit into several categories: 1. standardized neural simulators, 2. shared computational resources, 3. declarative model descriptors, ontologies and standardized annotations; 4. model sharing repositories and sharing standards. Conclusion A number of complementary innovations have been proposed to enhance sharing, transparency and reproducibility. The individual user can be encouraged to make use of version control, commenting, documentation and modularity in development of models. The community can help by requiring model sharing as a condition of publication and funding. Significance Model management will become increasingly important as multiscale models become larger, more detailed and correspondingly more difficult to manage by any single investigator or single laboratory. Additional big data management complexity will come as the models become more useful in interpreting experiments, thus increasing the need to ensure clear alignment between modeling data, both parameters and results, and experiment. PMID:27046845

Reproducibility of myelin content-based human habenula segmentation at 3 Tesla.

Science.gov (United States)

Kim, Joo-Won; Naidich, Thomas P; Joseph, Joshmi; Nair, Divya; Glasser, Matthew F; O'halloran, Rafael; Doucet, Gaelle E; Lee, Won Hee; Krinsky, Hannah; Paulino, Alejandro; Glahn, David C; Anticevic, Alan; Frangou, Sophia; Xu, Junqian

2018-03-26

In vivo morphological study of the human habenula, a pair of small epithalamic nuclei adjacent to the dorsomedial thalamus, has recently gained significant interest for its role in reward and aversion processing. However, segmenting the habenula from in vivo magnetic resonance imaging (MRI) is challenging due to the habenula's small size and low anatomical contrast. Although manual and semi-automated habenula segmentation methods have been reported, the test-retest reproducibility of the segmented habenula volume and the consistency of the boundaries of habenula segmentation have not been investigated. In this study, we evaluated the intra- and inter-site reproducibility of in vivo human habenula segmentation from 3T MRI (0.7-0.8 mm isotropic resolution) using our previously proposed semi-automated myelin contrast-based method and its fully-automated version, as well as a previously published manual geometry-based method. The habenula segmentation using our semi-automated method showed consistent boundary definition (high Dice coefficient, low mean distance, and moderate Hausdorff distance) and reproducible volume measurement (low coefficient of variation). Furthermore, the habenula boundary in our semi-automated segmentation from 3T MRI agreed well with that in the manual segmentation from 7T MRI (0.5 mm isotropic resolution) of the same subjects. Overall, our proposed semi-automated habenula segmentation showed reliable and reproducible habenula localization, while its fully-automated version offers an efficient way for large sample analysis. © 2018 Wiley Periodicals, Inc.

Reproducing oil paint gloss in print for the purpose of creating reproductions of Old Masters

Science.gov (United States)

Elkhuizen, Willemijn S.; Lenseigne, Boris A. J.; Baar, Teun; Verhofstad, Wim; Tempelman, Erik; Geraedts, Jo M. P.; Dik, Joris

2015-03-01

In the field of Fine Art reproduction, 3D scanning plus 3D printing, combined with dedicated software, now allows to capture and reproduce the color and texture of oil paintings. However, for life-like reproduction of the material appearance of such paintings, the typical gloss and translucency must also be included, which is currently not the case. The aim of this paper is to elaborate on the challenges and results of capturing and reproducing oil paint gloss (next to texture and color) using a scanning and printing system. A sample was hand-made using oil paint and acrylic varnish, and its gloss was then reproduced. A gloss map of the painted sample was acquired using a high end DLSR camera and a simple acquisition protocol. Next, Océ High Resolution 3D printing technology was used to create samples with spatially varying gloss. For this, two different strategies were combined: (1) multilevel half-toning of the colors was used to reproduce matte color layers, and (2) varnish was half-toned on top in increasing coverage to recreate increasing gloss levels. This paper presents an overview of the state-of-the-art literature in gloss reproduction and perception, our process of reproduction as well as the visual evaluation of the quality of the created reproduction.

Reproducibility of computer-aided detection system in digital mammograms

International Nuclear Information System (INIS)

Kim, Seung Ja; Cho, Nariya; Cha, Joo Hee; Chung, Hye Kyung; Lee, Sin Ho; Cho, Kyung Soo; Kim, Sun Mi; Moon, Woo Kyung

2005-01-01

To evaluate the reproducibility of the computer-aided detection (CAD) system for digital mammograms. We applied the CAD system (ImageChecker M1000-DM, version 3.1; R2 Technology) to full field digital mammograms. These mammograms were taken twice at an interval of 10-45 days (mean:25 days) for 34 preoperative patients (breast cancer n=27, benign disease n=7, age range:20-66 years, mean age:47.9 years). On the mammograms, lesions were visible in 19 patients and these were depicted as 15 masses and 12 calcification clusters. We analyzed the sensitivity, the false positive rate (FPR) and the reproducibility of the CAD marks. The broader sensitivities of the CAD system were 80% (12 of 15), 67%(10 of 15) for masses and those for calcification clusters were 100% (12 of 12). The strict sensitivities were 50% (15 of 30) and 50% (15 of 30) for masses and 92% (22 of 24) and 79% (19 of 24) for the clusters. The FPR for the masses was 0.21-0.22/image, the FPR for the clusters was 0.03-0.04/image and the total FPR was 0.24-0.26/image. Among 132 mammography images, the identical images regardless of the existence of CAD marks were 59% (78 of 132), and the identical images with CAD marks were 22% (15 of 69). The reproducibility of the CAD marks for the true positive mass was 67% (12 of 18) and 71% (17 of 24) for the true positive cluster. The reproducibility of CAD marks for the false positive mass was 8% (4 of 53), and the reproducibility of CAD marks for the false positive clusters was 14% (1 of 7). The reproducibility of the total mass marks was 23% (16 of 71), and the reproducibility of the total cluster marks was 58% (18 of 31). CAD system showed higher sensitivity and reproducibility of CAD marks for the calcification clusters which are related to breast cancer. Yet the overall reproducibility of CAD marks was low; therefore, the CAD system must be applied considering this limitation

PC database for high energy preprint collections

International Nuclear Information System (INIS)

Haymaker, R.

1985-06-01

We describe a microcomputer database used by the high energy group to keep track of preprints in our collection. It is used as a supplement to the SLAC-SPIRES database to retrieve preprints on hand. This was designed as a low overhead system for a small group

High-throughput miniaturized bioreactors for cell culture process development: reproducibility, scalability, and control.

Science.gov (United States)

Rameez, Shahid; Mostafa, Sigma S; Miller, Christopher; Shukla, Abhinav A

2014-01-01

Decreasing the timeframe for cell culture process development has been a key goal toward accelerating biopharmaceutical development. Advanced Microscale Bioreactors (ambr™) is an automated micro-bioreactor system with miniature single-use bioreactors with a 10-15 mL working volume controlled by an automated workstation. This system was compared to conventional bioreactor systems in terms of its performance for the production of a monoclonal antibody in a recombinant Chinese Hamster Ovary cell line. The miniaturized bioreactor system was found to produce cell culture profiles that matched across scales to 3 L, 15 L, and 200 L stirred tank bioreactors. The processes used in this article involve complex feed formulations, perturbations, and strict process control within the design space, which are in-line with processes used for commercial scale manufacturing of biopharmaceuticals. Changes to important process parameters in ambr™ resulted in predictable cell growth, viability and titer changes, which were in good agreement to data from the conventional larger scale bioreactors. ambr™ was found to successfully reproduce variations in temperature, dissolved oxygen (DO), and pH conditions similar to the larger bioreactor systems. Additionally, the miniature bioreactors were found to react well to perturbations in pH and DO through adjustments to the Proportional and Integral control loop. The data presented here demonstrates the utility of the ambr™ system as a high throughput system for cell culture process development. © 2014 American Institute of Chemical Engineers.

Stability and reproducibility of a single-sample urinary C-peptide/creatinine ratio and its correlation with 24-h urinary C-peptide.

Science.gov (United States)

McDonald, Tim J; Knight, Bridget A; Shields, Beverley M; Bowman, Pamela; Salzmann, Maurice B; Hattersley, Andrew T

2009-11-01

C-peptide measurement in blood or 24-h urine samples provides useful information regarding endogenous insulin secretion, but problems related to the rapid degradation of C-peptide in blood and difficulty of 24-h urine collection have limited widespread routine clinical use of this test. We assessed the feasibility of measuring urinary C-peptide (UCP) with correction for creatinine concentration in single urine samples. We analyzed UCP using a routine electrochemiluminescence immunoassay in samples from 21 healthy volunteers. We investigated the stability of UCP with different preservatives and storage conditions and compared the reproducibility of urinary C-peptide/creatinine ratio (UCPCR) in first- and second-void fasting urines, then assessed correlations with 24-h collections. UCPCR was unchanged at room temperature for 24 h and at 4 degrees C for 72 h even in the absence of preservative. UCPCR collected in boric acid was stable at room temperature for 72 h. UCPCR remained stable after 7 freeze-thaw cycles but decreased with freezer storage time and dropped to 82%-84% of baseline by 90 days at -20 degrees C. Second-void fasting UCPCRs were lower than first-void (median 0.78 vs 1.31, P = 0.0003) and showed less variation (CV 33% vs 52%), as second-void UCPCRs were not influenced by evening food-related insulin secretion. Second-void fasting UCPCR was highly correlated with 24-h UCP (r = 0.8, P = 0.00006). Second-void fasting UCPCR is a reproducible measure that correlates well with 24-h UCP in normal samples. The 3-day stability of UCPCR at room temperature greatly increases its potential clinical utility.

ZIF-8 Membranes with Improved Reproducibility Fabricated from Sputter-Coated ZnO/Alumina Supports

KAUST Repository

Yu, Jian

2015-11-10

Zeolitic imidazolate framework-8 (ZIF-8) membrane has shown great potential for propylene/propane separation based on molecular sieving mechanism. Although diverse synthesis strategies were applied to prepare ZIF-8 membranes, it is still a challenge for reproducible fabrication of high-quality membranes. In this study, high-quality ZIF-8 membranes were prepared through hydrothermal synthesis under the partial self-conversion of sputter-coated ZnO layer on porous α-alumina supports. The reproducibility was significantly improved, compared with that from sol-gel coated ZnO layer, due to the highly controllable sputtering deposition of ZnO precursor. The relationship between the quality of as-synthesized membrane and amount of deposited ZnO was also determined. The effect of pressure drop in C3H6/C3H8 separation on separating performance was also examined.

Collective dynamics in dense Hg vapour

International Nuclear Information System (INIS)

Ishikawa, D; Inui, M; Matsuda, K; Tamura, K; Baron, A Q R; Tsutsui, S; Tanaka, Y; Ishikawa, T

2004-01-01

The dynamic structure factor, S(Q,ο), of dense Hg vapour has been measured by high resolution inelastic x-ray scattering for densities of 3.0, 2.1 and 1.0 g cm -3 corresponding to 0.52, 0.36 and 0.17 times the critical density, respectively, and for momentum transfers between 2.0 and 48 nm -1 . Analysis of the longitudinal current-current correlation function in the framework of generalized hydrodynamics reveals that the frequencies of the collective excitations increase faster with Q than estimated from the macroscopic speed of sound. The ratios of the frequencies were found to be 1.27 at 3.0 g cm -3 , 1.12 at 2.1 g cm -3 and 1.10 at 1.0 g cm -3 . The sound velocity obtained from the present experiments is well reproduced by a wavenumber dependent adiabatic sound velocity, which means that the collective modes remain in the spectra of dense Hg vapour. (letter to the editor)

Tackling the Reproducibility Problem in Systems Research with Declarative Experiment Specifications

Energy Technology Data Exchange (ETDEWEB)

Jimenez, Ivo [Univ. of California, Santa Cruz, CA (United States); Maltzahn, Carlos [Univ. of California, Santa Cruz, CA (United States); Lofstead, Jay [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Moody, Adam [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Mohror, Kathryn [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Arpaci-Dusseau, Remzi [Univ. of Wisconsin, Madison, WI (United States); Arpaci-Dusseau, Andrea [Univ. of Wisconsin, Madison, WI (United States)

2015-05-04

Validating experimental results in the field of computer systems is a challenging task, mainly due to the many changes in software and hardware that computational environments go through. Determining if an experiment is reproducible entails two separate tasks: re-executing the experiment and validating the results. Existing reproducibility efforts have focused on the former, envisioning techniques and infrastructures that make it easier to re-execute an experiment. In this work we focus on the latter by analyzing the validation workflow that an experiment re-executioner goes through. We notice that validating results is done on the basis of experiment design and high-level goals, rather than exact quantitative metrics. Based on this insight, we introduce a declarative format for specifying the high-level components of an experiment as well as describing generic, testable conditions that serve as the basis for validation. We present a use case in the area of storage systems to illustrate the usefulness of this approach. We also discuss limitations and potential benefits of using this approach in other areas of experimental systems research.

Reproducible Bioinformatics Research for Biologists

Science.gov (United States)

This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

Reproducibility, controllability, and optimization of LENR experiments

Energy Technology Data Exchange (ETDEWEB)

Nagel, David J. [The George Washington University, Washington DC 20052 (United States)

2006-07-01

Low-energy nuclear reaction (LENR) measurements are significantly, and increasingly reproducible. Practical control of the production of energy or materials by LENR has yet to be demonstrated. Minimization of costly inputs and maximization of desired outputs of LENR remain for future developments. The paper concludes by underlying that it is now clearly that demands for reproducible experiments in the early years of LENR experiments were premature. In fact, one can argue that irreproducibility should be expected for early experiments in a complex new field. As emphasized in the paper and as often happened in the history of science, experimental and theoretical progress can take even decades. It is likely to be many years before investments in LENR experiments will yield significant returns, even for successful research programs. However, it is clearly that a fundamental understanding of the anomalous effects observed in numerous experiments will significantly increase reproducibility, improve controllability, enable optimization of processes, and accelerate the economic viability of LENR.

Reproducibility, controllability, and optimization of LENR experiments

International Nuclear Information System (INIS)

Nagel, David J.

2006-01-01

Low-energy nuclear reaction (LENR) measurements are significantly, and increasingly reproducible. Practical control of the production of energy or materials by LENR has yet to be demonstrated. Minimization of costly inputs and maximization of desired outputs of LENR remain for future developments. The paper concludes by underlying that it is now clearly that demands for reproducible experiments in the early years of LENR experiments were premature. In fact, one can argue that irreproducibility should be expected for early experiments in a complex new field. As emphasized in the paper and as often happened in the history of science, experimental and theoretical progress can take even decades. It is likely to be many years before investments in LENR experiments will yield significant returns, even for successful research programs. However, it is clearly that a fundamental understanding of the anomalous effects observed in numerous experiments will significantly increase reproducibility, improve controllability, enable optimization of processes, and accelerate the economic viability of LENR

Automated Generation of Technical Documentation and Provenance for Reproducible Research

Science.gov (United States)

Jolly, B.; Medyckyj-Scott, D.; Spiekermann, R.; Ausseil, A. G.

2017-12-01

Data provenance and detailed technical documentation are essential components of high-quality reproducible research, however are often only partially addressed during a research project. Recording and maintaining this information during the course of a project can be a difficult task to get right as it is a time consuming and often boring process for the researchers involved. As a result, provenance records and technical documentation provided alongside research results can be incomplete or may not be completely consistent with the actual processes followed. While providing access to the data and code used by the original researchers goes some way toward enabling reproducibility, this does not count as, or replace, data provenance. Additionally, this can be a poor substitute for good technical documentation and is often more difficult for a third-party to understand - particularly if they do not understand the programming language(s) used. We present and discuss a tool built from the ground up for the production of well-documented and reproducible spatial datasets that are created by applying a series of classification rules to a number of input layers. The internal model of the classification rules required by the tool to process the input data is exploited to also produce technical documentation and provenance records with minimal additional user input. Available provenance records that accompany input datasets are incorporated into those that describe the current process. As a result, each time a new iteration of the analysis is performed the documentation and provenance records are re-generated to provide an accurate description of the exact process followed. The generic nature of this tool, and the lessons learned during its creation, have wider application to other fields where the production of derivative datasets must be done in an open, defensible, and reproducible way.

Validity and Reproducibility of the Iodine Dietary Intake Questionnaire Assessment Conducted for Young Polish Women

Science.gov (United States)

Malowaniec, Ewa

2017-01-01

The aim of this study was to analyse a designed brief iodine dietary intake questionnaire based on a food frequency assessment (IOdine Dietary INtake Evaluation-Food Frequency Questionnaire—IODINE-FFQ), including the assessment of validity and reproducibility in a group of 90 Polish women aged 20–35 years. Participants collected 3-day dietary records and filled in the IODINE-FFQ twice (FFQ1—directly after the dietary record and FFQ2—6 weeks later). The analysis included an assessment of validity (comparison with the results of the 3-day dietary record) and of reproducibility (comparison of the results obtained twice—FFQ1 and FFQ2). In the analysis of validity, a Bland-Altman index of 5.5% and 4.4% was recorded, respectively for FFQ1 and FFQ2. In the analysis of reproducibility it was 6.7%, but the share of individuals correctly classified into tertiles was over 70% (weighted κ of 0.675). It was stated, that assessment of IODINE-FFQ revealed a satisfactory level of validity and reproducibility in the analysis of Bland-Alman plot. The IODINE-FFQ may be indicated as a tool for the assessment of iodine intake in the young women in Poland, however further studies should be considered in order to obtain the practical tool for public health specialists. Due to the lack of validated iodine-specific food frequency questionnaires for countries of Eastern Europe, the IODINE-FFQ may be adjusted for courtiers other than Poland including iodine-fortified products. PMID:28661461

Reproducing Kernels and Coherent States on Julia Sets

Energy Technology Data Exchange (ETDEWEB)

Thirulogasanthar, K., E-mail: santhar@cs.concordia.ca; Krzyzak, A. [Concordia University, Department of Computer Science and Software Engineering (Canada)], E-mail: krzyzak@cs.concordia.ca; Honnouvo, G. [Concordia University, Department of Mathematics and Statistics (Canada)], E-mail: g_honnouvo@yahoo.fr

2007-11-15

We construct classes of coherent states on domains arising from dynamical systems. An orthonormal family of vectors associated to the generating transformation of a Julia set is found as a family of square integrable vectors, and, thereby, reproducing kernels and reproducing kernel Hilbert spaces are associated to Julia sets. We also present analogous results on domains arising from iterated function systems.

Reproducing Kernels and Coherent States on Julia Sets

International Nuclear Information System (INIS)

Thirulogasanthar, K.; Krzyzak, A.; Honnouvo, G.

2007-01-01

We construct classes of coherent states on domains arising from dynamical systems. An orthonormal family of vectors associated to the generating transformation of a Julia set is found as a family of square integrable vectors, and, thereby, reproducing kernels and reproducing kernel Hilbert spaces are associated to Julia sets. We also present analogous results on domains arising from iterated function systems

Reproducibility of studies on text mining for citation screening in systematic reviews: Evaluation and checklist.

Science.gov (United States)

Olorisade, Babatunde Kazeem; Brereton, Pearl; Andras, Peter

2017-09-01

Independent validation of published scientific results through study replication is a pre-condition for accepting the validity of such results. In computation research, full replication is often unrealistic for independent results validation, therefore, study reproduction has been justified as the minimum acceptable standard to evaluate the validity of scientific claims. The application of text mining techniques to citation screening in the context of systematic literature reviews is a relatively young and growing computational field with high relevance for software engineering, medical research and other fields. However, there is little work so far on reproduction studies in the field. In this paper, we investigate the reproducibility of studies in this area based on information contained in published articles and we propose reporting guidelines that could improve reproducibility. The study was approached in two ways. Initially we attempted to reproduce results from six studies, which were based on the same raw dataset. Then, based on this experience, we identified steps considered essential to successful reproduction of text mining experiments and characterized them to measure how reproducible is a study given the information provided on these steps. 33 articles were systematically assessed for reproducibility using this approach. Our work revealed that it is currently difficult if not impossible to independently reproduce the results published in any of the studies investigated. The lack of information about the datasets used limits reproducibility of about 80% of the studies assessed. Also, information about the machine learning algorithms is inadequate in about 27% of the papers. On the plus side, the third party software tools used are mostly free and available. The reproducibility potential of most of the studies can be significantly improved if more attention is paid to information provided on the datasets used, how they were partitioned and utilized, and

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.

Reproducibility of food consumption frequencies derived from the Children's Eating Habits Questionnaire used in the IDEFICS study.

Science.gov (United States)

Lanfer, A; Hebestreit, A; Ahrens, W; Krogh, V; Sieri, S; Lissner, L; Eiben, G; Siani, A; Huybrechts, I; Loit, H-M; Papoutsou, S; Kovács, E; Pala, V

2011-04-01

To investigate the reproducibility of food consumption frequencies derived from the food frequency section of the Children's Eating Habits Questionnaire (CEHQ-FFQ) that was developed and used in the IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) project to assess food habits in 2- to 9-year-old European children. From a subsample of 258 children who participated in the IDEFICS baseline examination, parental questionnaires of the CEHQ were collected twice to assess reproducibility of questionnaire results from 0 to 354 days after the first examination. Weighted Cohen's kappa coefficients (κ) and Spearman's correlation coefficients (r) were calculated to assess agreement between the first and second questionnaires for each food item of the CEHQ-FFQ. Stratification was performed for sex, age group, geographical region and length of period between the first and second administrations. Fisher's Z transformation was applied to test correlation coefficients for significant differences between strata. For all food items analysed, weighted Cohen's kappa coefficients (κ) and Spearman's correlation coefficients (r) were significant and positive (P128 days) between the first and second administrations resulted in a generally lower, yet still acceptable, reproducibility. Results indicate that the CEHQ-FFQ gives reproducible estimates of the consumption frequency of 43 food items from 14 food groups in European children.

An investigation of the reproducibility of ultrasound measures of abdominal muscle activation in patients with chronic non-specific low back pain

Science.gov (United States)

Maher, Chris G.; Latimer, Jane; Hodges, Paul W.; Shirley, Debra

2009-01-01

Ultrasound (US) measures are used by clinicians and researchers to evaluate improvements in activity of the abdominal muscles in patients with low back pain. Studies evaluating the reproducibility of these US measures provide some information; however, little is known about the reproducibility of these US measures over time in patients with low back pain. The objectives of this study were to estimate the reproducibility of ultrasound measurements of automatic activation of the lateral abdominal wall muscles using a leg force task in patients with chronic low back pain. Thirty-five participants from an existing randomised, blinded, placebo-controlled trial participated in the study. A reproducibility analysis was undertaken from all patients using data collected at baseline and after treatment. The reproducibility of measurements of thickness, muscle activation (thickness changes) and muscle improvement/deterioration after intervention (differences in thickness changes from single images made before and after treatment) was analysed. The reproducibility of static images (thickness) was excellent (ICC2,1 = 0.97, 95% CI = 0.96–0.97, standard error of the measurement (SEM) = 0.04 cm, smallest detectable change (SDC) = 0.11 cm), the reproducibility of thickness changes was moderate (ICC2,1 = 0.72, 95% CI 0.65–0.76, SEM = 15%, SDC 41%), while the reproducibility of differences in thickness changes from single images with statistical adjustment for duplicate measures was poor (ICC2,1 = 0.44, 95% CI 0.33–0.58, SEM = 21%, SDC = 66.5%). Improvements in the testing protocol must be performed in order to enhance reproducibility of US as an outcome measure for abdominal muscle activation. PMID:19415347

Equipment for collecting samples of radioactive solutions

International Nuclear Information System (INIS)

Raggenbass, A.; Fradin, J.; Joubert, G.

1958-01-01

The authors present an equipment aimed at collecting samples of fission products to perform radio-chemical analysis. As the sample must have a total activity between 1 and 50 micro-Curie, this installation comprises a sampling system and a dilution device which aims at bringing the sample to the suitable activity. Samples are collected by means of needles. The sample reproducibility is discussed. The dilution device is described

Empirical questions for collective-behaviour modelling

Indian Academy of Sciences (India)

The collective behaviour of groups of social animals has been an active topic of study ... Models have been successful at reproducing qualitative features of ... quantitative and detailed empirical results for a range of animal systems. ... standard method [23], the redundant information recorded by the cameras can be used to.

Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format.

Science.gov (United States)

Pinheiro, Leonardo B; O'Brien, Helen; Druce, Julian; Do, Hongdo; Kay, Pippa; Daniels, Marissa; You, Jingjing; Burke, Daniel; Griffiths, Kate; Emslie, Kerry R

2017-11-07

Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.

Multiparticle Collectivity from Initial State Correlations in High Energy Proton-Nucleus Collisions

Science.gov (United States)

Dusling, Kevin; Mace, Mark; Venugopalan, Raju

2018-01-01

Qualitative features of multiparticle correlations in light-heavy ion (p +A ) collisions at RHIC and LHC are reproduced in a simple initial state model of partons in the projectile coherently scattering off localized domains of color charge in the heavy nuclear target. These include (i) the ordering of the magnitudes of the azimuthal angle n th Fourier harmonics of two-particle correlations vn{2 }, (ii) the energy and transverse momentum dependence of the four-particle Fourier harmonic v2{4 }, and (iii) the energy dependence of four-particle symmetric cumulants measuring correlations between different Fourier harmonics. Similar patterns are seen in an Abelian version of the model, where we observe v2{2 }>v2{4 }≈v2{6 }≈v2{8 } of two, four, six, and eight particle correlations. While such patterns are often interpreted as signatures of collectivity arising from hydrodynamic flow, our results provide an alternative description of the multiparticle correlations seen in p +A collisions.

A Fast, High Quality, and Reproducible Parallel Lagged-Fibonacci Pseudorandom Number Generator

Science.gov (United States)

Mascagni, Michael; Cuccaro, Steven A.; Pryor, Daniel V.; Robinson, M. L.

1995-07-01

We study the suitability of the additive lagged-Fibonacci pseudo-random number generator for parallel computation. This generator has relatively short period with respect to the size of its seed. However, the short period is more than made up for with the huge number of full-period cycles it contains. These different full period cycles are called equivalence classes. We show how to enumerate the equivalence classes and how to compute seeds to select a given equivalence class, In addition, we present some theoretical measures of quality for this generator when used in parallel. Next, we conjecture on the size of these measures of quality for this generator. Extensive empirical evidence supports this conjecture. In addition, a probabilistic interpretation of these measures leads to another conjecture similarly supported by empirical evidence. Finally we give an explicit parallelization suitable for a fully reproducible asynchronous MIMD implementation.

Reproducible diagnosis of Chronic Lymphocytic Leukemia by flow cytometry

DEFF Research Database (Denmark)

Rawstron, Andy C; Kreuzer, Karl-Anton; Soosapilla, Asha

2018-01-01

The diagnostic criteria for CLL rely on morphology and immunophenotype. Current approaches have limitations affecting reproducibility and there is no consensus on the role of new markers. The aim of this project was to identify reproducible criteria and consensus on markers recommended for the di...

Validity and reproducibility of self-reported working hours among Japanese male employees.

Science.gov (United States)

Imai, Teppei; Kuwahara, Keisuke; Miyamoto, Toshiaki; Okazaki, Hiroko; Nishihara, Akiko; Kabe, Isamu; Mizoue, Tetsuya; Dohi, Seitaro

2016-07-22

Working long hours is a potential health hazard. Although self-reporting of working hours in various time frames has been used in epidemiologic studies, its validity is unclear. The objective of this study was to examine the validity and reproducibility of self-reported working hours among Japanese male employees. The participants were 164 male employees of four large-scale companies in Japan. For validity, the Spearman correlation between self-reported working hours in the second survey and the working hours recorded by the company was calculated for the following four time frames: daily working hours, monthly overtime working hours in the last month, average overtime working hours in the last 3 months, and the frequency of long working months (≥45 h/month) within the last 12 months. For reproducibility, the intraclass correlation between the first (September 2013) and second surveys (December 2013) was calculated for each of the four time frames. The Spearman correlations between self-reported working hours and those based on company records were 0.74, 0.81, 0.85, and 0.89 for daily, monthly, 3-monthly, and yearly time periods, respectively. The intraclass correlations for self-reported working hours between the two questionnaire surveys were 0.63, 0.66, 0.73, and 0.87 for the respective time frames. The results of the present study among Japanese male employees suggest that the validity of self-reported working hours is high for all four time frames, whereas the reproducibility is moderate to high.

Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets.

Science.gov (United States)

Scott, D J; Devonshire, A S; Adeleye, Y A; Schutte, M E; Rodrigues, M R; Wilkes, T M; Sacco, M G; Gribaldo, L; Fabbri, M; Coecke, S; Whelan, M; Skinner, N; Bennett, A; White, A; Foy, C A

2011-11-28

The application of toxicogenomics as a predictive tool for chemical risk assessment has been under evaluation by the toxicology community for more than a decade. However, it predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we assessed whether the current generation of microarray technology in combination with an in vitro experimental design was capable of generating robust, reproducible data of sufficient quality to show promise as a tool for regulatory risk assessment. To this end, we designed a prospective collaborative study to determine the level of inter- and intra-laboratory reproducibility between three independent laboratories. All test centres (TCs) adopted the same protocols for all aspects of the toxicogenomic experiment including cell culture, chemical exposure, RNA extraction, microarray data generation and analysis. As a case study, the genotoxic carcinogen benzo[a]pyrene (B[a]P) and the human hepatoma cell line HepG2 were used to generate three comparable toxicogenomic data sets. High levels of technical reproducibility were demonstrated using a widely employed gene expression microarray platform. While differences at the global transcriptome level were observed between the TCs, a common subset of B[a]P responsive genes (n=400 gene probes) was identified at all TCs which included many genes previously reported in the literature as B[a]P responsive. These data show promise that the current generation of microarray technology, in combination with a standard in vitro experimental design, can produce robust data that can be generated reproducibly in independent laboratories. Future work will need to determine whether such reproducible in vitro model(s) can be predictive for a range of toxic chemicals with different mechanisms of action and thus be considered as part of future testing regimes for regulatory risk assessment. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Reproducibility of LiF:Mg, Cup thermoluminescent dosimeter on kilo voltage and megavoltage photon beam using different preheat rate:A glow curve study

International Nuclear Information System (INIS)

Mohd Fahmi Mohd Yusof; Robert, T.S.B.; Puteri Norkhatijah Abdul Hamid; Nor Shazleen Abdul Shukor; Mohd Sazarman Mohd Salleh

2013-01-01

Full-text: Post-irradiation annealing or preheat of the LiF based TLD prior readout is commonly practiced for routine dosimetry to eliminate low temperature glow peaks. The aim of this study is to determine the effect of different preheating rate technique prior readout on the reproducibility and glow curve structure of LiF:Mg, Cu, P or TLD-1OOH exposed to low (109kVp) energy and high energy (6MV) photon beam. TLD chips were read after 24 hours of irradiation with three different preheat techniques; no preheat, low preheat rate (100 degree Celsius/ 10 minutes) and high preheat rate (135 degree Celsius/ 10 seconds) and reproducibility of TL signals were assessed in term of Standard Deviation (SD) and glow curve peaks. The high preheat rate technique was the most reproducible method for low energy photon with 1.05 % of mean reproducibility followed by low preheat rate (1.16 %) and no-preheat (1.33 %) techniques. The high preheat rate techniques was also the most reproducible method for high energy photon with 0.767 % of mean reproducibility as compared to low preheat rate (1.281 %). However the high preheat technique record highest TL signal lost with 10.35 % and 6.04 % for 24 and 72 hours of delayed TLD readout with respectively compared to 9.27 % and 4.51 % for 24 and 72 hours by low preheat rate. The low preheat was found to be optimal to eliminate low peaks (peak 1 and 2) but enable to remove peak 3 as it was shifted up word to combine with the main peak 4 of TL glow peak. It can be concluded that the reproducibility and structure of glow curve was strongly influenced by preheat technique prior readout. (author)

A Framework for Reproducible Latent Fingerprint Enhancements.

Science.gov (United States)

Carasso, Alfred S

2014-01-01

Photoshop processing of latent fingerprints is the preferred methodology among law enforcement forensic experts, but that appproach is not fully reproducible and may lead to questionable enhancements. Alternative, independent, fully reproducible enhancements, using IDL Histogram Equalization and IDL Adaptive Histogram Equalization, can produce better-defined ridge structures, along with considerable background information. Applying a systematic slow motion smoothing procedure to such IDL enhancements, based on the rapid FFT solution of a Lévy stable fractional diffusion equation, can attenuate background detail while preserving ridge information. The resulting smoothed latent print enhancements are comparable to, but distinct from, forensic Photoshop images suitable for input into automated fingerprint identification systems, (AFIS). In addition, this progressive smoothing procedure can be reexamined by displaying the suite of progressively smoother IDL images. That suite can be stored, providing an audit trail that allows monitoring for possible loss of useful information, in transit to the user-selected optimal image. Such independent and fully reproducible enhancements provide a valuable frame of reference that may be helpful in informing, complementing, and possibly validating the forensic Photoshop methodology.

Parameter optimization for reproducible cardiac 1 H-MR spectroscopy at 3 Tesla.

Science.gov (United States)

de Heer, Paul; Bizino, Maurice B; Lamb, Hildo J; Webb, Andrew G

2016-11-01

frequency selective excitation water suppression (7.0%). Using the optimized parameters an intrasession limits of agreement of the myocardial triglyceride content of -0.11% to +0.04%, and an intersession of -0.15% to +0.9%, were achieved. The coefficient of variation was 5% for the intrasession reproducibility and 6.5% for the intersession reproducibility. Using approaches designed to optimize SNR and minimize the variation in inter-average signal intensities and frequencies/phases, a protocol was developed to perform cardiac MR spectroscopy on a clinical 3T system with high reproducibility. J. Magn. Reson. Imaging 2016;44:1151-1158. © 2016 International Society for Magnetic Resonance in Medicine.

Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry.

Science.gov (United States)

Fu, Qin; Kowalski, Michael P; Mastali, Mitra; Parker, Sarah J; Sobhani, Kimia; van den Broek, Irene; Hunter, Christie L; Van Eyk, Jennifer E

2018-01-05

Sample preparation for protein quantification by mass spectrometry requires multiple processing steps including denaturation, reduction, alkylation, protease digestion, and peptide cleanup. Scaling these procedures for the analysis of numerous complex biological samples can be tedious and time-consuming, as there are many liquid transfer steps and timed reactions where technical variations can be introduced and propagated. We established an automated sample preparation workflow with a total processing time for 96 samples of 5 h, including a 2 h incubation with trypsin. Peptide cleanup is accomplished by online diversion during the LC/MS/MS analysis. In a selected reaction monitoring (SRM) assay targeting 6 plasma biomarkers and spiked β-galactosidase, mean intraday and interday cyclic voltammograms (CVs) for 5 serum and 5 plasma samples over 5 days were samples repeated on 3 separate days had total CVs below 20%. Similar results were obtained when the workflow was transferred to a second site: 93% of peptides had CVs below 20%. An automated trypsin digestion workflow yields uniformly processed samples in less than 5 h. Reproducible quantification of peptides was observed across replicates, days, instruments, and laboratory sites, demonstrating the broad applicability of this approach.

The construction of a two-dimensional reproducing kernel function and its application in a biomedical model.

Science.gov (United States)

Guo, Qi; Shen, Shu-Ting

2016-04-29

There are two major classes of cardiac tissue models: the ionic model and the FitzHugh-Nagumo model. During computer simulation, each model entails solving a system of complex ordinary differential equations and a partial differential equation with non-flux boundary conditions. The reproducing kernel method possesses significant applications in solving partial differential equations. The derivative of the reproducing kernel function is a wavelet function, which has local properties and sensitivities to singularity. Therefore, study on the application of reproducing kernel would be advantageous. Applying new mathematical theory to the numerical solution of the ventricular muscle model so as to improve its precision in comparison with other methods at present. A two-dimensional reproducing kernel function inspace is constructed and applied in computing the solution of two-dimensional cardiac tissue model by means of the difference method through time and the reproducing kernel method through space. Compared with other methods, this method holds several advantages such as high accuracy in computing solutions, insensitivity to different time steps and a slow propagation speed of error. It is suitable for disorderly scattered node systems without meshing, and can arbitrarily change the location and density of the solution on different time layers. The reproducing kernel method has higher solution accuracy and stability in the solutions of the two-dimensional cardiac tissue model.

Adaptive Learning in Cartesian Product of Reproducing Kernel Hilbert Spaces

OpenAIRE

Yukawa, Masahiro

2014-01-01

We propose a novel adaptive learning algorithm based on iterative orthogonal projections in the Cartesian product of multiple reproducing kernel Hilbert spaces (RKHSs). The task is estimating/tracking nonlinear functions which are supposed to contain multiple components such as (i) linear and nonlinear components, (ii) high- and low- frequency components etc. In this case, the use of multiple RKHSs permits a compact representation of multicomponent functions. The proposed algorithm is where t...

Math Games 180 Reproducible Activities to Motivate, Excite, and Challenge Students, Grades 6-12

CERN Document Server

Muschla, Judith A

2011-01-01

Math Games offers a dynamic collection of 180 reproducible activity sheets to stimulate and challenge your students in all areas of math - from whole numbers to data analysis - while emphasizing problem solving, critical thinking, and the use of technology for today's curriculum! Each of the book's activities can help you teach students in grades 6 through 12 how to think with numbers, recognize relationships, and make connections between mathematical concepts. You pick the activity appropriate for their needs . . . encourage the use of a calculator . . . or provide further challenges with act

Reproducibility and reliability of repeated semen analyses in male partners of subfertile couples

NARCIS (Netherlands)

Leushuis, Esther; van der Steeg, Jan Willem; Steures, Pieternel; Repping, Sjoerd; Bossuyt, Patrick M. M.; Blankenstein, Marinus A.; Mol, Ben Willem J.; van der Veen, Fulco; Hompes, Peter G. A.

2010-01-01

Objective: To determine the precise degree of variability that is represented by the reproducibility and reliability of semen analysis. The general assumption is that semen analyses need to be repeated because of a high degree of within-individual variability. However, the precise degree of

Validation and reproducibility of an Australian caffeine food frequency questionnaire.

Science.gov (United States)

Watson, E J; Kohler, M; Banks, S; Coates, A M

2017-08-01

The aim of this study was to measure validity and reproducibility of a caffeine food frequency questionnaire (C-FFQ) developed for the Australian population. The C-FFQ was designed to assess average daily caffeine consumption using four categories of food and beverages including; energy drinks; soft drinks/soda; coffee and tea and chocolate (food and drink). Participants completed a seven-day food diary immediately followed by the C-FFQ on two consecutive days. The questionnaire was first piloted in 20 adults, and then, a validity/reproducibility study was conducted (n = 90 adults). The C-FFQ showed moderate correlations (r = .60), fair agreement (mean difference 63 mg) and reasonable quintile rankings indicating fair to moderate agreement with the seven-day food diary. To test reproducibility, the C-FFQ was compared to itself and showed strong correlations (r = .90), good quintile rankings and strong kappa values (κ = 0.65), indicating strong reproducibility. The C-FFQ shows adequate validity and reproducibility and will aid researchers in Australia to quantify caffeine consumption.

Non-collective oblate states in iodine isotopes at high spin

Energy Technology Data Exchange (ETDEWEB)

Paul, E S; Ali, I; Cullen, D M; Fallon, P; Forbes, S A; Hanna, F; Nolan, P J [Liverpool Univ. (United Kingdom). Oliver Lodge Lab.; Bentley, M A; Bruce, A M; Simpson, J [Daresbury Lab. (United Kingdom); Clark, R M; Regan, P H; Wadsworth, R [York Univ. (United Kingdom). Dept. of Physics; Fossan, D B; Hughes, J R; Lafosse, D R; Vaska, P; Waring, M P [Department of Physics, SUNY at Stony Brook, NY (United States); Liang, Y [Argonne National Lab., IL (United States); Ma, R [Brookhaven National Lab., Upton, NY (United States)

1992-08-01

Competition between single-particle and collective modes of excitation has been observed in the odd-A {sup 113-119}I isotopes at high spin. A maximally-aligned non-collective 43/2{sup -} configuration at {gamma}=+ 60 degrees is seen at similar excitation energies in these nuclei. 7 refs., 4 figs.

Collective properties and shapes of nuclei at very high spins

International Nuclear Information System (INIS)

Johnson, N.R.

1991-01-01

A topic which has been of major interest to us for some years now involves the evolution of nuclear collectivity at high rotational frequencies and the accompanying changes in the shapes of nuclei in these extreme conditions. We carry out these studies by determining the dynamic electromagnetic multipole moments which are a reflection of the collective aspects of the nuclear wave functions. The most direct way to get these multipole moments is by measurements of excited-state lifetimes which provide the transition matrix elements in a fairly straightforward fashion. Although the primary emphasis of this paper is on the collectivity of the high-spin states in 160 Yb and 164 Yb, it is important to review briefly some work we began about ten years ago lifetime studies of moderately high spins in nuclei near N=90 using the recoil-distance (RD) method. These nuclei are just at the onset of permanent deformation and are known to be very soft with respect to deformation changes. This softness is clearly illustrated in contour diagrams of their potential-energy surfaces. For example, the potential energy surface of 160 Yb reveals that the minimum in the potential occurs around var-epsilon ∼ 0.2 and that it is very shallow in the γ degree of freedom. Because of their γ softness, we have studied several nuclei near N=90 to assess to what extent the polarization effects induced by rotation alignment of high-j quasiparticles affect their collectivity

Automation of cDNA Synthesis and Labelling Improves Reproducibility

Directory of Open Access Journals (Sweden)

Daniel Klevebring

2009-01-01

Full Text Available Background. Several technologies, such as in-depth sequencing and microarrays, enable large-scale interrogation of genomes and transcriptomes. In this study, we asses reproducibility and throughput by moving all laboratory procedures to a robotic workstation, capable of handling superparamagnetic beads. Here, we describe a fully automated procedure for cDNA synthesis and labelling for microarrays, where the purification steps prior to and after labelling are based on precipitation of DNA on carboxylic acid-coated paramagnetic beads. Results. The fully automated procedure allows for samples arrayed on a microtiter plate to be processed in parallel without manual intervention and ensuring high reproducibility. We compare our results to a manual sample preparation procedure and, in addition, use a comprehensive reference dataset to show that the protocol described performs better than similar manual procedures. Conclusions. We demonstrate, in an automated gene expression microarray experiment, a reduced variance between replicates, resulting in an increase in the statistical power to detect differentially expressed genes, thus allowing smaller differences between samples to be identified. This protocol can with minor modifications be used to create cDNA libraries for other applications such as in-depth analysis using next-generation sequencing technologies.

Reproducibility of preclinical animal research improves with heterogeneity of study samples

Science.gov (United States)

Vogt, Lucile; Sena, Emily S.; Würbel, Hanno

2018-01-01

Single-laboratory studies conducted under highly standardized conditions are the gold standard in preclinical animal research. Using simulations based on 440 preclinical studies across 13 different interventions in animal models of stroke, myocardial infarction, and breast cancer, we compared the accuracy of effect size estimates between single-laboratory and multi-laboratory study designs. Single-laboratory studies generally failed to predict effect size accurately, and larger sample sizes rendered effect size estimates even less accurate. By contrast, multi-laboratory designs including as few as 2 to 4 laboratories increased coverage probability by up to 42 percentage points without a need for larger sample sizes. These findings demonstrate that within-study standardization is a major cause of poor reproducibility. More representative study samples are required to improve the external validity and reproducibility of preclinical animal research and to prevent wasting animals and resources for inconclusive research. PMID:29470495

Relative validity and reproducibility of a food frequency questionnaire for identifying the dietary patterns of toddlers in New Zealand.

Science.gov (United States)

Mills, Virginia C; Skidmore, Paula M L; Watson, Emily O; Taylor, Rachael W; Fleming, Elizabeth A; Heath, Anne-Louise M

2015-04-01

Dietary patterns provide insight into relationships between diet and disease. Food frequency questionnaires (FFQs) can identify dietary patterns in adults, but similar analyses have not been performed for toddlers. The aim of the Eating Assessment in Toddlers study was to evaluate the relative validity and reproducibility of dietary patterns from an FFQ developed for toddlers aged 12 to 24 months. Participants were 160 toddlers aged 12 to 24 months and their primary caregiver who completed an FFQ twice, approximately 5 weeks apart (FFQ1 and FFQ2). A 5-day weighed food record was collected on nonconsecutive days between FFQ administrations. Principal component analysis identified three major dietary patterns similar across FFQ1, FFQ2, and the 5-day weighted food record. The sweet foods and fries pattern was characterized by high intakes of sweet foods, fries and roast potato and kumara (sweet potato), butter and margarines, processed meat, sweet drinks, and fruit or milk drinks. The vegetables and meat pattern was characterized by high intakes of vegetables, meat, eggs and beans, and fruit. The milk and fruit pattern was characterized by high intakes of milk and milk products and fruit, and low intakes of breastmilk and infant and follow-up formula. The FFQ (FFQ1) correctly classified 43.1% to 51.0% of toddlers into the same quartile of pattern score as the 5-day weighted food record, and Pearson correlations ranged from 0.56 to 0.68 for the three patterns. Reliability coefficients ranged from 0.71 to 0.72 for all three dietary patterns. the Eating Assessment in Toddlers study FFQ shows acceptable relative validity and high reproducibility for identifying dietary patterns in toddlers. Copyright © 2015 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

Reproducibility of temporomandibular joint tomography. Influence of shifted X-ray beam and tomographic focal plane on reproducibility

International Nuclear Information System (INIS)

Saito, Masashi

1999-01-01

Proper tomographic focal plane and x-ray beam direction are the most important factors to obtain accurate images of the temporomandibular joint (TMJ). In this study, to clarify the magnitude of effect of these two factors on the image quality. We evaluated the reproducibility of tomograms by measuring the distortion when the x-ray beam was shifted from the correct center of the object. The effects of the deviation of the tomographic focal plane on image quality were evaluated by the MTF (Modulation Transfer Function). Two types of tomograms, one the plane type, the other the rotational type were used in this study. A TMJ model was made from Teflon for the purpose of evaluation by shifting the x-ray beam. The x-ray images were obtained by tilting the model from 0 to 10 degrees 2-degree increments. These x-ray images were processed for computer image analysis, and then the distance between condyle and the joint space was measured. To evaluate the influence of the shifted tomographic focal plane on image sharpness, the x-ray images from each setting were analyzed by MTF. To obtain the MTF, ''knife-edge'' made from Pb was used. The images were scanned with a microdensitometer at the central focal plane, and 0, 0.5, 1 mm away respectively. The density curves were analyzed by Fourier analysis and the MTF was calculated. The reproducibility of images became worse by shifting the x-ray beam. This tendency was similar for both tomograms. Object characteristics such as anterior and posterior portion of the joint space affected the deterioration of reproducibility of the tomography. The deviation of the tomographic focal plane also decreased the reproducibility of the x-ray images. The rotational type showed a better MTF, but it became seriously unfavorable with slight changes of the tomographic focal plane. Contrarily, the plane type showed a lower MTF, but the image was stable with shifting of the tomographic focal plane. (author)

A national drug related problems database: evaluation of use in practice, reliability and reproducibility

DEFF Research Database (Denmark)

Kjeldsen, Lene Juel; Birkholm, Trine; Fischer, Hanne Lis

2014-01-01

Background A drug related problems database (DRP-database) was developed on request by clinical pharmacists. The information from the DRP-database has only been used locally e.g. to identify focus areas and to communicate identified DRPs to the hospital wards. Hence the quality of the data...... by clinical pharmacists with categorization performed by the project group. Reproducibility was explored by re-categorization of a sample of existing records in the DRP-database by two project group members individually. Main outcome measures Observed proportion of agreement and Fleiss' kappa as measures...... reliability study of 34 clinical pharmacists showed high inter-rater reliability with the project group (Fleiss' kappa = 0.79 with 95 % CI (0.70; 0.88)), and the reproducibility study also documented high inter-rater reliability of a sample of 379 records from the DRP-database re-categorized by two project...

