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.

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.

Major NSSS design features of the Korean next generation reactor

International Nuclear Information System (INIS)

Kim, Insk; Kim, Dong-Su

1999-01-01

In order to meet national needs for increasing electric power generation in the Republic of Korea in the 2000s, the Korean nuclear development group (KNDG) is developing a standardized evolutionary advanced light water reactor (ALWR), the Korean Next Generation Reactor (KNGR). It is an advanced version of the successful Korean Standard Nuclear Power Plant (KSNP) design, which meets utility needs for safety enhancement, performance improvement and ease of operation and maintenance. The KNGR design starts fro the proven design concept of the currently operating KSNPs with uprated power and advanced design features required by the utility. The KNGR design is currently in the final stage of the basic design, and the paper describes the major nuclear steam supply system (NSSS) design features of the KNGR together with introduction of the KNGR development program. (author)

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.

Genetic Association of Major Depression With Atypical Features and Obesity-Related Immunometabolic Dysregulations

NARCIS (Netherlands)

Milaneschi, Yuri; Lamers, Femke; Peyrot, Wouter J; Baune, Bernhard T; Breen, Gerome; Dehghan, Abbas; Forstner, Andreas J; Grabe, Hans J; Homuth, Georg; Kan, Carol; Lewis, Cathryn M; Mullins, Niamh; Nauck, Matthias; Pistis, Giorgio; Preisig, Martin; Rivera, Margarita; Rietschel, Marcella; Streit, Fabian; Strohmaier, Jana; Teumer, Alexander; Van der Auwera, Sandra; Wray, Naomi R; Boomsma, Dorret I; Penninx, Brenda W J H

2017-01-01

Importance: The association between major depressive disorder (MDD) and obesity may stem from shared immunometabolic mechanisms particularly evident in MDD with atypical features, characterized by increased appetite and/or weight (A/W) during an active episode. Objective: To determine whether

Mining CANDELS for Tidal Features to Constrain Major Merging During Cosmic Noon

Science.gov (United States)

McIntosh, Daniel H.; Mantha, Kameswara; Ciaschi, Cody; Evan, Rubyet A.; Fries, Logan B.; Landry, Luther; Thompson, Scott E.; Snyder, Gregory; Guo, Yicheng; Ceverino, Daniel; Häuβler, Boris; Primack, Joel; Simons, Raymond C.; Zheng, Xianzhong; Cosmic Assembly Near-Infrared Deep Extragalactic Legacy Survey (CANDELS) Team

2018-01-01

The role of major merging in the rapid buildup and development of massive galaxies at z>1 remains an open question. New theories and observations suggest that non-merging processes like violent disk instabilities may be more vital than previously thought at assembling bulges, producing clumps, and inducing morphological disturbances that may be misinterpreted as the product of major merging. We will present initial results on a systematic search for hallmark tidal indicators of major merging in a complete sample of nearly 6000 massive z>1 galaxies from CANDELS (Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey), the premiere HST/WFC3 Treasury program. We have visually inspected published GALFIT F160W residual (image-model) maps and produced a comprehensive new catalog of Sersic residual characteristics based on a variety of natural features and poor-fit artifacts. Using this catalog, we find the frequency of galaxies with tidal signatures is very small in CANDELS data. Accounting for the brief time scale associated with faint transient tidal features, our preliminary finding indicates that merger fractions derived from the CANDELS morphological classification efforts are substantially overestimated. We are using the database of residual classifications as a baseline to (1) produce improved multi-component residual maps using GALFIT_M, (2) automatically extract and quantify plausible tidal indicators and substructures (clumps vs. multiple nuclei), (3) develop a new deep-learning classification pipeline to robustly identify merger indicators in imaging data, and (4) inform the systematic analyses of synthetic mock (CANDELized) images from zoom-in hydrodynamic simulations to thoroughly quantify the impacts of cosmological dimming, and calibrate the observability timescale of tidal feature detections. Our study will ultimately yield novel constraints on merger rates at z>1 and a definitive census of massive high-noon galaxies with tidal and double

Reproducibility of the World Health Organization 2008 criteria for myelodysplastic syndromes.