Dysplastic naevus: histological criteria and their inter-observer reproducibility.

Science.gov (United States)

Hastrup, N; Clemmensen, O J; Spaun, E; Søndergaard, K

1994-06-01

Forty melanocytic lesions were examined in a pilot study, which was followed by a final series of 100 consecutive melanocytic lesions, in order to evaluate the inter-observer reproducibility of the histological criteria proposed for the dysplastic naevus. The specimens were examined in a blind fashion by four observers. Analysis by kappa statistics showed poor reproducibility of nuclear features, while reproducibility of architectural features was acceptable, improving in the final series. Consequently, we cannot apply the combined criteria of cytological and architectural features with any confidence in the diagnosis of dysplastic naevus, and, until further studies have documented that architectural criteria alone will suffice in the diagnosis of dysplastic naevus, we, as pathologists, shall avoid this term.

Reproducible and controllable induction voltage adder for scaled beam experiments

Energy Technology Data Exchange (ETDEWEB)

Sakai, Yasuo; Nakajima, Mitsuo; Horioka, Kazuhiko [Department of Energy Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8502 (Japan)

2016-08-15

A reproducible and controllable induction adder was developed using solid-state switching devices and Finemet cores for scaled beam compression experiments. A gate controlled MOSFET circuit was developed for the controllable voltage driver. The MOSFET circuit drove the induction adder at low magnetization levels of the cores which enabled us to form reproducible modulation voltages with jitter less than 0.3 ns. Preliminary beam compression experiments indicated that the induction adder can improve the reproducibility of modulation voltages and advance the beam physics experiments.

GeoTrust Hub: A Platform For Sharing And Reproducing Geoscience Applications

Science.gov (United States)

Malik, T.; Tarboton, D. G.; Goodall, J. L.; Choi, E.; Bhatt, A.; Peckham, S. D.; Foster, I.; Ton That, D. H.; Essawy, B.; Yuan, Z.; Dash, P. K.; Fils, G.; Gan, T.; Fadugba, O. I.; Saxena, A.; Valentic, T. A.

2017-12-01

Recent requirements of scholarly communication emphasize the reproducibility of scientific claims. Text-based research papers are considered poor mediums to establish reproducibility. Papers must be accompanied by "research objects", aggregation of digital artifacts that together with the paper provide an authoritative record of a piece of research. We will present GeoTrust Hub (http://geotrusthub.org), a platform for creating, sharing, and reproducing reusable research objects. GeoTrust Hub provides tools for scientists to create `geounits'--reusable research objects. Geounits are self-contained, annotated, and versioned containers that describe and package computational experiments in an efficient and light-weight manner. Geounits can be shared on public repositories such as HydroShare and FigShare, and also using their respective APIs reproduced on provisioned clouds. The latter feature enables science applications to have a lifetime beyond sharing, wherein they can be independently verified and trust be established as they are repeatedly reused. Through research use cases from several geoscience laboratories across the United States, we will demonstrate how tools provided from GeoTrust Hub along with Hydroshare as its public repository for geounits is advancing the state of reproducible research in the geosciences. For each use case, we will address different computational reproducibility requirements. Our first use case will be an example of setup reproducibility which enables a scientist to set up and reproduce an output from a model with complex configuration and development environments. Our second use case will be an example of algorithm/data reproducibility, where in a shared data science model/dataset can be substituted with an alternate one to verify model output results, and finally an example of interactive reproducibility, in which an experiment is dependent on specific versions of data to produce the result. Toward this we will use software and data

NRFixer: Sentiment Based Model for Predicting the Fixability of Non-Reproducible Bugs

Directory of Open Access Journals (Sweden)

Anjali Goyal

2017-08-01

Full Text Available Software maintenance is an essential step in software development life cycle. Nowadays, software companies spend approximately 45\\% of total cost in maintenance activities. Large software projects maintain bug repositories to collect, organize and resolve bug reports. Sometimes it is difficult to reproduce the reported bug with the information present in a bug report and thus this bug is marked with resolution non-reproducible (NR. When NR bugs are reconsidered, a few of them might get fixed (NR-to-fix leaving the others with the same resolution (NR. To analyse the behaviour of developers towards NR-to-fix and NR bugs, the sentiment analysis of NR bug report textual contents has been conducted. The sentiment analysis of bug reports shows that NR bugs' sentiments incline towards more negativity than reproducible bugs. Also, there is a noticeable opinion drift found in the sentiments of NR-to-fix bug reports. Observations driven from this analysis were an inspiration to develop a model that can judge the fixability of NR bugs. Thus a framework, {NRFixer,} which predicts the probability of NR bug fixation, is proposed. {NRFixer} was evaluated with two dimensions. The first dimension considers meta-fields of bug reports (model-1 and the other dimension additionally incorporates the sentiments (model-2 of developers for prediction. Both models were compared using various machine learning classifiers (Zero-R, naive Bayes, J48, random tree and random forest. The bug reports of Firefox and Eclipse projects were used to test {NRFixer}. In Firefox and Eclipse projects, J48 and Naive Bayes classifiers achieve the best prediction accuracy, respectively. It was observed that the inclusion of sentiments in the prediction model shows a rise in the prediction accuracy ranging from 2 to 5\\% for various classifiers.

Reproducibility of NMR analysis of urine samples: impact of sample preparation, storage conditions, and animal health status.

Science.gov (United States)

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining (1)H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after (1)H NMR spectroscopy. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at -20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions.

Reproducibility of NMR Analysis of Urine Samples: Impact of Sample Preparation, Storage Conditions, and Animal Health Status

Directory of Open Access Journals (Sweden)

Christina Schreier

2013-01-01

Full Text Available Introduction. Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining 1H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing and the health status of the animals, which may influence urine pH and osmolarity. Methods. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after 1H NMR spectroscopy. Results. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at −20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Conclusion. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions.

Comparative validity and reproducibility study of various landmark-oriented reference planes in 3-dimensional computed tomographic analysis for patients receiving orthognathic surgery.

Science.gov (United States)

Lin, Hsiu-Hsia; Chuang, Ya-Fang; Weng, Jing-Ling; Lo, Lun-Jou

2015-01-01

Three-dimensional computed tomographic imaging has become popular in clinical evaluation, treatment planning, surgical simulation, and outcome assessment for maxillofacial intervention. The purposes of this study were to investigate whether there is any correlation among landmark-based horizontal reference planes and to validate the reproducibility and reliability of landmark identification. Preoperative and postoperative cone-beam computed tomographic images of patients who had undergone orthognathic surgery were collected. Landmark-oriented reference planes including the Frankfort horizontal plane (FHP) and the lateral semicircular canal plane (LSP) were established. Four FHPs were defined by selecting 3 points from the orbitale, porion, or midpoint of paired points. The LSP passed through both the lateral semicircular canal points and nasion. The distances between the maxillary or mandibular teeth and the reference planes were measured, and the differences between the 2 sides were calculated and compared. The precision in locating the landmarks was evaluated by performing repeated tests, and the intraobserver reproducibility and interobserver reliability were assessed. A total of 30 patients with facial deformity and malocclusion--10 patients with facial symmetry, 10 patients with facial asymmetry, and 10 patients with cleft lip and palate--were recruited. Comparing the differences among the 5 reference planes showed no statistically significant difference among all patient groups. Regarding intraobserver reproducibility, the mean differences in the 3 coordinates varied from 0 to 0.35 mm, with correlation coefficients between 0.96 and 1.0, showing high correlation between repeated tests. Regarding interobserver reliability, the mean differences among the 3 coordinates varied from 0 to 0.47 mm, with correlation coefficients between 0.88 and 1.0, exhibiting high correlation between the different examiners. The 5 horizontal reference planes were reliable and

Diffusion Properties and 3D Architecture of Human Lower Leg Muscles Assessed with Ultra-High-Field-Strength Diffusion-Tensor MR Imaging and Tractography: Reproducibility and Sensitivity to Sex Difference and Intramuscular Variability.

Science.gov (United States)

Fouré, Alexandre; Ogier, Augustin C; Le Troter, Arnaud; Vilmen, Christophe; Feiweier, Thorsten; Guye, Maxime; Gondin, Julien; Besson, Pierre; Bendahan, David

2018-05-01

Purpose To demonstrate the reproducibility of the diffusion properties and three-dimensional structural organization measurements of the lower leg muscles by using diffusion-tensor imaging (DTI) assessed with ultra-high-field-strength (7.0-T) magnetic resonance (MR) imaging and tractography of skeletal muscle fibers. On the basis of robust statistical mapping analyses, this study also aimed at determining the sensitivity of the measurements to sex difference and intramuscular variability. Materials and Methods All examinations were performed with ethical review board approval; written informed consent was obtained from all volunteers. Reproducibility of diffusion tensor indexes assessment including eigenvalues, mean diffusivity, and fractional anisotropy (FA) as well as muscle volume and architecture (ie, fiber length and pennation angle) were characterized in lower leg muscles (n = 8). Intramuscular variability and sex differences were characterized in young healthy men and women (n = 10 in each group). Student t test, statistical parametric mapping, correlation coefficients (Spearman rho and Pearson product-moment) and coefficient of variation (CV) were used for statistical data analysis. Results High reproducibility of measurements (mean CV ± standard deviation, 4.6% ± 3.8) was determined in diffusion properties and architectural parameters. Significant sex differences were detected in FA (4.2% in women for the entire lower leg; P = .001) and muscle volume (21.7% in men for the entire lower leg; P = .008), whereas architecture parameters were almost identical across sex. Additional differences were found independently of sex in diffusion properties and architecture along several muscles of the lower leg. Conclusion The high-spatial-resolution DTI assessed with 7.0-T MR imaging allows a reproducible assessment of structural organization of superficial and deep muscles, giving indirect information on muscle function. © RSNA, 2018 Online supplemental material is

[Reproducibility of Fuhrman nuclear grade: advantages of a two-grade system].

Science.gov (United States)

Letourneux, Hervé; Lindner, Véronique; Lang, Hervé; Massfelder, Thierry; Meyer, Nicolas; Saussine, Christian; Jacqmin, Didier

2006-06-01

The Fuhrman nuclear grade is the reference histoprognostic grading system routinely used all over the world for renal cell carcinoma. Studies measuring the inter-observer and intra-observer concordance of Fuhrman grade show poor results in terms of reproducibility and repeatability. These variations are due to a certain degree of subjectivity of the pathologist in application of the definition of tumour grade, particularly nuclear grade. Elements able to account for this subjectivity in renal cell carcinoma are identified from a review of the literature. To improve the reliability of nuclear grade, the territory occupied by the highest grade must be specified and the grades should probably be combined. At the present time, regrouping of grade 1 and 2 tumours as low grade and grade 3 and 4 tumours as high grade would achieve better reproducibility, while preserving the prognostic: value for overall survival. The development of new treatment modalities and their use in adjuvant situations will imply the use of reliable histoprognostic factors to specify, indications.

Reproducibility of intrarenal kinetics of Gd-DOTA with rabbits with dynamic MRI

International Nuclear Information System (INIS)

Grenier, N.; Broussin, J.; Barat, J.L.; Ducassou, D.

1989-01-01

Ten normal rabbits and seven rabbits with experimental acute renal failure by tubular necrosis were studied with dynamic MR to evaluate the reproducibility of intrarenal kinetics of Gd-DOTA. Sequential spin-echo sequences with short TR (200 msec)/TE (26 msec) were used yielding a 29 sec acquisition time. A usual semi-quantitative analysis of intrarenal contrast demonstrated the reproducilibity of some phases of the dynamic sequence in particular a drop in the signal within inner medulla between the third and the fourth minute after infusion. This effect, related to a high concentration of Gd-DOTA within the tubules was observed in 9 over 10 normal rabbits and in none of the rabbits with acute renal failure. The quantitative analysis calculation was based on relative signal intensity and contrast-to-noise ratio from the absolute signal intensity measure on regions-of-interest (ROI) on the cortex, outer medulla and inner medulla. No reproducibility of the variations with time of these parameters could be assessed. A gread number of factors of variations or error, mainly during the measurements of signal intensity with ROI, could explain this lack of reproducibility. At the present, dynamic MR is therefore not able to quantitatively evaluate the renal function. Only a semi-quantitative estimation of tubular concentration can be deduced [fr

Magnetic resonance elastography of the pancreas: Measurement reproducibility and relationship with age.

Science.gov (United States)

Kolipaka, Arunark; Schroeder, Samuel; Mo, Xiaokui; Shah, Zarine; Hart, Phil A; Conwell, Darwin L

2017-10-01

To determine magnetic resonance elastography (MRE)-derived stiffness of pancreas in healthy volunteers with emphasis on: 1) short term and midterm repeatability; and 2) variance as a function of age. Pancreatic MRE was performed on 22 healthy volunteers (age range:20-64years) in a 3T-scanner. For evaluation of reproducibility of stiffness estimates, the scans were repeated per volunteer on the same day (short term) and one month apart (midterm). MRE wave images were analyzed using 3D inversion to estimate the stiffness of overall pancreas and different anatomic regions (i.e., head, neck, body, and tail). Concordance and Spearman correlation tests were performed to determine reproducibility of stiffness measurements and relationship to age. A strong concordance correlation (ρ c =0.99; p-value0.81; p45yrs) had significantly higher stiffness compared to the younger group (≤45yrs) (p0.05) in stiffness measurements was observed between different anatomical regions of pancreas, except neck stiffness was slightly lower (ppancreas at month 1. MRE-derived pancreatic stiffness measurements are highly reproducible in the short and midterm and increase linearly with age in healthy volunteers. Further studies are needed to examine these effects in patients with various pancreatic diseases to understand potential clinical applications. Copyright © 2017 Elsevier Inc. All rights reserved.

Reproducibility of NMR Analysis of Urine Samples: Impact of Sample Preparation, Storage Conditions, and Animal Health Status

OpenAIRE

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Introduction. Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining 1H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. Methods. We treated rats wit...

Reproducibility problems of in-service ultrasonic testing results

International Nuclear Information System (INIS)

Honcu, E.

1974-01-01

The reproducibility of the results of ultrasonic testing is the basic precondition for its successful application in in-service inspection of changes in the quality of components of nuclear power installations. The results of periodic ultrasonic inspections are not satisfactory from the point of view of reproducibility. Regardless, the ultrasonic pulse-type method is suitable for evaluating the quality of most components of nuclear installations and often the sole method which may be recommended for inspection with regard to its technical and economic aspects. (J.B.)

Effective Form of Reproducing the Total Financial Potential of Ukraine

Directory of Open Access Journals (Sweden)

Portna Oksana V.

2015-03-01

Full Text Available Development of scientific principles of reproducing the total financial potential of the country and its effective form is an urgent problem both in theoretical and practical aspects of the study, the solution of which is intended to ensure the active mobilization and effective use of the total financial potential of Ukraine, and as a result — its expanded reproduction as well, which would contribute to realization of the internal capacities for stabilization of the national economy. The purpose of the article is disclosing the essence of the effective form of reproducing the total financial potential of the country, analyzing the results of reproducing the total financial potential of Ukraine. It has been proved that the basis for the effective form of reproducing the total financial potential of the country is the volume and flow of resources, which are associated with the «real» economy, affect the dynamics of GDP and define it, i.e. resource and process forms of reproducing the total financial potential of Ukraine (which precede the effective one. The analysis of reproducing the total financial potential of Ukraine has shown that in the analyzed period there was an increase in the financial possibilities of the country, but steady dynamics of reduction of the total financial potential was observed. If we consider the amount of resources involved in production, creating a net value added and GDP, it occurs on a restricted basis. Growth of the total financial potential of Ukraine is connected only with extensive quantitative factors rather than intensive qualitative changes.

The MIMIC Code Repository: enabling reproducibility in critical care research.

Science.gov (United States)

Johnson, Alistair Ew; Stone, David J; Celi, Leo A; Pollard, Tom J

2018-01-01

Lack of reproducibility in medical studies is a barrier to the generation of a robust knowledge base to support clinical decision-making. In this paper we outline the Medical Information Mart for Intensive Care (MIMIC) Code Repository, a centralized code base for generating reproducible studies on an openly available critical care dataset. Code is provided to load the data into a relational structure, create extractions of the data, and reproduce entire analysis plans including research studies. Concepts extracted include severity of illness scores, comorbid status, administrative definitions of sepsis, physiologic criteria for sepsis, organ failure scores, treatment administration, and more. Executable documents are used for tutorials and reproduce published studies end-to-end, providing a template for future researchers to replicate. The repository's issue tracker enables community discussion about the data and concepts, allowing users to collaboratively improve the resource. The centralized repository provides a platform for users of the data to interact directly with the data generators, facilitating greater understanding of the data. It also provides a location for the community to collaborate on necessary concepts for research progress and share them with a larger audience. Consistent application of the same code for underlying concepts is a key step in ensuring that research studies on the MIMIC database are comparable and reproducible. By providing open source code alongside the freely accessible MIMIC-III database, we enable end-to-end reproducible analysis of electronic health records. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Reproducibility of tomographic evaluation of posterolateral lumbar arthrodesis consolidation

Directory of Open Access Journals (Sweden)

Marcelo Italo Risso Neto

2015-06-01

Full Text Available OBJECTIVE: To evaluate interobserver agreement of Glassman classification for posterolateral lumbar spine arthrodesis.METHODS: One hundred and thirty-four CT scans from patients who underwent posterolateral arthrodesis of the lumbar and lumbosacral spine were evaluated by four observers, namely two orthopedic surgeons experienced in spine surgery and two in training in this area. Using the reconstructed tomographic images at oblique coronal plane, 299 operated levels were systematically analyzed looking for arthrodesis signals. The appearance of bone healing in each operated level was classified in five categories as proposed by Glassman to the posterolateral arthrodesis: 1 bilateral solid arthrodesis; 2 unilateral solid arthrodesis; 3 bilateral partial arthrodesis; 4 unilateral partial arthrodesis; 5 absence of arthrodesis. In a second step, the evaluation of each operated level was divided into two categories: fusion (including type 1, 2, 3, and 4 and non fusion (type 5. Statistical analysis was performed by calculating the Kappa coefficient considering the paired analysis between the two experienced observers and between the two observers in training.RESULTS: The interobserver reproducibility by the kappa coefficient for arthrodesis consolidation analysis for the classification proposed, divided into 5 types, was 0.729 for both experienced surgeons and training surgeons. Considering only two categories kappa coefficient was 0.745 between experienced surgeons and 0.795 between training surgeons. In all analyzes, we obtained high concordance power.CONCLUSION: Interobserver reproducibility was observed with high concordance in the classification proposed by Glassman for posterolateral arthrodesis of the lumbar and lumbosacral spine.

Composting in small laboratory pilots: Performance and reproducibility

International Nuclear Information System (INIS)

Lashermes, G.; Barriuso, E.; Le Villio-Poitrenaud, M.; Houot, S.

2012-01-01

Highlights: ► We design an innovative small-scale composting device including six 4-l reactors. ► We investigate the performance and reproducibility of composting on a small scale. ► Thermophilic conditions are established by self-heating in all replicates. ► Biochemical transformations, organic matter losses and stabilisation are realistic. ► The organic matter evolution exhibits good reproducibility for all six replicates. - Abstract: Small-scale reactors ( 2 consumption and CO 2 emissions, and characterising the biochemical evolution of organic matter. A good reproducibility was found for the six replicates with coefficients of variation for all parameters generally lower than 19%. An intense self-heating ensured the existence of a spontaneous thermophilic phase in all reactors. The average loss of total organic matter (TOM) was 46% of the initial content. Compared to the initial mixture, the hot water soluble fraction decreased by 62%, the hemicellulose-like fraction by 68%, the cellulose-like fraction by 50% and the lignin-like fractions by 12% in the final compost. The TOM losses, compost stabilisation and evolution of the biochemical fractions were similar to observed in large reactors or on-site experiments, excluding the lignin degradation, which was less important than in full-scale systems. The reproducibility of the process and the quality of the final compost make it possible to propose the use of this experimental device for research requiring a mass reduction of the initial composted waste mixtures.

Analysis of polymorphisms in milk proteins from cloned and sexually reproduced goats.

Science.gov (United States)

Xing, H; Shao, B; Gu, Y Y; Yuan, Y G; Zhang, T; Zang, J; Cheng, Y

2015-12-08

This study evaluates the relationship between the genotype and milk protein components in goats. Milk samples were collected from cloned goats and normal white goats during different postpartum (or abortion) phases. Two cloned goats, originated from the same somatic line of goat mammary gland epithelial cells, and three sexually reproduced normal white goats with no genetic relationships were used as the control. The goats were phylogenetically analyzed by polymerase chain reaction-restriction fragment length polymorphism. The milk protein components were identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results indicated that despite the genetic fingerprints being identical, the milk protein composition differed between the two cloned goats. The casein content of cloned goat C-50 was significantly higher than that of cloned goat C-4. Conversely, although the genetic fingerprints of the normal white goats N-1, N-2, and N-3 were not identical, the milk protein profiles did not differ significantly in their milk samples (obtained on postpartum day 15, 20, 25, 30, and 150). These results indicated an association between milk protein phenotypes and genetic polymorphisms, epigenetic regulation, and/or non-chromosomal factors. This study extends the knowledge of goat milk protein polymorphisms, and provides new strategies for the breeding of high milk-yielding goats.

Characterization and reproducibility of HepG2 hanging drop spheroids toxicology in vitro.

Science.gov (United States)

Hurrell, Tracey; Ellero, Andrea Antonio; Masso, Zelie Flavienne; Cromarty, Allan Duncan

2018-02-21

Hepatotoxicity remains a major challenge in drug development despite preclinical toxicity screening using hepatocytes of human origin. To overcome some limitations of reproducing the hepatic phenotype, more structurally and functionally authentic cultures in vitro can be introduced by growing cells in 3D spheroid cultures. Characterisation and reproducibility of HepG2 spheroid cultures using a high-throughput hanging drop technique was performed and features contributing to potential phenotypic variation highlighted. Cultured HepG2 cells were seeded into Perfecta 3D® 96-well hanging drop plates and assessed over time for morphology, viability, cell cycle distribution, protein content and protein-mass profiles. Divergent aspects which were assessed included cell stocks, seeding density, volume of culture medium and use of extracellular matrix additives. Hanging drops are advantageous due to no complex culture matrix being present, enabling background free extractions for downstream experimentation. Varying characteristics were observed across cell stocks and batches, seeding density, culture medium volume and extracellular matrix when using immortalized HepG2 cells. These factors contribute to wide-ranging cellular responses and highlights concerns with respect to generating a reproducible phenotype in HepG2 hanging drop spheroids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reproducibility and day time bias correction of optoelectronic leg volumetry: a prospective cohort study.

Science.gov (United States)

Engelberger, Rolf P; Blazek, Claudia; Amsler, Felix; Keo, Hong H; Baumann, Frédéric; Blättler, Werner; Baumgartner, Iris; Willenberg, Torsten

2011-10-05

Leg edema is a common manifestation of various underlying pathologies. Reliable measurement tools are required to quantify edema and monitor therapeutic interventions. Aim of the present work was to investigate the reproducibility of optoelectronic leg volumetry over 3 weeks' time period and to eliminate daytime related within-individual variability. Optoelectronic leg volumetry was performed in 63 hairdressers (mean age 45 ± 16 years, 85.7% female) in standing position twice within a minute for each leg and repeated after 3 weeks. Both lower leg (legBD) and whole limb (limbBF) volumetry were analysed. Reproducibility was expressed as analytical and within-individual coefficients of variance (CVA, CVW), and as intra-class correlation coefficients (ICC). A total of 492 leg volume measurements were analysed. Both legBD and limbBF volumetry were highly reproducible with CVA of 0.5% and 0.7%, respectively. Within-individual reproducibility of legBD and limbBF volumetry over a three weeks' period was high (CVW 1.3% for both; ICC 0.99 for both). At both visits, the second measurement revealed a significantly higher volume compared to the first measurement with a mean increase of 7.3 ml ± 14.1 (0.33% ± 0.58%) for legBD and 30.1 ml ± 48.5 ml (0.52% ± 0.79%) for limbBF volume. A significant linear correlation between absolute and relative leg volume differences and the difference of exact day time of measurement between the two study visits was found (P correction formula permitted further improvement of CVW. Leg volume changes can be reliably assessed by optoelectronic leg volumetry at a single time point and over a 3 weeks' time period. However, volumetry results are biased by orthostatic and daytime-related volume changes. The bias for day-time related volume changes can be minimized by a time-correction formula.

Reproducibility and day time bias correction of optoelectronic leg volumetry: a prospective cohort study

Directory of Open Access Journals (Sweden)

Baumgartner Iris

2011-10-01

Full Text Available Abstract Background Leg edema is a common manifestation of various underlying pathologies. Reliable measurement tools are required to quantify edema and monitor therapeutic interventions. Aim of the present work was to investigate the reproducibility of optoelectronic leg volumetry over 3 weeks' time period and to eliminate daytime related within-individual variability. Methods Optoelectronic leg volumetry was performed in 63 hairdressers (mean age 45 ± 16 years, 85.7% female in standing position twice within a minute for each leg and repeated after 3 weeks. Both lower leg (legBD and whole limb (limbBF volumetry were analysed. Reproducibility was expressed as analytical and within-individual coefficients of variance (CVA, CVW, and as intra-class correlation coefficients (ICC. Results A total of 492 leg volume measurements were analysed. Both legBD and limbBF volumetry were highly reproducible with CVA of 0.5% and 0.7%, respectively. Within-individual reproducibility of legBD and limbBF volumetry over a three weeks' period was high (CVW 1.3% for both; ICC 0.99 for both. At both visits, the second measurement revealed a significantly higher volume compared to the first measurement with a mean increase of 7.3 ml ± 14.1 (0.33% ± 0.58% for legBD and 30.1 ml ± 48.5 ml (0.52% ± 0.79% for limbBF volume. A significant linear correlation between absolute and relative leg volume differences and the difference of exact day time of measurement between the two study visits was found (P W. Conclusions Leg volume changes can be reliably assessed by optoelectronic leg volumetry at a single time point and over a 3 weeks' time period. However, volumetry results are biased by orthostatic and daytime-related volume changes. The bias for day-time related volume changes can be minimized by a time-correction formula.

Reproducibility of esophageal scintigraphy using semi-solid yoghurt

Energy Technology Data Exchange (ETDEWEB)

Imai, Yukinori; Kinoshita, Manabu; Asakura, Yasushi; Kakinuma, Tohru; Shimoji, Katsunori; Fujiwara, Kenji; Suzuki, Kenji; Miyamae, Tatsuya [Saitama Medical School, Moroyama (Japan)

1999-10-01

Esophageal scintigraphy is a non-invasive method which evaluate esophageal function quantitatively. We applied new technique using semi-solid yoghurt, which can evaluate esophageal function in a sitting position. To evaluate the reproducibility of this method, scintigraphy were performed in 16 healthy volunteers. From the result of four swallows except the first one, the mean coefficients of variation in esophageal transit time and esophageal emptying time were 12.8% and 13.4% respectively (interday variation). As regards the interday variation, this method had also good reproducibility from the result on the 2 separate days. (author)

Novel burn device for rapid, reproducible burn wound generation.

Science.gov (United States)

Kim, J Y; Dunham, D M; Supp, D M; Sen, C K; Powell, H M

2016-03-01

Scarring following full thickness burns leads to significant reductions in range of motion and quality of life for burn patients. To effectively study scar development and the efficacy of anti-scarring treatments in a large animal model (female red Duroc pigs), reproducible, uniform, full-thickness, burn wounds are needed to reduce variability in observed results that occur with burn depth. Prior studies have proposed that initial temperature of the burner, contact time with skin, thermal capacity of burner material, and the amount of pressure applied to the skin need to be strictly controlled to ensure reproducibility. The purpose of this study was to develop a new burner that enables temperature and pressure to be digitally controlled and monitored in real-time throughout burn wound creation and compare it to a standard burn device. A custom burn device was manufactured with an electrically heated burn stylus and a temperature control feedback loop via an electronic microstat. Pressure monitoring was controlled by incorporation of a digital scale into the device, which measured downward force. The standard device was comprised of a heat resistant handle with a long rod connected to the burn stylus, which was heated using a hot plate. To quantify skin surface temperature and internal stylus temperature as a function of contact time, the burners were heated to the target temperature (200±5°C) and pressed into the skin for 40s to create the thermal injuries. Time to reach target temperature and elapsed time between burns were recorded. In addition, each unit was evaluated for reproducibility within and across three independent users by generating burn wounds at contact times spanning from 5 to 40s at a constant pressure and at pressures of 1 or 3lbs with a constant contact time of 40s. Biopsies were collected for histological analysis and burn depth quantification using digital image analysis (ImageJ). The custom burn device maintained both its internal

One-Step Printable Perovskite Films Fabricated under Ambient Conditions for Efficient and Reproducible Solar Cells.

Science.gov (United States)

Jung, Yen-Sook; Hwang, Kyeongil; Heo, Youn-Jung; Kim, Jueng-Eun; Lee, Donmin; Lee, Cheol-Ho; Joh, Han-Ik; Yeo, Jun-Seok; Kim, Dong-Yu

2017-08-23

Despite the potential of roll-to-roll processing for the fabrication of perovskite films, the realization of highly efficient and reproducible perovskite solar cells (PeSCs) through continuous coating techniques and low-temperature processing is still challenging. Here, we demonstrate that efficient and reliable CH 3 NH 3 PbI 3 (MAPbI 3 ) films fabricated by a printing process can be achieved through synergetic effects of binary processing additives, N-cyclohexyl-2-pyrrolidone (CHP) and dimethyl sulfoxide (DMSO). Notably, these perovskite films are deposited from premixed perovskite solutions for facile one-step processing under a room-temperature and ambient atmosphere. The CHP molecules result in the uniform and homogeneous perovskite films even in the one-step slot-die system, which originate from the high boiling point and low vapor pressure of CHP. Meanwhile, the DMSO molecules facilitate the growth of perovskite grains by forming intermediate states with the perovskite precursor molecules. Consequently, fully printed PeSC based on the binary additive system exhibits a high PCE of 12.56% with a high reproducibility.

Estimating the reproducibility of psychological science

NARCIS (Netherlands)

Aarts, Alexander A.; Anderson, Joanna E.; Anderson, Christopher J.; Attridge, Peter R.; Attwood, Angela; Axt, Jordan; Babel, Molly; Bahnik, Stepan; Baranski, Erica; Barnett-Cowan, Michael; Bartmess, Elizabeth; Beer, Jennifer; Bell, Raoul; Bentley, Heather; Beyan, Leah; Binion, Grace; Borsboom, Denny; Bosch, Annick; Bosco, Frank A.; Bowman, Sara D.; Brandt, Mark J.; Braswell, Erin; Brohmer, Hilmar; Brown, Benjamin T.; Brown, Kristina; Bruening, Jovita; Calhoun-Sauls, Ann; Chagnon, Elizabeth; Callahan, Shannon P.; Chandler, Jesse; Chartier, Christopher R.; Cheung, Felix; Cillessen, Linda; Christopherson, Cody D.; Clay, Russ; Cleary, Hayley; Cloud, Mark D.; Cohn, Michael; Cohoon, Johanna; Columbus, Simon; Cordes, Andreas; Costantini, Giulio; Hartgerink, Chris; Krijnen, Job; Nuijten, Michele B.; van 't Veer, Anna E.; Van Aert, Robbie; van Assen, M.A.L.M.; Wissink, Joeri; Zeelenberg, Marcel

2015-01-01

INTRODUCTION Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. Scientific claims should not gain credence because of the status or authority of their originator but by the replicability of their supporting evidence. Even research

Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements.

Science.gov (United States)

Taumer, Christoph; Griesbaum, Lena; Kovacevic, Alen; Soufi, Boumediene; Nalpas, Nicolas C; Macek, Boris

2018-03-29

Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms data-dependent acquisition (DDA) in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple heterogeneous phosphopeptide-enriched samples and conclude that PRM shows a great promise in bacterial phosphoproteomics analyses where reproducible detection and quantification of a relatively small set of phosphopeptides is desired. Bacterial phosphorylated peptides occur in low abundance compared to their unmodified counterparts, and are therefore rarely reproducibly detected in shotgun (DDA) proteomics measurements. Here we show that parallel reaction monitoring complements DDA analyses and makes detection of known, targeted phosphopeptides more reproducible. This will be of significance in replicated MS measurements that have a goal to reproducibly detect and quantify phosphopeptides of interest. Copyright �

The Morris Nathanson Design Collection

Directory of Open Access Journals (Sweden)

Christopher Muller

2013-07-01

Full Text Available For more than a half century, Morris Nathanson has been at the forefront of creative interior design for the hospitality industry. He has nurtured, trained, and mentored scores of designers and project managers, while helping to launch the concept and brand development for dozens of landmark restaurant companies. Several images are reproduced from a vast collection of original drawings that have been donated to Boston University.

Magnet stability and reproducibility

CERN Document Server

Marks, N

2010-01-01

Magnet stability and reproducibility have become increasingly important as greater precision and beams with smaller dimension are required for research, medical and other purpose. The observed causes of mechanical and electrical instability are introduced and the engineering arrangements needed to minimize these problems discussed; the resulting performance of a state-of-the-art synchrotron source (Diamond) is then presented. The need for orbit feedback to obtain best possible beam stability is briefly introduced, but omitting any details of the necessary technical equipment, which is outside the scope of the presentation.

The LHC Cryomagnet Supports in Glass-Fiber Reinforced Epoxy A Large Scale Industrial Production with High Reproducibility in Performance

CERN Document Server

Poncet, A; Trigo, J; Parma, V

2008-01-01

The about 1700 LHC main ring super-conducting magnets are supported within their cryostats on 4700 low heat in leak column-type supports. The supports were designed to ensure a precise and stable positioning of the heavy dipole and quadrupole magnets while keeping thermal conduction heat loads within budget. A trade-off between mechanical and thermal properties, as well as cost considerations, led to the choice of glass fibre reinforced epoxy (GFRE). Resin Transfer Moulding (RTM), featuring a high level of automation and control, was the manufacturing process retained to ensure the reproducibility of the performance of the supports throughout the large production. The Spanish aerospace company EADS-CASA Espacio developed the specific RTM process, and produced the total quantity of supports between 2001 and 2004. This paper describes the development and the production of the supports, and presents the production experience and the achieved performance.

THE LHC CRYOMAGNET SUPPORTS IN GLASS-FIBER REINFORCED EPOXY: A LARGE SCALE INDUSTRIAL PRODUCTION WITH HIGH REPRODUCIBILITY IN PERFORMANCE

International Nuclear Information System (INIS)

Poncet, A.; Struik, M.; Parma, V.; Trigo, J.

2008-01-01

The about 1700 LHC main ring super-conducting magnets are supported within their cryostats on 4700 low heat in leak column-type supports. The supports were designed to ensure a precise and stable positioning of the heavy dipole and quadrupole magnets while keeping thermal conduction heat loads within budget. A trade-off between mechanical and thermal properties, as well as cost considerations, led to the choice of glass fibre reinforced epoxy (GFRE). Resin Transfer Moulding (RTM), featuring a high level of automation and control, was the manufacturing process retained to ensure the reproducibility of the performance of the supports throughout the large production.The Spanish aerospace company EADS-CASA Espacio developed the specific RTM process, and produced the total quantity of supports between 2001 and 2004.This paper describes the development and the production of the supports, and presents the production experience and the achieved performance

Collective Quadrupole Excitations of Transactinide Nuclei

CERN Document Server

Zajac, K; Pomorski, K; Rohozinski, S G; Srebrny, J

2003-01-01

The quadrupole excitations of transuranic nuclei are described in the frame of the microscopic Bohr Hamiltonian modified by adding the coupling with the collective pairing vibrations. The energies of the states from the ground-state bands in U to No even-even isotopes as well as the B(E2) transition probabilities are reproduced within the model containing no adjustable parameters.

Additive Manufacturing: Reproducibility of Metallic Parts

Directory of Open Access Journals (Sweden)

Konda Gokuldoss Prashanth

2017-02-01

Full Text Available The present study deals with the properties of five different metals/alloys (Al-12Si, Cu-10Sn and 316L—face centered cubic structure, CoCrMo and commercially pure Ti (CP-Ti—hexagonal closed packed structure fabricated by selective laser melting. The room temperature tensile properties of Al-12Si samples show good consistency in results within the experimental errors. Similar reproducible results were observed for sliding wear and corrosion experiments. The other metal/alloy systems also show repeatable tensile properties, with the tensile curves overlapping until the yield point. The curves may then follow the same path or show a marginal deviation (~10 MPa until they reach the ultimate tensile strength and a negligible difference in ductility levels (of ~0.3% is observed between the samples. The results show that selective laser melting is a reliable fabrication method to produce metallic materials with consistent and reproducible properties.

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.

Directory of Open Access Journals (Sweden)

Andrea Maesani

2015-11-01

Full Text Available The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs-locomotor bouts-matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior.

Diffusion weighted imaging of the normal breast: reproducibility of apparent diffusion coefficient measurements and variation with menstrual cycle and menopausal status

International Nuclear Information System (INIS)

O'Flynn, Elizabeth A.M.; Morgan, Veronica A.; Giles, Sharon L.; de Souza, Nandita M.

2012-01-01

To establish the reproducibility of apparent diffusion coefficient (ADC) measurements in normal fibroglandular breast tissue and to assess variation in ADC values with phase of the menstrual cycle and menopausal status. Thirty-one volunteers (13 premenopausal, 18 postmenopausal) underwent magnetic resonance twice (interval 11-22 days) using diffusion-weighted MRI. ADC total and a perfusion-insensitive ADC high (omitting b = 0) were calculated. Reproducibility and inter-observer variability of mean ADC values were assessed. The difference in mean ADC values between the two phases of the menstrual cycle and the postmenopausal breast were evaluated. ADC total and ADC high showed good reproducibility (r% = 17.6, 22.4). ADC high showed very good inter-observer agreement (kappa = 0.83). The intraclass correlation coefficients (ICC) were 0.93 and 0.91. Mean ADC values were significantly lower in the postmenopausal breast (ADC total 1.46 ± 0.3 x 10 -3 mm 2 /s, ADC high 1.33 ± 0.3 x 10 -3 mm 2 /s) compared with the premenopausal breast (ADC total 1.84 ± 0.26 x 10 -3 mm 2 /s, ADC high 1.77 ± 0.26 x 10 -3 mm 2 /s; both P total P = 0.2, ADC high P = 0.24) or between postmenopausal women taking or not taking oestrogen supplements (ADC total P = 0.6, ADC high P = 0.46). ADC values in fibroglandular breast tissue are reproducible. Lower ADC values within the postmenopausal breast may reduce diffusion-weighted contrast and have implications for accurately detecting tumours. (orig.)

Emotional Climate and High Quality Learning Experiences in Science Teacher Education

Science.gov (United States)

Bellocchi, Alberto; Ritchie, Stephen M.; Tobin, Kenneth; King, Donna; Sandhu, Maryam; Henderson, Senka

2014-01-01

The role of emotion during learning encounters in science teacher education is under-researched and under-theorized. In this case study, we explore the emotional climates (ECs), that is, the collective states of emotional arousal, of a preservice secondary science education class to illuminate practice for producing and reproducing high quality…

Disposable collection kit for rapid and reliable collection of saliva.

Science.gov (United States)

Yamaguchi, Masaki; Tezuka, Yuki; Takeda, Kazunori; Shetty, Vivek

2015-01-01

To describe and evaluate disposable saliva collection kit for rapid, reliable, and reproducible collection of saliva samples. The saliva collection kit comprised of a saliva absorbent swab and an extractor unit was used to retrieve whole saliva samples from 10 subjects. The accuracy and precision of the extracted volumes (3, 10, and 30 μl) were compared to similar volumes drawn from control samples obtained by passive drool. Additionally, the impact of kit collection method on subsequent immunoassay results was verified by assessing salivary cortisol levels in the samples and comparing them to controls. The recovered volumes for the whole saliva samples were 3.85 ± 0.28, 10.79 ± 0.95, and 31.18 ± 1.72 μl, respectively (CV = 8.76%) and 2.91 ± 0.19, 9.75 ± 0.43, and 29.64 ± 0.91 μl, respectively, (CV = 6.36%) for the controls. There was a close correspondence between the salivary cortisol levels from the saliva samples obtained by the collection kit and the controls (R(2)  > 0.96). The disposable saliva collection kit allows accurate and repeatable collection of fixed amounts of whole saliva and does not interfere with subsequent measurements of salivary cortisol. The simple collection process, lack of elaborate specimen recovery steps, and the short turnaround time (<3 min) should render the kit attractive to test subjects and researchers alike. © 2015 Wiley Periodicals, Inc.

INFORMATIVE ENERGY METRIC FOR SIMILARITY MEASURE IN REPRODUCING KERNEL HILBERT SPACES

Directory of Open Access Journals (Sweden)

Songhua Liu

2012-02-01

Full Text Available In this paper, information energy metric (IEM is obtained by similarity computing for high-dimensional samples in a reproducing kernel Hilbert space (RKHS. Firstly, similar/dissimilar subsets and their corresponding informative energy functions are defined. Secondly, IEM is proposed for similarity measure of those subsets, which converts the non-metric distances into metric ones. Finally, applications of this metric is introduced, such as classification problems. Experimental results validate the effectiveness of the proposed method.

Determining the optimal number of independent components for reproducible transcriptomic data analysis.

Science.gov (United States)

Kairov, Ulykbek; Cantini, Laura; Greco, Alessandro; Molkenov, Askhat; Czerwinska, Urszula; Barillot, Emmanuel; Zinovyev, Andrei

2017-09-11

Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data. Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets. We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

Reproducibility and Variability of I/O Performance on BG/Q: Lessons Learned from a Data Aggregation Algorithm

Energy Technology Data Exchange (ETDEWEB)

Tessier, Francois [Argonne National Lab. (ANL), Argonne, IL (United States); Vishwanath, Venkatram [Argonne National Lab. (ANL), Argonne, IL (United States)

2017-11-28

Reading and writing data efficiently from different tiers of storage is necessary for most scientific simulations to achieve good performance at scale. Many software solutions have been developed to decrease the I/O bottleneck. One wellknown strategy, in the context of collective I/O operations, is the two-phase I/O scheme. This strategy consists of selecting a subset of processes to aggregate contiguous pieces of data before performing reads/writes. In our previous work, we implemented the two-phase I/O scheme with a MPI-based topology-aware algorithm. Our algorithm showed very good performance at scale compared to the standard I/O libraries such as POSIX I/O and MPI I/O. However, the algorithm had several limitations hindering a satisfying reproducibility of our experiments. In this paper, we extend our work by 1) identifying the obstacles we face to reproduce our experiments and 2) discovering solutions that reduce the unpredictability of our results.

Handgrip force steadiness in young and older adults: a reproducibility study.

Science.gov (United States)

Blomkvist, Andreas W; Eika, Fredrik; de Bruin, Eling D; Andersen, Stig; Jorgensen, Martin

2018-04-02

Force steadiness is a quantitative measure of the ability to control muscle tonus. It is an independent predictor of functional performance and has shown to correlate well with different degrees of motor impairment following stroke. Despite being clinically relevant, few studies have assessed the validity of measuring force steadiness. The aim of this study was to explore the reproducibility of handgrip force steadiness, and to assess age difference in steadiness. Intrarater reproducibility (the degree to which a rating gives consistent result on separate occasions) was investigated in a test-retest design with seven days between sessions. Ten young and thirty older adults were recruited and handgrip steadiness was tested at 5%, 10% and 25% of maximum voluntary contraction (MVC) using Nintendo Wii Balance Board (WBB). Coefficients of variation were calculated from the mean force produced (CVM) and the target force (CVT). Area between the force curve and the target force line (Area) was also calculated. For the older adults we explored reliability using intraclass correlation coefficient (ICC) and agreement using standard error of measurement (SEM), limits of agreement (LOA) and smallest real difference (SRD). A systematic improvement in handgrip steadiness was found between sessions for all measures (CVM, CVT, Area). CVM and CVT at 5% of MVC showed good to high reliability, while Area had poor reliability for all percentages of MVC. Averaged ICC for CVM, CVT and Area was 0.815, 0.806 and 0.464, respectively. Averaged ICC on 5%, 10%, and 25% of MVC was 0.751, 0.667 and 0.668, respectively. Measures of agreement showed similar trends with better results for CVM and CVT than for Area. Young adults had better handgrip steadiness than older adults across all measures. The CVM and CVT measures demonstrated good reproducibility at lower percentages of MVC using the WBB, and could become relevant measures in the clinical setting. The Area measure had poor reproducibility

Reproducibility in cyclostratigraphy: initiating an intercomparison project

Science.gov (United States)

Sinnesael, Matthias; De Vleeschouwer, David; Zeeden, Christian; Claeys, Philippe

2017-04-01

The study of astronomical climate forcing and the application of cyclostratigraphy have experienced a spectacular growth over the last decades. In the field of cyclostratigraphy a broad range in methodological approaches exist. However, comparative study between the different approaches is lacking. Different cases demand different approaches, but with the growing importance of the field, questions arise about reproducibility, uncertainties and standardization of results. The radioisotopic dating community, in particular, has done far-reaching efforts to improve reproducibility and intercomparison of radioisotopic dates and their errors. To satisfy this need in cyclostratigraphy, we initiate a comparable framework for the community. The aims are to investigate and quantify reproducibility of, and uncertainties related to cyclostratigraphic studies and to provide a platform to discuss the merits and pitfalls of different methodologies, and their applicabilities. With this poster, we ask the feedback from the community on how to design this comparative framework in a useful, meaningful and productive manner. In parallel, we would like to discuss how reproducibility should be tested and what uncertainties should stand for in cyclostratigraphy. On the other hand, we intend to trigger interest for a cyclostratigraphic intercomparison project. This intercomparison project would imply the analysis of artificial and genuine geological records by individual researchers. All participants would be free to determine their method of choice. However, a handful of criterions will be required for an outcome to be comparable. The different results would be compared (e.g. during a workshop or a special session), and the lessons learned from the comparison could potentially be reported in a review paper. The aim of an intercomparison project is not to rank the different methods according to their merits, but to get insight into which specific methods are most suitable for which

The quest for improved reproducibility in MALDI mass spectrometry.

Science.gov (United States)

O'Rourke, Matthew B; Djordjevic, Steven P; Padula, Matthew P

2018-03-01

Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018. © 2016 Wiley Periodicals, Inc.

The MARS for squat, countermovement, and standing long jump performance analyses: are measures reproducible?

Science.gov (United States)

Hébert-Losier, Kim; Beaven, C Martyn

2014-07-01

Jump tests are often used to assess the effect of interventions because their outcomes are reported valid indicators of functional performance. In this study, we examined the reproducibility of performance parameters from 3 common jump tests obtained using the commercially available Kistler Measurement, Analysis and Reporting Software (MARS). On 2 separate days, 32 men performed 3 squat jumps (SJs), 3 countermovement jumps (CMJs), and 3 standing long jumps (LJs) on a Kistler force-plate. On both days, the performance measures from the best jump of each series were extracted using the MARS. Changes in the mean scores, intraclass correlation coefficients (ICCs), and coefficients of variations (CVs) were computed to quantify the between-day reproducibility of each parameter. Moreover, the reproducibility quantifiers specific to the 3 separate jumps were compared using nonparametric tests. Overall, an acceptable between-day reproducibility (mean ± SD, ICC, and CV) of SJ (0.88 ± 0.06 and 7.1 ± 3.8%), CMJ (0.84 ± 0.17 and 5.9 ± 4.1%), and LJ (0.80 ± 0.13 and 8.1 ± 4.1%) measures was found using the MARS, except for parameters directly relating to the rate of force development (i.e., time to maximal force) and change in momentum during countermovement (i.e., negative force impulse) where reproducibility was lower. A greater proportion of the performance measures from the standing LJs had low ICCs and/or high CVs values most likely owing to the complex nature of the LJ test. Practitioners and researchers can use most of the jump test parameters from the MARS with confidence to quantify changes in the functional ability of individuals over time, except for those relating to the rate of force development or change in momentum during countermovement phases of jumps.

Reproducibility of the cutoff probe for the measurement of electron density

Energy Technology Data Exchange (ETDEWEB)

Kim, D. W.; Oh, W. Y. [Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701 (Korea, Republic of); You, S. J., E-mail: sjyou@cnu.ac.kr [Department of Physics, Chungnam National University, Daejeon 305-701 (Korea, Republic of); Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H., E-mail: jhkim86@kriss.re.kr [Center for Vacuum Technology, Korea Research Institute of Standards and Science, Daejeon 305-306 (Korea, Republic of); Yoon, J.-S. [Plasma Technology Research Center, National Fusion Research Institute, Gunsan 573-540 (Korea, Republic of)

2016-06-15

Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

Reproducibility of the cutoff probe for the measurement of electron density

International Nuclear Information System (INIS)

Kim, D. W.; Oh, W. Y.; You, S. J.; Kwon, J. H.; You, K. H.; Seo, B. H.; Kim, J. H.; Yoon, J.-S.

2016-01-01

Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great reproducibility for the electron density measurement, i.e., there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.

Reproducibility between conventional and digital periapical radiography for bone height measurement

Directory of Open Access Journals (Sweden)

Miguel Simancas Pallares

2015-10-01

Conclusions. Reproducibility between methods was considered poor, including subgroup analysis, therefore, reproducibility between methods is minimal. Usage of these methods in periodontics should be made implementing the whole knowledge of the technical features and the advantages of these systems.

Reproducibility of urodynamic filling sensation at weekly interval in healthy volunteers and in women with detrusor overactivity.

Science.gov (United States)

Van Meel, Tom David; Wyndaele, Jean-Jacques

2011-11-01

To evaluate the reproducibility of bladder sensation during standardized filling cystometry in female volunteers and overactive bladder (OAB) patients, repeated with weekly interval. We recruited 13 female nulliparous volunteers (age 21-47) and 17 female patients with OAB between (age 18-72). They participated in three investigation periods, each separated by 7 days to assess reproducibility of sensation related to standardized cystometry. Subjects were asked to report all sensations they felt during bladder filling. The previously described pattern of sensation was reported during bladder filling in all. Consecutive sensations corresponded to statistically higher bladder volumes. Volumes, at which different sensations of bladder filling were reported, were significantly higher in controls than in OAB patients [first sensation of filling (FSF) P = 0.003, first desire to void (FDV) P sensation/volume ratios were significantly higher in patients with OAB than in the healthy volunteers: FSF occurred at mean 46% and FDV at mean 73% of SDV in OAB patients, compared to 36% and 64% in healthy volunteers. Sensations proved highly reproducible when determined with weekly interval. Our data demonstrate that cystometric filling sensation determined in a standardized way with weekly interval is highly reproducible in healthy and in OAB patients. This finding has, in our opinion, clinical importance as it shows that the technique is reliable both for a sensory evaluation of the LUT as to study influence of treatment aimed at changing this sensation. Copyright © 2011 Wiley Periodicals, Inc.

Tumor budding is a strong and reproducible prognostic marker in T3N0 colorectal cancer.

LENUS (Irish Health Repository)

Wang, Lai Mun

2012-02-01

BACKGROUND: Tumor budding along the advancing front of colorectal adenocarcinoma is an early event in the metastatic process. A reproducible, prognostic budding scoring system based on outcomes in early stage colorectal cancer has not been established. DESIGN: One hundred twenty-eight T3N0M0 colorectal carcinoma patients with known outcome were identified. Tumor budding was defined as isolated tumor cells or clusters of <5 cells at the invasive tumor front. Tumor bud counts were generated in 5 regions at 200x by 2 pathologists (conventional bud count method). The median bud count per case was used to divide cases into low (median=0) and high budding (median > or =1) groups. Forty cases were reevaluated to assess reproducibility using the conventional and a novel rapid bud count method. RESULTS: Fifty-seven (45%) carcinomas had high and 71 (55%) had low budding scores. High budding was associated with an infiltrative growth pattern (P<0.0001) and lymphovascular invasion (P=0.005). Five-year cancer-specific survival was significantly poorer in high compared with low budding groups: 63% versus 91%, respectively, P<0.0001. Multivariate analysis demonstrated tumor budding to be independently prognostic (hazard ratio=4.76, P<0.001). Interobserver agreement was at least equivalent comparing the conventional to the rapid bud count methods: 87.5% agreement (kappa=0.75) versus 92.5% agreement (kappa=0.85), respectively. CONCLUSIONS: Tumor budding is a strong, reproducible, and independent prognostic marker of outcome that is easily assessed on hematoxylin and eosin slides. This may be useful for identifying the subset of T3N0M0 patients at high risk of recurrence who may benefit from adjuvant therapy.

Reproducibility Between Brain Uptake Ratio Using Anatomic Standardization and Patlak-Plot Methods.

Science.gov (United States)

Shibutani, Takayuki; Onoguchi, Masahisa; Noguchi, Atsushi; Yamada, Tomoki; Tsuchihashi, Hiroko; Nakajima, Tadashi; Kinuya, Seigo

2015-12-01

The Patlak-plot and conventional methods of determining brain uptake ratio (BUR) have some problems with reproducibility. We formulated a method of determining BUR using anatomic standardization (BUR-AS) in a statistical parametric mapping algorithm to improve reproducibility. The objective of this study was to demonstrate the inter- and intraoperator reproducibility of mean cerebral blood flow as determined using BUR-AS in comparison to the conventional-BUR (BUR-C) and Patlak-plot methods. The images of 30 patients who underwent brain perfusion SPECT were retrospectively used in this study. The images were reconstructed using ordered-subset expectation maximization and processed using an automatic quantitative analysis for cerebral blood flow of ECD tool. The mean SPECT count was calculated from axial basal ganglia slices of the normal side (slices 31-40) drawn using a 3-dimensional stereotactic region-of-interest template after anatomic standardization. The mean cerebral blood flow was calculated from the mean SPECT count. Reproducibility was evaluated using coefficient of variation and Bland-Altman plotting. For both inter- and intraoperator reproducibility, the BUR-AS method had the lowest coefficient of variation and smallest error range about the Bland-Altman plot. Mean CBF obtained using the BUR-AS method had the highest reproducibility. Compared with the Patlak-plot and BUR-C methods, the BUR-AS method provides greater inter- and intraoperator reproducibility of cerebral blood flow measurement. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

[HPV primary test in the cervical cancer screening: reproducibility assessment and investigation on cytological outcome of Hybrid Capture 2 borderline samples].

Science.gov (United States)

Burroni, Elena; Sani, Cristina; Bisanzi, Simonetta; Ocello, Cristina

2016-01-01

to evaluate the reproducibility of the High-Risk Hybrid Capture 2 (HC2-HR, Qiagen) test within the frame of cervical cancer screening with HPV, for samples with values very close to the cut-off (borderline), that is 0.80≤RLU/CO≤0.99 (RLU/CO: relative light units/cut-off) and to assess any possible presence of high grade lesions. all borderline samples collected from January 2014 to August 2015 were repeated with HR-HC2 test within two weeks from the first test. For HPV-positive samples, cytology and colposcopy results (if present) were analysed. national and international directions recommend the use of HPV testing as a primary test for cervical cancer screening for women aged 30/34-64 years. In Tuscany Region (Central Italy) the primary screening with HPV test was introduced in 2013 and the HPV test currently used, HR-HC2, has a positive cut-off≥1 RLU/CO. proportion of HPV-positive tests at repetition, then stratified by type of material (ThinPrep, STM) and for the following subclasses of RLU/CO: 0.80-0.89 and 0.90-0.99. 253 samples were borderline at first test with HR-HC2 (about 0.4% of all samples tested). About 83% (209/253) of the samples was confirmed to be negative at the HPV test repetition: 88% for RLU/CO=0.80-0.89 and 76% for RLU/CO=0.90-0.99 (p-value=0.014). Median RLU/CO value of 44 HPV-positive samples at repetition is 1.4, with a maximum RLU/CO value of 16.7. In addition, 90% of HPV-positive samples at repetition has a RLU/CO values below or equal to 3.6. Even the used sampling system affects reproducibility: 26.4% (33/125) of the samples resulted positive at the repetition were in ThinPrep vs. 8.6% (11/128) of those in STM (p-valuecut-off (0.90-0.99), confirming the intrinsic limit to all analytical methods near to the cut-off. Moreover, even if the difference in reproducibility between the two systems of sampling is statistically significant, in samples that resulted positive at repetition high-grade lesions were not found at the time of HPV

SU-F-T-55: Reproducibility of Interstitial HDR Brachytherapy Plans

Energy Technology Data Exchange (ETDEWEB)

Lee, S; Ellis, R; Traughber, B; Podder, T [University Hospitals Case Medical Center, Cleveland, OH (United States)

2016-06-15

Purpose: Treating gynecological cancers with interstitial high-dose-rate (HDR) brachytherapy requires precise reconstruction of catheter positions to obtain accurate dosimetric plans. In this study, we investigated the degree of reproducibility of dosimetric plans for Syed HDR brachytherapy. Methods: We randomly selected five patients having cervix-vaginal cancer who were recently treated in our clinic with interstitial HDR brachytherapy with a prescription dose of 25–30 Gy in five fractions. Interstitial needles/catheters were placed under fluoroscopic guidance and intra-operative 3T MRI scan was performed to confirm the desired catheter placement for adequate target volume coverage. A CT scan was performed and fused with the MRI for delineating high-risk CTV (HR-CTV), intermediate-risk CTV (IR-CTV) and OARs. HDR treatment plans were generated using Oncentra planning software. A single plan was used for all five fractions of treatment for each patient. For this study, we took the original clinical plan and removed all the reconstructed catheters from the plan keeping the original contours unchanged. Then, we manually reconstructed all the catheters and entered the same dwell time from the first original clinical plan. The dosimetric parameters studied were: D90 for HR-CTV and IR-CV, and D2cc for bladder, rectum, sigmoid and bowel. Results: The mean of absolute differences in dosimetric coverage (D90) were (range): 1.3% (1.0–2.0%) and 2.0% (0.9–3.6%) for HR-CTV and IR-CTV, respectively. In case of OARs, the mean of absolute variations in D2cc were (range): 4.7% (0.7–8.9%) for bladder, 1.60% (0.3–3.2%) for rectum, 1.6% (0–3.9%) for sigmoid, and 1.8% (0–5.1%) for bowel. Conclusion: Overall, the reproducibility of interstitial HDR plans was within clinically acceptable limit. Observed maximum variation in D2cc for bladder. If number of catchers and dwell points were relatively low or any one catheter was heavily loaded, then reproducibility of the plan

An analysis of reproducibility and non-determinism in HEP software and ROOT data

Science.gov (United States)

Ivie, Peter; Zheng, Charles; Lannon, Kevin; Thain, Douglas

2017-10-01

Reproducibility is an essential component of the scientific method. In order to validate the correctness or facilitate the extension of a computational result, it should be possible to re-run a published result and verify that the same results are produced. However, reproducing a computational result is surprisingly difficult: non-determinism and other factors may make it impossible to get the same result, even when running the same code on the same machine on the same day. We explore this problem in the context of HEP codes and data, showing three high level methods for dealing with non-determinism in general: 1) Domain specific methods; 2) Domain specific comparisons; and 3) Virtualization adjustments. Using a CMS workflow with output data stored in ROOT files, we use these methods to prevent, detect, and eliminate some sources of non-determinism. We observe improved determinism using pre-determined random seeds, a predictable progression of system timestamps, and fixed process identifiers. Unfortunately, sources of non-determinism continue to exist despite the combination of all three methods. Hierarchical data comparisons also allow us to appropriately ignore some non-determinism when it is unavoidable. We conclude that there is still room for improvement, and identify directions that can be taken in each method to make an experiment more reproducible.

Spatial aspects of sound quality - and by multichannel systems subjective assessment of sound reproduced by stereo

DEFF Research Database (Denmark)

Choisel, Sylvain

the fidelity with which sound reproduction systems can re-create the desired stereo image, a laser pointing technique was developed to accurately collect subjects' responses in a localization task. This method is subsequently applied in an investigation of the effects of loudspeaker directivity...... on the perceived direction of panned sources. The second part of the thesis addresses the identification of auditory attributes which play a role in the perception of sound reproduced by multichannel systems. Short musical excerpts were presented in mono, stereo and several multichannel formats to evoke various...

Reproducibility of 3.0 Tesla Magnetic Resonance Spectroscopy for Measuring Hepatic Fat Content

NARCIS (Netherlands)

van Werven, Jochem R.; Hoogduin, Johannes M.; Nederveen, Aart J.; van Vliet, Andre A.; Wajs, Ewa; Vandenberk, Petra; Stroes, Erik S. G.; Stoker, Jaap

Purpose: To investigate reproducibility of proton magnetic resonance spectroscopy (H-1-MRS) to measure hepatic triglyceride content (HTGC). Materials and Methods: In 24 subjects, HTGC was evaluated using H-1-MRS at 3.0 Tesla. We studied "between-weeks" reproducibility and reproducibility of H-1-MRS

Completely reproducible description of digital sound data with cellular automata

International Nuclear Information System (INIS)

Wada, Masato; Kuroiwa, Jousuke; Nara, Shigetoshi

2002-01-01

A novel method of compressive and completely reproducible description of digital sound data by means of rule dynamics of CA (cellular automata) is proposed. The digital data of spoken words and music recorded with the standard format of a compact disk are reproduced completely by this method with use of only two rules in a one-dimensional CA without loss of information

Efficient and reproducible mammalian cell bioprocesses without probes and controllers?

Science.gov (United States)

Tissot, Stéphanie; Oberbek, Agata; Reclari, Martino; Dreyer, Matthieu; Hacker, David L; Baldi, Lucia; Farhat, Mohamed; Wurm, Florian M

2011-07-01

Bioprocesses for recombinant protein production with mammalian cells are typically controlled for several physicochemical parameters including the pH and dissolved oxygen concentration (DO) of the culture medium. Here we studied whether these controls are necessary for efficient and reproducible bioprocesses in an orbitally shaken bioreactor (OSR). Mixing, gas transfer, and volumetric power consumption (P(V)) were determined in both a 5-L OSR and a 3-L stirred-tank bioreactor (STR). The two cultivation systems had a similar mixing intensity, but the STR had a lower volumetric mass transfer coefficient of oxygen (k(L)a) and a higher P(V) than the OSR. Recombinant CHO cell lines expressing either tumor necrosis factor receptor as an Fc fusion protein (TNFR:Fc) or an anti-RhesusD monoclonal antibody were cultivated in the two systems. The 5-L OSR was operated in an incubator shaker with 5% CO(2) in the gas environment but without pH and DO control whereas the STR was operated with or without pH and DO control. Higher cell densities and recombinant protein titers were obtained in the OSR as compared to both the controlled and the non-controlled STRs. To test the reproducibility of a bioprocess in a non-controlled OSR, the two CHO cell lines were each cultivated in parallel in six 5-L OSRs. Similar cell densities, cell viabilities, and recombinant protein titers along with similar pH and DO profiles were achieved in each group of replicates. Our study demonstrated that bioprocesses can be performed in OSRs without pH or DO control in a highly reproducible manner, at least at the scale of operation studied here. Copyright © 2011 Elsevier B.V. All rights reserved.

Reproducibility of the Portuguese version of the PEDro Scale

Directory of Open Access Journals (Sweden)

Silvia Regina Shiwa

2011-10-01

Full Text Available The objective of this study was to test the inter-rater reproducibility of the Portuguese version of the PEDro Scale. Seven physiotherapists rated the methodological quality of 50 reports of randomized controlled trials written in Portuguese indexed on the PEDro database. Each report was also rated using the English version of the PEDro Scale. Reproducibility was evaluated by comparing two separate ratings of reports written in Portuguese and comparing the Portuguese PEDro score with the English version of the scale. Kappa coefficients ranged from 0.53 to 1.00 for individual item and an intraclass correlation coefficient (ICC of 0.82 for the total PEDro score was observed. The standard error of the measurement of the scale was 0.58. The Portuguese version of the scale was comparable with the English version, with an ICC of 0.78. The inter-rater reproducibility of the Brazilian Portuguese PEDro Scale is adequate and similar to the original English version.

Reproducibility of the Internal Load and Performance-Based Responses to Simulated Amateur Boxing.

Science.gov (United States)

Thomson, Edward D; Lamb, Kevin L

2017-12-01

Thomson, ED and Lamb, KL. Reproducibility of the internal load and performance-based responses to simulated amateur boxing. J Strength Cond Res 31(12): 3396-3402, 2017-The aim of this study was to examine the reproducibility of the internal load and performance-based responses to repeated bouts of a three-round amateur boxing simulation protocol (boxing conditioning and fitness test [BOXFIT]). Twenty-eight amateur boxers completed 2 familiarization trials before performing 2 complete trials of the BOXFIT, separated by 4-7 days. To characterize the internal load, mean (HRmean) and peak (HRpeak) heart rate, breath-by-breath oxygen uptake (V[Combining Dot Above]O2), aerobic energy expenditure, excess carbon dioxide production (CO2excess), and ratings of perceived exertion were recorded throughout each round, and blood lactate determined post-BOXFIT. Additionally, an indication of the performance-based demands of the BOXFIT was provided by a measure of acceleration of the punches thrown in each round. Analyses revealed there were no significant differences (p > 0.05) between repeated trials in any round for all dependent measures. The typical error (coefficient variation %) for all but 1 marker of internal load (CO2excess) was 1.2-16.5% and reflected a consistency that was sufficient for the detection of moderate changes in variables owing to an intervention. The reproducibility of the punch accelerations was high (coefficient of variance % range = 2.1-2.7%). In general, these findings suggest that the internal load and performance-based efforts recorded during the BOXFIT are reproducible and, thereby, offer practitioners a method by which meaningful changes impacting on performance could be identified.

Evaluation of MidIR fibre optic reflectance: Detection limit, reproducibility and binary mixture discrimination

Science.gov (United States)

Sessa, Clarimma; Bagán, Héctor; García, José Francisco

2013-11-01

MidIR fibre optic reflectance (MidIR-FORS) is a promising analytical technique in the field of science conservation, especially because it is non-destructive. Another advantage of MidIR-FORS is that the obtained information is representative, as a large amount of spectral data can be collected. Although the technique has a high potential and is almost routinely applied, its quality parameters have not been thoroughly studied in the specific application of analysis of artistic materials. The objective of this study is to evaluate the instrumental capabilities of MidIR-FORS for the analysis of artwork materials in terms of detection limit, reproducibility, and mixture characterisation. The study has been focused on oil easel painting and several paints of known composition have been analysed. Paint layers include blue pigments not only because of their important role along art history, but also because their physical and spectroscopic characteristics allow a better evaluation of the MidIR-FORS capabilities. The results of the analysis indicate that MidIR-FORS supplies a signal affected by different factors, such as the optical, morphological and physical properties of the surface, in addition to the composition of materials analysed. Consequently, the detection limits established are relatively high for artistic objects (Prussian blue - PB 2.1-6.5%; Phthalocyanine blue - Pht 6.3-10.2%; synthetic Ultramarine blue - UM 12.1%) and may therefore lead to an incomplete description of the artwork. Reproducibility of the technique over time and across surface has been determined. The results show that the major sources of dispersion are the heterogeneity of the pigments distribution, physical features, and band shape distortions. The total dispersion is around 4% for the most intense bands (oil) and increases up to 26% when weak or overlapped bands are considered (PB, Pht, UM). The application of different pre-treatments (cutoff of fibres absorption, Savizky-Golay smoothing

Combination of dynamic and integral methods for generating reproducible functional CBF images

International Nuclear Information System (INIS)

Lammertsma, A.A.; Cunningham, V.J.; Deiber, M.P.; Heather, J.D.; Bloomfield, P.M.; Nutt, J.; Frackowiak, R.S.; Jones, T.

1990-01-01

A new method to measure regional CBF is presented, applying both dynamic and integral analyses to a dynamic sequence of positron emission tomographic scans collected during and following the administration of H2(15)O (inhalation of C15O2). The dynamic analysis is used to correct continuously monitored arterial whole-blood activity for delay and dispersion relative to tissue scans. An integral analysis including corrections for this delay and dispersion is then used to calculate CBF on a pixel-by-pixel basis. Normal values and reproducibility over a 2-h period are presented, together with the results of validation and simulation studies. The results indicate that the single-tissue compartment model adequately describes the distribution of H2(15)O in the brain, without recourse to postulating a nonexchanging water pool

Long-term reproducibility of in vivo measures of specific binding of radioligands in rat brain

Energy Technology Data Exchange (ETDEWEB)

Kilbourn, Michael R. E-mail: mkilbour@umich.edu

2004-07-01

The long-term reproducibility of measures of in vivo specific binding of radiolabeled forms of (+)-{alpha}-dihydrotetrabenazine (DTBZ) and d-threo-methylphenidate (MPH) in rat brain was examined. All studies were done using a consistent bolus plus infusion protocol and calculation of equilibrium distribution volume ratios (DVR). Over a period of eight years striatal DVR values for DTBZ binding to the vesicular monoamine transporter 2 (VMAT2) in young adult (8-10 wks old) rats showed very good reproducibility (3.62{+-}0.33, N=35). Equivalent values were obtained using either tritiated or carbon-11 labeled DTBZ, and were irrespective of sex of animals. Older animals (78 wks old) showed losses (-45%) of specific binding. Striatal binding of MPH to the dopamine transporter (DAT) showed a similar reproducibility over a five year period (DVR=2.17{+-}0.39, N=52), again irrespective of radionuclide or sex. These studies demonstrate that use of a consistent in vivo technique can provide reliable measures of specific binding of radioligands to high affinity sites in the rat brain.

An empirical analysis of journal policy effectiveness for computational reproducibility.

Science.gov (United States)

Stodden, Victoria; Seiler, Jennifer; Ma, Zhaokun

2018-03-13

A key component of scientific communication is sufficient information for other researchers in the field to reproduce published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for reproducibility be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by ( i ) requesting data and code from authors and ( ii ) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44% of our sample and were able to reproduce the findings for 26%. We find this policy-author remission of data and code postpublication upon request-an improvement over no policy, but currently insufficient for reproducibility.

ANALYSIS OF INDIVIDUAL BIOLOGICAL CHARACTERISTICS OF AMUR CARP (CYPRINUS CARPIO HAEMATOPTERUS REPRODUCED USING CRYOPRESERVED SPERM

Directory of Open Access Journals (Sweden)

N. Kolisnyk

2014-12-01

Full Text Available Purpose. To reproduce Amur carp population using cryopreserved sperm and analyze some biological and fish culture peculiarities of the reproduced fish stock. Methodology. Generally accepted methods for fish culture [1]. Experimental reproduction was carried out in pond conditions of «Carpathian vodogray» LTD (Lisnevychi village, Pustomytivsky district, Lviv region. Hydrochemical analysis was carried out classically by O. Alуokin (1970 [2], hydrobiological studies in the fatting ponds according to V. Zhadin (1956, 1960 [3, 4]. Haemoglobin concentration was determined by hemocyanin method of G. Dervis, A. Vorobiov [5]. Blood for this method was collected from fish heart with the use of Pasteur pipettes in Eppendorf tubes with heparin. Following exterior morphometric parameters were analysed: body weight (m, g, standard fish body length (l, cm, largest body height (H, cm and body circumference (O cm. Following exterior indices were calculated based on these parameters: body depth index (l/H, body circumference index (l/O and Fulton’s condition factor (Kv. The study was carried out using two groups of carp: control and experimental. The first group was reproduced from the native sperm, the second from the cryopreserved sperm. Findings. Carp reproduction and growing was carried out using native and cryopreserved sperm. This work contains the results of growing 1+ Amur carp of experimental and control groups. Hydrochemical and hydrobiological parameters of the fattening ponds were studied. Peculiarities of the exterior and some hematological parameters of the carp of different origin were characterized. Originality. For the first time we performed a comparison of some biological parameters of Amur carp reproduced using native and cryopreserved sperm. Practical Value. Considering the economic importance of Amur carp due to its use in hybridization, reproduction of its population plays an important role in the development of the stocks of the pure

Reproducing Kernel Method for Solving Nonlinear Differential-Difference Equations

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Reza Mokhtari

2012-01-01

Full Text Available On the basis of reproducing kernel Hilbert spaces theory, an iterative algorithm for solving some nonlinear differential-difference equations (NDDEs is presented. The analytical solution is shown in a series form in a reproducing kernel space, and the approximate solution , is constructed by truncating the series to terms. The convergence of , to the analytical solution is also proved. Results obtained by the proposed method imply that it can be considered as a simple and accurate method for solving such differential-difference problems.

Archiving Reproducible Research with R and Dataverse

DEFF Research Database (Denmark)

Leeper, Thomas

2014-01-01

Reproducible research and data archiving are increasingly important issues in research involving statistical analyses of quantitative data. This article introduces the dvn package, which allows R users to publicly archive datasets, analysis files, codebooks, and associated metadata in Dataverse...

Short term reproducibility of a high contrast 3-D isotropic optic nerve imaging sequence in healthy controls

Science.gov (United States)

Harrigan, Robert L.; Smith, Alex K.; Mawn, Louise A.; Smith, Seth A.; Landman, Bennett A.

2016-03-01

The optic nerve (ON) plays a crucial role in human vision transporting all visual information from the retina to the brain for higher order processing. There are many diseases that affect the ON structure such as optic neuritis, anterior ischemic optic neuropathy and multiple sclerosis. Because the ON is the sole pathway for visual information from the retina to areas of higher level processing, measures of ON damage have been shown to correlate well with visual deficits. Increased intracranial pressure has been shown to correlate with the size of the cerebrospinal fluid (CSF) surrounding the ON. These measures are generally taken at an arbitrary point along the nerve and do not account for changes along the length of the ON. We propose a high contrast and high-resolution 3-D acquired isotropic imaging sequence optimized for ON imaging. We have acquired scan-rescan data using the optimized sequence and a current standard of care protocol for 10 subjects. We show that this sequence has superior contrast-to-noise ratio to the current standard of care while achieving a factor of 11 higher resolution. We apply a previously published automatic pipeline to segment the ON and CSF sheath and measure the size of each individually. We show that these measures of ON size have lower short- term reproducibility than the population variance and the variability along the length of the nerve. We find that the proposed imaging protocol is (1) useful in detecting population differences and local changes and (2) a promising tool for investigating biomarkers related to structural changes of the ON.

Reproducibility of cervical range of motion in patients with neck pain

NARCIS (Netherlands)

Pool, JJM; van Mameren, H; Deville, WJLM; Assendelft, WJJ; de Vet, HCW; de Winter, AF; Koes, BW; Bouter, LM; Hoving, J.L.

2005-01-01

Background: Reproducibility measurements of the range of motion are an important prerequisite for the interpretation of study results. The aim of the study is to assess the intra-rater and interrater reproducibility of the measurement of active Range of Motion ( ROM) in patients with neck pain using

Reproducibility study of TLD-100 micro-cubes at radiotherapy dose level

International Nuclear Information System (INIS)

Rosa, Luiz Antonio R. da; Regulla, Dieter F.; Fill, Ute A.

1999-01-01

The precision of the thermoluminescent response of Harshaw micro-cube dosimeters (TLD-100), evaluated in both Harshaw thermoluminescent readers 5500 and 3500, for 1 Gy dose value, was investigated. The mean reproducibility for micro-cubes, pre-readout annealed at 100 deg. C for 15 min, evaluated with the manual planchet reader 3500, is 0.61% (1 standard deviation). When micro-cubes are evaluated with the automated hot-gas reader 5500, reproducibility values are undoubtedly worse, mean reproducibility for numerically stabilised dosimeters being equal to 3.27% (1 standard deviation). These results indicate that the reader model 5500, or, at least, the instrument used for the present measurements, is not adequate for micro-cube evaluation, if precise and accurate dosimetry is required. The difference in precision is apparently due to geometry inconsistencies in the orientation of the imperfect micro-cube faces during readout, requiring careful and manual reproducible arrangement of the selected micro-cube faces in contact with the manual reader planchet

Cystic fibrosis in adults. Short-term and long-term reproducibility of the Brody score for lung morphology in low-dose MDCT scans

Energy Technology Data Exchange (ETDEWEB)

Weber, K.; Paolini, M.; Schmitz, M.; Coppenrath, E.; Reiser, M.; Mueller-Lisse, U.G. [Ludwig-Maximilians-Univ. Muenchen (Germany). Inst. fuer Klinische Radiologie; Fischer, R.; Huber, R. [Ludwig-Maximilians-Univ. Muenchen (Germany). Medical Hospital V

2014-01-15

Purpose: The semi-quantitative Brody score measures the severity of cystic fibrosis (CF)-related lung disease. We investigated the short-term (28 - 60 days) and long-term (2 - 7 years) intra- and inter-observer reproducibility of the Brody score in low-dose multidetector row computed tomography examinations performed in inspiration (LDCTs) of adult CF patients. Materials and Methods: Composite Brody scores and respective underlying bronchiectasis, mucus plugging, peribronchial thickening, parenchymal opacity, and hyperinflation subscores were evaluated twice (time interval, 1 - 84 months) by each of 3 independent radiologists (1 - 20 years of professional diagnostic radiology experience) in LDCTs (4 - 64 rows, 120 KVp, 10 - 15 mAs/slice, CTDIw approx. 1.0 mGy, effective dose approx. 0.5 mSv) of 15 adult patients with CF-related lung disease (8 female, 7 male, age, 18 - 50 years, mean, 33 years). Results: The average reproducibility of the Brody score was within +/-7 % (range, 2 - 30 %) between radiologists, and +/-6 % (3 - 12 %) within radiologists (short-term, 28 - 60 days, 4 %, 0 - 12 %, long-term, 2 - 7 years, 12 %, 1 - 36 %). For the different subscores, the reproducibility was within +/-25 % (15 - 41 %) between radiologists and +/-23 % (12 - 46 %) within radiologists. Conclusion: The Brody score shows high average inter-observer reproducibility in LDCTs of adult CF patients. The Brody score also demonstrates high average intra-observer reproducibility if subsequent assessments are made within 28 - 61 days. With time intervals of 2 - 7 years between subsequent evaluations, however, intra-observer reproducibility decreases. Respective subscores each demonstrate lower intra- and inter-observer reproducibility than does the composite Brody score. (orig.)

Scapular dyskinesis in trapezius myalgia and intraexaminer reproducibility of clinical tests

DEFF Research Database (Denmark)

Juul-Kristensen, Birgit; Hilt, Kenneth; Enoch, Flemming

2011-01-01

dyskinesis, general health, and work ability, and 19 cases and 14 controls participated in the reproducibility study. Intraexaminer reproducibility was good to excellent for 6 of 10 clinical variables (Intraclass Correlation Coefficient [ICC] 0.76-0.91; kappa 0.84-1.00), and fair to good for four variables...

Reproducibility of cervical range of motion in patients with neck pain

NARCIS (Netherlands)

Hoving, Jan Lucas; Pool, Jan J. M.; van Mameren, Henk; Devillé, Walter J. L. M.; Assendelft, Willem J. J.; de Vet, Henrica C. W.; de Winter, Andrea F.; Koes, Bart W.; Bouter, Lex M.

2005-01-01

BACKGROUND: Reproducibility measurements of the range of motion are an important prerequisite for the interpretation of study results. The aim of the study is to assess the intra-rater and inter-rater reproducibility of the measurement of active Range of Motion (ROM) in patients with neck pain using

Accuracy and reproducibility of adipose tissue measurements in young infants by whole body magnetic resonance imaging.

Science.gov (United States)

Bauer, Jan Stefan; Noël, Peter Benjamin; Vollhardt, Christiane; Much, Daniela; Degirmenci, Saliha; Brunner, Stefanie; Rummeny, Ernst Josef; Hauner, Hans

2015-01-01

MR might be well suited to obtain reproducible and accurate measures of fat tissues in infants. This study evaluates MR-measurements of adipose tissue in young infants in vitro and in vivo. MR images of ten phantoms simulating subcutaneous fat of an infant's torso were obtained using a 1.5T MR scanner with and without simulated breathing. Scans consisted of a cartesian water-suppression turbo spin echo (wsTSE) sequence, and a PROPELLER wsTSE sequence. Fat volume was quantified directly and by MR imaging using k-means clustering and threshold-based segmentation procedures to calculate accuracy in vitro. Whole body MR was obtained in sleeping young infants (average age 67±30 days). This study was approved by the local review board. All parents gave written informed consent. To obtain reproducibility in vivo, cartesian and PROPELLER wsTSE sequences were repeated in seven and four young infants, respectively. Overall, 21 repetitions were performed for the cartesian sequence and 13 repetitions for the PROPELLER sequence. In vitro accuracy errors depended on the chosen segmentation procedure, ranging from 5.4% to 76%, while the sequence showed no significant influence. Artificial breathing increased the minimal accuracy error to 9.1%. In vivo reproducibility errors for total fat volume of the sleeping infants ranged from 2.6% to 3.4%. Neither segmentation nor sequence significantly influenced reproducibility. With both cartesian and PROPELLER sequences an accurate and reproducible measure of body fat was achieved. Adequate segmentation was mandatory for high accuracy.

Accuracy and reproducibility of adipose tissue measurements in young infants by whole body magnetic resonance imaging.

Directory of Open Access Journals (Sweden)

Jan Stefan Bauer

Full Text Available MR might be well suited to obtain reproducible and accurate measures of fat tissues in infants. This study evaluates MR-measurements of adipose tissue in young infants in vitro and in vivo.MR images of ten phantoms simulating subcutaneous fat of an infant's torso were obtained using a 1.5T MR scanner with and without simulated breathing. Scans consisted of a cartesian water-suppression turbo spin echo (wsTSE sequence, and a PROPELLER wsTSE sequence. Fat volume was quantified directly and by MR imaging using k-means clustering and threshold-based segmentation procedures to calculate accuracy in vitro. Whole body MR was obtained in sleeping young infants (average age 67±30 days. This study was approved by the local review board. All parents gave written informed consent. To obtain reproducibility in vivo, cartesian and PROPELLER wsTSE sequences were repeated in seven and four young infants, respectively. Overall, 21 repetitions were performed for the cartesian sequence and 13 repetitions for the PROPELLER sequence.In vitro accuracy errors depended on the chosen segmentation procedure, ranging from 5.4% to 76%, while the sequence showed no significant influence. Artificial breathing increased the minimal accuracy error to 9.1%. In vivo reproducibility errors for total fat volume of the sleeping infants ranged from 2.6% to 3.4%. Neither segmentation nor sequence significantly influenced reproducibility.With both cartesian and PROPELLER sequences an accurate and reproducible measure of body fat was achieved. Adequate segmentation was mandatory for high accuracy.

Quantized correlation coefficient for measuring reproducibility of ChIP-chip data

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Kuroda Mitzi I

2010-07-01

Full Text Available Abstract Background Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip is used to study protein-DNA interactions and histone modifications on a genome-scale. To ensure data quality, these experiments are usually performed in replicates, and a correlation coefficient between replicates is used often to assess reproducibility. However, the correlation coefficient can be misleading because it is affected not only by the reproducibility of the signal but also by the amount of binding signal present in the data. Results We develop the Quantized correlation coefficient (QCC that is much less dependent on the amount of signal. This involves discretization of data into set of quantiles (quantization, a merging procedure to group the background probes, and recalculation of the Pearson correlation coefficient. This procedure reduces the influence of the background noise on the statistic, which then properly focuses more on the reproducibility of the signal. The performance of this procedure is tested in both simulated and real ChIP-chip data. For replicates with different levels of enrichment over background and coverage, we find that QCC reflects reproducibility more accurately and is more robust than the standard Pearson or Spearman correlation coefficients. The quantization and the merging procedure can also suggest a proper quantile threshold for separating signal from background for further analysis. Conclusions To measure reproducibility of ChIP-chip data correctly, a correlation coefficient that is robust to the amount of signal present should be used. QCC is one such measure. The QCC statistic can also be applied in a variety of other contexts for measuring reproducibility, including analysis of array CGH data for DNA copy number and gene expression data.

Quantized correlation coefficient for measuring reproducibility of ChIP-chip data.

Science.gov (United States)

Peng, Shouyong; Kuroda, Mitzi I; Park, Peter J

2010-07-27

Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip) is used to study protein-DNA interactions and histone modifications on a genome-scale. To ensure data quality, these experiments are usually performed in replicates, and a correlation coefficient between replicates is used often to assess reproducibility. However, the correlation coefficient can be misleading because it is affected not only by the reproducibility of the signal but also by the amount of binding signal present in the data. We develop the Quantized correlation coefficient (QCC) that is much less dependent on the amount of signal. This involves discretization of data into set of quantiles (quantization), a merging procedure to group the background probes, and recalculation of the Pearson correlation coefficient. This procedure reduces the influence of the background noise on the statistic, which then properly focuses more on the reproducibility of the signal. The performance of this procedure is tested in both simulated and real ChIP-chip data. For replicates with different levels of enrichment over background and coverage, we find that QCC reflects reproducibility more accurately and is more robust than the standard Pearson or Spearman correlation coefficients. The quantization and the merging procedure can also suggest a proper quantile threshold for separating signal from background for further analysis. To measure reproducibility of ChIP-chip data correctly, a correlation coefficient that is robust to the amount of signal present should be used. QCC is one such measure. The QCC statistic can also be applied in a variety of other contexts for measuring reproducibility, including analysis of array CGH data for DNA copy number and gene expression data.

Reproducibility of the dynamics of facial expressions in unilateral facial palsy.

Science.gov (United States)

Alagha, M A; Ju, X; Morley, S; Ayoub, A

2018-02-01

The aim of this study was to assess the reproducibility of non-verbal facial expressions in unilateral facial paralysis using dynamic four-dimensional (4D) imaging. The Di4D system was used to record five facial expressions of 20 adult patients. The system captured 60 three-dimensional (3D) images per second; each facial expression took 3-4seconds which was recorded in real time. Thus a set of 180 3D facial images was generated for each expression. The procedure was repeated after 30min to assess the reproducibility of the expressions. A mathematical facial mesh consisting of thousands of quasi-point 'vertices' was conformed to the face in order to determine the morphological characteristics in a comprehensive manner. The vertices were tracked throughout the sequence of the 180 images. Five key 3D facial frames from each sequence of images were analyzed. Comparisons were made between the first and second capture of each facial expression to assess the reproducibility of facial movements. Corresponding images were aligned using partial Procrustes analysis, and the root mean square distance between them was calculated and analyzed statistically (paired Student t-test, PFacial expressions of lip purse, cheek puff, and raising of eyebrows were reproducible. Facial expressions of maximum smile and forceful eye closure were not reproducible. The limited coordination of various groups of facial muscles contributed to the lack of reproducibility of these facial expressions. 4D imaging is a useful clinical tool for the assessment of facial expressions. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

Directory of Open Access Journals (Sweden)

Dazard Jean-Eudes

2012-06-01

Full Text Available Abstract Background Affinity-Purification Mass-Spectrometry (AP-MS provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. Methods To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. Results We illustrate the performance of our method by applying

Search for Correlations between Prolate-Shape Collective and Oblate-Shape Non-Collective Nuclear Rotation: High Spin States in 159,160 Yb

International Nuclear Information System (INIS)

Byrski, T.; Beck, F.A.; Sharpey-Schafer, J.F.

1987-01-01

High-spin states of 159,160 Yb have been studied using the escape-suppressed array TESSA 2. Extensions of yrast and lateral bands have been found up to I ∼40. Experimental data suggest strong correlations between maximum alignment configurations of the valence nucleons and related collective states. Theoretical analysis fully supports the idea of prolate-collective vs. oblate-non-collective correlations. Band termination interpretation is discussed

Reproducing kernel Hilbert spaces of Gaussian priors

NARCIS (Netherlands)

Vaart, van der A.W.; Zanten, van J.H.; Clarke, B.; Ghosal, S.

2008-01-01

We review definitions and properties of reproducing kernel Hilbert spaces attached to Gaussian variables and processes, with a view to applications in nonparametric Bayesian statistics using Gaussian priors. The rate of contraction of posterior distributions based on Gaussian priors can be described

Reproducibility, Controllability, and Optimization of Lenr Experiments

Science.gov (United States)

Nagel, David J.

2006-02-01

Low-energy nuclear reaction (LENR) measurements are significantly and increasingly reproducible. Practical control of the production of energy or materials by LENR has yet to be demonstrated. Minimization of costly inputs and maximization of desired outputs of LENR remain for future developments.

Intra- and inter-observer reproducibility of global and regional magnetic resonance feature tracking derived strain parameters of the left and right ventricle

Energy Technology Data Exchange (ETDEWEB)

Schmidt, Björn, E-mail: bjoernschmidt1989@gmx.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Dick, Anastasia, E-mail: anastasia-dick@web.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Treutlein, Melanie, E-mail: melanie-treutlein@web.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Schiller, Petra, E-mail: petra.schiller@uni-koeln.de [Institute of Medical Statistics, Informatics and Epidemiology, University of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Bunck, Alexander C., E-mail: alexander.bunck@uk-koeln.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Maintz, David, E-mail: david.maintz@uk-koeln.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany); Baeßler, Bettina, E-mail: bettina.baessler@uk-koeln.de [Department of Radiology, University Hospital of Cologne, Kerpener Str. 62, D-50937, Cologne (Germany)

2017-04-15

Highlights: • Left and right ventricular CMR feature tracking is highly reproducible. • The only exception is radial strain and strain rate. • Sample size estimations are presented as a practical reference for future studies. - Abstract: Objectives: To investigate the reproducibility of regional and global strain and strain rate (SR) parameters of both ventricles and to determine sample sizes for all investigated strain and SR parameters in order to generate a practical reference for future studies. Materials and methods: The study population consisted of 20 healthy individuals and 20 patients with acute myocarditis. Cine sequences in three horizontal long axis views and a stack of short axis views covering the entire left and right ventricle (LV, RV) were retrospectively analysed using a dedicated feature tracking (FT) software algorithm (TOMTEC). For intra-observer analysis, one observer analysed CMR images of all patients and volunteers twice. For inter-observer analysis, three additional blinded observers analysed the same datasets once. Intra- and inter-observer reproducibility were tested in all patients and controls using Bland-Altman analyses, intra-class correlation coefficients (ICCs) and coefficients of variation. Results: Intra-observer reproducibility of global LV strain and SR parameters was excellent (range of ICCs: 0.81–1.00), the only exception being global radial SR with a poor reproducibility (ICC 0.23). On a regional level, basal and midventricular strain and SR parameters were more reproducible when compared to apical parameters. Inter-observer reproducibility of all LV parameters was slightly lower than intra-observer reproducibility, yet still good to excellent for all global and regional longitudinal and circumferential strain and SR parameters (range of ICCs: 0.66–0.93). Similar to the LV, all global RV longitudinal and circumferential strain and SR parameters showed an excellent reproducibility, (range of ICCs: 0.75–0

Intra- and inter-observer reproducibility of global and regional magnetic resonance feature tracking derived strain parameters of the left and right ventricle

International Nuclear Information System (INIS)

Schmidt, Björn; Dick, Anastasia; Treutlein, Melanie; Schiller, Petra; Bunck, Alexander C.; Maintz, David; Baeßler, Bettina

2017-01-01

Highlights: • Left and right ventricular CMR feature tracking is highly reproducible. • The only exception is radial strain and strain rate. • Sample size estimations are presented as a practical reference for future studies. - Abstract: Objectives: To investigate the reproducibility of regional and global strain and strain rate (SR) parameters of both ventricles and to determine sample sizes for all investigated strain and SR parameters in order to generate a practical reference for future studies. Materials and methods: The study population consisted of 20 healthy individuals and 20 patients with acute myocarditis. Cine sequences in three horizontal long axis views and a stack of short axis views covering the entire left and right ventricle (LV, RV) were retrospectively analysed using a dedicated feature tracking (FT) software algorithm (TOMTEC). For intra-observer analysis, one observer analysed CMR images of all patients and volunteers twice. For inter-observer analysis, three additional blinded observers analysed the same datasets once. Intra- and inter-observer reproducibility were tested in all patients and controls using Bland-Altman analyses, intra-class correlation coefficients (ICCs) and coefficients of variation. Results: Intra-observer reproducibility of global LV strain and SR parameters was excellent (range of ICCs: 0.81–1.00), the only exception being global radial SR with a poor reproducibility (ICC 0.23). On a regional level, basal and midventricular strain and SR parameters were more reproducible when compared to apical parameters. Inter-observer reproducibility of all LV parameters was slightly lower than intra-observer reproducibility, yet still good to excellent for all global and regional longitudinal and circumferential strain and SR parameters (range of ICCs: 0.66–0.93). Similar to the LV, all global RV longitudinal and circumferential strain and SR parameters showed an excellent reproducibility, (range of ICCs: 0.75–0

Diffusion weighted imaging of the normal breast: reproducibility of apparent diffusion coefficient measurements and variation with menstrual cycle and menopausal status

Energy Technology Data Exchange (ETDEWEB)

O' Flynn, Elizabeth A.M.; Morgan, Veronica A.; Giles, Sharon L. [Cancer Research UK and ESPSRC Cancer Imaging Centre, Clinical Magnetic Resonance Group, Surrey (United Kingdom); deSouza, Nandita M. [Royal Marsden NHS Foundation Trust, Clinical Magnetic Resonance Group, Institute of Cancer Research, Surrey (United Kingdom)

2012-07-15

To establish the reproducibility of apparent diffusion coefficient (ADC) measurements in normal fibroglandular breast tissue and to assess variation in ADC values with phase of the menstrual cycle and menopausal status. Thirty-one volunteers (13 premenopausal, 18 postmenopausal) underwent magnetic resonance twice (interval 11-22 days) using diffusion-weighted MRI. ADC{sub total} and a perfusion-insensitive ADC{sub high} (omitting b = 0) were calculated. Reproducibility and inter-observer variability of mean ADC values were assessed. The difference in mean ADC values between the two phases of the menstrual cycle and the postmenopausal breast were evaluated. ADC{sub total} and ADC{sub high} showed good reproducibility (r% = 17.6, 22.4). ADC{sub high} showed very good inter-observer agreement (kappa = 0.83). The intraclass correlation coefficients (ICC) were 0.93 and 0.91. Mean ADC values were significantly lower in the postmenopausal breast (ADC{sub total} 1.46 {+-} 0.3 x 10{sup -3} mm{sup 2}/s, ADC{sub high} 1.33 {+-} 0.3 x 10{sup -3} mm{sup 2}/s) compared with the premenopausal breast (ADC{sub total} 1.84 {+-} 0.26 x 10{sup -3} mm{sup 2}/s, ADC{sub high} 1.77 {+-} 0.26 x 10{sup -3} mm{sup 2}/s; both P < 0.001). No significant difference was seen in ADC values in relation to menstrual cycle (ADC{sub total} P = 0.2, ADC{sub high} P = 0.24) or between postmenopausal women taking or not taking oestrogen supplements (ADC{sub total} P = 0.6, ADC{sub high} P = 0.46). ADC values in fibroglandular breast tissue are reproducible. Lower ADC values within the postmenopausal breast may reduce diffusion-weighted contrast and have implications for accurately detecting tumours. (orig.)

Accuracy, reproducibility, and time efficiency of dental measurements using different technologies.

Science.gov (United States)

Grünheid, Thorsten; Patel, Nishant; De Felippe, Nanci L; Wey, Andrew; Gaillard, Philippe R; Larson, Brent E

2014-02-01

Historically, orthodontists have taken dental measurements on plaster models. Technological advances now allow orthodontists to take these measurements on digital models. In this study, we aimed to assess the accuracy, reproducibility, and time efficiency of dental measurements taken on 3 types of digital models. emodels (GeoDigm, Falcon Heights, Minn), SureSmile models (OraMetrix, Richardson, Tex), and AnatoModels (Anatomage, San Jose, Calif) were made for 30 patients. Mesiodistal tooth-width measurements taken on these digital models were timed and compared with those on the corresponding plaster models, which were used as the gold standard. Accuracy and reproducibility were assessed using the Bland-Altman method. Differences in time efficiency were tested for statistical significance with 1-way analysis of variance. Measurements on SureSmile models were the most accurate, followed by those on emodels and AnatoModels. Measurements taken on SureSmile models were also the most reproducible. Measurements taken on SureSmile models and emodels were significantly faster than those taken on AnatoModels and plaster models. Tooth-width measurements on digital models can be as accurate as, and might be more reproducible and significantly faster than, those taken on plaster models. Of the models studied, the SureSmile models provided the best combination of accuracy, reproducibility, and time efficiency of measurement. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Massive and Reproducible Production of Liver Buds Entirely from Human Pluripotent Stem Cells

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Takanori Takebe

2017-12-01

Full Text Available Summary: Organoid technology provides a revolutionary paradigm toward therapy but has yet to be applied in humans, mainly because of reproducibility and scalability challenges. Here, we overcome these limitations by evolving a scalable organ bud production platform entirely from human induced pluripotent stem cells (iPSC. By conducting massive “reverse” screen experiments, we identified three progenitor populations that can effectively generate liver buds in a highly reproducible manner: hepatic endoderm, endothelium, and septum mesenchyme. Furthermore, we achieved human scalability by developing an omni-well-array culture platform for mass producing homogeneous and miniaturized liver buds on a clinically relevant large scale (>108. Vascularized and functional liver tissues generated entirely from iPSCs significantly improved subsequent hepatic functionalization potentiated by stage-matched developmental progenitor interactions, enabling functional rescue against acute liver failure via transplantation. Overall, our study provides a stringent manufacturing platform for multicellular organoid supply, thus facilitating clinical and pharmaceutical applications especially for the treatment of liver diseases through multi-industrial collaborations. : With the goal of clinical translation of liver bud transplant therapy, Takebe et al. established a massive organoid production platform from endoderm, endothelial, and mesenchymal progenitor populations specified entirely from human iPSCs, reproducibly demonstrating functionality both in vitro and in vivo. Keywords: iPSC, liver bud, organoid, transplantation, self-organization, endothelial, mesenchymal, liver failure, clinical grade

PSYCHOLOGY. Estimating the reproducibility of psychological science.

Science.gov (United States)

2015-08-28

Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams. Copyright © 2015, American Association for the Advancement of Science.

Examining the Reproducibility of 6 Published Studies in Public Health Services and Systems Research.

Science.gov (United States)

Harris, Jenine K; B Wondmeneh, Sarah; Zhao, Yiqiang; Leider, Jonathon P

2018-02-23

Research replication, or repeating a study de novo, is the scientific standard for building evidence and identifying spurious results. While replication is ideal, it is often expensive and time consuming. Reproducibility, or reanalysis of data to verify published findings, is one proposed minimum alternative standard. While a lack of research reproducibility has been identified as a serious and prevalent problem in biomedical research and a few other fields, little work has been done to examine the reproducibility of public health research. We examined reproducibility in 6 studies from the public health services and systems research subfield of public health research. Following the methods described in each of the 6 papers, we computed the descriptive and inferential statistics for each study. We compared our results with the original study results and examined the percentage differences in descriptive statistics and differences in effect size, significance, and precision of inferential statistics. All project work was completed in 2017. We found consistency between original and reproduced results for each paper in at least 1 of the 4 areas examined. However, we also found some inconsistency. We identified incorrect transcription of results and omitting detail about data management and analyses as the primary contributors to the inconsistencies. Increasing reproducibility, or reanalysis of data to verify published results, can improve the quality of science. Researchers, journals, employers, and funders can all play a role in improving the reproducibility of science through several strategies including publishing data and statistical code, using guidelines to write clear and complete methods sections, conducting reproducibility reviews, and incentivizing reproducible science.

Recovery and Stability of Δ9-Tetrahydrocannabinol Using the Oral-Eze® Oral Fluid Collection System and Intercept® Oral Specimen Collection Device.

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Samano, Kimberly L; Anne, Lakshmi; Johnson, Ted; Tang, Kenneth; Sample, R H Barry

2015-10-01

Oral fluid (OF) is increasingly used for clinical, forensic and workplace drug testing as an alternative to urine. Uncertainties surrounding OF collection device performance, drug stability and testing reproducibility may be partially responsible for delays in the implementation of OF testing in regulated drug testing programs. Stability of Δ(9)-tetrahydrocannabinol (THC) fortified and authentic specimens was examined after routine collection, transport and laboratory testing. Acceptable recovery and stability were observed when THC-fortified OF (1.5 and 4.5 ng/mL) was applied to Oral-Eze devices. Neat OF samples collected with Oral-Eze, processed per the package insert, and fortified with THC (3 and 6 ng/mL) were stable (±20%) at room temperature (21-25°C), refrigerated (2-8°C) and frozen (-25 to -15°C) conditions up to 1 month, while samples collected with Intercept devices showed decreases at refrigerated and room temperatures. After long-term refrigerated or frozen storage, maximum reductions in THC concentrations were 42% for Oral-Eze and 69% for Intercept. After ≥1 year frozen storage, 80.7% of laboratory specimens positive for THC (3 ng/mL cut-off) by GC-MS were reconfirmed positive (within 25%), with an average THC decrease of 4.2%. Specimens (n = 47) processed with Oral-Eze (diluted) and tested via enzyme immunoassay were concordant with LC-MS-MS results and showed 100% sensitivity and 95% specificity. Paired specimens collected with Oral-Eze and Intercept exhibited 98% overall agreement between the immunoassay test systems. Collectively, these data demonstrate consistent and reproducible recovery and stability of THC in OF after collection, transport and laboratory testing using the Oral-Eze OF Collection System. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies.

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Li, Robin; Lin, Xiao; Geng, Haijiang; Li, Zhihui; Li, Jiabing; Lu, Tao; Yan, Fangrong

2015-12-29

Personalized cancer treatments depend on the determination of a patient's genetic status according to known genetic profiles for which targeted treatments exist. Such genetic profiles must be scientifically validated before they is applied to general patient population. Reproducibility of findings that support such genetic profiles is a fundamental challenge in validation studies. The percentage of overlapping genes (POG) criterion and derivative methods produce unstable and misleading results. Furthermore, in a complex disease, comparisons between different tumor subtypes can produce high POG scores that do not capture the consistencies in the functions. We focused on the quality rather than the quantity of the overlapping genes. We defined the rank value of each gene according to importance or quality by PageRank on basis of a particular topological structure. Then, we used the p-value of the rank-sum of the overlapping genes (PRSOG) to evaluate the quality of reproducibility. Though the POG scores were low in different studies of the same disease, the PRSOG was statistically significant, which suggests that sets of differentially expressed genes might be highly reproducible. Evaluations of eight datasets from breast cancer, lung cancer and four other disorders indicate that quality-based PRSOG method performs better than a quantity-based method. Our analysis of the components of the sets of overlapping genes supports the utility of the PRSOG method.

Understanding reproducibility of human IVF traits to predict next IVF cycle outcome.

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Wu, Bin; Shi, Juanzi; Zhao, Wanqiu; Lu, Suzhen; Silva, Marta; Gelety, Timothy J

2014-10-01

Evaluating the failed IVF cycle often provides useful prognostic information. Before undergoing another attempt, patients experiencing an unsuccessful IVF cycle frequently request information about the probability of future success. Here, we introduced the concept of reproducibility and formulae to predict the next IVF cycle outcome. The experimental design was based on the retrospective review of IVF cycle data from 2006 to 2013 in two different IVF centers and statistical analysis. The reproducibility coefficients (r) of IVF traits including number of oocytes retrieved, oocyte maturity, fertilization, embryo quality and pregnancy were estimated using the interclass correlation coefficient between the repeated IVF cycle measurements for the same patient by variance component analysis. The formulae were designed to predict next IVF cycle outcome. The number of oocytes retrieved from patients and their fertilization rate had the highest reproducibility coefficients (r = 0.81 ~ 0.84), which indicated a very close correlation between the first retrieval cycle and subsequent IVF cycles. Oocyte maturity and number of top quality embryos had middle level reproducibility (r = 0.38 ~ 0.76) and pregnancy rate had a relative lower reproducibility (r = 0.23 ~ 0.27). Based on these parameters, the next outcome for these IVF traits might be accurately predicted by the designed formulae. The introduction of the concept of reproducibility to our human IVF program allows us to predict future IVF cycle outcomes. The traits of oocyte numbers retrieved, oocyte maturity, fertilization, and top quality embryos had higher or middle reproducibility, which provides a basis for accurate prediction of future IVF outcomes. Based on this prediction, physicians may counsel their patients or change patient's stimulation plans, and laboratory embryologists may improve their IVF techniques accordingly.

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

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Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

Analysis method of high-order collective-flow correlations based on the concept of correlative degree

International Nuclear Information System (INIS)

Zhang Weigang

2000-01-01

Based on the concept of correlative degree, a new method of high-order collective-flow measurement is constructed, with which azimuthal correlations, correlations of final state transverse momentum magnitude and transverse correlations can be inspected respectively. Using the new method the contributions of the azimuthal correlations of particles distribution and the correlations of transverse momentum magnitude of final state particles to high-order collective-flow correlations are analyzed respectively with 4π experimental events for 1.2 A GeV Ar + BaI 2 collisions at the Bevalac stream chamber. Comparing with the correlations of transverse momentum magnitude, the azimuthal correlations of final state particles distribution dominate high-order collective-flow correlations in experimental samples. The contributions of correlations of transverse momentum magnitude of final state particles not only enhance the strength of the high-order correlations of particle group, but also provide important information for the measurement of the collectivity of collective flow within the more constraint district

Reproducibility of ad libitum energy intake with the use of a computerized vending machine system123

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Votruba, Susanne B; Franks, Paul W; Krakoff, Jonathan; Salbe, Arline D

2010-01-01

Background: Accurate assessment of energy intake is difficult but critical for the evaluation of eating behavior and intervention effects. Consequently, methods to assess ad libitum energy intake under controlled conditions have been developed. Objective: Our objective was to evaluate the reproducibility of ad libitum energy intake with the use of a computerized vending machine system. Design: Twelve individuals (mean ± SD: 36 ± 8 y old; 41 ± 8% body fat) consumed a weight-maintaining diet for 3 d; subsequently, they self-selected all food with the use of a computerized vending machine system for an additional 3 d. Mean daily energy intake was calculated from the actual weight of foods consumed and expressed as a percentage of weight-maintenance energy needs (%WMEN). Subjects repeated the study multiple times during 2 y. The within-person reproducibility of energy intake was determined through the calculation of the intraclass correlation coefficients (ICCs) between visits. Results: Daily energy intake for all subjects was 5020 ± 1753 kcal during visit 1 and 4855 ± 1615 kcal during visit 2. There were no significant associations between energy intake and body weight, body mass index, or percentage body fat while subjects used the vending machines, which indicates that intake was not driven by body size or need. Despite overconsumption (%WMEN = 181 ± 57%), the reproducibility of intake between visits, whether expressed as daily energy intake (ICC = 0.90), %WMEN (ICC = 0.86), weight of food consumed (ICC = 0.87), or fat intake (g/d; ICC = 0.87), was highly significant (P < 0.0001). Conclusion: Although ad libitum energy intake exceeded %WMEN, the within-person reliability of this intake across multiple visits was high, which makes this a reproducible method for the measurement of ad libitum intake in subjects who reside in a research unit. This trial was registered at clinicaltrials.gov as NCT00342732. PMID:19923376

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

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Ling-Hong Hung

Full Text Available Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11 graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

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Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Introducing Discrete Frequency Infrared Technology for High-Throughput Biofluid Screening

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Hughes, Caryn; Clemens, Graeme; Bird, Benjamin; Dawson, Timothy; Ashton, Katherine M.; Jenkinson, Michael D.; Brodbelt, Andrew; Weida, Miles; Fotheringham, Edeline; Barre, Matthew; Rowlette, Jeremy; Baker, Matthew J.

2016-02-01

Accurate early diagnosis is critical to patient survival, management and quality of life. Biofluids are key to early diagnosis due to their ease of collection and intimate involvement in human function. Large-scale mid-IR imaging of dried fluid deposits offers a high-throughput molecular analysis paradigm for the biomedical laboratory. The exciting advent of tuneable quantum cascade lasers allows for the collection of discrete frequency infrared data enabling clinically relevant timescales. By scanning targeted frequencies spectral quality, reproducibility and diagnostic potential can be maintained while significantly reducing acquisition time and processing requirements, sampling 16 serum spots with 0.6, 5.1 and 15% relative standard deviation (RSD) for 199, 14 and 9 discrete frequencies respectively. We use this reproducible methodology to show proof of concept rapid diagnostics; 40 unique dried liquid biopsies from brain, breast, lung and skin cancer patients were classified in 2.4 cumulative seconds against 10 non-cancer controls with accuracies of up to 90%.

A new strategy to deliver synthetic protein drugs: self-reproducible biologics using minicircles.

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Yi, Hyoju; Kim, Youngkyun; Kim, Juryun; Jung, Hyerin; Rim, Yeri Alice; Jung, Seung Min; Park, Sung-Hwan; Ju, Ji Hyeon

2014-08-05

Biologics are the most successful drugs used in anticytokine therapy. However, they remain partially unsuccessful because of the elevated cost of their synthesis and purification. Development of novel biologics has also been hampered by the high cost. Biologics are made of protein components; thus, theoretically, they can be produced in vivo. Here we tried to invent a novel strategy to allow the production of synthetic drugs in vivo by the host itself. The recombinant minicircles encoding etanercept or tocilizumab, which are synthesized currently by pharmaceutical companies, were injected intravenously into animal models. Self-reproduced etanercept and tocilizumab were detected in the serum of mice. Moreover, arthritis subsided in mice that were injected with minicircle vectors carrying biologics. Self-reproducible biologics need neither factory facilities for drug production nor clinical processes, such as frequent drug injection. Although this novel strategy is in its very early conceptual stage, it seems to represent a potential alternative method for the delivery of biologics.

Relevant principal factors affecting the reproducibility of insect primary culture.

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Ogata, Norichika; Iwabuchi, Kikuo

2017-06-01

The primary culture of insect cells often suffers from problems with poor reproducibility in the quality of the final cell preparations. The cellular composition of the explants (cell number and cell types), surgical methods (surgical duration and surgical isolation), and physiological and genetic differences between donors may be critical factors affecting the reproducibility of culture. However, little is known about where biological variation (interindividual differences between donors) ends and technical variation (variance in replication of culture conditions) begins. In this study, we cultured larval fat bodies from the Japanese rhinoceros beetle, Allomyrina dichotoma, and evaluated, using linear mixed models, the effect of interindividual variation between donors on the reproducibility of the culture. We also performed transcriptome analysis of the hemocyte-like cells mainly seen in the cultures using RNA sequencing and ultrastructural analyses of hemocytes using a transmission electron microscope, revealing that the cultured cells have many characteristics of insect hemocytes.

Evaluation of multichannel reproduced sound

DEFF Research Database (Denmark)

Choisel, Sylvain; Wickelmaier, Florian Maria

2007-01-01

A study was conducted with the goal of quantifying auditory attributes which underlie listener preference for multichannel reproduced sound. Short musical excerpts were presented in mono, stereo and several multichannel formats to a panel of forty selected listeners. Scaling of auditory attributes......, as well as overall preference, was based on consistency tests of binary paired-comparison judgments and on modeling the choice frequencies using probabilistic choice models. As a result, the preferences of non-expert listeners could be measured reliably at a ratio scale level. Principal components derived...

Reproducible positioning in chest X-ray radiography

International Nuclear Information System (INIS)

1974-01-01

A device is described that can be used to ensure reproducibility in the positioning of the patient during X-ray radiography of the thorax. Signals are taken from an electrocardiographic monitor and from a device recording the respiratory cycle. Radiography is performed only when two preselected signals coincide

Reproducibility of Manual Platelet Estimation Following Automated Low Platelet Counts

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Zainab S Al-Hosni

2016-11-01

Full Text Available Objectives: Manual platelet estimation is one of the methods used when automated platelet estimates are very low. However, the reproducibility of manual platelet estimation has not been adequately studied. We sought to assess the reproducibility of manual platelet estimation following automated low platelet counts and to evaluate the impact of the level of experience of the person counting on the reproducibility of manual platelet estimates. Methods: In this cross-sectional study, peripheral blood films of patients with platelet counts less than 100 × 109/L were retrieved and given to four raters to perform manual platelet estimation independently using a predefined method (average of platelet counts in 10 fields using 100× objective multiplied by 20. Data were analyzed using intraclass correlation coefficient (ICC as a method of reproducibility assessment. Results: The ICC across the four raters was 0.840, indicating excellent agreement. The median difference of the two most experienced raters was 0 (range: -64 to 78. The level of platelet estimate by the least-experienced rater predicted the disagreement (p = 0.037. When assessing the difference between pairs of raters, there was no significant difference in the ICC (p = 0.420. Conclusions: The agreement between different raters using manual platelet estimation was excellent. Further confirmation is necessary, with a prospective study using a gold standard method of platelet counts.

Reproducibility in the assessment of acute pancreatitis with computed tomography

International Nuclear Information System (INIS)

Freire Filho, Edison de Oliveira; Vieira, Renata La Rocca; Yamada, Andre Fukunishi; Shigueoka, David Carlos; Bekhor, Daniel; Freire, Maxime Figueiredo de Oliveira; Ajzen, Sergio; D'Ippolito, Giuseppe

2007-01-01

Objective: To evaluate the reproducibility of unenhanced and contrast-enhanced computed tomography in the assessment of patients with acute pancreatitis. Materials and methods: Fifty-one unenhanced and contrast-enhanced abdominal computed tomography studies of patients with acute pancreatitis were blindly reviewed by two radiologists (observers 1 and 2). The morphological index was separately calculated for unenhanced and contrast-enhanced computed tomography and the disease severity index was established. Intraobserver and interobserver reproducibility of computed tomography was measured by means of the kappa index (κ). Results: Interobserver agreement was κ 0.666, 0.705, 0.648, 0.547 and 0.631, respectively for unenhanced and contrast-enhanced morphological index, presence of pancreatic necrosis, pancreatic necrosis extension, and disease severity index. Intraobserver agreement (observers 1 and 2, respectively) was κ = 0.796 and 0.732 for unenhanced morphological index; κ 0.725 and 0.802 for contrast- enhanced morphological index; κ = 0.674 and 0.849 for presence of pancreatic necrosis; κ = 0.606 and 0.770 for pancreatic necrosis extension; and κ = 0.801 and 0.687 for disease severity index at computed tomography. Conclusion: Computed tomography for determination of morphological index and disease severity index in the staging of acute pancreatitis is a quite reproducible method. The absence of contrast- enhancement does not affect the computed tomography morphological index reproducibility. (author)

An Open Framework for the Reproducible Study of the Iterated Prisoner’s Dilemma

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Vincent Knight

2016-08-01

Full Text Available The Axelrod library is an open source Python package that allows for reproducible game theoretic research into the Iterated Prisoner’s Dilemma. This area of research began in the 1980s but suffers from a lack of documentation and test code. The goal of the library is to provide such a resource, with facilities for the design of new strategies and interactions between them, as well as conducting tournaments and ecological simulations for populations of strategies. With a growing collection of 139 strategies, the library is a also a platform for an original tournament that, in itself, is of interest to the game theoretic community. This paper describes the Iterated Prisoner’s Dilemma, the Axelrod library and its development, and insights gained from some novel research.

Reproducibility of UAV-based earth surface topography based on structure-from-motion algorithms.

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Clapuyt, François; Vanacker, Veerle; Van Oost, Kristof

2014-05-01

A representation of the earth surface at very high spatial resolution is crucial to accurately map small geomorphic landforms with high precision. Very high resolution digital surface models (DSM) can then be used to quantify changes in earth surface topography over time, based on differencing of DSMs taken at various moments in time. However, it is compulsory to have both high accuracy for each topographic representation and consistency between measurements over time, as DSM differencing automatically leads to error propagation. This study investigates the reproducibility of reconstructions of earth surface topography based on structure-from-motion (SFM) algorithms. To this end, we equipped an eight-propeller drone with a standard reflex camera. This equipment can easily be deployed in the field, as it is a lightweight, low-cost system in comparison with classic aerial photo surveys and terrestrial or airborne LiDAR scanning. Four sets of aerial photographs were created for one test field. The sets of airphotos differ in focal length, and viewing angles, i.e. nadir view and ground-level view. In addition, the importance of the accuracy of ground control points for the construction of a georeferenced point cloud was assessed using two different GPS devices with horizontal accuracy at resp. the sub-meter and sub-decimeter level. Airphoto datasets were processed with SFM algorithm and the resulting point clouds were georeferenced. Then, the surface representations were compared with each other to assess the reproducibility of the earth surface topography. Finally, consistency between independent datasets is discussed.

Inter-examiner reproducibility of tests for lumbar motor control

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Elkjaer Arne

2011-05-01

Full Text Available Abstract Background Many studies show a relation between reduced lumbar motor control (LMC and low back pain (LBP. However, test circumstances vary and during test performance, subjects may change position. In other words, the reliability - i.e. reproducibility and validity - of tests for LMC should be based on quantitative data. This has not been considered before. The aim was to analyse the reproducibility of five different quantitative tests for LMC commonly used in daily clinical practice. Methods The five tests for LMC were: repositioning (RPS, sitting forward lean (SFL, sitting knee extension (SKE, and bent knee fall out (BKFO, all measured in cm, and leg lowering (LL, measured in mm Hg. A total of 40 subjects (14 males, 26 females 25 with and 15 without LBP, with a mean age of 46.5 years (SD 14.8, were examined independently and in random order by two examiners on the same day. LBP subjects were recruited from three physiotherapy clinics with a connection to the clinic's gym or back-school. Non-LBP subjects were recruited from the clinic's staff acquaintances, and from patients without LBP. Results The means and standard deviations for each of the tests were 0.36 (0.27 cm for RPS, 1.01 (0.62 cm for SFL, 0.40 (0.29 cm for SKE, 1.07 (0.52 cm for BKFO, and 32.9 (7.1 mm Hg for LL. All five tests for LMC had reproducibility with the following ICCs: 0.90 for RPS, 0.96 for SFL, 0.96 for SKE, 0.94 for BKFO, and 0.98 for LL. Bland and Altman plots showed that most of the differences between examiners A and B were less than 0.20 cm. Conclusion These five tests for LMC displayed excellent reproducibility. However, the diagnostic accuracy of these tests needs to be addressed in larger cohorts of subjects, establishing values for the normal population. Also cut-points between subjects with and without LBP must be determined, taking into account age, level of activity, degree of impairment and participation in sports. Whether reproducibility of these

Reproducibility of trabecular bone score with different scan modes using dual-energy X-ray absorptiometry: a phantom study

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Bandirali, Michele; Messina, Carmelo [Universita degli Studi di Milano, Scuola di Specializzazione in Radiodiagnostica, Milano (Italy); Di Leo, Giovanni [Unita di Radiologia, IRCCS Policlinico San Donato, San Donato Milanese (Italy); Pastor Lopez, Maria Juana; Ulivieri, Fabio M. [Servizio di Medicina Nucleare, Ospedale Maggiore, Mineralometria Ossea Computerizzata e Ambulatorio Malattie Metabolismo Minerale e Osseo, Milano (Italy); Mai, Alessandro [Universita degli Studi di Milano, Tecniche di Radiologia Medica, per Immagini e Radioterapia, Milano (Italy); Sardanelli, Francesco [Unita di Radiologia, IRCCS Policlinico San Donato, San Donato Milanese (Italy); Universita degli Studi di Milano, Dipartimento di Scienze Biomediche per la Salute, San Donato Milanese (Italy)

2014-08-12

The trabecular bone score (TBS) accounts for the bone microarchitecture and is calculated on dual-energy X-ray absorptiometry (DXA). We estimated the reproducibility of the TBS using different scan modes compared to the reproducibility bone mineral density (BMD). A spine phantom was used with a Hologic QDR-Discovery A densitometer. For each scan mode [fast array, array, high definition (HD)], 25 scans were automatically performed without phantom repositioning; a further 25 scans were performed with phantom repositioning. For each scan, the TBS was obtained. The coefficient of variation (CoV) was calculated as the ratio between standard deviation and mean; percent least significant change (LSC%) as 2.8 x CoV; reproducibility as the complement to 100 % of LSC%. Differences among scan modes were assessed using ANOVA. Without phantom repositioning, the mean TBS (mm{sup -1}) was: 1.352 (fast array), 1.321 (array), and 1.360 (HD); with phantom repositioning, it was 1.345, 1.332, and 1.362, respectively. Reproducibility of the TBS without phantom repositioning was 97.7 % (fast array), 98.3 % (array), and 98.2 % (HD); with phantom repositioning, it was 97.9 %, 98.7 %, and 98.4 %, respectively. LSC% was ≤2.26 %. Differences among scan modes were all statistically significant (p ≤ 0.019). Reproducibility of BMD was 99.1 % with all scan modes, while LSC% was from 0.86 % to 0.91 %. Reproducibility error of the TBS was 2-3-fold higher than that of BMD. Although statistically significant, differences in TBS among scan modes were within the highest LSC%. Thus, the three scan modes can be considered interchangeable. (orig.)

Reproducibility of heart rate variability parameters measured in healthy subjects at rest and after a postural change maneuver

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E.M. Dantas

2010-10-01

Full Text Available Heart rate variability (HRV provides important information about cardiac autonomic modulation. Since it is a noninvasive and inexpensive method, HRV has been used to evaluate several parameters of cardiovascular health. However, the internal reproducibility of this method has been challenged in some studies. Our aim was to determine the intra-individual reproducibility of HRV parameters in short-term recordings obtained in supine and orthostatic positions. Electrocardiographic (ECG recordings were obtained from 30 healthy subjects (20-49 years, 14 men using a digital apparatus (sampling ratio = 250 Hz. ECG was recorded for 10 min in the supine position and for 10 min in the orthostatic position. The procedure was repeated 2-3 h later. Time and frequency domain analyses were performed. Frequency domain included low (LF, 0.04-0.15 Hz and high frequency (HF, 0.15-0.4 Hz bands. Power spectral analysis was performed by the autoregressive method and model order was set at 16. Intra-subject agreement was assessed by linear regression analysis, test of difference in variances and limits of agreement. Most HRV measures (pNN50, RMSSD, LF, HF, and LF/HF ratio were reproducible independent of body position. Better correlation indexes (r > 0.6 were obtained in the orthostatic position. Bland-Altman plots revealed that most values were inside the agreement limits, indicating concordance between measures. Only SDNN and NNv in the supine position were not reproducible. Our results showed reproducibility of HRV parameters when recorded in the same individual with a short time between two exams. The increased sympathetic activity occurring in the orthostatic position probably facilitates reproducibility of the HRV indexes.

Reduction of collectivity at very high spins in 134Nd: Expanding the projected-shell-model basis up to 10-quasiparticle states

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Wang, Long-Jun; Sun, Yang; Mizusaki, Takahiro; Oi, Makito; Ghorui, Surja K.

2016-03-01

Background: The recently started physics campaign with the new generation of γ -ray spectrometers, "GRETINA" and "AGATA," will possibly produce many high-quality γ rays from very fast-rotating nuclei. Microscopic models are needed to understand these states. Purpose: It is a theoretical challenge to describe high-spin states in a shell-model framework by the concept of configuration mixing. To meet the current needs, one should overcome the present limitations and vigorously extend the quasiparticle (qp) basis of the projected shell model (PSM). Method: With the help of the recently proposed Pfaffian formulas, we apply the new algorithm and develop a new PSM code that extends the configuration space to include up to 10-qp states. The much-enlarged multi-qp space enables us to investigate the evolutional properties at very high spins in fast-rotating nuclei. Results: We take 134Nd as an example to demonstrate that the known experimental yrast and the several negative-parity side bands in this nucleus could be well described by the calculation. The variations in moment of inertia with spin are reproduced and explained in terms of successive band crossings among the 2-qp, 4-qp, 6-qp, 8-qp, and 10-qp states. Moreover, the electric quadrupole transitions in these bands are studied. Conclusions: A pronounced decrease in the high-spin B (E 2 ) of 134Nd is predicted, which suggests reduction of collectivity at very high spins because of increased level density and complex band mixing. The possibility for a potential application of the present development in the study of highly excited states in warm nuclei is mentioned.

Reproducibility of Perfusion Parameters of Optic Disc and Macula in Rhesus Monkeys by Optical Coherence Tomography Angiography.

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Li, Jing; Yang, Yi-Quan; Yang, Di-Ya; Liu, Xiang-Xiang; Sun, Yun-Xiao; Wei, Shi-Fei; Wang, Ning-Li

2016-05-05

Optical coherence tomography (OCT) angiography is a novel technique by which we can detect the local perfusion of fundus directly. The aim of this study was to evaluate the reproducibility of optic disc and macular flow perfusion parameters in rhesus monkeys using OCT angiography. Eighteen healthy monkeys (18 eyes) were subjected to optic disc and macula flow index measurements via a high-speed and high-resolution spectral-domain OCT XR Avanti with a split-spectrum amplitude de-correlation angiography algorithm. Right eye was imaged 3 times during the first examination and once during each of the two following examinations. The intra-visit and inter-visit intraclass correlation coefficients (ICCs) were both determined. The average flow indices of the four optic disc area layers were 0.171 ± 0.009 (optic nerve head), 0.015 ± 0.004 (vitreous), 0.052 ± 0.009 (radial peripapillary capillary), and 0.167 ± 0.011 (choroid). Average flow indices of the four macula area layers were 0.044 ± 0.011 (superficial retina), 0.036 ± 0.011 (deep retina), 0.016 ± 0.009 (outer retina), and 0.155 ± 0.013 (choroid). Intra-visit (ICC value: 0.821-0.954) and inter-visit (ICC value: 0.844-0.899) repeatability were both high. The study is about the reproducibility of optic disc and macular perfusion parameters as measured by OCT angiography in healthy rhesus monkeys. Flow index measurement reproducibility is high for both the optic disc and macula of normal monkey eyes. OCT angiography might be a useful technique to assess changes when examining monkeys with experimental ocular diseases.

Reproducibility of prompts in computer-aided detection (CAD) of breast cancer

International Nuclear Information System (INIS)

Taylor, C.G.; Champness, J.; Reddy, M.; Taylor, P.; Potts, H.W.W.; Given-Wilson, R.

2003-01-01

AIM: We evaluated the reproducibility of prompts using the R2 ImageChecker M2000 computer-aided detection (CAD) system. MATERIALS AND METHODS: Forty selected two-view mammograms of women with breast cancer were digitized and analysed using the ImageChecker on 10 separate occasions. The mammograms were chosen to provide both straightforward and subtle signs of malignancy. Data analysed included mammographic abnormality, pathology, and whether the cancer was prompted or given an emphasized prompt. RESULTS: Correct prompts were generated in 86 out of 100 occasions for screen-detected cancers. Reproducibility was less in the other categories of more subtle cancers: 21% for cancers previously missed by CAD, a group that contained more grade 1 and small (<10 mm) tumours. Prompts for calcifications were more reproducible than those for masses (76% versus 53%) and these cancers were more likely to have an emphasized prompt. CONCLUSIONS: Probably the most important cause of variability of prompts is shifts in film position between sequential digitizations. Consequently subtle lesions that are only just above the threshold for display may not be prompted on repeat scanning. However, users of CAD should be aware that even emphasized prompts are not consistently reproducible

Reproducing {sup 137}Cs vertical migration in Spanish soils - Reproducing {sup 137}Cs and {sup 90}Sr vertical migration in Spanish mainland

Energy Technology Data Exchange (ETDEWEB)

Olondo, C.; Legarda, F.; Herranz, M.; Idoeta, R. [The University of the Basque Country - UPV/EHU, Nuclear Engineering and Fluid Mechanics Dept. Faculty of Engineering, Alda. Urquijo 48013, Bilbao (Spain)

2014-07-01

As a result of caesium's and strontium's activity migration study developed in Spanish mainland soils, there has been obtained convective - diffusive migration equation that will reproduce adequately the movement that an activity deposit would follow in this land. Taking into account the dependence on rain that apparent convection velocity shows, it has been defined a new migration parameter that depends only on soil's properties. By means of a least square method and fitting the migration equation to experimental activity profiles, the values showed by the migration parameters in the studied soils, characteristics of that area, have been obtained. After that, there have been obtained the mean values of these parameters for each defined group that, depending on soil's texture, have been observed in the study performed about the movement of both radionuclides in soils and to whom these soils belong. Using these mean values and obtained equation, it has been properly reproduce those vertical activity profiles that were experimentally determined. In order to validate these values, a new sampling programme is carrying out in the north of Spain and, with obtained new sampling points' information, is going to verify if, indeed, obtained mean values also reproduce these new sampling points' activity vertical profile. (authors)

Optimizing silver-capped silicon nanopillars to simultaneously realize macroscopic, practical-level SERS signal reproducibility and high enhancement at low costs

DEFF Research Database (Denmark)

Wu, Kaiyu; Rindzevicius, Tomas; Schmidt, Michael Stenbæk

2017-01-01

and show that the improved structures exhibit unrivalled macroscale SERS uniformities (RSD: ∼2.5% in millimeter scale, ∼7% in wafer scale) and reproducibility (RSD: ∼1.5% across 3 wafers), while at the same time exhibiting a very large average SERS enhancement factor of >108. The obtained SERS uniformity...

Reproducibility of up-flow column percolation tests for contaminated soils.

Directory of Open Access Journals (Sweden)

Tetsuo Yasutaka

Full Text Available Up-flow column percolation tests are used at laboratory scale to assess the leaching behavior of hazardous substance from contaminated soils in a specific condition as a function of time. Monitoring the quality of these test results inter or within laboratory is crucial, especially if used for Environment-related legal policy or for routine testing purposes. We tested three different sandy loam type soils (Soils I, II and III to determine the reproducibility (variability inter laboratory of test results and to evaluate the difference in the test results within laboratory. Up-flow column percolation tests were performed following the procedure described in the ISO/TS 21268-3. This procedure consists of percolating solution (calcium chloride 1 mM from bottom to top at a flow rate of 12 mL/h through softly compacted soil contained in a column of 5 cm diameter and 30 ± 5 cm height. Eluate samples were collected at liquid-to-solid ratio of 0.1, 0.2, 0.5, 1, 2, 5 and 10 L/kg and analyzed for quantification of the target elements (Cu, As, Se, Cl, Ca, F, Mg, DOC and B in this research. For Soil I, 17 institutions in Japan joined this validation test. The up-flow column experiments were conducted in duplicate, after 48 h of equilibration time and at a flow rate of 12 mL/h. Column percolation test results from Soils II and III were used to evaluate the difference in test results from the experiments conducted in duplicate in a single laboratory, after 16 h of equilibration time and at a flow rate of 36 mL/h. Overall results showed good reproducibility (expressed in terms of the coefficient of variation, CV, calculated by dividing the standard deviation by the mean, as the CV was lower than 30% in more than 90% of the test results associated with Soil I. Moreover, low variability (expressed in terms of difference between the two test results divided by the mean was observed in the test results related to Soils II and III, with a variability lower than 30

Paleomagnetic analysis of curved thrust belts reproduced by physical models

Science.gov (United States)

Costa, Elisabetta; Speranza, Fabio

2003-12-01

This paper presents a new methodology for studying the evolution of curved mountain belts by means of paleomagnetic analyses performed on analogue models. Eleven models were designed aimed at reproducing various tectonic settings in thin-skinned tectonics. Our models analyze in particular those features reported in the literature as possible causes for peculiar rotational patterns in the outermost as well as in the more internal fronts. In all the models the sedimentary cover was reproduced by frictional low-cohesion materials (sand and glass micro-beads), which detached either on frictional or on viscous layers. These latter were reproduced in the models by silicone. The sand forming the models has been previously mixed with magnetite-dominated powder. Before deformation, the models were magnetized by means of two permanent magnets generating within each model a quasi-linear magnetic field of intensity variable between 20 and 100 mT. After deformation, the models were cut into closely spaced vertical sections and sampled by means of 1×1-cm Plexiglas cylinders at several locations along curved fronts. Care was taken to collect paleomagnetic samples only within virtually undeformed thrust sheets, avoiding zones affected by pervasive shear. Afterwards, the natural remanent magnetization of these samples was measured, and alternating field demagnetization was used to isolate the principal components. The characteristic components of magnetization isolated were used to estimate the vertical-axis rotations occurring during model deformation. We find that indenters pushing into deforming belts from behind form non-rotational curved outer fronts. The more internal fronts show oroclinal-type rotations of a smaller magnitude than that expected for a perfect orocline. Lateral symmetrical obstacles in the foreland colliding with forward propagating belts produce non-rotational outer curved fronts as well, whereas in between and inside the obstacles a perfect orocline forms

Reproducibility of a 3-dimensional gyroscope in measuring shoulder anteflexion and abduction

Directory of Open Access Journals (Sweden)

Penning Ludo I F

2012-07-01

Full Text Available Abstract Background Few studies have investigated the use of a 3-dimensional gyroscope for measuring the range of motion (ROM in the impaired shoulder. Reproducibility of digital inclinometer and visual estimation is poor. This study aims to investigate the reproducibility of a tri axial gyroscope in measurement of anteflexion, abduction and related rotations in the impaired shoulder. Methods Fifty-eight patients with either subacromial impingement (27 or osteoarthritis of the shoulder (31 participated. Active anteflexion, abduction and related rotations were measured with a tri axial gyroscope according to a test retest protocol. Severity of shoulder impairment and patient perceived pain were assessed by the Disability of Arm Shoulder and Hand score (DASH and the Visual Analogue Scale (VAS. VAS scores were recorded before and after testing. Results In two out of three hospitals patients with osteoarthritis (n = 31 were measured, in the third hospital patients with subacromial impingement (n = 27. There were significant differences among hospitals for the VAS and DASH scores measured before and after testing. The mean differences between the test and retest means for anteflexion were −6 degrees (affected side, 9 (contralateral side and for abduction 15 degrees (affected side and 10 degrees (contralateral side. Bland & Altman plots showed that the confidence intervals for the mean differences fall within −6 up to 15 degrees, individual test - retest differences could exceed these limits. A simulation according to ‘Generalizability Theory’ produces very good coefficients for anteflexion and related rotation as a comprehensive measure of reproducibility. Optimal reproducibility is achieved with 2 repetitions for anteflexion. Conclusions Measurements were influenced by patient perceived pain. Differences in VAS and DASH might be explained by different underlying pathology. These differences in shoulder pathology however did not alter

Reproducibility of liver position using active breathing coordinator for liver cancer radiotherapy

International Nuclear Information System (INIS)

Eccles, Cynthia; Brock, Kristy K.; Bissonnette, Jean-Pierre; Hawkins, Maria; Dawson, Laura A.

2006-01-01

Purpose: To measure the intrabreath-hold liver motion and the intrafraction and interfraction reproducibility of liver position relative to vertebral bodies using an active breathing coordinator (ABC) in patients with unresectable liver cancer treated with hypofractionated stereotactic body radiation therapy (SBRT). Methods: Tolerability of ABC and organ motion during ABC was assessed using kV fluoroscopy in 34 patients. For patients treated with ABC, repeat breath-hold CT scans in the ABC breath-hold position were acquired at simulation to estimate the volumetric intrafraction reproducibility of the liver relative to the vertebral bodies. In addition, preceding each radiation therapy fraction, with the liver immobilized using ABC, repeat anteroposterior (AP) megavoltage verification images were obtained. Off-line alignments were completed to determine intrafraction reproducibility (from repeat images obtained before one treatment) and interfraction reproducibility (from comparisons of the final image for each fraction with the AP) of diaphragm position relative to vertebral bodies. For each image set, the vertebral bodies were aligned, and the resultant craniocaudal (CC) offset in diaphragm position was measured. Liver position during ABC was also evaluated from kV fluoroscopy acquired at the time of simulation, kV fluoroscopy at the time of treatment, and from MV beam's-eye view movie loops acquired during treatment. Results: Twenty-one of 34 patients were screened to be suitable for ABC. The average free breathing range of these patients was 13 mm (range, 5-1 mm). Fluoroscopy revealed that the average maximal diaphragm motion during ABC breath-hold was 1.4 mm (range, 0-3.4 mm). The MV treatment movie loops confirmed diaphragm stability during treatment. For a measure of intrafraction reproducibility, an analysis of 36 repeat ABC computed tomography (CT) scans in 14 patients was conducted. The average mean difference in the liver surface position was -0.9 mm, -0

The reproducibility of random amplified polymorphic DNA (RAPD ...

African Journals Online (AJOL)

RAPD) profiles of Streptococcus thermophilus strains by using the polymerase chain reaction (PCR). Several factors can cause the amplification of false and non reproducible bands in the RAPD profiles. We tested three primers, OPI-02 MOD, ...

Reproducibility of 5-HT2A receptor measurements and sample size estimations with [18F]altanserin PET using a bolus/infusion approach

DEFF Research Database (Denmark)

Haugbøl, Steven; Pinborg, Lars H; Arfan, Haroon M

2006-01-01

PURPOSE: To determine the reproducibility of measurements of brain 5-HT2A receptors with an [18F]altanserin PET bolus/infusion approach. Further, to estimate the sample size needed to detect regional differences between two groups and, finally, to evaluate how partial volume correction affects...... reproducibility and the required sample size. METHODS: For assessment of the variability, six subjects were investigated with [18F]altanserin PET twice, at an interval of less than 2 weeks. The sample size required to detect a 20% difference was estimated from [18F]altanserin PET studies in 84 healthy subjects....... Regions of interest were automatically delineated on co-registered MR and PET images. RESULTS: In cortical brain regions with a high density of 5-HT2A receptors, the outcome parameter (binding potential, BP1) showed high reproducibility, with a median difference between the two group measurements of 6...

Assessment of intercentre reproducibility and epidemiological concordance of Legionella pneumophila serogroup 1 genotyping by amplified fragment length polymorphism analysis

DEFF Research Database (Denmark)

Fry, N K; Bangsborg, Jette Marie; Bernander, S

2000-01-01

The aims of this work were to assess (i) the intercentre reproducibility and epidemiological concordance of amplified fragment length polymorphism analysis for epidemiological typing of Legionella pneumophila serogroup 1, and (ii) the suitability of the method for standardisation and implementation...... by members of the European Working Group on Legionella Infections. Fifty coded isolates comprising two panels of well-characterised strains, a "reproducibility" panel (n=20) and an "epidemiologically related" panel (n=30), were sent to 13 centres in 12 European countries. Analysis was undertaken in each...... using gel analysis software yielded R=1.00 and E=1.00, with 12, 13 or 14 types. This method can be used as a simple, rapid screening tool for epidemiological typing of isolates of Legionella pneumophila serogroup 1. Results demonstrate that the method can be highly reproducible (R=1...

Reproducibility and Transparency in Ocean-Climate Modeling

Science.gov (United States)

Hannah, N.; Adcroft, A.; Hallberg, R.; Griffies, S. M.

2015-12-01

Reproducibility is a cornerstone of the scientific method. Within geophysical modeling and simulation achieving reproducibility can be difficult, especially given the complexity of numerical codes, enormous and disparate data sets, and variety of supercomputing technology. We have made progress on this problem in the context of a large project - the development of new ocean and sea ice models, MOM6 and SIS2. Here we present useful techniques and experience.We use version control not only for code but the entire experiment working directory, including configuration (run-time parameters, component versions), input data and checksums on experiment output. This allows us to document when the solutions to experiments change, whether due to code updates or changes in input data. To avoid distributing large input datasets we provide the tools for generating these from the sources, rather than provide raw input data.Bugs can be a source of non-determinism and hence irreproducibility, e.g. reading from or branching on uninitialized memory. To expose these we routinely run system tests, using a memory debugger, multiple compilers and different machines. Additional confidence in the code comes from specialised tests, for example automated dimensional analysis and domain transformations. This has entailed adopting a code style where we deliberately restrict what a compiler can do when re-arranging mathematical expressions.In the spirit of open science, all development is in the public domain. This leads to a positive feedback, where increased transparency and reproducibility makes using the model easier for external collaborators, who in turn provide valuable contributions. To facilitate users installing and running the model we provide (version controlled) digital notebooks that illustrate and record analysis of output. This has the dual role of providing a gross, platform-independent, testing capability and a means to documents model output and analysis.

Properties of galaxies reproduced by a hydrodynamic simulation

Science.gov (United States)

Vogelsberger, M.; Genel, S.; Springel, V.; Torrey, P.; Sijacki, D.; Xu, D.; Snyder, G.; Bird, S.; Nelson, D.; Hernquist, L.

2014-05-01

Previous simulations of the growth of cosmic structures have broadly reproduced the `cosmic web' of galaxies that we see in the Universe, but failed to create a mixed population of elliptical and spiral galaxies, because of numerical inaccuracies and incomplete physical models. Moreover, they were unable to track the small-scale evolution of gas and stars to the present epoch within a representative portion of the Universe. Here we report a simulation that starts 12 million years after the Big Bang, and traces 13 billion years of cosmic evolution with 12 billion resolution elements in a cube of 106.5 megaparsecs a side. It yields a reasonable population of ellipticals and spirals, reproduces the observed distribution of galaxies in clusters and characteristics of hydrogen on large scales, and at the same time matches the `metal' and hydrogen content of galaxies on small scales.

Optimising diffusion weighted MRI for imaging metastatic and myeloma bone disease and assessing reproducibility

International Nuclear Information System (INIS)

Messiou, C.; Collins, D.J.; Morgan, V.A.; DeSouza, N.M.

2011-01-01

To establish normal bone marrow values of apparent diffusion coefficient (ADC) over an age range, compare them with metastatic and myelomatous involvement, to establish reproducibility and to optimise b values. The ADCs of bone marrow in 7 volunteers (mean age 29.7 years), 34 volunteers (mean age 63.3 years) and 43 patients with metastatic and myelomatous involvement (mean age 65.5 years) were measured. In 9 volunteers diffusion weighted MRI was repeated within 7 days. b values were derived to optimise contrast between normal and pathological marrow. The mean ADC of bone marrow in younger volunteers was significantly higher than that of older volunteers. The coefficient of reproducibility was 14.8%. The ADC mean of metastatic and myeloma bone disease was 1054+/-456 x 10 -6 mm 2 s -1 . An ADC threshold of 655 x 10 -6 mm 2 s -1 separated normal and abnormal marrow with a sensitivity and specificity of 90% and 93% respectively. Contrast between normal and abnormal marrow was optimal at b = 1389 smm -2 . The reproducibility of ADC measurements in bone is equivalent to published data for soft tissue with a high sensitivity and specificity for separating abnormal from age matched normal bone marrow. A b value of around 1,400 smm -2 is optimal for imaging bone marrow. (orig.)

Optimising diffusion weighted MRI for imaging metastatic and myeloma bone disease and assessing reproducibility

Energy Technology Data Exchange (ETDEWEB)

Messiou, C. [Institute of Cancer Research and Royal Marsden, NHS Foundation Trust, Cancer Research UK Clinical Magnetic Resonance Research Group, Surrey (United Kingdom); Institute of Cancer Research and Royal Marsden, NHS Foundation Trust, MRI Department, Surrey (United Kingdom); Collins, D.J.; Morgan, V.A.; DeSouza, N.M. [Institute of Cancer Research and Royal Marsden, NHS Foundation Trust, Cancer Research UK Clinical Magnetic Resonance Research Group, Surrey (United Kingdom)

2011-08-15

To establish normal bone marrow values of apparent diffusion coefficient (ADC) over an age range, compare them with metastatic and myelomatous involvement, to establish reproducibility and to optimise b values. The ADCs of bone marrow in 7 volunteers (mean age 29.7 years), 34 volunteers (mean age 63.3 years) and 43 patients with metastatic and myelomatous involvement (mean age 65.5 years) were measured. In 9 volunteers diffusion weighted MRI was repeated within 7 days. b values were derived to optimise contrast between normal and pathological marrow. The mean ADC of bone marrow in younger volunteers was significantly higher than that of older volunteers. The coefficient of reproducibility was 14.8%. The ADC mean of metastatic and myeloma bone disease was 1054+/-456 x 10{sup -6} mm{sup 2}s{sup -1}. An ADC threshold of 655 x 10{sup -6} mm{sup 2}s{sup -1} separated normal and abnormal marrow with a sensitivity and specificity of 90% and 93% respectively. Contrast between normal and abnormal marrow was optimal at b = 1389 smm{sup -2}. The reproducibility of ADC measurements in bone is equivalent to published data for soft tissue with a high sensitivity and specificity for separating abnormal from age matched normal bone marrow. A b value of around 1,400 smm{sup -2} is optimal for imaging bone marrow. (orig.)

A reproducible accelerated in vitro release testing method for PLGA microspheres.

Science.gov (United States)

Shen, Jie; Lee, Kyulim; Choi, Stephanie; Qu, Wen; Wang, Yan; Burgess, Diane J

2016-02-10

The objective of the present study was to develop a discriminatory and reproducible accelerated in vitro release method for long-acting PLGA microspheres with inner structure/porosity differences. Risperidone was chosen as a model drug. Qualitatively and quantitatively equivalent PLGA microspheres with different inner structure/porosity were obtained using different manufacturing processes. Physicochemical properties as well as degradation profiles of the prepared microspheres were investigated. Furthermore, in vitro release testing of the prepared risperidone microspheres was performed using the most common in vitro release methods (i.e., sample-and-separate and flow through) for this type of product. The obtained compositionally equivalent risperidone microspheres had similar drug loading but different inner structure/porosity. When microsphere particle size appeared similar, porous risperidone microspheres showed faster microsphere degradation and drug release compared with less porous microspheres. Both in vitro release methods investigated were able to differentiate risperidone microsphere formulations with differences in porosity under real-time (37 °C) and accelerated (45 °C) testing conditions. Notably, only the accelerated USP apparatus 4 method showed good reproducibility for highly porous risperidone microspheres. These results indicated that the accelerated USP apparatus 4 method is an appropriate fast quality control tool for long-acting PLGA microspheres (even with porous structures). Copyright © 2015 Elsevier B.V. All rights reserved.

Reproducibility of 5-HT2A receptor measurements and sample size estimations with [18F]altanserin PET using a bolus/infusion approach

International Nuclear Information System (INIS)

Haugboel, Steven; Pinborg, Lars H.; Arfan, Haroon M.; Froekjaer, Vibe M.; Svarer, Claus; Knudsen, Gitte M.; Madsen, Jacob; Dyrby, Tim B.

2007-01-01

To determine the reproducibility of measurements of brain 5-HT 2A receptors with an [ 18 F]altanserin PET bolus/infusion approach. Further, to estimate the sample size needed to detect regional differences between two groups and, finally, to evaluate how partial volume correction affects reproducibility and the required sample size. For assessment of the variability, six subjects were investigated with [ 18 F]altanserin PET twice, at an interval of less than 2 weeks. The sample size required to detect a 20% difference was estimated from [ 18 F]altanserin PET studies in 84 healthy subjects. Regions of interest were automatically delineated on co-registered MR and PET images. In cortical brain regions with a high density of 5-HT 2A receptors, the outcome parameter (binding potential, BP 1 ) showed high reproducibility, with a median difference between the two group measurements of 6% (range 5-12%), whereas in regions with a low receptor density, BP 1 reproducibility was lower, with a median difference of 17% (range 11-39%). Partial volume correction reduced the variability in the sample considerably. The sample size required to detect a 20% difference in brain regions with high receptor density is approximately 27, whereas for low receptor binding regions the required sample size is substantially higher. This study demonstrates that [ 18 F]altanserin PET with a bolus/infusion design has very low variability, particularly in larger brain regions with high 5-HT 2A receptor density. Moreover, partial volume correction considerably reduces the sample size required to detect regional changes between groups. (orig.)

Test-Retest Reproducibility of the Microperimeter MP3 With Fundus Image Tracking in Healthy Subjects and Patients With Macular Disease.

Science.gov (United States)

Palkovits, Stefan; Hirnschall, Nino; Georgiev, Stefan; Leisser, Christoph; Findl, Oliver

2018-02-01

To evaluate the test-retest reproducibility of a novel microperimeter with fundus image tracking (MP3, Nidek Co, Japan) in healthy subjects and patients with macular disease. Ten healthy subjects and 20 patients suffering from range of macular diseases were included. After training measurements, two additional microperimetry measurements were scheduled. Test-retest reproducibility was assessed for mean retinal sensitivity, pointwise sensitivity, and deep scotoma size using the coefficient of repeatability and Bland-Altman diagrams. In addition, in a subgroup of patients microperimetry was compared with conventional perimetry. Average differences in mean retinal sensitivity between the two study measurements were 0.26 ± 1.7 dB (median 0 dB; interquartile range [IQR] -1 to 1) for the healthy and 0.36 ± 2.5 dB (median 0 dB; IQR -1 to 2) for the macular patient group. Coefficients of repeatability for mean retinal sensitivity and pointwise retinal sensitivity were 1.2 and 3.3 dB for the healthy subjects and 1.6 and 5.0 dB for the macular disease patients, respectively. Absolute agreement in deep scotoma size between both study days was found in 79.9% of the test loci. The microperimeter MP3 shows an adequate test-retest reproducibility for mean retinal sensitivity, pointwise retinal sensitivity, and deep scotoma size in healthy subjects and patients suffering from macular disease. Furthermore, reproducibility of microperimetry is higher than conventional perimetry. Reproducibility is an important measure for each diagnostic device. Especially in a clinical setting high reproducibility set the basis to achieve reliable results using the specific device. Therefore, assessment of the reproducibility is of eminent importance to interpret the findings of future studies.

Regulating Ultrasound Cavitation in order to Induce Reproducible Sonoporation

Science.gov (United States)

Mestas, J.-L.; Alberti, L.; El Maalouf, J.; Béra, J.-C.; Gilles, B.

2010-03-01

Sonoporation would be linked to cavitation, which generally appears to be a non reproducible and unstationary phenomenon. In order to obtain an acceptable trade-off between cell mortality and transfection, a regulated cavitation generator based on an acoustical cavitation measurement was developed and tested. The medium to be sonicated is placed in a sample tray. This tray is immersed in in degassed water and positioned above the face of a flat ultrasonic transducer (frequency: 445 kHz; intensity range: 0.08-1.09 W/cm2). This technical configuration was admitted to be conducive to standing-wave generation through reflection at the air/medium interface in the well thus enhancing the cavitation phenomenon. Laterally to the transducer, a homemade hydrophone was oriented to receive the acoustical signal from the bubbles. From this spectral signal recorded at intervals of 5 ms, a cavitation index was calculated as the mean of the cavitation spectrum integration in a logarithmic scale, and the excitation power is automatically corrected. The device generates stable and reproducible cavitation level for a wide range of cavitation setpoint from stable cavitation condition up to full-developed inertial cavitation. For the ultrasound intensity range used, the time delay of the response is lower than 200 ms. The cavitation regulation device was evaluated in terms of chemical bubble collapse effect. Hydroxyl radical production was measured on terephthalic acid solutions. In open loop, the results present a great variability whatever the excitation power. On the contrary the closed loop allows a great reproducibility. This device was implemented for study of sonodynamic effect. The regulation provides more reproducible results independent of cell medium and experimental conditions (temperature, pressure). Other applications of this regulated cavitation device concern internalization of different particles (Quantum Dot) molecules (SiRNA) or plasmids (GFP, DsRed) into different

Reproducible high-resolution multispectral image acquisition in dermatology

Science.gov (United States)

Duliu, Alexandru; Gardiazabal, José; Lasser, Tobias; Navab, Nassir

2015-07-01

Multispectral image acquisitions are increasingly popular in dermatology, due to their improved spectral resolution which enables better tissue discrimination. Most applications however focus on restricted regions of interest, imaging only small lesions. In this work we present and discuss an imaging framework for high-resolution multispectral imaging on large regions of interest.

Reproducibility of the serum lipid response to coffee oil in healthy volunteers

Directory of Open Access Journals (Sweden)

Katan Martijn B

2003-10-01

Full Text Available Abstract Background Humans and animals show a certain consistency in the response of their serum lipids to fat-modified diets. This may indicate a genetic basis underlying this response. Coffee oil might be used as a model substance to investigate which genes determine differences in the serum lipid response. Before carrying out such studies our objective was to investigate to what extent the effect of coffee oil on serum lipid concentrations is reproducible within subjects. Methods The serum lipid response of 32 healthy volunteers was measured twice in separate five-week periods in which coffee oil was administered (69 mg cafestol / day. Results Total cholesterol levels increased by 24% in period 1 (range:0;52% and 18% in period 2 (1;48%, LDL cholesterol by 29 % (-9;71% and 20% (-12;57%, triglycerides by 66% (16;175% and 58% (-13;202%, and HDL cholesterol did not change significantly: The range of the HDL response was -19;25% in period 1 and -20;33% in period 2. The correlation between the two responses was 0.20 (95%CI -0.16, 0.51 for total cholesterol, 0.16 (95%CI -0.20, 0.48 for LDL, 0.67 (95%CI 0.42, 0.83 for HDL, and 0.77 (95%CI 0.56, 0.88 for triglycerides. Conclusions The responses of total and LDL cholesterol to coffee oil were poorly reproducible within subjects. The responses of HDL and triglycerides, however, appeared to be highly reproducible. Therefore, investigating the genetic sources of the variation in the serum-lipid response to coffee oil is more promising for HDL and triglycerides.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Science.gov (United States)

Addona, Terri A; Abbatiello, Susan E; Schilling, Birgit; Skates, Steven J; Mani, D R; Bunk, David M; Spiegelman, Clifford H; Zimmerman, Lisa J; Ham, Amy-Joan L; Keshishian, Hasmik; Hall, Steven C; Allen, Simon; Blackman, Ronald K; Borchers, Christoph H; Buck, Charles; Cardasis, Helene L; Cusack, Michael P; Dodder, Nathan G; Gibson, Bradford W; Held, Jason M; Hiltke, Tara; Jackson, Angela; Johansen, Eric B; Kinsinger, Christopher R; Li, Jing; Mesri, Mehdi; Neubert, Thomas A; Niles, Richard K; Pulsipher, Trenton C; Ransohoff, David; Rodriguez, Henry; Rudnick, Paul A; Smith, Derek; Tabb, David L; Tegeler, Tony J; Variyath, Asokan M; Vega-Montoto, Lorenzo J; Wahlander, Åsa; Waldemarson, Sofia; Wang, Mu; Whiteaker, Jeffrey R; Zhao, Lei; Anderson, N Leigh; Fisher, Susan J; Liebler, Daniel C; Paulovich, Amanda G; Regnier, Fred E; Tempst, Paul; Carr, Steven A

2010-01-01

Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low µg/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma. PMID:19561596

Reproducibility of heart rate variability, blood pressure variability and baroreceptor sensitivity during rest and head-up tilt

DEFF Research Database (Denmark)

Højgaard, Michael V; Agner, Erik; Kanters, Jørgen K

2005-01-01

OBJECTIVE: Previous studies have indicated moderate-to-poor reproducibility of heart rate variability (HRV) but the reproducibility of blood pressure variability (BPV) and spectral measures of baroreceptor sensitivity (BRS) are not well established. METHODS: We measured normal-to-normal heart beat...... pressures were extracted for the assessment of day-to-day and short-term reproducibility. Power spectrum analysis (Fourier) and transfer function analysis was performed. Reproducibility was assessed using the coefficient of variation (CV). The reproducibility of the mean RR interval, mean systolic......, diastolic and mean blood pressure was good (CVspectral parameters of HRV (CV range 18-36%) and BPV (16-44%) and moderate reproducibility of BRS (14-20%). CONCLUSION: Spectral estimates of BRS had only moderate reproducibility although...

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

Science.gov (United States)

Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

2017-01-01

, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.

Reproducibility of quantitative planar thallium-201 scintigraphy: quantitative criteria for reversibility of myocardial perfusion defects

International Nuclear Information System (INIS)

Sigal, S.L.; Soufer, R.; Fetterman, R.C.; Mattera, J.A.; Wackers, F.J.

1991-01-01

Fifty-two paired stress/delayed planar 201 TI studies (27 exercise studies, 25 dipyridamole studies) were processed twice by seven technologists to assess inter- and intraobserver variability. The reproducibility was inversely related to the size of 201 Tl perfusion abnormalities. Intraobserver variability was not different between exercise and dipyridamole studies for lesions of similar size. Based upon intraobserver variability, objective quantitative criteria for reversibility of perfusion abnormalities were defined. These objective criteria were tested prospectively in a separate group of 35 201 Tl studies and compared with the subjective interpretation of quantitative circumferential profiles. Overall, exact agreement existed in 78% of images (kappa statistic k = 0.66). We conclude that quantification of planar 201 Tl scans is highly reproducible, with acceptable inter- and intraobserver variability. Objective criteria for lesion reversibility correlated well with analysis by experienced observers

Reproducibility Test for Thermoluminescence Dosimeter (TLD) Using TLD Radpro

International Nuclear Information System (INIS)

Nur Khairunisa Zahidi; Ahmad Bazlie Abdul Kadir; Faizal Azrin Abdul Razalim

2016-01-01

Thermoluminescence dosimeters (TLD) as one type of dosimeter which are often used to substitute the film badge. Like a film badge, it is worn for a period of time and then must be processed to determine the dose received. This study was to test the reproducibility of TLD using Radpro reader. This study aimed to determine the dose obtained by TLD-100 chips when irradiated with Co-60 gamma source and to test the effectiveness of TLD Radpro reader as a machine to analyse the TLD. Ten chips of TLD -100 were irradiated using Eldorado machine with Co-60 source at a distance of 5 meters from the source with 2 mSv dose exposure. After the irradiation process, TLD-100 chips were read using the TLD Radpro reader. These steps will be repeated for nine times to obtain reproducibility coefficient, r i . The readings of dose obtained from experiment was almost equivalent to the actual dose. Results shows that the average value obtained for reproducibility coefficient, r i is 6.39 % which is less than 10 %. As conclusion, the dose obtained from experiment considered accurate because its value were almost equivalent to the actual dose and TLD Radpro was verified as a good reader to analyse the TLD. (author)

Repeatability and Reproducibility of Fibre-Based Nanogenerator Synthesized by Electrospinning Machine

International Nuclear Information System (INIS)

Suyitno; Huda, Sholiehul; Arifin, Zainal; Hadi, Syamsul; Lambang, Raymundus Lullus

2014-01-01

Zinc oxide fibres-based nanogenerators synthesized easily by electrospinning machine are promising to harvest electricity from mechanical energy. However, the repeatability and reproducibility were two major factors needed to be investigated to minimize product failure and to determine the feasibility of mass production of nanogenerators. The green fibres of zinc oxide were produced by electrospinning machine of zinc acetate and polyvinyl alcohol solution at a flow rate of 4 μL/min followed by sintering at temperature 550°C with heating rate 240°C/h. Each 10 nanogenerators was tested by three trained operators with three times of repetition at compressive load 0.5 kg. The nanogenerators revealed the maximum output voltage ranging from 203 to 217 mV. The value of repeatability and reproducibility of nanogenerators was approximately 24.29% showing that nanogenerators were still acceptable to be mass-produced. The relatively low reproducibility was mainly due to the operators, so that the checklist needed to be made easier and simpler for all the variables affecting to the quality of the fibres. Reducing the value of the repeatability and reproducibility is interesting to study further by creating a rotating collector so that the thickness and orientation of fibres can be arranged better

Assessing Cognitive Performance in Badminton Players: A Reproducibility and Validity Study

Directory of Open Access Journals (Sweden)

van de Water Tanja

2017-01-01

Full Text Available Fast reaction and good inhibitory control are associated with elite sports performance. To evaluate the reproducibility and validity of a newly developed Badminton Reaction Inhibition Test (BRIT, fifteen elite (25 ± 4 years and nine non-elite (24 ± 4 years Dutch male badminton players participated in the study. The BRIT measured four components: domain-general reaction time, badminton-specific reaction time, domain-general inhibitory control and badminton-specific inhibitory control. Five participants were retested within three weeks on the badminton-specific components. Reproducibility was acceptable for badminton-specific reaction time (ICC = 0.626, CV = 6% and for badminton-specific inhibitory control (ICC = 0.317, CV = 13%. Good construct validity was shown for badminton-specific reaction time discriminating between elite and non-elite players (F = 6.650, p 0.05. Concurrent validity for domain-general reaction time was good, as it was associated with a national ranking for elite (p = 0.70, p 0.05. In conclusion, reproducibility and validity of inhibitory control assessment was not confirmed, however, the BRIT appears a reproducible and valid measure of reaction time in badminton players. Reaction time measured with the BRIT may provide input for training programs aiming to improve badminton players’ performance.

Assessing Cognitive Performance in Badminton Players: A Reproducibility and Validity Study.

Science.gov (United States)

van de Water, Tanja; Huijgen, Barbara; Faber, Irene; Elferink-Gemser, Marije

2017-01-01

Fast reaction and good inhibitory control are associated with elite sports performance. To evaluate the reproducibility and validity of a newly developed Badminton Reaction Inhibition Test (BRIT), fifteen elite (25 ± 4 years) and nine non-elite (24 ± 4 years) Dutch male badminton players participated in the study. The BRIT measured four components: domain-general reaction time, badminton-specific reaction time, domain-general inhibitory control and badminton-specific inhibitory control. Five participants were retested within three weeks on the badminton-specific components. Reproducibility was acceptable for badminton-specific reaction time (ICC = 0.626, CV = 6%) and for badminton-specific inhibitory control (ICC = 0.317, CV = 13%). Good construct validity was shown for badminton-specific reaction time discriminating between elite and non-elite players (F = 6.650, p 0.05). Concurrent validity for domain-general reaction time was good, as it was associated with a national ranking for elite (p = 0.70, p badminton-specific reaction time, nor both components of inhibitory control (p > 0.05). In conclusion, reproducibility and validity of inhibitory control assessment was not confirmed, however, the BRIT appears a reproducible and valid measure of reaction time in badminton players. Reaction time measured with the BRIT may provide input for training programs aiming to improve badminton players' performance.

Open and reproducible global land use classification

Science.gov (United States)

Nüst, Daniel; Václavík, Tomáš; Pross, Benjamin

2015-04-01

Researchers led by the Helmholtz Centre for Environmental research (UFZ) developed a new world map of land use systems based on over 30 diverse indicators (http://geoportal.glues.geo.tu-dresden.de/stories/landsystemarchetypes.html) of land use intensity, climate and environmental and socioeconomic factors. They identified twelve land system archetypes (LSA) using a data-driven classification algorithm (self-organizing maps) to assess global impacts of land use on the environment, and found unexpected similarities across global regions. We present how the algorithm behind this analysis can be published as an executable web process using 52°North WPS4R (https://wiki.52north.org/bin/view/Geostatistics/WPS4R) within the GLUES project (http://modul-a.nachhaltiges-landmanagement.de/en/scientific-coordination-glues/). WPS4R is an open source collaboration platform for researchers, analysts and software developers to publish R scripts (http://www.r-project.org/) as a geo-enabled OGC Web Processing Service (WPS) process. The interoperable interface to call the geoprocess allows both reproducibility of the analysis and integration of user data without knowledge about web services or classification algorithms. The open platform allows everybody to replicate the analysis in their own environments. The LSA WPS process has several input parameters, which can be changed via a simple web interface. The input parameters are used to configure both the WPS environment and the LSA algorithm itself. The encapsulation as a web process allows integration of non-public datasets, while at the same time the publication requires a well-defined documentation of the analysis. We demonstrate this platform specifically to domain scientists and show how reproducibility and open source publication of analyses can be enhanced. We also discuss future extensions of the reproducible land use classification, such as the possibility for users to enter their own areas of interest to the system and

Device Engineering Towards Improved Tin Sulfide Solar Cell Performance and Performance Reproducibility

Energy Technology Data Exchange (ETDEWEB)

Steinmann, Vera; Chakraborty, Rupak; Rekemeyer, Paul; Siol, Sebastian; Martinot, Loic; Polizzotti, Alex; Yang, Chuanxi; Hartman, Katy; Gradecak, Silvija; Zakutayev, Andriy; Gordon, Roy G.; Buonassisi, Tonio

2016-11-21

As novel absorber materials are developed and screened for their photovoltaic (PV) properties, the challenge remains to rapidly test promising candidates in high-performing PV devices. There is a need to engineer new compatible device architectures, including the development of novel transparent conductive oxides and buffer layers. Here, we consider the two approaches of a substrate-style and a superstrate-style device architecture for novel thin-film solar cells. We use tin sulfide as a test absorber material. Upon device engineering, we demonstrate new approaches to improve device performance and performance reproducibility.

A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

Science.gov (United States)

Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

2017-06-20

With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Geometry of the self-consistent collective-coordinate method for the large-amplitude collective motion

International Nuclear Information System (INIS)

Sakata, Fumihiko; Marumori, Toshio; Hashimoto, Yukio; Une, Tsutomu.

1983-05-01

The geometry of the self-consistent collective-coordinate (SCC) method formulated within the framework of the time-dependent Hartree-Fock (TDHF) theory is investigated by associating the variational parameters with a symplectic manifold (a TDHF manifold). With the use of a canonical-variables parametrization, it is shown that the TDHF equation is equivalent to the canonical equations of motion in classical mechanics in the TDHF manifold. This enables us to investigate geometrical structure of the SCC method in the language of the classical mechanics. The SCC method turns out to give a prescription how to dynamically extract a ''maximally-decoupled'' collective submanifold (hypersurface) out of the TDHF manifold, in such a way that a certain kind of trajectories corresponding to the large-amplitude collective motion under consideration can be reproduced on the hypersurface as precisely as possible. The stability of the hypersurface at each point on it is investigated, in order to see whether the hypersurface obtained by the SCC method is really an approximate integral surface in the TDHF manifold or not. (author)

Intercenter reproducibility of binary typing for Staphylococcus aureus

NARCIS (Netherlands)

van Leeuwen, Willem B.; Snoeijers, Sandor; van der Werken-Libregts, Christel; Tuip, Anita; van der Zee, Anneke; Egberink, Diane; de Proost, Monique; Bik, Elisabeth; Lunter, Bjorn; Kluytmans, Jan; Gits, Etty; van Duyn, Inge; Heck, Max; van der Zwaluw, Kim; Wannet, Wim; Noordhoek, Gerda T.; Mulder, Sije; Renders, Nicole; Boers, Miranda; Zaat, Sebastiaan; van der Riet, Daniëlle; Kooistra, Mirjam; Talens, Adriaan; Dijkshoorn, Lenie; van der Reyden, Tanny; Veenendaal, Dick; Bakker, Nancy; Cookson, Barry; Lynch, Alisson; Witte, Wolfgang; Cuny, Christa; Blanc, Dominique; Vernez, Isabelle; Hryniewicz, Waleria; Fiett, Janusz; Struelens, Marc; Deplano, Ariane; Landegent, Jim; Verbrugh, Henri A.; van Belkum, Alex

2002-01-01

The reproducibility of the binary typing (BT) protocol developed for epidemiological typing of Staphylococcus aureus was analyzed in a biphasic multicenter study. In a Dutch multicenter pilot study, 10 genetically unique isolates of methicillin-resistant S. aureus (MRSA) were characterized by the BT

Visual-stratigraphic dating of the GISP2 ice core: Basis, reproducibility, and application

Science.gov (United States)

Alley, R. B.; Shuman, C. A.; Meese, D. A.; Gow, A. J.; Taylor, K. C.; Cuffey, K. M.; Fitzpatrick, J. J.; Grootes, P. M.; Zielinski, G. A.; Ram, M.; Spinelli, G.; Elder, B.

1997-11-01

Annual layers are visible in the Greenland Ice Sheet Project 2 ice core from central Greenland, allowing rapid dating of the core. Changes in bubble and grain structure caused by near-surface, primarily summertime formation of hoar complexes provide the main visible annual marker in the Holocene, and changes in "cloudiness" of the ice correlated with dustiness mark Wisconsinan annual cycles; both markers are evident and have been intercalibrated in early Holocene ice. Layer counts are reproducible between different workers and for one worker at different times, with 1% error over century-length times in the Holocene. Reproducibility is typically 5% in Wisconsinan ice-age ice and decreases with increasing age and depth. Cumulative ages from visible stratigraphy are not significantly different from independent ages of prominent events for ice older than the historical record and younger than approximately 50,000 years. Visible observations are not greatly degraded by "brittle ice" or many other core-quality problems, allowing construction of long, consistently sampled time series. High accuracy requires careful study of the core by dedicated observers.

Intra-observer reproducibility and diagnostic performance of breast shear-wave elastography in Asian women.

Science.gov (United States)

Park, Hye Young; Han, Kyung Hwa; Yoon, Jung Hyun; Moon, Hee Jung; Kim, Min Jung; Kim, Eun-Kyung

2014-06-01

Our aim was to evaluate intra-observer reproducibility of shear-wave elastography (SWE) in Asian women. Sixty-four breast masses (24 malignant, 40 benign) were examined with SWE in 53 consecutive Asian women (mean age, 44.9 y old). Two SWE images were obtained for each of the lesions. The intra-observer reproducibility was assessed by intra-class correlation coefficients (ICC). We also evaluated various clinicoradiologic factors that can influence reproducibility in SWE. The ICC of intra-observer reproducibility was 0.789. In clinicoradiologic factor evaluation, masses surrounded by mixed fatty and glandular tissue (ICC: 0.619) showed lower intra-observer reproducibility compared with lesions that were surrounded by glandular tissue alone (ICC: 0.937; p breast SWE was excellent in Asian women. However, it may decrease when breast tissue is in a heterogeneous background. Therefore, SWE should be performed carefully in these cases. Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

SU-D-207B-01: Radiomics Feature Reproducibility From Repeat CT Scans of Patients with Rectal Cancer

Energy Technology Data Exchange (ETDEWEB)

Hu, P; Wang, J; Zhong, H; Zhou, Z; Shen, L; Hu, W; Zhang, Z [Fudan University Shanghai Cancer Center, Shanghai, Shanghai (China)

2016-06-15

Purpose: To evaluate the reproducibility of radiomics features by repeating computed tomographic (CT) scans in rectal cancer. To choose stable radiomics features for rectal cancer. Methods: 40 rectal cancer patients were enrolled in this study, each of whom underwent two CT scans within average 8.7 days (5 days to 17 days), before any treatment was delivered. The rectal gross tumor volume (GTV) was distinguished and segmented by an experienced oncologist in both CTs. Totally, more than 2000 radiomics features were defined in this study, which were divided into four groups (I: GLCM, II: GLRLM III: Wavelet GLCM and IV: Wavelet GLRLM). For each group, five types of features were extracted (Max slice: features from the largest slice of target images, Max value: features from all slices of target images and choose the maximum value, Min value: minimum value of features for all slices, Average value: average value of features for all slices, Matrix sum: all slices of target images translate into GLCM and GLRLM matrices and superpose all matrices, then extract features from the superposed matrix). Meanwhile a LOG (Laplace of Gauss) filter with different parameters was applied to these images. Concordance correlation coefficients (CCC) and inter-class correlation coefficients (ICC) were calculated to assess the reproducibility. Results: 403 radiomics features were extracted from each type of patients’ medical images. Features of average type are the most reproducible. Different filters have little effect for radiomics features. For the average type features, 253 out of 403 features (62.8%) showed high reproducibility (ICC≥0.8), 133 out of 403 features (33.0%) showed medium reproducibility (0.8≥ICC≥0.5) and 17 out of 403 features (4.2%) showed low reproducibility (ICC≥0.5). Conclusion: The average type radiomics features are the most stable features in rectal cancer. Further analysis of these features of rectal cancer can be warranted for treatment monitoring and

The salience of social referents: a field experiment on collective norms and harassment behavior in a school social network.

Science.gov (United States)

Paluck, Elizabeth Levy; Shepherd, Hana

2012-12-01

Persistent, widespread harassment in schools can be understood as a product of collective school norms that deem harassment, and behavior allowing harassment to escalate, as typical and even desirable. Thus, one approach to reducing harassment is to change students' perceptions of these collective norms. Theory suggests that the public behavior of highly connected and chronically salient actors in a group, called social referents, may provide influential cues for individuals' perception of collective norms. Using repeated, complete social network surveys of a public high school, we demonstrate that changing the public behavior of a randomly assigned subset of student social referents changes their peers' perceptions of school collective norms and their harassment behavior. Social referents exert their influence over peers' perceptions of collective norms through the mechanism of everyday social interaction, particularly interaction that is frequent and personally motivated, in contrast to interaction shaped by institutional channels like shared classes. These findings clarify the development of collective social norms: They depend on certain patterns of and motivations for social interactions within groups across time, and are not static but constantly reshaped and reproduced through these interactions. Understanding this process creates opportunities for changing collective norms and behavior. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

Transition questions in clinical practice - validity and reproducibility

DEFF Research Database (Denmark)

Lauridsen, Henrik Hein

2008-01-01

Transition questions in CLINICAL practice - validity and reproducibility Lauridsen HH1, Manniche C3, Grunnet-Nilsson N1, Hartvigsen J1,2 1   Clinical Locomotion Science, Institute of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark. e-mail: hlauridsen......@health.sdu.dk 2   Nordic Institute of Chiropractic and Clinical Biomechanics, Part of Clinical Locomotion Science, Odense, Denmark 3   Backcenter Funen, Part of Clinical Locomotion Science, Ringe, Denmark   Abstract  Understanding a change score is indispensable for interpretation of results from clinical studies...... are reproducible in patients with low back pain and/or leg pain. Despite critique of several biases, our results have reinforced the construct validity of TQ’s as an outcome measure since only 1 hypothesis was rejected. On the basis of our findings we have outlined a proposal for a standardised use of transition...

Reproducing American Sign Language Sentences: Cognitive Scaffolding in Working Memory

Directory of Open Access Journals (Sweden)

Ted eSupalla

2014-08-01

Full Text Available The American Sign Language Sentence Reproduction Test (ASL-SRT requires the precise reproduction of a series of ASL sentences increasing in complexity and length. Error analyses of such tasks provides insight into working memory and scaffolding processes. Data was collected from three groups expected to differ in fluency: deaf children, deaf adults and hearing adults, all users of ASL. Quantitative (correct/incorrect recall and qualitative error analyses were performed. Percent correct on the reproduction task supports its sensitivity to fluency as test performance clearly differed across the three groups studied. A linguistic analysis of errors further documented differing strategies and bias across groups. Subjects’ recall projected the affordance and constraints of deep linguistic representations to differing degrees, with subjects resorting to alternate processing strategies in the absence of linguistic knowledge. A qualitative error analysis allows us to capture generalizations about the relationship between error pattern and the cognitive scaffolding, which governs the sentence reproduction process. Highly fluent signers and less-fluent signers share common chokepoints on particular words in sentences. However, they diverge in heuristic strategy. Fluent signers, when they make an error, tend to preserve semantic details while altering morpho-syntactic domains. They produce syntactically correct sentences with equivalent meaning to the to-be-reproduced one, but these are not verbatim reproductions of the original sentence. In contrast, less-fluent signers tend to use a more linear strategy, preserving lexical status and word ordering while omitting local inflections, and occasionally resorting to visuo-motoric imitation. Thus, whereas fluent signers readily use top-down scaffolding in their working memory, less fluent signers fail to do so. Implications for current models of working memory across spoken and signed modalities are

Reproducibility of isotope ratio measurements

International Nuclear Information System (INIS)

Elmore, D.

1981-01-01

The use of an accelerator as part of a mass spectrometer has improved the sensitivity for measuring low levels of long-lived radionuclides by several orders of magnitude. However, the complexity of a large tandem accelerator and beam transport system has made it difficult to match the precision of low energy mass spectrometry. Although uncertainties for accelerator measured isotope ratios as low as 1% have been obtained under favorable conditions, most errors quoted in the literature for natural samples are in the 5 to 20% range. These errors are dominated by statistics and generally the reproducibility is unknown since the samples are only measured once

Reproducibility of the results in ultrasonic testing

International Nuclear Information System (INIS)

Chalaye, M.; Launay, J.P.; Thomas, A.

1980-12-01

This memorandum reports on the conclusions of the tests carried out in order to evaluate the reproducibility of ultrasonic tests made on welded joints. FRAMATOME have started a study to assess the dispersion of results afforded by the test line and to characterize its behaviour. The tests covered sensors and ultrasonic generators said to be identical to each other (same commercial batch) [fr

Test–Retest Reproducibility of the Microperimeter MP3 With Fundus Image Tracking in Healthy Subjects and Patients With Macular Disease

Science.gov (United States)

Palkovits, Stefan; Hirnschall, Nino; Georgiev, Stefan; Leisser, Christoph

2018-01-01

Purpose To evaluate the test–retest reproducibility of a novel microperimeter with fundus image tracking (MP3, Nidek Co, Japan) in healthy subjects and patients with macular disease. Methods Ten healthy subjects and 20 patients suffering from range of macular diseases were included. After training measurements, two additional microperimetry measurements were scheduled. Test–retest reproducibility was assessed for mean retinal sensitivity, pointwise sensitivity, and deep scotoma size using the coefficient of repeatability and Bland-Altman diagrams. In addition, in a subgroup of patients microperimetry was compared with conventional perimetry. Results Average differences in mean retinal sensitivity between the two study measurements were 0.26 ± 1.7 dB (median 0 dB; interquartile range [IQR] −1 to 1) for the healthy and 0.36 ± 2.5 dB (median 0 dB; IQR −1 to 2) for the macular patient group. Coefficients of repeatability for mean retinal sensitivity and pointwise retinal sensitivity were 1.2 and 3.3 dB for the healthy subjects and 1.6 and 5.0 dB for the macular disease patients, respectively. Absolute agreement in deep scotoma size between both study days was found in 79.9% of the test loci. Conclusion The microperimeter MP3 shows an adequate test–retest reproducibility for mean retinal sensitivity, pointwise retinal sensitivity, and deep scotoma size in healthy subjects and patients suffering from macular disease. Furthermore, reproducibility of microperimetry is higher than conventional perimetry. Translational Relevance Reproducibility is an important measure for each diagnostic device. Especially in a clinical setting high reproducibility set the basis to achieve reliable results using the specific device. Therefore, assessment of the reproducibility is of eminent importance to interpret the findings of future studies. PMID:29430338

Fishing out collective memory of migratory schools

DEFF Research Database (Denmark)

De Luca, G.; Mariani, Patrizio; MacKenzie, Brian

2014-01-01

Animals form groups for many reasons but there are costs and benefit associated with group formation. One of the benefits is collective memory. In groups on the move, social interactions play a crucial role in the cohesion and the ability to make consensus decisions. When migrating from spawning...... to feeding areas fish schools need to retain a collective memory of the destination site over thousand of kilometers and changes in group formation or individual preference can produce sudden changes in migration pathways. We propose a modelling framework, based on stochastic adaptive networks, that can...... reproduce this collective behaviour. We assume that three factors control group formation and school migration behaviour: the intensity of social interaction, the relative number of informed individuals and the preference that each individual has for the particular migration area. We treat these factors...

Reproducibility in light microscopy: Maintenance, standards and SOPs.

Science.gov (United States)

Deagle, Rebecca C; Wee, Tse-Luen Erika; Brown, Claire M

2017-08-01

Light microscopy has grown to be a valuable asset in both the physical and life sciences. It is a highly quantitative method available in individual research laboratories and often centralized in core facilities. However, although quantitative microscopy is becoming a customary tool in research, it is rarely standardized. To achieve accurate quantitative microscopy data and reproducible results, three levels of standardization must be considered: (1) aspects of the microscope, (2) the sample, and (3) the detector. The accuracy of the data is only as reliable as the imaging system itself, thereby imposing the need for routine standard performance testing. Depending on the task some maintenance procedures should be performed once a month, some before each imaging session, while others conducted annually. This text should be implemented as a resource for researchers to integrate with their own standard operating procedures to ensure the highest quality quantitative microscopy data. Copyright © 2017. Published by Elsevier Ltd.

Reproducibility of 3D kinematics and surface electromyography measurements of mastication.

Science.gov (United States)

Remijn, Lianne; Groen, Brenda E; Speyer, Renée; van Limbeek, Jacques; Nijhuis-van der Sanden, Maria W G

2016-03-01

The aim of this study was to determine the measurement reproducibility for a procedure evaluating the mastication process and to estimate the smallest detectable differences of 3D kinematic and surface electromyography (sEMG) variables. Kinematics of mandible movements and sEMG activity of the masticatory muscles were obtained over two sessions with four conditions: two food textures (biscuit and bread) of two sizes (small and large). Twelve healthy adults (mean age 29.1 years) completed the study. The second to the fifth chewing cycle of 5 bites were used for analyses. The reproducibility per outcome variable was calculated with an intraclass correlation coefficient (ICC) and a Bland-Altman analysis was applied to determine the standard error of measurement relative error of measurement and smallest detectable differences of all variables. ICCs ranged from 0.71 to 0.98 for all outcome variables. The outcome variables consisted of four bite and fourteen chewing cycle variables. The relative standard error of measurement of the bite variables was up to 17.3% for 'time-to-swallow', 'time-to-transport' and 'number of chewing cycles', but ranged from 31.5% to 57.0% for 'change of chewing side'. The relative standard error of measurement ranged from 4.1% to 24.7% for chewing cycle variables and was smaller for kinematic variables than sEMG variables. In general, measurements obtained with 3D kinematics and sEMG are reproducible techniques to assess the mastication process. The duration of the chewing cycle and frequency of chewing were the best reproducible measurements. Change of chewing side could not be reproduced. The published measurement error and smallest detectable differences will aid the interpretation of the results of future clinical studies using the same study variables. Copyright © 2015 Elsevier Inc. All rights reserved.

Variability and reproducibility of rubidium-82 kinetic parameters in the myocardium of the anesthetized canine

International Nuclear Information System (INIS)

Coxson, P.G.; Brennan, K.M.; Huesman, R.H.

1995-01-01

Kinetic analysis of 82 Rb (I) dynamic PET data produces quantitative measures which could be used to evaluate ischemic heart disease. These measures have the potential to generate objective comparisons of different patients or the same patient at different times. To achieve this potential, it is essential to determine the variability and reproducibility of the kinetic parameters. A total of 48 I dynamic PET datasets were acquired from two pure bred beagles. Each animal underwent eight I PET studies with essentially the same protocol for three successive weeks. Data were acquired with the Donner 600-Crystal Positron Tomograph (PET600). In each week, single-slice dynamic I PET datasets were collected with the animal at rest at three different gantry positions separated by 5 mm. Additional dataset were collected after dipyridamole infusion and after administration of aminophylline to induce a return to rest. A two-compartment kinetic model with correction for myocardial vasculature and spillover from the left ventricular blood pool was used to analyze the dynamic datasets. Model parameters for uptake (k 1 ), washout (k 2 ) and vascular fraction (f v ) were estimated in 11-14 myocardial regions of interest (ROIs) using a weighted least-squares criterion. Statistical fluctuation due to the PET acquisition process was minimized by using a relatively high I dose (about 30 mCi) to take advantage of the high count rate capacity of the PET600. The variation in mean k 1 , where the mean is taken over the myocardial ROIs was 10%-20% (Dog 1) and 15%-50% (Dog 2) among the rest studies conducted on the same data. Similar variation was evident in comparing studies in the same animal for different weeks. Spatial and temporal variation in estimates of the uptake rate (k 1 ) of I in the resting myocardium of the anesthetized canine are small in relation to the functional increase in k 1 , following dipyridamole stress. 17 refs., 14 figs

T2-mapping of the sacroiliac joints at 1.5 Tesla: a feasibility and reproducibility study.

Science.gov (United States)

Albano, Domenico; Chianca, Vito; Cuocolo, Renato; Bignone, Rodolfo; Ciccia, Francesco; Sconfienza, Luca Maria; Midiri, Massimo; Brunetti, Arturo; Lagalla, Roberto; Galia, Massimo

2018-04-20

To evaluate the reproducibility of T2 relaxation time measurements of the sacroiliac joints at 1.5 T. Healthy volunteers underwent an oblique axial multislice multiecho spin-echo sequence of the sacroiliac joints at 1.5 T. Regions of interest were manually drawn using a dedicated software by two musculoskeletal radiologists to include the cartilaginous part of the sacroiliac joints. A senior radiologist performed the measurement twice, while a resident measured once. Intra- and inter-observer reproducibility was tested using the Bland-Altman method. Association between sex and T2 relaxation times was tested using the Mann-Whitney U test. Correlation between T2 relaxation times and body mass index (BMI) was tested using the Spearman's rho. Eighty sacroiliac joints of 40 subjects (mean age: 28 ± 4.8 years, range: 20-43; mean BMI: 23.3 ± 3.1, range: 18.9-30) were imaged. The mean T2 values obtained by the senior radiologist in the first series of measurements were 42 ± 4.4 ms, whereas in the second series were 40.7 ± 4.5 ms. The mean T2 values obtained by the radiology resident were 41.1 ± 4.2 ms. Intra-observer reproducibility was 88% (coefficient of repeatability = 3.8; bias = 1.28; p sacroiliac joints seems to be highly reproducible at 1.5 T. Further studies could investigate the potential clinical application of this tool in the sacroiliac joints.

Automated analysis of phantom images for the evaluation of long-term reproducibility in digital mammography

International Nuclear Information System (INIS)

Gennaro, G; Ferro, F; Contento, G; Fornasin, F; Di Maggio, C

2007-01-01

The performance of an automatic software package was evaluated with phantom images acquired by a full-field digital mammography unit. After the validation, the software was used, together with a Leeds TORMAS test object, to model the image acquisition process. Process modelling results were used to evaluate the sensitivity of the method in detecting changes of exposure parameters from routine image quality measurements in digital mammography, which is the ultimate purpose of long-term reproducibility tests. Image quality indices measured by the software included the mean pixel value and standard deviation of circular details and surrounding background, contrast-to-noise ratio and relative contrast; detail counts were also collected. The validation procedure demonstrated that the software localizes the phantom details correctly and the difference between automatic and manual measurements was within few grey levels. Quantitative analysis showed sufficient sensitivity to relate fluctuations in exposure parameters (kV p or mAs) to variations in image quality indices. In comparison, detail counts were found less sensitive in detecting image quality changes, even when limitations due to observer subjectivity were overcome by automatic analysis. In conclusion, long-term reproducibility tests provided by the Leeds TORMAS phantom with quantitative analysis of multiple IQ indices have been demonstrated to be effective in predicting causes of deviation from standard operating conditions and can be used to monitor stability in full-field digital mammography

Entangled states that cannot reproduce original classical games in their quantum version

International Nuclear Information System (INIS)

Shimamura, Junichi; Oezdemir, S.K.; Morikoshi, Fumiaki; Imoto, Nobuyuki

2004-01-01

A model of a quantum version of classical games should reproduce the original classical games in order to be able to make a comparative analysis of quantum and classical effects. We analyze a class of symmetric multipartite entangled states and their effect on the reproducibility of the classical games. We present the necessary and sufficient condition for the reproducibility of the original classical games. Satisfying this condition means that complete orthogonal bases can be constructed from a given multipartite entangled state provided that each party is restricted to two local unitary operators. We prove that most of the states belonging to the class of symmetric states with respect to permutations, including the N-qubit W state, do not satisfy this condition

Fixed-flexion radiography of the knee provides reproducible joint space width measurements in osteoarthritis

International Nuclear Information System (INIS)

Kothari, Manish; Sieffert, Martine; Block, Jon E.; Peterfy, Charles G.; Guermazi, Ali; Ingersleben, Gabriele von; Miaux, Yves; Stevens, Randall

2004-01-01

The validity of a non-fluoroscopic fixed-flexion radiographic acquisition and analysis protocol for measurement of joint space width (JSW) in knee osteoarthritis is determined. A cross-sectional study of 165 patients with documented knee osteoarthritis participating in a multicenter, prospective study of chondroprotective agents was performed. All patients had posteroanterior, weight-bearing, fixed-flexion radiography with 10 caudal beam angulation. A specially designed frame (SynaFlexer) was used to standardize the positioning. Minimum medial and lateral JSW were measured manually and twice by an automated analysis system to determine inter-technique and intra-reader concordance and reliability. A random subsample of 30 patients had repeat knee radiographs 2 weeks apart to estimate short-term reproducibility using automated analysis. Concordance between manual and automated medial JSW measurements was high (ICC=0.90); lateral compartment measurements showed somewhat less concordance (ICC=0.72). There was excellent concordance between repeated automated JSW measurements performed 6 months apart for the medial (ICC=0.94) and lateral (ICC=0.86) compartments. Short-term reproducibility for the subsample of 30 cases with repeat acquisitions demonstrated an average SD of 0.14 mm for medial JSW (CV=4.3%) and 0.23 mm for lateral JSW (CV=4.0%). Fixed-flexion radiography of the knee using a positioning device provides consistent, reliable and reproducible measurement of minimum JSW in knee osteoarthritis without the need for concurrent fluoroscopic guidance. (orig.)

Convergence of macrostates under reproducible processes

International Nuclear Information System (INIS)

Rau, Jochen

2010-01-01

I show that whenever a system undergoes a reproducible macroscopic process the mutual distinguishability of macrostates, as measured by their relative entropy, diminishes. This extends the second law which regards only ordinary entropies, and hence only the distinguishability between macrostates and one specific reference state (equidistribution). The new result holds regardless of whether the process is linear or nonlinear. Its proof hinges on the monotonicity of quantum relative entropy under arbitrary coarse grainings, even those that cannot be represented by trace-preserving completely positive maps.

Reproducibility of retinal nerve fiber layer thickness measures using eye tracking in children with nonglaucomatous optic neuropathy.

Science.gov (United States)

Rajjoub, Raneem D; Trimboli-Heidler, Carmelina; Packer, Roger J; Avery, Robert A

2015-01-01

To determine the intra- and intervisit reproducibility of circumpapillary retinal nerve fiber layer (RNFL) thickness measures using eye tracking-assisted spectral-domain optical coherence tomography (SD OCT) in children with nonglaucomatous optic neuropathy. Prospective longitudinal study. Circumpapillary RNFL thickness measures were acquired with SD OCT using the eye-tracking feature at 2 separate study visits. Children with normal and abnormal vision (visual acuity ≥ 0.2 logMAR above normal and/or visual field loss) who demonstrated clinical and radiographic stability were enrolled. Intra- and intervisit reproducibility was calculated for the global average and 9 anatomic sectors by calculating the coefficient of variation and intraclass correlation coefficient. Forty-two subjects (median age 8.6 years, range 3.9-18.2 years) met inclusion criteria and contributed 62 study eyes. Both the abnormal and normal vision cohort demonstrated the lowest intravisit coefficient of variation for the global RNFL thickness. Intervisit reproducibility remained good for those with normal and abnormal vision, although small but statistically significant increases in the coefficient of variation were observed for multiple anatomic sectors in both cohorts. The magnitude of visual acuity loss was significantly associated with the global (ß = 0.026, P < .01) and temporal sector coefficient of variation (ß = 0.099, P < .01). SD OCT with eye tracking demonstrates highly reproducible RNFL thickness measures. Subjects with vision loss demonstrate greater intra- and intervisit variability than those with normal vision. Copyright © 2015 Elsevier Inc. All rights reserved.

Microfluidic Air Sampler for Highly Efficient Bacterial Aerosol Collection and Identification.

Science.gov (United States)

Bian, Xiaojun; Lan, Ying; Wang, Bing; Zhang, Yu Shrike; Liu, Baohong; Yang, Pengyuan; Zhang, Weijia; Qiao, Liang

2016-12-06

The early warning capability of the presence of biological aerosol threats is an urgent demand in ensuing civilian and military safety. Efficient and rapid air sample collection in relevant indoor or outdoor environment is a key step for subsequent analysis of airborne microorganisms. Herein, we report a portable battery-powered sampler that is capable of highly efficient bioaerosol collection. The essential module of the sampler is a polydimethylsiloxane (PDMS) microfluidic chip, which consisted of a 3-loop double-spiral microchannel featuring embedded herringbone and sawtooth wave-shaped structures. Vibrio parahemolyticus (V. parahemolyticus) as a model microorganism, was initially employed to validate the bioaerosol collection performance of the device. Results showed that the sampling efficacy reached as high as >99.9%. The microfluidic sampler showed greatly improved capturing efficiency compared with traditional plate sedimentation methods. The high performance of our device was attributed to the horizontal inertial centrifugal force and the vertical turbulence applied to airflow during sampling. The centrifugation field and turbulence were generated by the specially designed herringbone structures when air circulated in the double-spiral microchannel. The sawtooth wave-shaped microstructure created larger specific surface area for accommodating more aerosols. Furthermore, a mixture of bacterial aerosols formed by V. parahemolyticus, Listeria monocytogenes, and Escherichia coli was extracted by the microfluidic sampler. Subsequent integration with mass spectrometry conveniently identified the multiple bacterial species captured by the sampler. Our developed stand-alone and cable-free sampler shows clear advantages comparing with conventional strategies, including portability, easy-to-use, and low cost, indicating great potential in future field applications.

Relative Validity and Reproducibility of an Interviewer Administered 14-Item FFQ to Estimate Flavonoid Intake Among Older Adults with Mild-Moderate Dementia.

Science.gov (United States)

Kent, Katherine; Charlton, Karen

2017-01-01

There is a large burden on researchers and participants when attempting to accurately measure dietary flavonoid intake using dietary assessment. Minimizing participant and researcher burden when collecting dietary data may improve the validity of the results, especially in older adults with cognitive impairment. A short 14-item food frequency questionnaire (FFQ) to measure flavonoid intake, and flavonoid subclasses (anthocyanins, flavan-3-ols, flavones, flavonols, and flavanones) was developed and assessed for validity and reproducibility against a 24-hour recall. Older adults with mild-moderate dementia (n = 49) attended two interviews 12 weeks apart. With the assistance of a family carer, a 24-h recall was collected at the first interview, and the flavonoid FFQ was interviewer-administered at both time-points. Validity and reproducibility was assessed using the Wilcoxon signed-rank sum test, Spearman's correlation coefficient, Bland-Altman Plots, and Cohen's kappa. Mean flavonoid intake was determined (FFQ1 = 795 ± 492.7 mg/day, 24-h recall = 515.6 ± 384.3 mg/day). Tests of validity indicated the FFQ was better at estimating total flavonoid intake than individual flavonoid subclasses compared with the 24-h recall. There was a significant difference in total flavonoid intake estimates between the FFQ and the 24-h recall (Wilcoxon signed-rank sum p Wilcoxon signed-rank sum test showed no significant difference, Spearman's correlation coefficient indicated excellent reliability (r = 0.75, p < 0.001), Bland-Altman plots visually showed small, nonsignificant bias and wide limits of agreement, and Cohen's kappa indicated fair agreement (κ = 0.429, p < 0.001). A 14-item FFQ developed to easily measure flavonoid intake in older adults with dementia demonstrates fair validity against a 24-h recall and good reproducibility.

High collection efficiency CVD diamond alpha detectors

International Nuclear Information System (INIS)

Bergonzo, P.; Foulon, F.; Marshall, R.D.; Jany, C.; Brambilla, A.; McKeag, R.D.; Jackman, R.B.

1998-01-01

Advances in Chemical Vapor Deposited (CVD) diamond have enabled the routine use of this material for sensor device fabrication, allowing exploitation of its unique combination of physical properties (low temperature susceptibility (> 500 C), high resistance to radiation damage (> 100 Mrad) and to corrosive media). A consequence of CVD diamond growth on silicon is the formation of polycrystalline films which has a profound influence on the physical and electronic properties with respect to those measured on monocrystalline diamond. The authors report the optimization of physical and geometrical device parameters for radiation detection in the counting mode. Sandwich and co-planar electrode geometries are tested and their performances evaluated with regard to the nature of the field profile and drift distances inherent in such devices. The carrier drift length before trapping was measured under alpha particles and values as high as 40% of the overall film thickness are reported. Further, by optimizing the device geometry, they show that a gain in collection efficiency, defined as the induced charge divided by the deposited charge within the material, can be achieved even though lower bias values are used

Aveiro method in reproducing kernel Hilbert spaces under complete dictionary

Science.gov (United States)

Mai, Weixiong; Qian, Tao

2017-12-01

Aveiro Method is a sparse representation method in reproducing kernel Hilbert spaces (RKHS) that gives orthogonal projections in linear combinations of reproducing kernels over uniqueness sets. It, however, suffers from determination of uniqueness sets in the underlying RKHS. In fact, in general spaces, uniqueness sets are not easy to be identified, let alone the convergence speed aspect with Aveiro Method. To avoid those difficulties we propose an anew Aveiro Method based on a dictionary and the matching pursuit idea. What we do, in fact, are more: The new Aveiro method will be in relation to the recently proposed, the so called Pre-Orthogonal Greedy Algorithm (P-OGA) involving completion of a given dictionary. The new method is called Aveiro Method Under Complete Dictionary (AMUCD). The complete dictionary consists of all directional derivatives of the underlying reproducing kernels. We show that, under the boundary vanishing condition, bring available for the classical Hardy and Paley-Wiener spaces, the complete dictionary enables an efficient expansion of any given element in the Hilbert space. The proposed method reveals new and advanced aspects in both the Aveiro Method and the greedy algorithm.

Reproducibility and validity of the Shanghai Women's Health Study physical activity questionnaire.

Science.gov (United States)

Matthews, Charles E; Shu, Xiao-Ou; Yang, Gong; Jin, Fan; Ainsworth, Barbara E; Liu, Dake; Gao, Yu-Tang; Zheng, Wei

2003-12-01

In this investigation, the authors evaluated the reproducibility and validity of the Shanghai Women's Health Study (SWHS) physical activity questionnaire (PAQ), which was administered in a cohort study of approximately 75,000 Chinese women aged 40-70 years. Reproducibility (2-year test-retest) was evaluated using kappa statistics and intraclass correlation coefficients (ICCs). Validity was evaluated by comparing Spearman correlations (r) for the SWHS PAQ with two criterion measures administered over a period of 12 months: four 7-day physical activity logs and up to 28 7-day PAQs. Women were recruited from the SWHS cohort (n = 200). Results indicated that the reproducibility of adolescent and adult exercise participation (kappa = 0.85 and kappa = 0.64, respectively) and years of adolescent exercise and adult exercise energy expenditure (ICC = 0.83 and ICC = 0.70, respectively) was reasonable. Reproducibility values for adult lifestyle activities were lower (ICC = 0.14-0.54). Significant correlations between the PAQ and criterion measures of adult exercise were observed for the first PAQ administration (physical activity log, r = 0.50; 7-day PAQ, r = 0.62) and the second PAQ administration (physical activity log, r = 0.74; 7-day PAQ, r = 0.80). Significant correlations between PAQ lifestyle activities and the 7-day PAQ were also noted (r = 0.33-0.88). These data indicate that the SWHS PAQ is a reproducible and valid measure of exercise behaviors and that it demonstrates utility in stratifying women by levels of important lifestyle activities (e.g., housework, walking, cycling).

A multicenter reproducibility study of single-voxel 1H-MRS of the medial temporal lobe

International Nuclear Information System (INIS)

Traeber, Frank; Block, Wolfgang; Guer, Okan; Schild, Hans H.; Freymann, Nikolaus; Heun, Reinhard; Jessen, Frank; Kucinski, Thomas; Hammen, Thilo; Ende, Gabriele; Pilatus, Ulrich; Hampel, Harald

2006-01-01

Proton magnetic resonance spectroscopy ( 1 H-MRS) has provided evidence for a reduction of N-acetyl-aspartate (NAA) in the medial temporal lobe (MTL) in cerebral disorders such as Alzheimer's Disease. Within the 1 H-MRS study of the German Research Network on Dementia, we determined the multicenter reproducibility of single-voxel 1 H-MRS of the MTL. At five sites with 1.5T MR systems, single-voxel 1 H spectra from the MTL of an identical healthy subject were measured. The same subject was also examined at one of the sites five times to assess intracenter stability. The protocol included water-suppressed spectra with TE 272 ms and TE 30 ms and unsuppressed spectra for absolute quantification of metabolite concentrations. The intracenter reproducibility of absolute NAA concentration, expressed as coefficient of variation (CV), was 1.8%. CV for the concentrations of creatine (Cr), choline (Cho), and myoinositol (MI) and for the ratios NAA/Cr, NAA/Cho, and MI/NAA varied by 11-16%. Intercenter CV was 3.9% for NAA and were below 10% for all other metabolites and metabolic ratios. Our study demonstrates that quantitative assessment of NAA with single-voxel MRS can be performed with high intercenter reproducibility. This is the basis for applying 1 H-MRS in large-scale early recognition and treatment studies in MTL affecting disorders. (orig.)

Controlling the reproducibility of Coulomb blockade phenomena for gold nanoparticles on an organic monolayer/silicon system.

Science.gov (United States)

Caillard, L; Sattayaporn, S; Lamic-Humblot, A-F; Casale, S; Campbell, P; Chabal, Y J; Pluchery, O

2015-02-13

Two types of highly ordered organic layers were prepared on silicon modified with an amine termination for binding gold nanoparticles (AuNPs). These two grafted organic monolayers (GOMs), consisting of alkyl chains with seven or 11 carbon atoms, were grafted on oxide-free Si(111) surfaces as tunnel barriers between the silicon electrode and the AuNPs. Three kinds of colloidal AuNPs were prepared by reducing HAuCl4 with three different reactants: citrate (Turkevich synthesis, diameter ∼16 nm), ascorbic acid (diameter ∼9 nm), or NaBH4 (Natan synthesis, diameter ∼7 nm). Scanning tunnel spectroscopy (STS) was performed in a UHV STM at 40 K, and Coulomb blockade behaviour was observed. The reproducibility of the Coulomb behavior was analysed as a function of several chemical and physical parameters: size, crystallinity of the AuNPs, influence of surrounding surfactant molecules, and quality of the GOM/Si interface (degree of oxidation after the full processing). Samples were characterized with scanning tunneling microscope, STS, atomic force microscope, Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy (XPS), and high resolution transmission electronic microscope. We show that the reproducibility in observing Coulomb behavior can be as high as ∼80% with the Natan synthesis of AuNPs and GOMs with short alkyl chains.

Timbral aspects of reproduced sound in small rooms. I

DEFF Research Database (Denmark)

Bech, Søren

1995-01-01

, has been simulated using an electroacoustic setup. The model included the direct sound, 17 individual reflections, and the reverberant field. The threshold of detection and just-noticeable differences for an increase in level were measured for individual reflections using eight subjects for noise......This paper reports some of the influences of individual reflections on the timbre of reproduced sound. A single loudspeaker with frequency-independent directivity characteristics, positioned in a listening room of normal size with frequency-independent absorption coefficients of the room surfaces...... and speech. The results have shown that the first-order floor and ceiling reflections are likely to individually contribute to the timbre of reproduced speech. For a noise signal, additional reflections from the left sidewall will contribute individually. The level of the reverberant field has been found...

Reproducibility of corneal, macular and retinal nerve fiber layer ...

African Journals Online (AJOL)

side the limits of a consulting room.5. Reproducibility of ... examination, intraocular pressure and corneal thickness ... All OCT measurements were taken between 2 and 5 pm ..... CAS-OCT, Slit-lamp OCT, RTVue-100) have shown ICC.

Evaluating the Reproducibility of Motion Analysis Scanning of the Spine during Walking

Directory of Open Access Journals (Sweden)

Aaron Gipsman

2014-01-01

Full Text Available The Formetric 4D dynamic system (Diers International GmbH, Schlangenbad, Germany is a rasterstereography based imaging system designed to evaluate spinal deformity, providing radiation-free imaging of the position, rotation, and shape of the spine during the gait cycle. Purpose. This study was designed to evaluate whether repeated measurements with the Formetric 4D dynamic system would be reproducible with a standard deviation of less than +/− 3 degrees. This study looked at real-time segmental motion, measuring kyphosis, lordosis, trunk length, pelvic, and T4 and L1 vertebral body rotation. Methods. Twenty healthy volunteers each underwent 3 consecutive scans. Measurements for kyphosis, lordosis, trunk length, and rotations of T4, L1, and the pelvis were recorded for each trial. Results. The average standard deviations of same-day repeat measurements were within +/− 3 degrees with a range of 0.51 degrees to 2.3 degrees. Conclusions. The surface topography system calculated reproducible measurements with error ranges comparable to the current gold standard in dynamic spinal motion analysis. Therefore, this technique should be considered of high clinical value for reliably evaluating segmental motion and spinal curvatures and should further be evaluated in the setting of adolescent idiopathic scoliosis.

REPRODUCIBILITY OF MACULAR PIGMENT OPTICAL DENSITY MEASUREMENT BY TWO-WAVELENGTH AUTOFLUORESCENCE IN A CLINICAL SETTING.

Science.gov (United States)

You, Qi Sheng; Bartsch, Dirk-Uwe G; Espina, Mark; Alam, Mostafa; Camacho, Natalia; Mendoza, Nadia; Freeman, William R

2016-07-01

-Altman plot showed 8.8%, 2.9%, and 4.4% points outside the 95% limits of agreement, respectively. The data for the reproducibility did not differ significantly among the various disease and normal eyes. Under routine examination conditions with pupil dilation, MPOD measurement by two-wavelength autofluorescence method showed a high reproducibility.

Highly Sensitive and Reproducible SERS Sensor for Biological pH Detection Based on a Uniform Gold Nanorod Array Platform.

Science.gov (United States)

Bi, Liyan; Wang, Yunqing; Yang, Ying; Li, Yuling; Mo, Shanshan; Zheng, Qingyin; Chen, Lingxin

2018-05-09

Conventional research on surface-enhanced Raman scattering (SERS)-based pH sensors often depends on nanoparticle aggregation, whereas the variability in nanoparticle aggregation gives rise to poor repeatability in the SERS signal. Herein, we fabricated a gold nanorod array platform via an efficient evaporative self-assembly method. The platform exhibits great SERS sensitivity with an enhancement factor of 5.6 × 10 7 and maintains excellent recyclability and reproducibility with relative standard deviation (RSD) values of less than 8%. On the basis of the platform, we developed a highly sensitive bovine serum albumin (BSA)-coated 4-mercaptopyridine (4-MPy)-linked (BMP) SERS-based pH sensor to report pH ranging from pH 3.0 to pH 8.0. The intensity ratio variation of 1004 and 1096 cm -1 in 4-MPy showed excellent pH sensitivity, which decreased as the surrounding pH increased. Furthermore, this BMP SERS-based pH sensor was employed to measure the pH value in C57BL/6 mouse blood. We have demonstrated that the pH sensor has great advantages such as good stability, reliability, and accuracy, which could be extended for the design of point-of-care devices.

The Accuracy and Reproducibility of Linear Measurements Made on CBCT-derived Digital Models.

Science.gov (United States)

Maroua, Ahmad L; Ajaj, Mowaffak; Hajeer, Mohammad Y

2016-04-01

To evaluate the accuracy and reproducibility of linear measurements made on cone-beam computed tomography (CBCT)-derived digital models. A total of 25 patients (44% female, 18.7 ± 4 years) who had CBCT images for diagnostic purposes were included. Plaster models were obtained and digital models were extracted from CBCT scans. Seven linear measurements from predetermined landmarks were measured and analyzed on plaster models and the corresponding digital models. The measurements included arch length and width at different sites. Paired t test and Bland-Altman analysis were used to evaluate the accuracy of measurements on digital models compared to the plaster models. Also, intraclass correlation coefficients (ICCs) were used to evaluate the reproducibility of the measurements in order to assess the intraobserver reliability. The statistical analysis showed significant differences on 5 out of 14 variables, and the mean differences ranged from -0.48 to 0.51 mm. The Bland-Altman analysis revealed that the mean difference between variables was (0.14 ± 0.56) and (0.05 ± 0.96) mm and limits of agreement between the two methods ranged from -1.2 to 0.96 and from -1.8 to 1.9 mm in the maxilla and the mandible, respectively. The intraobserver reliability values were determined for all 14 variables of two types of models separately. The mean ICC value for the plaster models was 0.984 (0.924-0.999), while it was 0.946 for the CBCT models (range from 0.850 to 0.985). Linear measurements obtained from the CBCT-derived models appeared to have a high level of accuracy and reproducibility.

77 FR 50470 - Proposed Information Collection; Comment Request; Atlantic Highly Migratory Species Recreational...

Science.gov (United States)

2012-08-21

..., West Atlantic sailfish, or North Atlantic swordfish in states (and the United States Virgin Islands and... Collection; Comment Request; Atlantic Highly Migratory Species Recreational Landings Reports AGENCY: National... provides important data used to monitor catches of Atlantic highly migratory species (HMS) and supplements...

Psychometric Evaluation of the Brachial Assessment Tool Part 1: Reproducibility.

Science.gov (United States)

Hill, Bridget; Williams, Gavin; Olver, John; Ferris, Scott; Bialocerkowski, Andrea

2018-04-01

To evaluate reproducibility (reliability and agreement) of the Brachial Assessment Tool (BrAT), a new patient-reported outcome measure for adults with traumatic brachial plexus injury (BPI). Prospective repeated-measure design. Outpatient clinics. Adults with confirmed traumatic BPI (N=43; age range, 19-82y). People with BPI completed the 31-item 4-response BrAT twice, 2 weeks apart. Results for the 3 subscales and summed score were compared at time 1 and time 2 to determine reliability, including systematic differences using paired t tests, test retest using intraclass correlation coefficient model 1,1 (ICC 1,1 ), and internal consistency using Cronbach α. Agreement parameters included standard error of measurement, minimal detectable change, and limits of agreement. BrAT. Test-retest reliability was excellent (ICC 1,1 =.90-.97). Internal consistency was high (Cronbach α=.90-.98). Measurement error was relatively low (standard error of measurement range, 3.1-8.8). A change of >4 for subscale 1, >6 for subscale 2, >4 for subscale 3, and >10 for the summed score is indicative of change over and above measurement error. Limits of agreement ranged from ±4.4 (subscale 3) to 11.61 (summed score). These findings support the use of the BrAT as a reproducible patient-reported outcome measure for adults with traumatic BPI with evidence of appropriate reliability and agreement for both individual and group comparisons. Further psychometric testing is required to establish the construct validity and responsiveness of the BrAT. Copyright © 2017 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Dynamic Data Citation through Provenance - new approach for reproducible science in Geoscience Australia.

Science.gov (United States)

Bastrakova, I.; Car, N.

2017-12-01

Geoscience Australia (GA) is recognised and respected as the National Repository and steward of multiple nationally significance data collections that provides geoscience information, services and capability to the Australian Government, industry and stakeholders. Internally, this brings a challenge of managing large volume (11 PB) of diverse and highly complex data distributed through a significant number of catalogues, applications, portals, virtual laboratories, and direct downloads from multiple locations. Externally, GA is facing constant changer in the Government regulations (e.g. open data and archival laws), growing stakeholder demands for high quality and near real-time delivery of data and products, and rapid technological advances enabling dynamic data access. Traditional approach to citing static data and products cannot satisfy increasing demands for the results from scientific workflows, or items within the workflows to be open, discoverable, thrusted and reproducible. Thus, citation of data, products, codes and applications through the implementation of provenance records is being implemented. This approach involves capturing the provenance of many GA processes according to a standardised data model and storing it, as well as metadata for the elements it references, in a searchable set of systems. This provides GA with ability to cite workflows unambiguously as well as each item within each workflow, including inputs and outputs and many other registered components. Dynamic objects can therefore be referenced flexibly in relation to their generation process - a dataset's metadata indicates where to obtain its provenance from - meaning the relevant facts of its dynamism need not be crammed into a single citation object with a single set of attributes. This allows for simple citations, similar to traditional static document citations such as references in journals, to be used for complex dynamic data and other objects such as software code.

The reproducibility of single photon absorptiometry in a clinical setting

International Nuclear Information System (INIS)

Valkema, R.; Blokland, J.A.K.; Pauwels, E.K.J.; Papapoulos, S.E.; Bijvoet, O.L.M.

1989-01-01

The reproducibility of single photon absorptiometry (SPA) results for detection of changes in bone mineral content (BMC) was evaluated in a clinical setting. During a period of 18 months with 4 different sources, the calibration scans of an aluminium standard had a variation of less than 1% unless the activity of the 125 I source was low. The calibration procedure was performed weekly and this was sufficient to correct for drift of the system. The short term reproducibility in patients was assessed with 119 duplicate measurements made in direct succession. The best reproducibility (CV=1.35%) was found for fat corrected BMC results expressed in g/cm, obtained at the site proximal to the 8 mm space between the radius and ulna. Analysis of all SPA scans made during 1 year (487 scans) showed a failure of the automatic procedure to detect the space of 8 mm between the forearm bones in 19 scans (3.9%). A space adjacent to the ulnar styloid was taken as the site for the first scan in these examinations. This problem may be recognized and corrected relatively easy. A significant correlation was found between BMC at the lower arm and BMC of the lumbar spine assessed with dual photon absorptiometry. However, the error of estimation of proximal BMC (SEE=20%) and distal BMC (SEE=19.4%) made these measurements of little value to predict BMC at the lumbar spine in individuals. The short term reproducibility in patients combined with long term stability of the equipment in our clinical setting showed that SPA is a reliable technique to assess changes in bone mass at the lower arm of 4% between 2 measurements with a confidence level of 95%. (orig.)

Reproducibility of Mammography Units, Film Processing and Quality Imaging

International Nuclear Information System (INIS)

Gaona, Enrique

2003-01-01

The purpose of this study was to carry out an exploratory survey of the problems of quality control in mammography and processors units as a diagnosis of the current situation of mammography facilities. Measurements of reproducibility, optical density, optical difference and gamma index are included. Breast cancer is the most frequently diagnosed cancer and is the second leading cause of cancer death among women in the Mexican Republic. Mammography is a radiographic examination specially designed for detecting breast pathology. We found that the problems of reproducibility of AEC are smaller than the problems of processors units because almost all processors fall outside of the acceptable variation limits and they can affect the mammography quality image and the dose to breast. Only four mammography units agree with the minimum score established by ACR and FDA for the phantom image

High-throughput genotyping for species identification and diversity assessment in germplasm collections.

Science.gov (United States)

Mason, Annaliese S; Zhang, Jing; Tollenaere, Reece; Vasquez Teuber, Paula; Dalton-Morgan, Jessica; Hu, Liyong; Yan, Guijun; Edwards, David; Redden, Robert; Batley, Jacqueline

2015-09-01

Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP array. Of these, 76 were provided on the basis of suspected misclassification and another 104 were sourced independently from the germplasm collection. Presence of the A- and C-genomes combined with principle components analysis clearly separated Brassica rapa, B. oleracea, B. napus, B. carinata and B. juncea samples into distinct species groups. Several lines were further validated using chromosome counts. Overall, 18% of samples (32/180) were misclassified on the basis of species. Within these 180 samples, 23/76 (30%) supplied on the basis of suspected misclassification were misclassified, and 9/105 (9%) of the samples randomly sourced from the Australian Grains Genebank were misclassified. Surprisingly, several individuals were also found to be the product of interspecific hybridization events. The SNP (single nucleotide polymorphism) array proved effective at confirming species, and provided useful information related to genetic diversity. As similar genomic resources become available for different crops, high-throughput molecular genotyping will offer an efficient and cost-effective method to screen germplasm collections worldwide, facilitating more effective use of these valuable resources by breeders and researchers. © 2015 John Wiley & Sons Ltd.

A highly reproducible solenoid micropump system for the analysis of total inorganic carbon and ammonium using gas-diffusion with conductimetric detection.

Science.gov (United States)

Henríquez, Camelia; Horstkotte, Burkhard; Cerdà, Víctor

2014-01-01

In this work, a simple, economic, and miniaturized flow-based analyzer based on solenoid micropumps is presented. It was applied to determine two parameters of high environmental interest: ammonium and total inorganic carbon (TIC) in natural waters. The method is based on gas diffusion (GD) of CO₂ and NH3 through a hydrophobic gas permeable membrane from an acidic or alkaline donor stream, respectively. The analytes are trapped in an acceptor solution, being slightly alkaline for CO₂ and slightly acidic for NH₃. The analytes are quantified using a homemade stainless steel conductimetric cell. The proposed system required five solenoid micro-pumps, one for each reagent and sample. Two especially made air bubble traps were placed down-stream of the solendoid pumps, which provided the acceptor solutions, by this increasing the method's reproducibility. Values of RSD lower than 1% were obtained. Achieved limits of detection were 0.27 µmol L⁻¹ for NH₄⁺ and 50 µmol L⁻¹ for TIC. Add-recovery tests were used to prove the trueness of the method and recoveries of 99.5 ± 7.5% were obtained for both analytes. The proposed system proved to be adequate for monitoring purpose of TIC and NH₄⁺ due to its high sample throughput and repeatability. © 2013 Published by Elsevier B.V.

Reproducibility of CT bone dosimetry: Operator versus automated ROI definition

International Nuclear Information System (INIS)

Louis, O.; Luypaert, R.; Osteaux, M.; Kalender, W.

1988-01-01

Intrasubject reproducibility with repeated determination of vertebral mineral density from a given set of CT images was investigated. The region of interest (ROI) in 10 patient scans was selected by four independent operators either manually or with an automated procedure separating cortical and spongeous bone, the operators being requested to interact in ROI selection. The mean intrasubject variation was found to be much lower with the automated process (0.3 to 0.6%) than with the conventional method (2.5 to 5.2%). In a second study, 10 patients were examined twice to determine the reproducibility of CT slice selection by the operator. The errors were of the same order of magnitude as in ROI selection. (orig.)

Reproducible analyses of microbial food for advanced life support systems

Science.gov (United States)

Petersen, Gene R.

1988-01-01

The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

The Impact of Collective Bargaining on Teacher Transfer Rates in Urban High-Poverty Schools

Science.gov (United States)

Nelson, F. Howard

2006-01-01

Data in this report reveals that collectively bargaining agreements are not the source of the teacher quality problem in urban school districts. The data shows that collective bargaining agreements are associated with reduced teacher transfer activity, especially in high-poverty schools, and less reliance on first-year teachers to staff…

Bad Behavior: Improving Reproducibility in Behavior Testing.

Science.gov (United States)

Andrews, Anne M; Cheng, Xinyi; Altieri, Stefanie C; Yang, Hongyan

2018-01-24

Systems neuroscience research is increasingly possible through the use of integrated molecular and circuit-level analyses. These studies depend on the use of animal models and, in many cases, molecular and circuit-level analyses. Associated with genetic, pharmacologic, epigenetic, and other types of environmental manipulations. We illustrate typical pitfalls resulting from poor validation of behavior tests. We describe experimental designs and enumerate controls needed to improve reproducibility in investigating and reporting of behavioral phenotypes.

Reproducibility of the Pleth Variability Index in premature infants

NARCIS (Netherlands)

Den Boogert, W.J. (Wilhelmina J.); H.A. van Elteren (Hugo); T.G. Goos (Tom); I.K.M. Reiss (Irwin); R.C.J. de Jonge (Rogier); V.J. van den Berg (Victor J.)

2017-01-01

textabstractThe aim was to assess the reproducibility of the Pleth Variability Index (PVI), developed for non-invasive monitoring of peripheral perfusion, in preterm neonates below 32 weeks of gestational age. Three PVI measurements were consecutively performed in stable, comfortable preterm

Development of a double-layered ceramic filter for aerosol filtration at high-temperatures: the filter collection efficiency.

Science.gov (United States)

de Freitas, Normanda L; Gonçalves, José A S; Innocentini, Murilo D M; Coury, José R

2006-08-25

The performance of double-layered ceramic filters for aerosol filtration at high temperatures was evaluated in this work. The filtering structure was composed of two layers: a thin granular membrane deposited on a reticulate ceramic support of high porosity. The goal was to minimize the high pressure drop inherent of granular structures, without decreasing their high collection efficiency for small particles. The reticulate support was developed using the technique of ceramic replication of polyurethane foam substrates of 45 and 75 pores per inch (ppi). The filtering membrane was prepared by depositing a thin layer of granular alumina-clay paste on one face of the support. Filters had their permeability and fractional collection efficiency analyzed for filtration of an airborne suspension of phosphatic rock in temperatures ranging from ambient to 700 degrees C. Results revealed that collection efficiency decreased with gas temperature and was enhanced with filtration time. Also, the support layer influenced the collection efficiency: the 75 ppi support was more effective than the 45 ppi. Particle collection efficiency dropped considerably for particles below 2 microm in diameter. The maximum collection occurred for particle diameters of approximately 3 microm, and decreased again for diameters between 4 and 8 microm. Such trend was successfully represented by the proposed correlation, which is based on the classical mechanisms acting on particle collection. Inertial impaction seems to be the predominant collection mechanism, with particle bouncing/re-entrainment acting as detachment mechanisms.

Device and method for enhanced collection and assay of chemicals with high surface area ceramic

Science.gov (United States)

Addleman, Raymond S.; Li, Xiaohong Shari; Chouyyok, Wilaiwan; Cinson, Anthony D.; Bays, John T.; Wallace, Krys

2016-02-16

A method and device for enhanced capture of target analytes is disclosed. This invention relates to collection of chemicals for separations and analysis. More specifically, this invention relates to a solid phase microextraction (SPME) device having better capability for chemical collection and analysis. This includes better physical stability, capacity for chemical collection, flexible surface chemistry and high affinity for target analyte.

Reproducibility of Quantitative Structural and Physiological MRI Measurements

Science.gov (United States)

2017-08-09

project.org/) and SPSS (IBM Corp., Armonk, NY) for data analysis. Mean and confidence inter- vals for each measure are found in Tables 1–7. To assess...visits, and was calculated using a two- way mixed model in SPSS MCV and MRD values closer to 0 are considered to be the most reproducible, and ICC

The collective bands of positive parity states in odd-A (fp) shell nuclei

International Nuclear Information System (INIS)

Ahalpara, D.P.

1979-01-01

The low-lying collective bands of positive parity states in (fp) shell nuclei are described in the deformed Hartree-Fock method by projecting states of definite angular momenta from 'the lowest energy intrinsic states in (sd)sup(-1)(fp)sup(n+1) configurations. The modified Kuo-Brown effective interaction for (fp) shell and modified surface delta interaction (MSDI) for a hole in (sd) shell with a particle in (fp) shell have been used. The collective bands of states are in general well reproduced by the effective interactions. The excitation energies of the band head states are however off by about one MeV. The calculated magnetic moments of the band head j = 3/2 + states are in reasonable agreement with experiment. Using effective charges esub(p) = 1.33 e and esub(n) = 0.64 e fairly good agreement is obtained for E(2) transitions. The hindered M(1) transition strengths are reproduced to the correct order, however they are slightly higher compared to the experiment. (author)

Validity and Reproducibility of a Food Frequency Questionnaire for Dietary Factors Related to Colorectal Cancer

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Daniel Nigusse Tollosa

2017-11-01

Full Text Available Dietary factors play a major role in the development of colorectal cancer. This study evaluated the reproducibility and validity of a 109-food item Food Frequency Questionnaire (FFQ to measure the consumption of foods and nutrients related to the development of colorectal cancer in a population aged ≥50 years in Flanders, Belgium. A semi-quantitative FFQ was administered two times in a period of two weeks to evaluate reproducibility (FFQ1 and FFQ2. The validity of the FFQ was assessed by comparing FFQ1 against the 3-day diary method (3 DD. A total of 162 respondents (mean age 57.5 years provided data for the FFQ, of whom 156 also participated in the validity assessment. Mean differences in the intake of foods and nutrients between FFQ1 and FFQ2 were, overall, small and statistically insignificant. However, a higher estimation was observed by FFQ1 as compared to the 3-DD method for the majority of food groups and nutrient intake in the validity assessment. A systematic mean difference (g/day was observed for eight food groups in the Bland–Altman agreement test; the largest was for fruit intake. Regarding the nutrients, a systematic mean difference was observed in calcium, fat, and vitamin D intake. Overall, the reproducibility of the FFQ was good, and its validity could be satisfactory for estimating absolute food and nutrient intakes and ranking individuals according to high and low intake categories.

Validity and Reproducibility of a Food Frequency Questionnaire for Dietary Factors Related to Colorectal Cancer.

Science.gov (United States)

Tollosa, Daniel Nigusse; Van Camp, John; Huybrechts, Inge; Huybregts, Lieven; Van Loco, Joris; De Smet, Stefaan; Sterck, Ellen; Rabâi, Céline; Van Hecke, Thomas; Vanhaecke, Lynn; Vossen, Els; Peeters, Marc; Lachat, Carl

2017-11-17

Dietary factors play a major role in the development of colorectal cancer. This study evaluated the reproducibility and validity of a 109-food item Food Frequency Questionnaire (FFQ) to measure the consumption of foods and nutrients related to the development of colorectal cancer in a population aged ≥50 years in Flanders, Belgium. A semi-quantitative FFQ was administered two times in a period of two weeks to evaluate reproducibility (FFQ1 and FFQ2). The validity of the FFQ was assessed by comparing FFQ1 against the 3-day diary method (3 DD). A total of 162 respondents (mean age 57.5 years) provided data for the FFQ, of whom 156 also participated in the validity assessment. Mean differences in the intake of foods and nutrients between FFQ1 and FFQ2 were, overall, small and statistically insignificant. However, a higher estimation was observed by FFQ1 as compared to the 3-DD method for the majority of food groups and nutrient intake in the validity assessment. A systematic mean difference (g/day) was observed for eight food groups in the Bland-Altman agreement test; the largest was for fruit intake. Regarding the nutrients, a systematic mean difference was observed in calcium, fat, and vitamin D intake. Overall, the reproducibility of the FFQ was good, and its validity could be satisfactory for estimating absolute food and nutrient intakes and ranking individuals according to high and low intake categories.

Reproducibility of contrast-enhanced transrectal ultrasound of the prostate

NARCIS (Netherlands)

Sedelaar, J. P.; Goossen, T. E.; Wijkstra, H.; de la Rosette, J. J.

2001-01-01

Transrectal three-dimensional (3-D) contrast-enhanced power Doppler ultrasound (US) is a novel technique for studying possible prostate malignancy. Before studies can be performed to investigate the clinical validity of the technique, reproducibility of the contrast US studies must be proven.

A Novel Approach to Calculation of Reproducing Kernel on Infinite Interval and Applications to Boundary Value Problems

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Jing Niu

2013-01-01

reproducing kernel on infinite interval is obtained concisely in polynomial form for the first time. Furthermore, as a particular effective application of this method, we give an explicit representation formula for calculation of reproducing kernel in reproducing kernel space with boundary value conditions.

In utero diffusion tensor imaging of the fetal brain: A reproducibility study.

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Jakab, András; Tuura, Ruth; Kellenberger, Christian; Scheer, Ianina

2017-01-01

Our purpose was to evaluate the within-subject reproducibility of in utero diffusion tensor imaging (DTI) metrics and the visibility of major white matter structures. Images for 30 fetuses (20-33. postmenstrual weeks, normal neurodevelopment: 6 cases, cerebral pathology: 24 cases) were acquired on 1.5 T or 3.0 T MRI. DTI with 15 diffusion-weighting directions was repeated three times for each case, TR/TE: 2200/63 ms, voxel size: 1 ∗ 1 mm, slice thickness: 3-5 mm, b-factor: 700 s/mm 2 . Reproducibility was evaluated from structure detectability, variability of DTI measures using the coefficient of variation (CV), image correlation and structural similarity across repeated scans for six selected structures. The effect of age, scanner type, presence of pathology was determined using Wilcoxon rank sum test. White matter structures were detectable in the following percentage of fetuses in at least two of the three repeated scans: corpus callosum genu 76%, splenium 64%, internal capsule, posterior limb 60%, brainstem fibers 40% and temporooccipital association pathways 60%. The mean CV of DTI metrics ranged between 3% and 14.6% and we measured higher reproducibility in fetuses with normal brain development. Head motion was negatively correlated with reproducibility, this effect was partially ameliorated by motion-correction algorithm using image registration. Structures on 3.0 T had higher variability both with- and without motion correction. Fetal DTI is reproducible for projection and commissural bundles during mid-gestation, however, in 16-30% of the cases, data were corrupted by artifacts, resulting in impaired detection of white matter structures. To achieve robust results for the quantitative analysis of diffusivity and anisotropy values, fetal-specific image processing is recommended and repeated DTI is needed to ensure the detectability of fiber pathways.

Reproducibility analysis of the stability and treatment of vertebral metastatic lesions

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Raphael de Rezende Pratali

2014-09-01

Full Text Available OBJECTIVES: To investigate the reproducibility among spine surgeons in defining the treatment of vertebral metastatic lesions, taking into account the mechanical stability of injuries. METHODS: Twenty cases of isolated vertebral metastatic lesions were presented to ten experts. Their opinion was then asked about the stability of the lesion, as well as their treatment option. RESULTS: The interobserver Kappa coefficient obtained both for stability analysis as to the decision of the treatment was poor (0.334 and 0.248, respectively. CONCLUSIONS: Poor interobserver reproducibility was observed in deciding the treatment of vertebral metastatic lesions when considering the stability of the lesions.

Validity and reproducibility of a food frequency questionnaire for adults of São Paulo, Brazil.

Science.gov (United States)

Selem, Soraya Sant'Ana de Castro; Carvalho, Aline Martins de; Verly-Junior, Eliseu; Carlos, Jackeline Venâncio; Teixeira, Juliana Araujo; Marchioni, Dirce Maria Lobo; Fisberg, Regina Mara

2014-12-01

To assess the validity and reproducibility of a food frequency questionnaire developed for estimating the food consumption of adults in São Paulo, Brazil, based population study. A sample of individuals aged above 20 years, of both genders, living in São Paulo, was used for the validation study (n = 77) and reproducibility study (n = 74) of the food frequency questionnaire. To verify the validity and reproducibility of energy and 19 nutrients were applied two food frequency questionnaires (60 items) and three 24-hour dietary recalls (24HR - reference method). The validity was verified by Spearman correlation coefficient (crude and de-attenuated) and weighted Kappa, and reproducibility by intraclass correlation coefficients and weighted kappa. In analyzes of validity de-attenuated correlation coefficients ranged from 0.21 (carbohydrate) to 0.74 (energy), and weighted kappa exceeded 0.40 for 30% of the nutrients. Polyunsaturated fat and folate did not show significant correlation and weighted kappa. In reproducibility correlation coefficients ranged from 0.36 (polyunsaturated fat) to 0.69 (calcium), and weighted kappa exceeded 0.40 for 80% of the nutrients. The food frequency questionnaire analyzed has good validity and reproducibility for estimating the food consumption of adults in São Paulo compared to the reference method, so it is an appropriate instrument to be used in epidemiological studies on similar populations. Estimates of polyunsaturated fat and folate should be interpreted with caution.

Cyberinfrastructure to Support Collaborative and Reproducible Computational Hydrologic Modeling

Science.gov (United States)

Goodall, J. L.; Castronova, A. M.; Bandaragoda, C.; Morsy, M. M.; Sadler, J. M.; Essawy, B.; Tarboton, D. G.; Malik, T.; Nijssen, B.; Clark, M. P.; Liu, Y.; Wang, S. W.

2017-12-01

Creating cyberinfrastructure to support reproducibility of computational hydrologic models is an important research challenge. Addressing this challenge requires open and reusable code and data with machine and human readable metadata, organized in ways that allow others to replicate results and verify published findings. Specific digital objects that must be tracked for reproducible computational hydrologic modeling include (1) raw initial datasets, (2) data processing scripts used to clean and organize the data, (3) processed model inputs, (4) model results, and (5) the model code with an itemization of all software dependencies and computational requirements. HydroShare is a cyberinfrastructure under active development designed to help users store, share, and publish digital research products in order to improve reproducibility in computational hydrology, with an architecture supporting hydrologic-specific resource metadata. Researchers can upload data required for modeling, add hydrology-specific metadata to these resources, and use the data directly within HydroShare.org for collaborative modeling using tools like CyberGIS, Sciunit-CLI, and JupyterHub that have been integrated with HydroShare to run models using notebooks, Docker containers, and cloud resources. Current research aims to implement the Structure For Unifying Multiple Modeling Alternatives (SUMMA) hydrologic model within HydroShare to support hypothesis-driven hydrologic modeling while also taking advantage of the HydroShare cyberinfrastructure. The goal of this integration is to create the cyberinfrastructure that supports hypothesis-driven model experimentation, education, and training efforts by lowering barriers to entry, reducing the time spent on informatics technology and software development, and supporting collaborative research within and across research groups.

A multicenter reproducibility study of single-voxel {sup 1}H-MRS of the medial temporal lobe

Energy Technology Data Exchange (ETDEWEB)

Traeber, Frank; Block, Wolfgang; Guer, Okan; Schild, Hans H. [University of Bonn, Department of Radiology, Bonn (Germany); Freymann, Nikolaus; Heun, Reinhard; Jessen, Frank [University of Bonn, Department of Psychiatry, Bonn (Germany); Kucinski, Thomas [University of Hamburg, Department of Neuroradiology, Hamburg (Germany); Hammen, Thilo [University of Erlangen, Department of Psychiatry, Erlangen (Germany); Ende, Gabriele [Central Institute of Mental Health, NMR Research in Psychiatry, Mannheim (Germany); Pilatus, Ulrich [University of Frankfurt, Department of Neuroradiology, Frankfurt (Germany); Hampel, Harald [University of Munich, Department of Psychiatry, Munich (Germany)

2006-05-15

Proton magnetic resonance spectroscopy ({sup 1}H-MRS) has provided evidence for a reduction of N-acetyl-aspartate (NAA) in the medial temporal lobe (MTL) in cerebral disorders such as Alzheimer's Disease. Within the {sup 1}H-MRS study of the German Research Network on Dementia, we determined the multicenter reproducibility of single-voxel {sup 1}H-MRS of the MTL. At five sites with 1.5T MR systems, single-voxel {sup 1}H spectra from the MTL of an identical healthy subject were measured. The same subject was also examined at one of the sites five times to assess intracenter stability. The protocol included water-suppressed spectra with TE 272 ms and TE 30 ms and unsuppressed spectra for absolute quantification of metabolite concentrations. The intracenter reproducibility of absolute NAA concentration, expressed as coefficient of variation (CV), was 1.8%. CV for the concentrations of creatine (Cr), choline (Cho), and myoinositol (MI) and for the ratios NAA/Cr, NAA/Cho, and MI/NAA varied by 11-16%. Intercenter CV was 3.9% for NAA and were below 10% for all other metabolites and metabolic ratios. Our study demonstrates that quantitative assessment of NAA with single-voxel MRS can be performed with high intercenter reproducibility. This is the basis for applying {sup 1}H-MRS in large-scale early recognition and treatment studies in MTL affecting disorders. (orig.)

Running an open experiment: transparency and reproducibility in soil and ecosystem science

Science.gov (United States)

Bond-Lamberty, Ben; Peyton Smith, A.; Bailey, Vanessa

2016-08-01

Researchers in soil and ecosystem science, and almost every other field, are being pushed—by funders, journals, governments, and their peers—to increase transparency and reproducibility of their work. A key part of this effort is a move towards open data as a way to fight post-publication data loss, improve data and code quality, enable powerful meta- and cross-disciplinary analyses, and increase trust in, and the efficiency of, publicly-funded research. Many scientists however lack experience in, and may be unsure of the benefits of, making their data and fully-reproducible analyses publicly available. Here we describe a recent ‘open experiment’, in which we documented every aspect of a soil incubation online, making all raw data, scripts, diagnostics, final analyses, and manuscripts available in real time. We found that using tools such as version control, issue tracking, and open-source statistical software improved data integrity, accelerated our team’s communication and productivity, and ensured transparency. There are many avenues to improve scientific reproducibility and data availability, of which is this only one example, and it is not an approach suited for every experiment or situation. Nonetheless, we encourage the communities in our respective fields to consider its advantages, and to lead rather than follow with respect to scientific reproducibility, transparency, and data availability.

Reproducibility of rest and exercise stress contrast-enhanced calf perfusion magnetic resonance imaging in peripheral arterial disease

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Jiji Ronny S

2013-01-01

Full Text Available Abstract Background The purpose was to determine the reproducibility and utility of rest, exercise, and perfusion reserve (PR measures by contrast-enhanced (CE calf perfusion magnetic resonance imaging (MRI of the calf in normal subjects (NL and patients with peripheral arterial disease (PAD. Methods Eleven PAD patients with claudication (ankle-brachial index 0.67 ±0.14 and 16 age-matched NL underwent symptom-limited CE-MRI using a pedal ergometer. Tissue perfusion and arterial input were measured at rest and peak exercise after injection of 0.1 mM/kg of gadolinium-diethylnetriamine pentaacetic acid (Gd-DTPA. Tissue function (TF and arterial input function (AIF measurements were made from the slope of time-intensity curves in muscle and artery, respectively, and normalized to proton density signal to correct for coil inhomogeneity. Perfusion index (PI = TF/AIF. Perfusion reserve (PR = exercise TF/ rest TF. Intraclass correlation coefficient (ICC was calculated from 11 NL and 10 PAD with repeated MRI on a different day. Results Resting TF was low in NL and PAD (mean ± SD 0.25 ± 0.18 vs 0.35 ± 0.71, p = 0.59 but reproducible (ICC 0.76. Exercise TF was higher in NL than PAD (5.5 ± 3.2 vs. 3.4 ± 1.6, p = 0.04. Perfusion reserve was similar between groups and highly variable (28.6 ± 19.8 vs. 42.6 ± 41.0, p = 0.26. Exercise TF and PI were reproducible measures (ICC 0.63 and 0.60, respectively. Conclusion Although rest measures are reproducible, they are quite low, do not distinguish NL from PAD, and lead to variability in perfusion reserve measures. Exercise TF and PI are the most reproducible MRI perfusion measures in PAD for use in clinical trials.

Appearance Constrained Semi-Automatic Segmentation from DCE-MRI is Reproducible and Feasible for Breast Cancer Radiomics: A Feasibility Study.

Science.gov (United States)

Veeraraghavan, Harini; Dashevsky, Brittany Z; Onishi, Natsuko; Sadinski, Meredith; Morris, Elizabeth; Deasy, Joseph O; Sutton, Elizabeth J

2018-03-19

We present a segmentation approach that combines GrowCut (GC) with cancer-specific multi-parametric Gaussian Mixture Model (GCGMM) to produce accurate and reproducible segmentations. We evaluated GCGMM using a retrospectively collected 75 invasive ductal carcinoma with ERPR+ HER2- (n = 15), triple negative (TN) (n = 9), and ER-HER2+ (n = 57) cancers with variable presentation (mass and non-mass enhancement) and background parenchymal enhancement (mild and marked). Expert delineated manual contours were used to assess the segmentation performance using Dice coefficient (DSC), mean surface distance (mSD), Hausdorff distance, and volume ratio (VR). GCGMM segmentations were significantly more accurate than GrowCut (GC) and fuzzy c-means clustering (FCM). GCGMM's segmentations and the texture features computed from those segmentations were the most reproducible compared with manual delineations and other analyzed segmentation methods. Finally, random forest (RF) classifier trained with leave-one-out cross-validation using features extracted from GCGMM segmentation resulted in the best accuracy for ER-HER2+ vs. ERPR+/TN (GCGMM 0.95, expert 0.95, GC 0.90, FCM 0.92) and for ERPR + HER2- vs. TN (GCGMM 0.92, expert 0.91, GC 0.77, FCM 0.83).

Modeling collective animal behavior with a cognitive perspective: a methodological framework.

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Sebastian Weitz

Full Text Available The last decades have seen an increasing interest in modeling collective animal behavior. Some studies try to reproduce as accurately as possible the collective dynamics and patterns observed in several animal groups with biologically plausible, individual behavioral rules. The objective is then essentially to demonstrate that the observed collective features may be the result of self-organizing processes involving quite simple individual behaviors. Other studies concentrate on the objective of establishing or enriching links between collective behavior researches and cognitive or physiological ones, which then requires that each individual rule be carefully validated. Here we discuss the methodological consequences of this additional requirement. Using the example of corpse clustering in ants, we first illustrate that it may be impossible to discriminate among alternative individual rules by considering only observational data collected at the group level. Six individual behavioral models are described: They are clearly distinct in terms of individual behaviors, they all reproduce satisfactorily the collective dynamics and distribution patterns observed in experiments, and we show theoretically that it is strictly impossible to discriminate two of these models even in the limit of an infinite amount of data whatever the accuracy level. A set of methodological steps are then listed and discussed as practical ways to partially overcome this problem. They involve complementary experimental protocols specifically designed to address the behavioral rules successively, conserving group-level data for the overall model validation. In this context, we highlight the importance of maintaining a sharp distinction between model enunciation, with explicit references to validated biological concepts, and formal translation of these concepts in terms of quantitative state variables and fittable functional dependences. Illustrative examples are provided of the

Leveraging High Performance Computing for Managing Large and Evolving Data Collections

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Ritu Arora

2014-10-01

Full Text Available The process of developing a digital collection in the context of a research project often involves a pipeline pattern during which data growth, data types, and data authenticity need to be assessed iteratively in relation to the different research steps and in the interest of archiving. Throughout a project’s lifecycle curators organize newly generated data while cleaning and integrating legacy data when it exists, and deciding what data will be preserved for the long term. Although these actions should be part of a well-oiled data management workflow, there are practical challenges in doing so if the collection is very large and heterogeneous, or is accessed by several researchers contemporaneously. There is a need for data management solutions that can help curators with efficient and on-demand analyses of their collection so that they remain well-informed about its evolving characteristics. In this paper, we describe our efforts towards developing a workflow to leverage open science High Performance Computing (HPC resources for routinely and efficiently conducting data management tasks on large collections. We demonstrate that HPC resources and techniques can significantly reduce the time for accomplishing critical data management tasks, and enable a dynamic archiving throughout the research process. We use a large archaeological data collection with a long and complex formation history as our test case. We share our experiences in adopting open science HPC resources for large-scale data management, which entails understanding usage of the open source HPC environment and training users. These experiences can be generalized to meet the needs of other data curators working with large collections.

Reproducibility of the Pleth Variability Index in premature infants

NARCIS (Netherlands)

Den Boogert, Wilhelmina J.; Van Elteren, Hugo A.; Goos, T.G.; Reiss, Irwin K.M.; De Jonge, Rogier C.J.; van Den Berg, Victor J.

2017-01-01

The aim was to assess the reproducibility of the Pleth Variability Index (PVI), developed for non-invasive monitoring of peripheral perfusion, in preterm neonates below 32 weeks of gestational age. Three PVI measurements were consecutively performed in stable, comfortable preterm neonates in the

Pancreatic fluid collections: What is the ideal imaging technique?

Science.gov (United States)

Dhaka, Narendra; Samanta, Jayanta; Kochhar, Suman; Kalra, Navin; Appasani, Sreekanth; Manrai, Manish; Kochhar, Rakesh

2015-12-28

Pancreatic fluid collections (PFCs) are seen in up to 50% of cases of acute pancreatitis. The Revised Atlanta classification categorized these collections on the basis of duration of disease and contents, whether liquid alone or a mixture of fluid and necrotic debris. Management of these different types of collections differs because of the variable quantity of debris; while patients with pseudocysts can be drained by straight-forward stent placement, walled-off necrosis requires multi-disciplinary approach. Differentiating these collections on the basis of clinical severity alone is not reliable, so imaging is primarily performed. Contrast-enhanced computed tomography is the commonly used modality for the diagnosis and assessment of proportion of solid contents in PFCs; however with certain limitations such as use of iodinated contrast material especially in renal failure patients and radiation exposure. Magnetic resonance imaging (MRI) performs better than computed tomography (CT) in characterization of pancreatic/peripancreatic fluid collections especially for quantification of solid debris and fat necrosis (seen as fat density globules), and is an alternative in those situations where CT is contraindicated. Also magnetic resonance cholangiopancreatography is highly sensitive for detecting pancreatic duct disruption and choledocholithiasis. Endoscopic ultrasound is an evolving technique with higher reproducibility for fluid-to-debris component estimation with the added advantage of being a single stage procedure for both diagnosis (solid debris delineation) and management (drainage of collection) in the same sitting. Recently role of diffusion weighted MRI and positron emission tomography/CT with (18)F-FDG labeled autologous leukocytes is also emerging for detection of infection noninvasively. Comparative studies between these imaging modalities are still limited. However we look forward to a time when this gap in literature will be fulfilled.

Submicroscopic malaria parasite carriage: how reproducible are polymerase chain reaction-based methods?

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Daniela Camargos Costa

2014-02-01

Full Text Available The polymerase chain reaction (PCR-based methods for the diagnosis of malaria infection are expected to accurately identify submicroscopic parasite carriers. Although a significant number of PCR protocols have been described, few studies have addressed the performance of PCR amplification in cases of field samples with submicroscopic malaria infection. Here, the reproducibility of two well-established PCR protocols (nested-PCR and real-time PCR for the Plasmodium 18 small subunit rRNA gene were evaluated in a panel of 34 blood field samples from individuals that are potential reservoirs of malaria infection, but were negative for malaria by optical microscopy. Regardless of the PCR protocol, a large variation between the PCR replicates was observed, leading to alternating positive and negative results in 38% (13 out of 34 of the samples. These findings were quite different from those obtained from the microscopy-positive patients or the unexposed individuals; the diagnosis of these individuals could be confirmed based on the high reproducibility and specificity of the PCR-based protocols. The limitation of PCR amplification was restricted to the field samples with very low levels of parasitaemia because titrations of the DNA templates were able to detect < 3 parasites/µL in the blood. In conclusion, conventional PCR protocols require careful interpretation in cases of submicroscopic malaria infection, as inconsistent and false-negative results can occur.

Collective effects in microscopic transport models

International Nuclear Information System (INIS)

Greiner, Carsten

2003-01-01

We give a reminder on the major inputs of microscopic hadronic transport models and on the physics aims when describing various aspects of relativistic heavy ion collisions at SPS energies. We then first stress that the situation of particle ratios being reproduced by a statistical description does not necessarily mean a clear hint for the existence of a fully isotropic momentum distribution at hydrochemical freeze-out. Second, a short discussion on the status of strangeness production is given. Third we demonstrate the importance of a new collective mechanism for producing (strange) antibaryons within a hardonic description, which guarantees sufficiently fast chemical equilibration

A study on reproducibility of three-dimensional measurement for an evaluation of craniofacial morphology

International Nuclear Information System (INIS)

Nagai, Yoshihiro; Nishiyama, Hideyoshi; Nihara, Jun; Tanaka, Ray; Yamaki, Masaki; Hayashi, Takafumi; Saito, Isao

2013-01-01

Materials including facial and oral pictures, frontal and lateral cephalograms, dental casts and CT are essential for orthodontic diagnosis with orthognathic surgery. Although a three-dimensional analysis has been prevalent in diagnosing patients with dentofacial deformity, little information is available as to the definition and reproducibility of the measurement points when conducting a three-dimensional analysis using CT. This study was therefore designed to evaluate reproducibility of three-dimensional landmarks defined on the multiplaner reconstruction (MPR) images. Seven presurgical CT data obtained from seven orthognathic patients (4 females and 3 males) were selected. Two orthodontists independently repeated the identification of 44 landmarks defined twice on the MPR image with the reference plane of the Frankfurt horizontal plane (FH plane) using DICOM viewer Exavision Lite (Ziosoft, Tokyo). The significance of intra-examiner and inter-examiner errors was assessed using ANOVA, and reproducibility of landmarks was evaluated by the standard deviation (SD) value of measurement error. While no significant differences were found in intra-examiner measurement values, a significant difference was identified in inter-examiner measurement values at 39 coordinates among 132 coordinates; 10, 15, and 14 coordinates were found in X-, Y- and Z-coordinates, respectively. Reproducibility of ramus posterior point (Ar), Gonion (Go) and greater palatine foramen were particularly poor. However, reproducibility of landmarks adopted was considered enough for the analysis of maxillofacial morphology since the SDs of those landmarks were small as compared to voxel size. In case the FH plane is set as the reference plane, much more reproducible measurement landmarks may be selected without an influence of changes in head posture. (author)

Reproducibility and discriminability of brain patterns of semantic categories enhanced by congruent audiovisual stimuli.

Directory of Open Access Journals (Sweden)

Yuanqing Li

Full Text Available One of the central questions in cognitive neuroscience is the precise neural representation, or brain pattern, associated with a semantic category. In this study, we explored the influence of audiovisual stimuli on the brain patterns of concepts or semantic categories through a functional magnetic resonance imaging (fMRI experiment. We used a pattern search method to extract brain patterns corresponding to two semantic categories: "old people" and "young people." These brain patterns were elicited by semantically congruent audiovisual, semantically incongruent audiovisual, unimodal visual, and unimodal auditory stimuli belonging to the two semantic categories. We calculated the reproducibility index, which measures the similarity of the patterns within the same category. We also decoded the semantic categories from these brain patterns. The decoding accuracy reflects the discriminability of the brain patterns between two categories. The results showed that both the reproducibility index of brain patterns and the decoding accuracy were significantly higher for semantically congruent audiovisual stimuli than for unimodal visual and unimodal auditory stimuli, while the semantically incongruent stimuli did not elicit brain patterns with significantly higher reproducibility index or decoding accuracy. Thus, the semantically congruent audiovisual stimuli enhanced the within-class reproducibility of brain patterns and the between-class discriminability of brain patterns, and facilitate neural representations of semantic categories or concepts. Furthermore, we analyzed the brain activity in superior temporal sulcus and middle temporal gyrus (STS/MTG. The strength of the fMRI signal and the reproducibility index were enhanced by the semantically congruent audiovisual stimuli. Our results support the use of the reproducibility index as a potential tool to supplement the fMRI signal amplitude for evaluating multimodal integration.

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

A how to guide to reproducible research

OpenAIRE

Whitaker, Kirstie

2018-01-01

This talk will discuss the perceived and actual barriers experienced by researchers attempting to do reproducible research, and give practical guidance on how they can be overcome. It will include suggestions on how to make your code and data available and usable for others (including a strong suggestion to document both clearly so you don't have to reply to lots of email questions from future users). Specifically it will include a brief guide to version control, collaboration and disseminati...

Equipment for collecting samples of radioactive solutions; Installation de prelevements d'echantillons de solutions radioactives

Energy Technology Data Exchange (ETDEWEB)

Raggenbass, A.; Fradin, J.; Joubert, G.

1958-12-03

The authors present an equipment aimed at collecting samples of fission products to perform radio-chemical analysis. As the sample must have a total activity between 1 and 50 micro-Curie, this installation comprises a sampling system and a dilution device which aims at bringing the sample to the suitable activity. Samples are collected by means of needles. The sample reproducibility is discussed. The dilution device is described.

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers

Science.gov (United States)

Prybol, Cameron J.; Kurtzer, Gregory M.

2017-01-01

Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub’s primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers. PMID:29186161

Reproducibility of Ultrasound and Magnetic Resonance Imaging Measurements of Tendon Size

International Nuclear Information System (INIS)

Brushoej, C.; Henriksen, B.M.; Albrecht-Beste, E.; Hoelmich, P.; Larsen, K.; Bachmann Nielsen, M.

2006-01-01

Purpose: To investigate the intra- and inter-tester reproducibility of measurements of the Achilles tendon, tibialis anterior tendon, and the tibialis posterior tendon in football players using ultrasound (US) and magnetic resonance imaging (MRI). Material and Methods: Eleven asymptomatic football players were examined. Using a standardized US scanning protocol, the tendons were examined by two observers with US for thickness, width, and cross-sectional area. One observer conducted the procedure twice. The subjects also underwent an MRI examination, and the assessment of tendon size was conducted twice by two observers. Results: The best reproducibility judged by coefficient of variation (CV) and 95% confidence interval was determined for the Achilles tendon on both US and MRI. The variability of US on measurements on the tibialis anterior and tibialis posterior tendons was less than that when using MRI. In 12 out of 18 measurements, there were systematic differences between observers as judged by one-sided F-test. Conclusion: The reproducibility of the three tendons was limited. Precaution should be taken when looking for minor quantitative changes, i.e., training-induced hypertrophy, and when doing so, the Achilles tendon should be used

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers.

Directory of Open Access Journals (Sweden)

Vanessa V Sochat

Full Text Available Here we present Singularity Hub, a framework to build and deploy Singularity containers for mobility of compute, and the singularity-python software with novel metrics for assessing reproducibility of such containers. Singularity containers make it possible for scientists and developers to package reproducible software, and Singularity Hub adds automation to this workflow by building, capturing metadata for, visualizing, and serving containers programmatically. Our novel metrics, based on custom filters of content hashes of container contents, allow for comparison of an entire container, including operating system, custom software, and metadata. First we will review Singularity Hub's primary use cases and how the infrastructure has been designed to support modern, common workflows. Next, we conduct three analyses to demonstrate build consistency, reproducibility metric and performance and interpretability, and potential for discovery. This is the first effort to demonstrate a rigorous assessment of measurable similarity between containers and operating systems. We provide these capabilities within Singularity Hub, as well as the source software singularity-python that provides the underlying functionality. Singularity Hub is available at https://singularity-hub.org, and we are excited to provide it as an openly available platform for building, and deploying scientific containers.

Reproducibility of MRI-Determined Proton Density Fat Fraction Across Two Different MR Scanner Platforms

Science.gov (United States)

Kang, Geraldine H.; Cruite, Irene; Shiehmorteza, Masoud; Wolfson, Tanya; Gamst, Anthony C.; Hamilton, Gavin; Bydder, Mark; Middleton, Michael S.; Sirlin, Claude B.

2016-01-01

Purpose To evaluate magnetic resonance imaging (MRI)-determined proton density fat fraction (PDFF) reproducibility across two MR scanner platforms and, using MR spectroscopy (MRS)-determined PDFF as reference standard, to confirm MRI-determined PDFF estimation accuracy. Materials and Methods This prospective, cross-sectional, crossover, observational pilot study was approved by an Institutional Review Board. Twenty-one subjects gave written informed consent and underwent liver MRI and MRS at both 1.5T (Siemens Symphony scanner) and 3T (GE Signa Excite HD scanner). MRI-determined PDFF was estimated using an axial 2D spoiled gradient-recalled echo sequence with low flip-angle to minimize T1 bias and six echo-times to permit correction of T2* and fat-water signal interference effects. MRS-determined PDFF was estimated using a stimulated-echo acquisition mode sequence with long repetition time to minimize T1 bias and five echo times to permit T2 correction. Interscanner reproducibility of MRI determined PDFF was assessed by correlation analysis; accuracy was assessed separately at each field strength by linear regression analysis using MRS-determined PDFF as reference standard. Results 1.5T and 3T MRI-determined PDFF estimates were highly correlated (r = 0.992). MRI-determined PDFF estimates were accurate at both 1.5T (regression slope/intercept = 0.958/−0.48) and 3T (slope/intercept = 1.020/0.925) against the MRS-determined PDFF reference. Conclusion MRI-determined PDFF estimation is reproducible and, using MRS-determined PDFF as reference standard, accurate across two MR scanner platforms at 1.5T and 3T. PMID:21769986

Reproducibility and validity of the Dutch translation of the de Morton Mobility Index (DEMMI) used by physiotherapists in older patients with knee or hip osteoarthritis.

Science.gov (United States)

Jans, Marielle P; Slootweg, Vera C; Boot, Cecile R; de Morton, Natalie A; van der Sluis, Geert; van Meeteren, Nico L

2011-11-01

To examine the reproducibility, construct validity, and unidimensionality of the Dutch translation of the de Morton Mobility Index (DEMMI), a performance-based measure of mobility for older patients. Cross-sectional study. Rehabilitation center (reproducibility study) and hospital (validity study). Patients (N=28; age >65y) after orthopedic surgery (reproducibility study) and patients (N=219; age >65y) waiting for total hip or total knee arthroplasty (validity study). Not applicable. Not applicable. The intraclass correlation coefficient for interrater reliability was high (.85; 95% confidence interval, 71-.93), and minimal detectable change with 90% confidence was 7 on the 100-point DEMMI scale. Rasch analysis identified that the Dutch translation of the DEMMI is a unidimensional measure of mobility in this population. DEMMI scores showed high correlations with scores on other performance-based measures of mobility (Timed Up and Go test, Spearman r=-.73; Chair Rise Time, r=-.69; walking test, r=.74). A lower correlation of .44 was identified with the self-report measure Western Ontario and McMaster Universities Osteoarthritis Index. The Dutch translation of the DEMMI is a reproducible and valid performance-based measure for assessing mobility in older patients with knee or hip osteoarthritis. Copyright © 2011 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Thickness of patellofemoral articular cartilage as measured on MR imaging: sequence comparison of accuracy, reproducibility, and interobserver variation

Energy Technology Data Exchange (ETDEWEB)

Van Leersum, M.D. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Schweitzer, M.E. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Gannon, F. [Dept. of Pathology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Vinitski, S. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Finkel, G. [Dept. of Pathology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Mitchell, D.G. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States)

1995-08-01

This study was undertaken to assess the accuracy, precision, and reliability of magnetic resonance (MR) measurements of articular cartilage. Fifteen cadaveric patellas were imaged in the axial plane at 1.5 T. Gradient echo and fat-suppressed FSE, T2-weighted, proton density, and T1-weighted sequences were performed. We measured each 5-mm section separately at three standardized positions, giving a total of 900 measurements. These findings were correlated with independently performed measurements of the corresponding anatomic sections. A hundred random measurements were also evaluated for reproducibility and interobserver variation. Although all sequences were highly accurate, the T1-weighted images were the most accurate, with a mean difference of 0.25 mm and a correlation coefficient of 0.85. All sequences were also highly reproducible with little inter-observer variation. In an attempt to improve the accuracy of the MR measurements further, we retrospectively evaluated all measurements with discrepancies greater than 1 mm from the specimen. All these differences were attributable to focal defects causing exaggeration of the thickness on MR imaging. (orig.)

Thickness of patellofemoral articular cartilage as measured on MR imaging: sequence comparison of accuracy, reproducibility, and interobserver variation

International Nuclear Information System (INIS)

Van Leersum, M.D.; Schweitzer, M.E.; Gannon, F.; Vinitski, S.; Finkel, G.; Mitchell, D.G.

1995-01-01

This study was undertaken to assess the accuracy, precision, and reliability of magnetic resonance (MR) measurements of articular cartilage. Fifteen cadaveric patellas were imaged in the axial plane at 1.5 T. Gradient echo and fat-suppressed FSE, T2-weighted, proton density, and T1-weighted sequences were performed. We measured each 5-mm section separately at three standardized positions, giving a total of 900 measurements. These findings were correlated with independently performed measurements of the corresponding anatomic sections. A hundred random measurements were also evaluated for reproducibility and interobserver variation. Although all sequences were highly accurate, the T1-weighted images were the most accurate, with a mean difference of 0.25 mm and a correlation coefficient of 0.85. All sequences were also highly reproducible with little inter-observer variation. In an attempt to improve the accuracy of the MR measurements further, we retrospectively evaluated all measurements with discrepancies greater than 1 mm from the specimen. All these differences were attributable to focal defects causing exaggeration of the thickness on MR imaging. (orig.)

Do detailed simulations with size-resolved microphysics reproduce basic features of observed cirrus ice size distributions?

Science.gov (United States)

Fridlind, A. M.; Atlas, R.; van Diedenhoven, B.; Ackerman, A. S.; Rind, D. H.; Harrington, J. Y.; McFarquhar, G. M.; Um, J.; Jackson, R.; Lawson, P.

2017-12-01

It has recently been suggested that seeding synoptic cirrus could have desirable characteristics as a geoengineering approach, but surprisingly large uncertainties remain in the fundamental parameters that govern cirrus properties, such as mass accommodation coefficient, ice crystal physical properties, aggregation efficiency, and ice nucleation rate from typical upper tropospheric aerosol. Only one synoptic cirrus model intercomparison study has been published to date, and studies that compare the shapes of observed and simulated ice size distributions remain sparse. Here we amend a recent model intercomparison setup using observations during two 2010 SPARTICUS campaign flights. We take a quasi-Lagrangian column approach and introduce an ensemble of gravity wave scenarios derived from collocated Doppler cloud radar retrievals of vertical wind speed. We use ice crystal properties derived from in situ cloud particle images, for the first time allowing smoothly varying and internally consistent treatments of nonspherical ice capacitance, fall speed, gravitational collection, and optical properties over all particle sizes in our model. We test two new parameterizations for mass accommodation coefficient as a function of size, temperature and water vapor supersaturation, and several ice nucleation scenarios. Comparison of results with in situ ice particle size distribution data, corrected using state-of-the-art algorithms to remove shattering artifacts, indicate that poorly constrained uncertainties in the number concentration of crystals smaller than 100 µm in maximum dimension still prohibit distinguishing which parameter combinations are more realistic. When projected area is concentrated at such sizes, the only parameter combination that reproduces observed size distribution properties uses a fixed mass accommodation coefficient of 0.01, on the low end of recently reported values. No simulations reproduce the observed abundance of such small crystals when the

Reproducibility Problems with the Abbott Laboratories LCx Assay for Chlamydia trachomatis and Neisseria gonorrhoeae

OpenAIRE

Gronowski, Ann M.; Copper, Susan; Baorto, David; Murray, Patrick R.

2000-01-01

This study demonstrates that significant reproducibility problems can occur during routine use of the Abbott Laboratories LCx assay for Chlamydia trachomatis and Neisseria gonorrhoeae. These problems can go undetected by the quality control procedures outlined in the manufacturer's package insert. We outline here procedures for detecting and preventing contamination and reproducibility problems.

Reproducibility and validity of the DynaPort KneeTest

NARCIS (Netherlands)

Mokkink, L.B.; Terwee, C.B.; Slikke, van der R.M.; Lummel, van R.C.; Benink, R.J.; Bouter, L.M.; Vet, de H.C.W.

2005-01-01

OBJECTIVE: To determine the reproducibility and validity of the DynaPort KneeTest, a performance-based test that measures quality of movement of patients undergoing total knee replacement (TKR). METHODS: A total of 92 patients with osteoarthritis (OA) of the knee performed the KneeTest twice on the

pH-Triggered Molecular Alignment for Reproducible SERS Detection via an AuNP/Nanocellulose Platform

Science.gov (United States)

Wei, Haoran; Vikesland, Peter J.

2015-12-01

The low affinity of neutral and hydrophobic molecules towards noble metal surfaces hinders their detection by surface-enhanced Raman spectroscopy (SERS). Herein, we present a method to enhance gold nanoparticle (AuNP) surface affinity by lowering the suspension pH below the analyte pKa. We developed an AuNP/bacterial cellulose (BC) nanocomposite platform and applied it to two common pollutants, carbamazepine (CBZ) and atrazine (ATZ) with pKa values of 2.3 and 1.7, respectively. Simple mixing of the analytes with AuNP/BC at pH < pKa resulted in consistent electrostatic alignment of the CBZ and ATZ molecules across the nanocomposite and highly reproducible SERS spectra. Limits of detection of 3 nM and 11 nM for CBZ and ATZ, respectively, were attained. Tests with additional analytes (melamine, 2,4-dichloroaniline, 4-chloroaniline, 3-bromoaniline, and 3-nitroaniline) further illustrate that the AuNP/BC platform provides reproducible analyte detection and quantification while avoiding the uncontrolled aggregation and flocculation of AuNPs that often hinder low pH detection.

Hot-Volumes as Uniform and Reproducible SERS-Detection Enhancers in Weakly-Coupled Metallic Nanohelices

Science.gov (United States)

Caridad, José M.; Winters, Sinéad; McCloskey, David; Duesberg, Georg S.; Donegan, John F.; Krstić, Vojislav

2017-03-01

Reproducible and enhanced optical detection of molecules in low concentrations demands simultaneously intense and homogeneous electric fields acting as robust signal amplifiers. To generate such sophisticated optical near-fields, different plasmonic nanostructures were investigated in recent years. These, however, exhibit either high enhancement factor (EF) or spatial homogeneity but not both. Small interparticle gaps or sharp nanostructures show enormous EFs but no near-field homogeneity. Meanwhile, approaches using rounded and separated monomers create uniform near-fields with moderate EFs. Here, guided by numerical simulations, we show how arrays of weakly-coupled Ag nanohelices achieve both homogeneous and strong near-field enhancements, reaching even the limit forreproducible detection of individual molecules. The unique near-field distribution of a single nanohelix consists of broad hot-spots, merging with those from neighbouring nanohelices in specific array configurations and generating a wide and uniform detection zone (“hot-volume”). We experimentally assessed these nanostructures via surface-enhanced Raman spectroscopy, obtaining a corresponding EF of ~107 and a relative standard deviation <10%. These values demonstrate arrays of nanohelices as state-of-the-art substrates for reproducible optical detection as well as compelling nanostructures for related fields such as near-field imaging.

Nonlinear Delta-f Particle Simulations of Collective Effects in High-Intensity Bunched Beams

CERN Document Server

Qin, Hong; Hudson, Stuart R; Startsev, Edward

2005-01-01

The collective effects in high-intensity 3D bunched beams are described self-consistently by the nonlinear Vlasov-Maxwell equations.* The nonlinear delta-f method,** a particle simulation method for solving the nonlinear Vlasov-Maxwell equations, is being used to study the collective effects in high-intensity 3D bunched beams. The delta-f method, as a nonlinear perturbative scheme, splits the distribution function into equilibrium and perturbed parts. The perturbed distribution function is represented as a weighted summation over discrete particles, where the particle orbits are advanced by equations of motion in the focusing field and self-consistent fields, and the particle weights are advanced by the coupling between the perturbed fields and the zero-order distribution function. The nonlinear delta-f method exhibits minimal noise and accuracy problems in comparison with standard particle-in-cell simulations. A self-consistent 3D kinetic equilibrium is first established for high intensity bunched beams. The...

Reproducibility of wrist home blood pressure measurement with position sensor and automatic data storage

Directory of Open Access Journals (Sweden)

Nickenig Georg

2009-05-01

Full Text Available Abstract Background Wrist blood pressure (BP devices have physiological limits with regards to accuracy, therefore they were not preferred for home BP monitoring. However some wrist devices have been successfully validated using etablished validation protocols. Therefore this study assessed the reproducibility of wrist home BP measurement with position sensor and automatic data storage. Methods To compare the reproducibility of three different(BP measurement methods: 1 office BP, 2 home BP (Omron wrist device HEM- 637 IT with position sensor, 3 24-hour ambulatory BP(24-h ABPM (ABPM-04, Meditech, Hunconventional sphygmomanometric office BP was measured on study days 1 and 7, 24-h ABPM on study days 7 and 14 and home BP between study days 1 and 7 and between study days 8 and 14 in 69 hypertensive and 28 normotensive subjects. The correlation coeffcient of each BP measurement method with echocardiographic left ventricular mass index was analyzed. The schedule of home readings was performed according to recently published European Society of Hypertension (ESH- guidelines. Results The reproducibility of home BP measurement analyzed by the standard deviation as well as the squared differeces of mean individual differences between the respective BP measurements was significantly higher than the reproducibility of office BP (p Conclusion The short-term reproducibility of home BP measurement with the Omron HEM-637 IT wrist device was superior to the reproducibility of office BP and 24- h ABPM measurement. Furthermore, home BP with the wrist device showed similar correlations to targed organ damage as recently reported for upper arm devices. Although wrist devices have to be used cautious and with defined limitations, the use of validated devices with position sensor according to recently recommended measurement schedules might have the potential to be used for therapy monitoring.

Inter-scan reproducibility of coronary calcium measurement using Multi Detector-Row Computed Tomography (MDCT)

International Nuclear Information System (INIS)

Sabour, Siamak; Rutten, A.; Schouw, Y. T. van der; Atsma, F.; Grobbee, D. E.; Mali, W. P.; Bartelink, M. E. L.; Bots, M. L.; Prokop, M.

2007-01-01

Purpose. To assess inter-scan reproducibility of coronary calcium measurements obtained from Multi Detector-Row CT (MDCT) images and to evaluate whether this reproducibility is affected by different measurement protocols, slice thickness, cardiovascular risk factors and/or technical variables.Design. Cross-sectional study with repeated measurements. Materials and methods. The study population comprised 76 healthy women. Coronary calcium was assessed in these women twice in one session using 16-MDCT (Philips Mx 8000 IDT 16). Images were reconstructed with 1.5 mm slice thickness and 3.0 mm slice thickness. The 76 repeated scans were scored. The Agatston score, a volume measurement and a mass measurement were assessed. Reproducibility was determined by estimation of mean, absolute, relative difference, the weighted kappa value for agreement and the Intra-class correlation coefficient (ICCC).Results. Fifty-five participants (72.4%) had a coronary calcification of more than zero in Agatston (1.5 mm slice thickness). The reproducibility of coronary calcium measurements between scans in terms of ranking was excellent with Intra-class correlation coefficients of >0.98, and kappa values above 0.80. The absolute difference in calcium score between scans increased with increasing calcium levels, indicating that measurement error increases with increasing calcium levels. However, no relation was found between the mean difference in scores and calcium levels, indicating that the increase in measurement error is likely to result in random misclassification in calcium score. Reproducibility results were similar for 1.5 mm slices and for 3.0 mm slices, and equal for Agatston, volume and mass measurements.Conclusion. Inter-scan reproducibility of measurement of coronary calcium using images from MDCT is excellent, irrespective of slice thickness and type of calcium parameter

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR—protein spectral assignment

Energy Technology Data Exchange (ETDEWEB)

Fenwick, Matthew; Hoch, Jeffrey C. [UConn Health, Department of Molecular Biology and Biophysics (United States); Ulrich, Eldon [University of Wisconsin-Madison, Department of Biochemistry (United States); Gryk, Michael R., E-mail: gryk@uchc.edu [UConn Health, Department of Molecular Biology and Biophysics (United States)

2015-10-15

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata.

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR—protein spectral assignment

International Nuclear Information System (INIS)

Fenwick, Matthew; Hoch, Jeffrey C.; Ulrich, Eldon; Gryk, Michael R.

2015-01-01

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata

On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners.

Science.gov (United States)

Chen, Kevin T; Izquierdo-Garcia, David; Poynton, Clare B; Chonde, Daniel B; Catana, Ciprian

2017-03-01

To propose an MR-based method for generating continuous-valued head attenuation maps and to assess its accuracy and reproducibility. Demonstrating that novel MR-based photon attenuation correction methods are both accurate and reproducible is essential prior to using them routinely in research and clinical studies on integrated PET/MR scanners. Continuous-valued linear attenuation coefficient maps ("μ-maps") were generated by combining atlases that provided the prior probability of voxel positions belonging to a certain tissue class (air, soft tissue, or bone) and an MR intensity-based likelihood classifier to produce posterior probability maps of tissue classes. These probabilities were used as weights to generate the μ-maps. The accuracy of this probabilistic atlas-based continuous-valued μ-map ("PAC-map") generation method was assessed by calculating the voxel-wise absolute relative change (RC) between the MR-based and scaled CT-based attenuation-corrected PET images. To assess reproducibility, we performed pair-wise comparisons of the RC values obtained from the PET images reconstructed using the μ-maps generated from the data acquired at three time points. The proposed method produced continuous-valued μ-maps that qualitatively reflected the variable anatomy in patients with brain tumor and agreed well with the scaled CT-based μ-maps. The absolute RC comparing the resulting PET volumes was 1.76 ± 2.33 %, quantitatively demonstrating that the method is accurate. Additionally, we also showed that the method is highly reproducible, the mean RC value for the PET images reconstructed using the μ-maps obtained at the three visits being 0.65 ± 0.95 %. Accurate and highly reproducible continuous-valued head μ-maps can be generated from MR data using a probabilistic atlas-based approach.

On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners

Energy Technology Data Exchange (ETDEWEB)

Chen, Kevin T. [Massachusetts General Hospital and Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Charlestown, MA (United States); Massachusetts Institute of Technology, Division of Health Sciences and Technology, Cambridge, MA (United States); Izquierdo-Garcia, David; Catana, Ciprian [Massachusetts General Hospital and Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Charlestown, MA (United States); Poynton, Clare B. [Massachusetts General Hospital and Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Charlestown, MA (United States); Massachusetts General Hospital, Department of Psychiatry, Boston, MA (United States); University of California, San Francisco, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States); Chonde, Daniel B. [Massachusetts General Hospital and Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Charlestown, MA (United States); Harvard University, Program in Biophysics, Cambridge, MA (United States)

2017-03-15

To propose an MR-based method for generating continuous-valued head attenuation maps and to assess its accuracy and reproducibility. Demonstrating that novel MR-based photon attenuation correction methods are both accurate and reproducible is essential prior to using them routinely in research and clinical studies on integrated PET/MR scanners. Continuous-valued linear attenuation coefficient maps (''μ-maps'') were generated by combining atlases that provided the prior probability of voxel positions belonging to a certain tissue class (air, soft tissue, or bone) and an MR intensity-based likelihood classifier to produce posterior probability maps of tissue classes. These probabilities were used as weights to generate the μ-maps. The accuracy of this probabilistic atlas-based continuous-valued μ-map (''PAC-map'') generation method was assessed by calculating the voxel-wise absolute relative change (RC) between the MR-based and scaled CT-based attenuation-corrected PET images. To assess reproducibility, we performed pair-wise comparisons of the RC values obtained from the PET images reconstructed using the μ-maps generated from the data acquired at three time points. The proposed method produced continuous-valued μ-maps that qualitatively reflected the variable anatomy in patients with brain tumor and agreed well with the scaled CT-based μ-maps. The absolute RC comparing the resulting PET volumes was 1.76 ± 2.33 %, quantitatively demonstrating that the method is accurate. Additionally, we also showed that the method is highly reproducible, the mean RC value for the PET images reconstructed using the μ-maps obtained at the three visits being 0.65 ± 0.95 %. Accurate and highly reproducible continuous-valued head μ-maps can be generated from MR data using a probabilistic atlas-based approach. (orig.)

The intersubject and intrasubject reproducibility of FMRI activation during three encoding tasks: implications for clinical applications

International Nuclear Information System (INIS)

Harrington, Greg S.; Tomaszewski Farias, Sarah; Buonocore, Michael H.; Yonelinas, Andrew P.

2006-01-01

The goal of the present study was to evaluate the inter- and intrasubject reproducibility of FMRI activation for three memory encoding tasks previously used in the context of presurgical functional mapping. The primary region of interest (ROI) was the medial temporal lobe (MTL). Comparative ROIs included the inferior frontal and fusiform gyri which are less affected by susceptibility-induced signal losses than the MTL regions. Eighteen subjects were scanned using three memory encoding paradigms: word-pair, pattern, and scene encoding. Nine subjects underwent repeat scanning. Intersubject reproducibility of FMRI activation was evaluated by examining the percent of subjects who showed activation within a given ROI and the range to which individual laterality indices (LIs) varied from the mean. Intrasubject test-retest reproducibility was evaluated by examining the LI test-retest correlation, the average difference between LIs from two separate imaging sessions, and concordance ratios of activation volumes (R volume and R overlap ). For scene encoding the reproducibility of activation volume and LIs within the MTL were as good as or better than the reproducibility within the fusiform and inferior frontal ROIs. For pattern encoding and word-pair encoding, the reproducibility of activation volume and LIs within the MTL tended to be worse compared to the fusiform and inferior frontal ROIs. The differences in FMRI reproducibility appeared more dependent on the task than the susceptibility effects. The results of this study suggest that FMRI-based assessment of the neural substrates of memory using a scene encoding task may be a useful clinical tool. (orig.)

The intersubject and intrasubject reproducibility of FMRI activation during three encoding tasks: implications for clinical applications

Energy Technology Data Exchange (ETDEWEB)

Harrington, Greg S. [Virginia Commonwealth University, Department of Radiology, Richmond, VA (United States); Tomaszewski Farias, Sarah [University of California at Davis, Department of Neurology, Sacramento (United States); Buonocore, Michael H. [University of California at Davis, Department of Radiology, Sacramento (United States); Yonelinas, Andrew P. [University of California at Davis, Department of Psychology, Davis (United States)

2006-07-15

The goal of the present study was to evaluate the inter- and intrasubject reproducibility of FMRI activation for three memory encoding tasks previously used in the context of presurgical functional mapping. The primary region of interest (ROI) was the medial temporal lobe (MTL). Comparative ROIs included the inferior frontal and fusiform gyri which are less affected by susceptibility-induced signal losses than the MTL regions. Eighteen subjects were scanned using three memory encoding paradigms: word-pair, pattern, and scene encoding. Nine subjects underwent repeat scanning. Intersubject reproducibility of FMRI activation was evaluated by examining the percent of subjects who showed activation within a given ROI and the range to which individual laterality indices (LIs) varied from the mean. Intrasubject test-retest reproducibility was evaluated by examining the LI test-retest correlation, the average difference between LIs from two separate imaging sessions, and concordance ratios of activation volumes (R{sub volume} and R{sub overlap}). For scene encoding the reproducibility of activation volume and LIs within the MTL were as good as or better than the reproducibility within the fusiform and inferior frontal ROIs. For pattern encoding and word-pair encoding, the reproducibility of activation volume and LIs within the MTL tended to be worse compared to the fusiform and inferior frontal ROIs. The differences in FMRI reproducibility appeared more dependent on the task than the susceptibility effects. The results of this study suggest that FMRI-based assessment of the neural substrates of memory using a scene encoding task may be a useful clinical tool. (orig.)

Multichannel electrogastrography under a magnifying glass--an in-depth study on reproducibility of fed state electrogastrograms.

Science.gov (United States)

Krusiec-Swidergoł, B; Jonderko, K

2008-06-01

We checked on reproducibility of parameters of a multichannel electrogastrogram in adults after intake of typical, applied in electrogastrography, test meals. Recordings of multichannel electrogastrograms were accomplished in four blocks comprising 18 subjects (nine healthy volunteers and nine patients with functional GI disorders) each. Every subject had two examinations taken 1-2 days apart, and a third one was accomplished at least 2 weeks before or after the two other sessions. The registration involved a 30-min fasted and a 2-h postprandial period after one of the meal stimuli tested within a given block: 400 mL water, 400 g yoghurt (378 kcal), a scrambled eggs sandwich (370 kcal), a pancake (355 kcal). From among the parameters reflecting the propagation of the gastric slow waves, the average percentage of slow wave coupling (APSWC) exhibited a good (coefficient of variation for paired examinations CV(p) < or = 10%) to moderate (10 < CV(p) < or = 30%) reproducibility. On the other hand, the reproducibility of the maximum dominant frequency difference and the spatial dominant power difference was found to be unsatisfactory. The reproducibility of the multichannel electrogastrographic parameters did not differ between healthy volunteers and patients with functional GI disorders. Gender or the kind of a test meal did not affect the reproducibility of the electrogastrographic parameters either. The medium-term reproducibility was not any worse than the short-term one. From among the parameters of a multichannel electrogastrogram intended to quantify the propagation of slow waves, only the APSWC offers a reproducibility potentially good enough for clinical applications.

From Quasiperiodic Partial Synchronization to Collective Chaos in Populations of Inhibitory Neurons with Delay.

Science.gov (United States)

Pazó, Diego; Montbrió, Ernest

2016-06-10

Collective chaos is shown to emerge, via a period-doubling cascade, from quasiperiodic partial synchronization in a population of identical inhibitory neurons with delayed global coupling. This system is thoroughly investigated by means of an exact model of the macroscopic dynamics, valid in the thermodynamic limit. The collective chaotic state is reproduced numerically with a finite population, and persists in the presence of weak heterogeneities. Finally, the relationship of the model's dynamics with fast neuronal oscillations is discussed.

Reproducible and expedient rice regeneration system using in vitro ...

African Journals Online (AJOL)

Inevitable prerequisite for expedient regeneration in rice is the selection of totipotent explant and developing an apposite combination of growth hormones. Here, we reported a reproducible regeneration protocol in which basal segments of the stem of the in vitro grown rice plants were used as ex-plant. Using the protocol ...

Collective efficacy in a high-fidelity simulation of an airline operations center

Science.gov (United States)

Jinkerson, Shanna

This study investigated the relationships between collective efficacy, teamwork, and team performance. Participants were placed into teams, where they worked together in a high-fidelity simulation of an airline operations center. Each individual was assigned a different role to represent different jobs within an airline (Flight Operations Coordinator, Crew Scheduling, Maintenance, Weather, Flight Scheduling, or Flight Planning.) Participants completed a total of three simulations with an After Action Review between each. Within this setting, both team performance and teamwork behaviors were shown to be positively related to expectations for subsequent performance (collective efficacy). Additionally, teamwork and collective efficacy were not shown to be concomitantly related to subsequent team performance. A chi-square test was used to evaluate existence of performance spirals, and they were not supported. The results of this study were likely impacted by lack of power, as well as a lack of consistency across the three simulations.

Apical serine protease activity is necessary for assembly of a high-resistance renal collecting duct epithelium

DEFF Research Database (Denmark)

Steensgaard, Mette; Svenningsen, Per; Tinning, Anne R

2010-01-01

Abstract AIM: We hypothesized that the serine protease prostasin is necessary for differentiation of a high resistance renal collecting duct epithelium governed by glucocorticoid. METHODS: Postnatal rat kidney and adult human kidney was used to study expression and localization of prostasin......-cadherin distribution did not change. CONCLUSION: Apical, GPI-anchored, lipid raft-associated serine protease activity, compatible with prostasin, is necessary for development of a high-resistance collecting duct epithelium....

Scan-rescan reproducibility of segmental aortic wall shear stress as assessed by phase-specific segmentation with 4D flow MRI in healthy volunteers.

Science.gov (United States)

van der Palen, Roel L F; Roest, Arno A W; van den Boogaard, Pieter J; de Roos, Albert; Blom, Nico A; Westenberg, Jos J M

2018-05-26

The aim was to investigate scan-rescan reproducibility and observer variability of segmental aortic 3D systolic wall shear stress (WSS) by phase-specific segmentation with 4D flow MRI in healthy volunteers. Ten healthy volunteers (age 26.5 ± 2.6 years) underwent aortic 4D flow MRI twice. Maximum 3D systolic WSS (WSSmax) and mean 3D systolic WSS (WSSmean) for five thoracic aortic segments over five systolic cardiac phases by phase-specific segmentations were calculated. Scan-rescan analysis and observer reproducibility analysis were performed. Scan-rescan data showed overall good reproducibility for WSSmean (coefficient of variation, COV 10-15%) with moderate-to-strong intraclass correlation coefficient (ICC 0.63-0.89). The variability in WSSmax was high (COV 16-31%) with moderate-to-good ICC (0.55-0.79) for different aortic segments. Intra- and interobserver reproducibility was good-to-excellent for regional aortic WSSmax (ICC ≥ 0.78; COV ≤ 17%) and strong-to-excellent for WSSmean (ICC ≥ 0.86; COV ≤ 11%). In general, ascending aortic segments showed more WSSmax/WSSmean variability compared to aortic arch or descending aortic segments for scan-rescan, intraobserver and interobserver comparison. Scan-rescan reproducibility was good for WSSmean and moderate for WSSmax for all thoracic aortic segments over multiple systolic phases in healthy volunteers. Intra/interobserver reproducibility for segmental WSS assessment was good-to-excellent. Variability of WSSmax is higher and should be taken into account in case of individual follow-up or in comparative rest-stress studies to avoid misinterpretation.

Reproducibility of non-invasive assessment of skin endothelial function using laser Doppler flowmetry and laser speckle contrast imaging.

Directory of Open Access Journals (Sweden)

Cyril Puissant

Full Text Available Endothelial dysfunction precedes atherosclerosis. Vasodilation induced by acetylcholine (ACh is a specific test of endothelial function. Reproducibility of laser techniques such as laser-Doppler-flowmetry (LDF and Laser-speckle-contrast-imaging (LSCI to detect ACh vasodilation is debated and results expressions lack standardization. We aimed to study at a 7-day interval (i the inter-subject reproducibility, (ii the intra-subjects reproducibility, and (iii the effect of the results expressions over variability.Using LDF and LSCI simultaneously, we performed two different ACh-iontophoresis protocols. The maximal ACh vasodilation (peak-ACh was expressed as absolute or normalized flow or conductance values. Inter-subject reproducibility was expressed as coefficient of variation (inter-CV,%. Intra-subject reproducibility was expressed as within subject coefficients of variation (intra-CV,%, and intra-class correlation coefficients (ICC. Fifteen healthy subjects were included. The inter-subject reproducibility of peak-ACh depended upon the expression of the results and ranged from 55% to 162% for LDF and from 17% to 83% for LSCI. The intra-subject reproducibility (intra-CV/ICC of peak-ACh was reduced when assessed with LSCI compared to LDF no matter how the results were expressed and whatever the protocol used. The highest intra-subject reproducibility was found using LSCI. It was 18.7%/0.87 for a single current stimulation (expressed as cutaneous vascular conductance and 11.4%/0.61 for multiple current stimulations (expressed as absolute value.ACh-iontophoresis coupled with LSCI is a promising test to assess endothelial function because it is reproducible, safe, and non-invasive. N°: NCT01664572.

Reproducible Hydrogeophysical Inversions through the Open-Source Library pyGIMLi

Science.gov (United States)

Wagner, F. M.; Rücker, C.; Günther, T.

2017-12-01

Many tasks in applied geosciences cannot be solved by a single measurement method and require the integration of geophysical, geotechnical and hydrological methods. In the emerging field of hydrogeophysics, researchers strive to gain quantitative information on process-relevant subsurface parameters by means of multi-physical models, which simulate the dynamic process of interest as well as its geophysical response. However, such endeavors are associated with considerable technical challenges, since they require coupling of different numerical models. This represents an obstacle for many practitioners and students. Even technically versatile users tend to build individually tailored solutions by coupling different (and potentially proprietary) forward simulators at the cost of scientific reproducibility. We argue that the reproducibility of studies in computational hydrogeophysics, and therefore the advancement of the field itself, requires versatile open-source software. To this end, we present pyGIMLi - a flexible and computationally efficient framework for modeling and inversion in geophysics. The object-oriented library provides management for structured and unstructured meshes in 2D and 3D, finite-element and finite-volume solvers, various geophysical forward operators, as well as Gauss-Newton based frameworks for constrained, joint and fully-coupled inversions with flexible regularization. In a step-by-step demonstration, it is shown how the hydrogeophysical response of a saline tracer migration can be simulated. Tracer concentration data from boreholes and measured voltages at the surface are subsequently used to estimate the hydraulic conductivity distribution of the aquifer within a single reproducible Python script.

Automating dChip: toward reproducible sharing of microarray data analysis

Directory of Open Access Journals (Sweden)

Li Cheng

2008-05-01

Full Text Available Abstract Background During the past decade, many software packages have been developed for analysis and visualization of various types of microarrays. We have developed and maintained the widely used dChip as a microarray analysis software package accessible to both biologist and data analysts. However, challenges arise when dChip users want to analyze large number of arrays automatically and share data analysis procedures and parameters. Improvement is also needed when the dChip user support team tries to identify the causes of reported analysis errors or bugs from users. Results We report here implementation and application of the dChip automation module. Through this module, dChip automation files can be created to include menu steps, parameters, and data viewpoints to run automatically. A data-packaging function allows convenient transfer from one user to another of the dChip software, microarray data, and analysis procedures, so that the second user can reproduce the entire analysis session of the first user. An analysis report file can also be generated during an automated run, including analysis logs, user comments, and viewpoint screenshots. Conclusion The dChip automation module is a step toward reproducible research, and it can prompt a more convenient and reproducible mechanism for sharing microarray software, data, and analysis procedures and results. Automation data packages can also be used as publication supplements. Similar automation mechanisms could be valuable to the research community if implemented in other genomics and bioinformatics software packages.

Intra-rater reproducibility and validity of Nintendo Wii Balance Tests in community-dwelling Older Adults

DEFF Research Database (Denmark)

Jørgensen, Martin; Læssøe, Uffe; Hendriksen, C

2014-01-01

The aims of the current study were to examine the intrarater intersession reproducibility of the Nintendo Wii agility and stillness tests and explore the concurrent validity in relation to gold-standard force-plate analysis. Within-day intersession reproducibility was examined in 30 older adults ...

Charge collection and charge pulse formation in highly irradiated silicon planar detectors

International Nuclear Information System (INIS)

Dezillie, B.; Li, Z.; Eremin, V.

1998-06-01

The interpretation of experimental data and predictions for future experiments for high-energy physics have been based on conventional methods like capacitance versus voltage (C-V) measurements. Experiments carried out on highly irradiated detectors show that the kinetics of the charge collection and the dependence of the charge pulse amplitude on the applied bias are deviated too far from those predicted by the conventional methods. The described results show that in highly irradiated detectors, at a bias lower than the real full depletion voltage (V fd ), the kinetics of the charge collection (Q) contains a fast and a slow component. At V = V fd *, which is the full depletion voltage traditionally determined by the extrapolation of the fast component amplitude of q versus bias to the maximum value or from the standard C-V measurements, the pulse has a slow component with significant amplitude. This slow component can only be eliminated by applying additional bias that amounts to the real full depletion voltage (V fd ) or more. The above mentioned regularities are explained in this paper in terms of a model of an irradiated detector with multiple regions. This model allows one to use C-V, in a modified way, as well as TChT (transient charge technique) measurements to determine the V fd for highly irradiated detectors

Anatomical Reproducibility of a Head Model Molded by a Three-dimensional Printer.

Science.gov (United States)

Kondo, Kosuke; Nemoto, Masaaki; Masuda, Hiroyuki; Okonogi, Shinichi; Nomoto, Jun; Harada, Naoyuki; Sugo, Nobuo; Miyazaki, Chikao

2015-01-01

We prepared rapid prototyping models of heads with unruptured cerebral aneurysm based on image data of computed tomography angiography (CTA) using a three-dimensional (3D) printer. The objective of this study was to evaluate the anatomical reproducibility and accuracy of these models by comparison with the CTA images on a monitor. The subjects were 22 patients with unruptured cerebral aneurysm who underwent preoperative CTA. Reproducibility of the microsurgical anatomy of skull bone and arteries, the length and thickness of the main arteries, and the size of cerebral aneurysm were compared between the CTA image and rapid prototyping model. The microsurgical anatomy and arteries were favorably reproduced, apart from a few minute regions, in the rapid prototyping models. No significant difference was noted in the measured lengths of the main arteries between the CTA image and rapid prototyping model, but errors were noted in their thickness (p printer. It was concluded that these models are useful tools for neurosurgical simulation. The thickness of the main arteries and size of cerebral aneurysm should be comprehensively judged including other neuroimaging in consideration of errors.

Design of reproducible polarized and non-polarized edge filters using genetic algorithm

International Nuclear Information System (INIS)

Ejigu, Efrem Kebede; Lacquet, B M

2010-01-01

Recent advancement in optical fibre communications technology is partly due to the advancement of optical thin film technology. The advancement of optical thin film technology includes the development of new and existing optical filter design methods. The genetic algorithm is one of the new design methods that show promising results in designing a number of complicated design specifications. It is the finding of this study that the genetic algorithm design method, through its optimization capability, can give more reliable and reproducible designs of any specifications. The design method in this study optimizes the thickness of each layer to get to the best possible solution. Its capability and unavoidable limitations in designing polarized and non-polarized edge filters from absorptive and dispersive materials is well demonstrated. It is also demonstrated that polarized and non-polarized designs from the genetic algorithm are reproducible with great success. This research has accomplished the great task of formulating a computer program using the genetic algorithm in a Matlab environment for the design of a reproducible polarized and non-polarized filters of any sort from any kind of materials

Reproducibility of kinematic measures of the thoracic spine, lumbar spine and pelvis during fast running.

Science.gov (United States)

Mason, D L; Preece, S J; Bramah, C A; Herrington, L C

2016-01-01

This study evaluated the reproducibility of the angular rotations of the thoracic spine, lumbar spine, pelvis and lower extremity during running. In addition, the study compared kinematic reproducibility between two methods for calculating kinematic trajectories: a six degrees of freedom (6DOF) approach and a global optimisation (GO) approach. With the first approach segments were treated independently, however with GO approach joint constraints were imposed to stop translation of adjacent segments. A total of 12 athletes were tested on two separate days whilst running over ground at a speed of 5.6ms(-1). The results demonstrated good between-day reproducibility for most kinematic parameters in the frontal and transverse planes with typical angular errors of 1.4-3°. Acceptable repeatability was also found in the sagittal plane. However, in this plane, although kinematic waveform shape was preserved between testing session, there were sometimes shifts in curve offset which lead to slightly higher angular errors, typically ranging from 1.9° to 3.5°. In general, the results demonstrated similar levels of reproducibility for both computational approaches (6DOF and, GO) and therefore suggest that GO may not lead to improved kinematic reproducibility during running. Copyright © 2013 Elsevier B.V. All rights reserved.

Sharing meanings: developing interoperable semantic technologies to enhance reproducibility in earth and environmental science research

Science.gov (United States)

Schildhauer, M.

2015-12-01

Earth and environmental scientists are familiar with the entities, processes, and theories germane to their field of study, and comfortable collecting and analyzing data in their area of interest. Yet, while there appears to be consistency and agreement as to the scientific "terms" used to describe features in their data and analyses, aside from a few fundamental physical characteristics—such as mass or velocity-- there can be broad tolerances, if not considerable ambiguity, in how many earth science "terms" map to the underlying "concepts" that they actually represent. This ambiguity in meanings, or "semantics", creates major problems for scientific reproducibility. It greatly impedes the ability to replicate results—by making it difficult to determine the specifics of the intended meanings of terms such as deforestation or carbon flux -- as to scope, composition, magnitude, etc. In addition, semantic ambiguity complicates assemblage of comparable data for reproducing results, due to ambiguous or idiosyncratic labels for measurements, such as percent cover of forest, where the term "forest" is undefined; or where a reported output of "total carbon-emissions" might just include CO2 emissions, but not methane emissions. In this talk, we describe how the NSF-funded DataONE repository for earth and environmental science data (http://dataone.org), is using W3C-standard languages (RDF/OWL) to build an ontology for clarifying concepts embodied in heterogeneous data and model outputs. With an initial focus on carbon cycling concepts using terrestrial biospheric model outputs and LTER productivity data, we describe how we are achieving interoperability with "semantic vocabularies" (or ontologies) from aligned earth and life science domains, including OBO-foundry ontologies such as ENVO and BCO; the ISO/OGC O&M; and the NSF Earthcube GeoLink project. Our talk will also discuss best practices that may be helpful for other groups interested in constructing their own

Signatures of collective flow in high multiplicity pp collisions

CERN Document Server

Kisiel, Adam

2011-01-01

A blast-wave parametrization, including a full set of hadronic resonances, is used to model a small system, with total particle multiplicity comparable to the one measured in the high-multiplicity pp collisions at the LHC. Calculations are preformed for three cases: with negligible, regular and strong radial flow on the blast-wave hypersurface. We investigate the effects of flow on inclusive p_T spectra as well as on 1D and 3D femtoscopic radii for pions. Special emphasis is put on the role of pions from resonance decays. In particular we show that they magnify the flow effects present in the blast-wave stage and significantly influence the shape of the correlation functions. A specific observable, the R^E_out/R^G_side ratio is proposed as a sensitive probe of the collective effects. Model results for the high multiplicity pp collisions, for scenarios with small and large radial flow are compared.

Three-dimensional accuracy and interfractional reproducibility of patient fixation and positioning using a stereotactic head mask system

International Nuclear Information System (INIS)

Karger, Christian P.; Jaekel, Oliver; Debus, Juergen; Kuhn, Sabine; Hartmann, Guenther H.

2001-01-01

Purpose: Conformal radiotherapy in the head and neck region requires precise and reproducible patient setup. The definition of safety margins around the clinical target volume has to take into account uncertainties of fixation and positioning. Data are presented to quantify the involved uncertainties for the system used. Methods and Materials: Interfractional reproducibility of fixation and positioning of a target point in the brain was evaluated by biplanar films. 118 film pairs obtained at 52 fractions in 4 patients were analyzed. The setup was verified at the actual treatment table position by diagnostic X-ray units aligned to the isocenter and by a stereotactic X-ray localization technique. The stereotactic coordinates of the treated isocenter, of fiducials on the mask, and of implanted internal markers within the patient were measured to determine systematic and random errors. The data are corrected for uncertainty of the localization method. Results: Displacements in target point positioning were 0.35±0.41 mm, 1.22±0.25 mm, and -0.74±0.32 mm in the x, y, and z direction, respectively. The reproducibility of the fixation of the patient's head within the mask was 0.48 mm (x), 0.67 mm (y), and 0.72 mm (z). Rotational uncertainties around an axis parallel to the x, y, and z axis were 0.72 deg., 0.43 deg., and 0.70 deg., respectively. A simulation, based on the acquired data, yields a typical radial overall uncertainty for positioning and fixation of 1.80±0.60 mm. Conclusions: The applied setup technique showed to be highly reproducible. The data suggest that for the applied technique, a safety margin between clinical and planning target volume of 1-2 mm along one axis is sufficient for a target at the base of skull

Emergent patterns of collective cell migration under tubular confinement.

Science.gov (United States)

Xi, Wang; Sonam, Surabhi; Beng Saw, Thuan; Ladoux, Benoit; Teck Lim, Chwee

2017-11-15

Collective epithelial behaviors are essential for the development of lumens in organs. However, conventional assays of planar systems fail to replicate cell cohorts of tubular structures that advance in concerted ways on out-of-plane curved and confined surfaces, such as ductal elongation in vivo. Here, we mimic such coordinated tissue migration by forming lumens of epithelial cell sheets inside microtubes of 1-10 cell lengths in diameter. We show that these cell tubes reproduce the physiological apical-basal polarity, and have actin alignment, cell orientation, tissue organization, and migration modes that depend on the extent of tubular confinement and/or curvature. In contrast to flat constraint, the cell sheets in a highly constricted smaller microtube demonstrate slow motion with periodic relaxation, but fast overall movement in large microtubes. Altogether, our findings provide insights into the emerging migratory modes for epithelial migration and growth under tubular confinement, which are reminiscent of the in vivo scenario.

Collective Thomson scattering of a high power electron cyclotron resonance heating beam in LHD

DEFF Research Database (Denmark)

Kubo, S.; Nishiura, M.; Tanaka, K.

2010-01-01

Collective Thomson scattering (CTS) system has been constructed at LHD making use of the high power ECRH system in LHD. The necessary features for CTS, high power probing beams and receiving beams, both with well defined Gaussian profile and with the fine controllability, are endowed in the ECRH ...

Ceramic molar crown reproducibility by digital workflow manufacturing: An in vitro study.

Science.gov (United States)

Jeong, Ii-Do; Kim, Woong-Chul; Park, Jinyoung; Kim, Chong-Myeong; Kim, Ji-Hwan

2017-08-01

This in vitro study aimed to analyze and compare the reproducibility of zirconia and lithium disilicate crowns manufactured by digital workflow. A typodont model with a prepped upper first molar was set in a phantom head, and a digital impression was obtained with a video intraoral scanner (CEREC Omnicam; Sirona GmbH), from which a single crown was designed and manufactured with CAD/CAM into a zirconia crown and lithium disilicate crown (n=12). Reproducibility of each crown was quantitatively retrieved by superimposing the digitized data of the crown in 3D inspection software, and differences were graphically mapped in color. Areas with large differences were analyzed with digital microscopy. Mean quadratic deviations (RMS) quantitatively obtained from each ceramic group were statistically analyzed with Student's t-test (α=.05). The RMS value of lithium disilicate crown was 29.2 (4.1) µm and 17.6 (5.5) µm on the outer and inner surfaces, respectively, whereas these values were 18.6 (2.0) µm and 20.6 (5.1) µm for the zirconia crown. Reproducibility of zirconia and lithium disilicate crowns had a statistically significant difference only on the outer surface ( P <.001). The outer surface of lithium disilicate crown showed over-contouring on the buccal surface and under-contouring on the inner occlusal surface. The outer surface of zirconia crown showed both over- and under-contouring on the buccal surface, and the inner surface showed under-contouring in the marginal areas. Restoration manufacturing by digital workflow will enhance the reproducibility of zirconia single crowns more than that of lithium disilicate single crowns.

On the reproducibility of apatite fission-track plateau-age dating

International Nuclear Information System (INIS)

Poupeau, G.; Baitelli, R.; Berbert, M.; Fonseca, A.

1985-01-01

Duplicate measurements as well as published data show that plateau-age measurements on apatites have a reproducibility - when made in optical microscopy - generally better than +- 5%, which may be accounted for by statistical errors on track density measurement. (Author) [pt

Reproducibility of an aerobic endurance test for nonexpert swimmers.

Science.gov (United States)

Veronese da Costa, Adalberto; Costa, Manoel da Cunha; Carlos, Daniel Medeiros; Guerra, Luis Marcos de Medeiros; Silva, Antônio José; Barbosa, Tiago Manoel Cabral Dos Santos

2012-01-01

This study aimed to verify the reproduction of an aerobic test to determine nonexpert swimmers' resistance. The sample consisted of 24 male swimmers (age: 22.79 ± 3.90 years; weight: 74.72 ± 11.44 kg; height: 172.58 ± 4.99 cm; and fat percentage: 15.19% ± 3.21%), who swim for 1 hour three times a week. A new instrument was used in this study (a Progressive Swim Test): the swimmer wore an underwater MP3 player and increased their swimming speed on hearing a beep after every 25 meters. Each swimmer's heart rate was recorded before the test (BHR) and again after the test (AHR). The rate of perceived exertion (RPE) and the number of laps performed (NLP) were also recorded. The sample size was estimated using G*Power software (v 3.0.10; Franz Faul, Kiel University, Kiel, Germany). The descriptive values were expressed as mean and standard deviation. After confirming the normality of the data using both the Shapiro-Wilk and Levene tests, a paired t-test was performed to compare the data. The Pearson's linear correlation (r) and intraclass coefficient correlation (ICC) tests were used to determine relative reproducibility. The standard error of measurement (SEM) and the coefficient of variation (CV) were used to determine absolute reproducibility. The limits of agreement and the bias of the absolute and relative values between days were determined by Bland-Altman plots. All values had a significance level of P 0.50 and ICC > 0.66. The SEM had a variation of ±2% and the CV was 0.90; SEM swimmers. The Progressive Swim Test for nonexpert swimmers produces comparable results for noncompetitive swimmers with a favorable degree of reproducibility, thus presenting possible applications for researching the physiological performance of nonexpert swimmers.

Reproducibility of TL measurements in a mixed field of thermal neutrons and photons

International Nuclear Information System (INIS)

Fernandes, A.C.; Goncalves, I.C.; Ferro Carvalho, A.; Santos, J.; Cardoso, J.; Santos, L.; Osvay, M.

2002-01-01

The reproducibility of measurements performed with GR-100 (LiF:Mg,Ti) from the Solid Dosimetric Detector and Method Laboratory (DML) China, GR-107 ( 7 LiF:Mg,Ti, DML), TLD-700H ( 7 LiF:Mg,Cu,P, Harshaw) and Al 2 O 3 :Mg,Y (Hungary) in photon and mixed photon-neutron fields was investigated. Mixed-field irradiations were performed in a thermal neutron field generated at a nuclear reactor. GR-100 sensitivity decreased after mixed-field irradiations, while no significant change was found for the other materials. Using GR-100 for the dosimetry of mixed and high-intensity fields requires careful procedures. (author)

Reproducibility and validity of the Nintendo Wii Balance Board for measuring shoulder sensorimotor control in prone lying.

Science.gov (United States)

Eshoj, H; Juul-Kristensen, Birgit; Jørgensen, Rene Gam Bender; Søgaard, Karen

2017-02-01

For the lower limbs, the Nintendo Wii Balance Board (NWBB) has been widely used to measure postural control. However, this has not been performed for upper limb measurements. Further, the NWBB has shown to produce more background noise with decreasing loads, which may be of concern when used for upper limb testing. The aim was to investigate reproducibility and validity of the NWBB. A test-retest design was performed with 68 subjects completing three different prone lying, upper limb weight-bearing balance tasks on a NWBB: two-arms, eyes closed (1) one-arm, non-dominant/non-injured (2) and one-arm, dominant/injured (3). Each task was repeated three times over the course of two test sessions with a 30-min break in between. Further, the level of background noise from a NWBB was compared with a force platform through systematic loading of both boards with increasing deadweights ranging from 5 to 90kg. Test-retest reproducibility was high with ICCs ranging from 0.95 to 0.97 (95% CI 0.92 to 0.98). However, systematic bias and tendencies for funnel effects in the Bland Altman plots for both one-armed tests were present. The concurrent validity of the NWBB was low (CCC 0.17 (95% CI 0.12-0.22)) due to large differences between the NWBB and force platform in noise sensitivity at low deadweights (especially below 50kg). The NWBB prone lying, shoulder sensorimotor control test was highly reproducible. Though, concurrent validity of the NWBB was poor compared to a force platform. Further investigation of the impact of the background noise, especially at low loads, is needed. Copyright © 2016 Elsevier B.V. All rights reserved.

An Analysis and Allocation System for Library Collections Budgets: The Comprehensive Allocation Process (CAP)

Science.gov (United States)

Lyons, Lucy Eleonore; Blosser, John

2012-01-01

The "Comprehensive Allocation Process" (CAP) is a reproducible decision-making structure for the allocation of new collections funds, for the reallocation of funds within stagnant budgets, and for budget cuts in the face of reduced funding levels. This system was designed to overcome common shortcomings of current methods. Its philosophical…

In vivo reproducibility of robotic probe placement for an integrated US-CT image-guided radiation therapy system

Science.gov (United States)

Lediju Bell, Muyinatu A.; Sen, H. Tutkun; Iordachita, Iulian; Kazanzides, Peter; Wong, John

2014-03-01

Radiation therapy is used to treat cancer by delivering high-dose radiation to a pre-defined target volume. Ultrasound (US) has the potential to provide real-time, image-guidance of radiation therapy to identify when a target moves outside of the treatment volume (e.g. due to breathing), but the associated probe-induced tissue deformation causes local anatomical deviations from the treatment plan. If the US probe is placed to achieve similar tissue deformations in the CT images required for treatment planning, its presence causes streak artifacts that will interfere with treatment planning calculations. To overcome these challenges, we propose robot-assisted placement of a real ultrasound probe, followed by probe removal and replacement with a geometrically-identical, CT-compatible model probe. This work is the first to investigate in vivo deformation reproducibility with the proposed approach. A dog's prostate, liver, and pancreas were each implanted with three 2.38-mm spherical metallic markers, and the US probe was placed to visualize the implanted markers in each organ. The real and model probes were automatically removed and returned to the same position (i.e. position control), and CT images were acquired with each probe placement. The model probe was also removed and returned with the same normal force measured with the real US probe (i.e. force control). Marker positions in CT images were analyzed to determine reproducibility, and a corollary reproducibility study was performed on ex vivo tissue. In vivo results indicate that tissue deformations with the real probe were repeatable under position control for the prostate, liver, and pancreas, with median 3D reproducibility of 0.3 mm, 0.3 mm, and 1.6 mm, respectively, compared to 0.6 mm for the ex vivo tissue. For the prostate, the mean 3D tissue displacement errors between the real and model probes were 0.2 mm under position control and 0.6 mm under force control, which are both within acceptable

Reproducing kernel method with Taylor expansion for linear Volterra integro-differential equations

Directory of Open Access Journals (Sweden)

Azizallah Alvandi

2017-06-01

Full Text Available This research aims of the present a new and single algorithm for linear integro-differential equations (LIDE. To apply the reproducing Hilbert kernel method, there is made an equivalent transformation by using Taylor series for solving LIDEs. Shown in series form is the analytical solution in the reproducing kernel space and the approximate solution $ u_{N} $ is constructed by truncating the series to $ N $ terms. It is easy to prove the convergence of $ u_{N} $ to the analytical solution. The numerical solutions from the proposed method indicate that this approach can be implemented easily which shows attractive features.

Reproducibility and diagnostic performance of shear wave elastography in evaluating breast solid mass.

Science.gov (United States)

Hong, Sun; Woo, Ok Hee; Shin, Hye Seon; Hwang, Soon-Young; Cho, Kyu Ran; Seo, Bo Kyoung

Shear wave elastography (SWE) was performed independently by two radiologists in 264 solid breast masses. The images were reviewed for color overlay pattern (COP) classification by the two radiologists, double blinded to any information. The interobserver agreement of the COP was almost perfect (κ=0.908) and high in E max (ICC=0.89). The AUC value of the COP (0.954) was significantly higher than that of E max (0.915) (p=0.002) but not significantly different from that of E max combined with COP (0.957) (p=0.098). The SWE color overlay pattern and E max of breast masses were highly reproducible. The COP had better diagnostic ability than E max , suggesting that COP may be a more reliable parameter for solid breast mass evaluation. Copyright © 2017 Elsevier Inc. All rights reserved.

Reproducibility of non-invasive measurement for left ventricular contractility using gated myocardial SPECT

International Nuclear Information System (INIS)

Kim, Kyeon Min; Lee, Dong Soo; Kim, Yu Kyeong; Cheon, Gi Jeong; Kim, Seok Ki; Chung, June Key; Lee, Myung Chul

2001-01-01

We tried to establish the reproducibility of the measurement of maximal elastance (Emax) and to compare the degree of the reproducibility of two estimation methods: single pressure-volume loop method and parameter optimization method. In 47 patients (42 males and 5 females, 53 ± 10 years old) with suspected coronary artery disease (ejection fraction; 22-68%), gated Tc-99m MIBI myocardial SPECT and arterial tonometry were acquired, In 11 patients among these 47 patients, gated SPECT and tonometry were performed twice consecutively with patients in situ. Emax and void volume (Vo) were estimated using single pressure-volume loop method of Lee and parameter optimization method based on linear approximation of Yoshizawa. Correlation between the consecutive measurements by each method and correlation between the two estimation methods were compared. Reproducibility of Emax (r=0.96) and Vo (r=0.99) by single pressure-volume method was better than the reporducibility of Emax (r=0.89) and Vo (r=0.64) by parameter optimization method. Correlations of Emax and Vo were fair between the two methods. The correlation of Emax (r=0.77) was better thn that of Vo (r=0.65). Reproducibiity of Emax measurement by single pressure-volume loop method using gated myocardial SPECT and arterial tonometry was excellent. Reproducibility by parameter optimization method was also but was less than that achieved by single pressure-volume method

Reproducibility and quantitativity of oblique-angle reconstruction in single photon emission computed tomography using Tl-201 myocardial phantom

International Nuclear Information System (INIS)

Bunko, Hisashi; Nanbu, Ichiro; Seki, Hiroyasu

1984-01-01

This study was carried out in order to evaluate reproducibility and quantitativity of oblique-angle reconstruction of myocardial phantom SPECT. Myocardial phantom with transmural and subendcardial defects, and off-axis phantom with wall thickness changing continuously from 0 to 23 mm were used. Sixty projection data in every 6 0 were aquired using dual-camera (ZLC) with high resolution collimators connected to Scintipac-2400 computer system. Oblique-angle reconstructed images were obtained by indicating the long axis of the phantom manually in the transaxial and vertical long axial tomograms. Reproducibility and quantitativity were evaluated by creating circumferential profile (CFP) of the finally reconstructed short axial images. Inter- and intra-operater reproducibility of relative counting ratio were less than 6.7% (C.V.) and 3.3% (C.V.), respectively. Both inter- and intraoperater reproducibility of absolute counts were better than that of counting ratio (less than 5.1% (C.V.) and 2.9% (C.V.), respectively). Variation of defect location in the reconstructed image and between the slices were less than 1 sampling interval of CFP (6 0 ) and 0.6 slice, respectively. Quantitativity of counts in the reconstructed images was poor in the transmulal defect, but was fair in the subendocardial defect. Counting ratio was greatly affected by wall thickness. Temporal quantitatibity or linearity of the counts in sequential SPECTs was good in non-defect area, especially when wall thickness was greater than 70% (16 mm) of maximum. In conclusion, three-dimensional oblique-angle reconstruction in Tl-201 myocardial SPECT could be applicable to relative and temporal quantitation of local myocardial activity other than defect area for the quantitative evaluation of Tl-201 myocardial wash-out. (J.P.N.)

Parallel magnetic resonance imaging as approximation in a reproducing kernel Hilbert space

International Nuclear Information System (INIS)

Athalye, Vivek; Lustig, Michael; Martin Uecker

2015-01-01

In magnetic resonance imaging data samples are collected in the spatial frequency domain (k-space), typically by time-consuming line-by-line scanning on a Cartesian grid. Scans can be accelerated by simultaneous acquisition of data using multiple receivers (parallel imaging), and by using more efficient non-Cartesian sampling schemes. To understand and design k-space sampling patterns, a theoretical framework is needed to analyze how well arbitrary sampling patterns reconstruct unsampled k-space using receive coil information. As shown here, reconstruction from samples at arbitrary locations can be understood as approximation of vector-valued functions from the acquired samples and formulated using a reproducing kernel Hilbert space with a matrix-valued kernel defined by the spatial sensitivities of the receive coils. This establishes a formal connection between approximation theory and parallel imaging. Theoretical tools from approximation theory can then be used to understand reconstruction in k-space and to extend the analysis of the effects of samples selection beyond the traditional image-domain g-factor noise analysis to both noise amplification and approximation errors in k-space. This is demonstrated with numerical examples. (paper)

Easy, Fast, and Reproducible Quantification of Cholesterol and Other Lipids in Human Plasma by Combined High Resolution MSX and FTMS Analysis

Science.gov (United States)

Gallego, Sandra F.; Højlund, Kurt; Ejsing, Christer S.

2018-01-01

Reliable, cost-effective, and gold-standard absolute quantification of non-esterified cholesterol in human plasma is of paramount importance in clinical lipidomics and for the monitoring of metabolic health. Here, we compared the performance of three mass spectrometric approaches available for direct detection and quantification of cholesterol in extracts of human plasma. These approaches are high resolution full scan Fourier transform mass spectrometry (FTMS) analysis, parallel reaction monitoring (PRM), and novel multiplexed MS/MS (MSX) technology, where fragments from selected precursor ions are detected simultaneously. Evaluating the performance of these approaches in terms of dynamic quantification range, linearity, and analytical precision showed that the MSX-based approach is superior to that of the FTMS and PRM-based approaches. To further show the efficacy of this approach, we devised a simple routine for extensive plasma lipidome characterization using only 8 μL of plasma, using a new commercially available ready-to-spike-in mixture with 14 synthetic lipid standards, and executing a single 6 min sample injection with combined MSX analysis for cholesterol quantification and FTMS analysis for quantification of sterol esters, glycerolipids, glycerophospholipids, and sphingolipids. Using this simple routine afforded reproducible and absolute quantification of 200 lipid species encompassing 13 lipid classes in human plasma samples. Notably, the analysis time of this procedure can be shortened for high throughput-oriented clinical lipidomics studies or extended with more advanced MSALL technology (Almeida R. et al., J. Am. Soc. Mass Spectrom. 26, 133-148 [1]) to support in-depth structural elucidation of lipid molecules. [Figure not available: see fulltext.

Can radiomics features be reproducibly measured from CBCT images for patients with non-small cell lung cancer?

Energy Technology Data Exchange (ETDEWEB)

Fave, Xenia, E-mail: xjfave@mdanderson.org; Fried, David [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and The University of Texas Graduate School of Biomedical Sciences at Houston, 6767 Bertner Avenue, Houston, Texas 77030 (United States); Mackin, Dennis; Yang, Jinzhong; Zhang, Joy; Balter, Peter; Followill, David [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); Gomez, Daniel [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); Kyle Jones, A. [Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); Stingo, Francesco [Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States); Fontenot, Jonas [Mary Bird Perkins Cancer Center, 4950 Essen Lane, Baton Rouge, Louisiana 70809 (United States); Court, Laurence [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 and Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030 (United States)

2015-12-15

Purpose: Increasing evidence suggests radiomics features extracted from computed tomography (CT) images may be useful in prognostic models for patients with nonsmall cell lung cancer (NSCLC). This study was designed to determine whether such features can be reproducibly obtained from cone-beam CT (CBCT) images taken using medical Linac onboard-imaging systems in order to track them through treatment. Methods: Test-retest CBCT images of ten patients previously enrolled in a clinical trial were retrospectively obtained and used to determine the concordance correlation coefficient (CCC) for 68 different texture features. The volume dependence of each feature was also measured using the Spearman rank correlation coefficient. Features with a high reproducibility (CCC > 0.9) that were not due to volume dependence in the patient test-retest set were further examined for their sensitivity to differences in imaging protocol, level of scatter, and amount of motion by using two phantoms. The first phantom was a texture phantom composed of rectangular cartridges to represent different textures. Features were measured from two cartridges, shredded rubber and dense cork, in this study. The texture phantom was scanned with 19 different CBCT imagers to establish the features’ interscanner variability. The effect of scatter on these features was studied by surrounding the same texture phantom with scattering material (rice and solid water). The effect of respiratory motion on these features was studied using a dynamic-motion thoracic phantom and a specially designed tumor texture insert of the shredded rubber material. The differences between scans acquired with different Linacs and protocols, varying amounts of scatter, and with different levels of motion were compared to the mean intrapatient difference from the test-retest image set. Results: Of the original 68 features, 37 had a CCC >0.9 that was not due to volume dependence. When the Linac manufacturer and imaging protocol

Collection, storage and management of high-water marks data: praxis and recommendations

Directory of Open Access Journals (Sweden)

Piotte Olivier

2016-01-01

Full Text Available High-water marks data, in its most general definition, is a precious source of information for the many stakeholders involved in risk culture, inundation mapping, river, estuarine or coastal studies, etc. Although there have already been many initiatives to collect and exploit existing data, as well as collecting new marks after flood events, a lack of harmonization and coordination remains. The French flood forecasting services, together with Cerema, decided to provide technical and organizational solutions in order to set up a collaborative management approach of high-water marks data. On the one hand, a methodological handbook has been produced, giving recommendations for post-flood field investigations. It comes with a dedicated PDA tool and a PC desktop software. On the other hand, a national repository has been built, making it possible to gather the large range of informations usually needed. This repository is combined with a collaborative web platform, which aims to be a way of public access to the available information, a working tool for technical users, and a front door to contribute to the inventory. The last step of this approach is the setting of an organization blue-print including all the stakeholders directly or indirectly involved in high-water marks knowledge.

Reproducibility of F18-FDG PET radiomic features for different cervical tumor segmentation methods, gray-level discretization, and reconstruction algorithms.

Science.gov (United States)

Altazi, Baderaldeen A; Zhang, Geoffrey G; Fernandez, Daniel C; Montejo, Michael E; Hunt, Dylan; Werner, Joan; Biagioli, Matthew C; Moros, Eduardo G

2017-11-01

Site-specific investigations of the role of radiomics in cancer diagnosis and therapy are emerging. We evaluated the reproducibility of radiomic features extracted from 18 Flourine-fluorodeoxyglucose ( 18 F-FDG) PET images for three parameters: manual versus computer-aided segmentation methods, gray-level discretization, and PET image reconstruction algorithms. Our cohort consisted of pretreatment PET/CT scans from 88 cervical cancer patients. Two board-certified radiation oncologists manually segmented the metabolic tumor volume (MTV 1 and MTV 2 ) for each patient. For comparison, we used a graphical-based method to generate semiautomated segmented volumes (GBSV). To address any perturbations in radiomic feature values, we down-sampled the tumor volumes into three gray-levels: 32, 64, and 128 from the original gray-level of 256. Finally, we analyzed the effect on radiomic features on PET images of eight patients due to four PET 3D-reconstruction algorithms: maximum likelihood-ordered subset expectation maximization (OSEM) iterative reconstruction (IR) method, fourier rebinning-ML-OSEM (FOREIR), FORE-filtered back projection (FOREFBP), and 3D-Reprojection (3DRP) analytical method. We extracted 79 features from all segmentation method, gray-levels of down-sampled volumes, and PET reconstruction algorithms. The features were extracted using gray-level co-occurrence matrices (GLCM), gray-level size zone matrices (GLSZM), gray-level run-length matrices (GLRLM), neighborhood gray-tone difference matrices (NGTDM), shape-based features (SF), and intensity histogram features (IHF). We computed the Dice coefficient between each MTV and GBSV to measure segmentation accuracy. Coefficient values close to one indicate high agreement, and values close to zero indicate low agreement. We evaluated the effect on radiomic features by calculating the mean percentage differences (d¯) between feature values measured from each pair of parameter elements (i.e. segmentation methods: MTV

HashDist: Reproducible, Relocatable, Customizable, Cross-Platform Software Stacks for Open Hydrological Science

Science.gov (United States)

Ahmadia, A. J.; Kees, C. E.

2014-12-01

Developing scientific software is a continuous balance between not reinventing the wheel and getting fragile codes to interoperate with one another. Binary software distributions such as Anaconda provide a robust starting point for many scientific software packages, but this solution alone is insufficient for many scientific software developers. HashDist provides a critical component of the development workflow, enabling highly customizable, source-driven, and reproducible builds for scientific software stacks, available from both the IPython Notebook and the command line. To address these issues, the Coastal and Hydraulics Laboratory at the US Army Engineer Research and Development Center has funded the development of HashDist in collaboration with Simula Research Laboratories and the University of Texas at Austin. HashDist is motivated by a functional approach to package build management, and features intelligent caching of sources and builds, parametrized build specifications, and the ability to interoperate with system compilers and packages. HashDist enables the easy specification of "software stacks", which allow both the novice user to install a default environment and the advanced user to configure every aspect of their build in a modular fashion. As an advanced feature, HashDist builds can be made relocatable, allowing the easy redistribution of binaries on all three major operating systems as well as cloud, and supercomputing platforms. As a final benefit, all HashDist builds are reproducible, with a build hash specifying exactly how each component of the software stack was installed. This talk discusses the role of HashDist in the hydrological sciences, including its use by the Coastal and Hydraulics Laboratory in the development and deployment of the Proteus Toolkit as well as the Rapid Operational Access and Maneuver Support project. We demonstrate HashDist in action, and show how it can effectively support development, deployment, teaching, and

MASSIVE DATA, THE DIGITIZATION OF SCIENCE, AND REPRODUCIBILITY OF RESULTS

CERN Multimedia

CERN. Geneva

2010-01-01

As the scientific enterprise becomes increasingly computational and data-driven, the nature of the information communicated must change. Without inclusion of the code and data with published computational results, we are engendering a credibility crisis in science. Controversies such as ClimateGate, the microarray-based drug sensitivity clinical trials under investigation at Duke University, and retractions from prominent journals due to unverified code suggest the need for greater transparency in our computational science. In this talk I argue that the scientific method be restored to (1) a focus on error control as central to scientific communication and (2) complete communication of the underlying methodology producing the results, ie. reproducibility. I outline barriers to these goals based on recent survey work (Stodden 2010), and suggest solutions such as the “Reproducible Research Standard” (Stodden 2009), giving open licensing options designed to create an intellectual property framework for scien...

Reproducibility of coronary calcification detection with electron-beam computed tomography

International Nuclear Information System (INIS)

Hernigou, A.; Challande, P.; Boudeville, J.C.; Sene, V.; Grataloup, C.; Plainfosse, M.

1996-01-01

If coronary calcification scores obtained with electron-beam computed tomography (EBT) were proved to be correlated to coronary atherosclerosis, the reproducibility of the technique had to be assessed before being useed for patient follow-up. A total of 150 patients, selected as a result of a cholesterol screening programme, were studied by EBT. Twelve contiguous 3-mm-thick transverse slices beginning on the proximal coronary arteries were obtained through the base of the heart. The amount of calcium was evaluated as the calcified area weighted by a coefficient depending on the density peak level. The value was expressed as a logarithmic scale. Intra-observer, inter-observer and inter-examination reproducibilities were calculated. They were 1.9, 1.3 and 7.2%, respectively. These results were good enough to allow the use of EBT for longitudinal studies. The influence of acquisition and calculation conditions on score computation were also analysed. (orig.)

Reproducibility of 3-Dimensional Ultrasound Measurements of Placental Volume at Gestational Ages 11 - 14 Weeks

DEFF Research Database (Denmark)

Larsen, M L; Naver, K V; Kjaer, M M

2015-01-01

.918 (0.812 - 0.966) and 0.983 (0.960- 0.993), LOA = [-22.9- 22.5] and [-14.3 - 12.1]), but interobserver reproducibility showed a wide range of agreement (LOA = [-50.5- 34.8]), particularly in cases with u-shaped placentas. CONCLUSION: The low interobserver reproducibility of VOCAL measurements...

Reproducibility of 3-Dimensional Ultrasound Measurements of Placental Volume at Gestational Ages 11 - 14 Weeks

DEFF Research Database (Denmark)

Larsen, M L; Naver, K V; Kjaer, M M

2016-01-01

.918 (0.812 - 0.966) and 0.983 (0.960- 0.993), LOA = [-22.9- 22.5] and [-14.3 - 12.1]), but interobserver reproducibility showed a wide range of agreement (LOA = [-50.5- 34.8]), particularly in cases with u-shaped placentas. CONCLUSION: The low interobserver reproducibility of VOCAL measurements...

Improvement of reproducibility and quality control of human growth hormone radioiodination

International Nuclear Information System (INIS)

Bartolini, P.; Ribela, M.T.C.P.; Camilo, M.A.

1988-01-01

The labelling reaction of human growth hormone (hGH) with 125 I and its chromatographic purification have been studied with emphasis on the reproducibility of the yields, quantitaTive recoveries and resulting activities. Through the accurate standardization of a monitoring technique, it is confirmed that there are no significant losses in radioactivity or protein during the labelling or purification process. By strict control of the reaction conditions a fairily good reproducibility is also obtained in the labelling of various hGH extracts with diferent 125 I shipments used after short or long storage. Finally, the specific activity (or absolute mass) of the radioiodinated protein is determined by this Analysis of the Reaction Mixture and compared to the widely used radioimmunological assay (Self-displacement). (M.A.C.) [pt

Hybrid engineered materials with high water-collecting efficiency inspired by Namib Desert beetles.

Science.gov (United States)

Zhu, Hai; Guo, Zhiguang

2016-05-21

Inspired by Namib Desert beetles, a hybrid superhydrophobic surface was fabricated, showing highly efficient fog harvesting with a water collection rate (WCR) of 1309.9 mg h(-1) cm(-2). And, the surface possessed an excellent robustness and self-cleaning property.

Highly Scalable Trip Grouping for Large Scale Collective Transportation Systems

DEFF Research Database (Denmark)

Gidofalvi, Gyozo; Pedersen, Torben Bach; Risch, Tore

2008-01-01

Transportation-related problems, like road congestion, parking, and pollution, are increasing in most cities. In order to reduce traffic, recent work has proposed methods for vehicle sharing, for example for sharing cabs by grouping "closeby" cab requests and thus minimizing transportation cost...... and utilizing cab space. However, the methods published so far do not scale to large data volumes, which is necessary to facilitate large-scale collective transportation systems, e.g., ride-sharing systems for large cities. This paper presents highly scalable trip grouping algorithms, which generalize previous...

The reproducibility of organ position using active breathing control (ABC) during liver radiotherapy

International Nuclear Information System (INIS)

Dawson, Laura A.; Brock, Kristy K.; Kazanjian, Sahira; Fitch, Dwight; McGinn, Cornelius J.; Lawrence, Theodore S.; Haken, Randall K. ten; Balter, James

2001-01-01

Purpose: To evaluate the intrafraction and interfraction reproducibility of liver immobilization using active breathing control (ABC). Methods and Materials: Patients with unresectable intrahepatic tumors who could comfortably hold their breath for at least 20 s were treated with focal liver radiation using ABC for liver immobilization. Fluoroscopy was used to measure any potential motion during ABC breath holds. Preceding each radiotherapy fraction, with the patient setup in the nominal treatment position using ABC, orthogonal radiographs were taken using room-mounted diagnostic X-ray tubes and a digital imager. The radiographs were compared to reference images using a 2D alignment tool. The treatment table was moved to produce acceptable setup, and repeat orthogonal verification images were obtained. The positions of the diaphragm and the liver (assessed by localization of implanted radiopaque intra-arterial microcoils) relative to the skeleton were subsequently analyzed. The intrafraction reproducibility (from repeat radiographs obtained within the time period of one fraction before treatment) and interfraction reproducibility (from comparisons of the first radiograph for each treatment with a reference radiograph) of the diaphragm and the hepatic microcoil positions relative to the skeleton with repeat breath holds using ABC were then measured. Caudal-cranial (CC), anterior-posterior (AP), and medial-lateral (ML) reproducibility of the hepatic microcoils relative to the skeleton were also determined from three-dimensional alignment of repeat CT scans obtained in the treatment position. Results: A total of 262 fractions of radiation were delivered using ABC breath holds in 8 patients. No motion of the diaphragm or hepatic microcoils was observed on fluoroscopy during ABC breath holds. From analyses of 158 sets of positioning radiographs, the average intrafraction CC reproducibility (σ) of the diaphragm and hepatic microcoil position relative to the skeleton

Computer-Aided Detection in Digital Mammography: False-Positive Marks and Their Reproducibility in Negative Mammograms

International Nuclear Information System (INIS)

Kim, Seung Ja; Moon, Woo Kyung; Cho, Nariya; Chang, Jung Min; Seong, Min Hyun

2009-01-01

Background: There are relatively few studies reporting the frequency of false-positive computer-aided detection (CAD) marks and their reproducibility in normal cases. Purpose: To evaluate retrospectively the false-positive mark rate of a CAD system and the reproducibility of false-positive marks in two sets of negative digital mammograms. Material and Methods: Two sets of negative digital mammograms were obtained in 360 women (mean age 57 years, range 30-76 years) with an approximate interval of 1 year (mean time 343.7 days), and a CAD system was applied. False-positive CAD marks and the reproducibility were determined. Results: Of the 360 patients, 252 (70.0%) and 240 (66.7%) patients had 1-7 CAD marks on the initial and second mammograms, respectively. The false-positive CAD mark rate was 1.5 (1.1 for masses and 0.4 for calcifications) and 1.4 (1.0 for masses and 0.4 for calcifications) per examination in the initial and second mammograms, respectively. The reproducibility of the false-positive CAD marks was 12.0% for both mass (81/680) and microcalcification (33/278) marks. Conclusion: False-positive CAD marks were seen in approximately 70% of normal cases. However, the reproducibility was very low. Radiologists must be familiar with the findings of false-positive CAD marks, since they are very common and can increase the recall rate in screening

Reproducibility of gallbladder ejection fraction measured by fatty meal cholescintigraphy

International Nuclear Information System (INIS)

Al-Muqbel, Kusai M.; Hani, M. N. Hani; Elheis, M. A.; Al-Omari, M. H.

2010-01-01

There are conflicting data in the literature regarding the reproducibility of the gallbladder ejection fraction (GBEF) measured by fatty meal cholescintigraphy (CS). We aimed to test the reproducibility of GBEF measured by fatty meal CS. Thirty-five subjects (25 healthy volunteers and 10 patients with chronic abdominal pain) underwent fatty meal CS twice in order to measure GBEF1 and GBEF2. The healthy volunteers underwent a repeat scan within 1-13 months from the first scan. The patients underwent a repeat scan within 1-4 years from the first scan and were not found to have chronic acalculous cholecystitis (CAC). Our standard fatty meal was composed of a 60-g Snickers chocolate bar and 200 ml full-fat yogurt. The mean ± SD values for GBEF1 and GBEF2 were 52±17% and 52±16%, respectively. There was a direct linear correlation between the values of GBEF1 and GBEF2 for the subjects, with a correlation coefficient of 0.509 (p=0.002). Subgroup data analysis of the volunteer group showed that there was significant linear correlation between volunteer values of GBEF1 and GBEF2, with a correlation coefficient of 0.473 (p=0.017). Subgroup data analysis of the non-CAC patient group showed no significant correlation between patient values of GBEF1 and GBEF2, likely due to limited sample size. This study showed that fatty meal CS is a reliable test in gallbladder motility evaluation and that GBEF measured by fatty meal CS is reproducible

Reproducibility of gallbladder ejection fraction measured by fatty meal cholescintigraphy

Energy Technology Data Exchange (ETDEWEB)

Al-Muqbel, Kusai M.; Hani, M. N. Hani; Elheis, M. A.; Al-Omari, M. H. [School of Medicine, Jordan University of Science and Technology, Irbid (Jordan)

2010-12-15

There are conflicting data in the literature regarding the reproducibility of the gallbladder ejection fraction (GBEF) measured by fatty meal cholescintigraphy (CS). We aimed to test the reproducibility of GBEF measured by fatty meal CS. Thirty-five subjects (25 healthy volunteers and 10 patients with chronic abdominal pain) underwent fatty meal CS twice in order to measure GBEF1 and GBEF2. The healthy volunteers underwent a repeat scan within 1-13 months from the first scan. The patients underwent a repeat scan within 1-4 years from the first scan and were not found to have chronic acalculous cholecystitis (CAC). Our standard fatty meal was composed of a 60-g Snickers chocolate bar and 200 ml full-fat yogurt. The mean {+-} SD values for GBEF1 and GBEF2 were 52{+-}17% and 52{+-}16%, respectively. There was a direct linear correlation between the values of GBEF1 and GBEF2 for the subjects, with a correlation coefficient of 0.509 (p=0.002). Subgroup data analysis of the volunteer group showed that there was significant linear correlation between volunteer values of GBEF1 and GBEF2, with a correlation coefficient of 0.473 (p=0.017). Subgroup data analysis of the non-CAC patient group showed no significant correlation between patient values of GBEF1 and GBEF2, likely due to limited sample size. This study showed that fatty meal CS is a reliable test in gallbladder motility evaluation and that GBEF measured by fatty meal CS is reproducible

On the reproducibility of expert-operated and robotic ultrasound acquisitions.