Science.gov (United States)

Senent, Leonor; Arenillas, Leonor; Luño, Elisa; Ruiz, Juan C; Sanz, Guillermo; Florensa, Lourdes

2013-04-01

The reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is uncertain and its assessment was the major aim of this study. The different peripheral blood and bone marrow variables required for an adequate morphological classification were blindly evaluated by four cytomorphologists in samples from 50 patients with myelodysplastic syndromes. The degree of agreement among observers was calculated using intraclass correlation coefficient and the generalized kappa statistic for multiple raters. The degree of agreement for the percentages of blasts in bone marrow and peripheral blood, ring sideroblasts in bone marrow, and erythroid, granulocytic and megakaryocytic dysplastic cells was strong (P<0.001 in all instances). After stratifying the percentages according to the categories required for the assignment of World Health Organization subtypes, the degree of agreement was not statistically significant for cases with 5-9% blasts in bone marrow (P=0.07), 0.1-1% blasts in peripheral blood (P=0.47), or percentage of erythroid dysplastic cells (P=0.49). Finally, the interobserver concordance for World Health Organization-defined subtypes showed a moderate overall agreement (P<0.001), the reproducibility being lower for cases with refractory anemia with excess of blasts type 1 (P=0.05) and refractory anemia with ring sideroblasts (P=0.09). In conclusion, the reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is acceptable but the defining criteria for blast cells and features of erythroid dysplasia need to be refined.

An Open Trial of a New Acceptance-Based Behavioral Treatment for Major Depression with Psychotic Features

Science.gov (United States)

Gaudiano, Brandon A.; Nowlan, Kathryn; Brown, Lily A.; Epstein-Lubow, Gary; Miller, Ivan W.

2013-01-01

Research suggests that cognitive and behavioral therapies produce significant benefits over medications alone in the treatment of severe, nonpsychotic major depression or primary psychotic disorders such as schizophrenia. However, previous research has not demonstrated the efficacy of psychotherapy for major depression with psychotic features. In…

Explicit signal to noise ratio in reproducing kernel Hilbert spaces

DEFF Research Database (Denmark)

Gomez-Chova, Luis; Nielsen, Allan Aasbjerg; Camps-Valls, Gustavo

2011-01-01

This paper introduces a nonlinear feature extraction method based on kernels for remote sensing data analysis. The proposed approach is based on the minimum noise fraction (MNF) transform, which maximizes the signal variance while also minimizing the estimated noise variance. We here propose...... an alternative kernel MNF (KMNF) in which the noise is explicitly estimated in the reproducing kernel Hilbert space. This enables KMNF dealing with non-linear relations between the noise and the signal features jointly. Results show that the proposed KMNF provides the most noise-free features when confronted...

European LeukemiaNet study on the reproducibility of bone marrow features in masked polycythemia vera and differentiation from essential thrombocythemia.

Science.gov (United States)

Kvasnicka, Hans Michael; Orazi, Attilio; Thiele, Juergen; Barosi, Giovanni; Bueso-Ramos, Carlos E; Vannucchi, Alessandro M; Hasserjian, Robert P; Kiladjian, Jean-Jacques; Gianelli, Umberto; Silver, Richard; Mughal, Tariq I; Barbui, Tiziano

2017-10-01

The purpose of the study was to assess consensus and interobserver agreement among an international panel of six hematopathologists regarding characterization and reproducibility of bone marrow (BM) histologic features used to diagnose early stage myeloproliferative neoplasms, in particular differentiation of so-called masked/prodromal polycythemia vera (mPV) from JAK2-mutated essential thrombocythemia (ET). The six members of the hematopathology panel evaluated 98 BM specimens independently and in a blinded fashion without knowledge of clinical data. The specimens included 48 cases of mPV according to the originally published hemoglobin threshold values for this entity (male: 16.0-18.4 g/dL, female: 15.0-16.4 g/dL), 31 cases with overt PV according to the updated 2016 WHO criteria, and 19 control cases. The latter group included cases of JAK2-mutated ET, primary myelofibrosis, myelodysplastic syndrome, and various reactive conditions. Inter-rater agreement between the panelists was very high (overall agreement 92.6%, kappa 0.812), particularly with respect to separating mPV from ET. Virtually all cases of mPV were correctly classified as PV according to their BM morphology. In conclusion, a central blinded review of histology slides by six hematopathologists demonstrated that highly reproducible specific histological pattern characterize PV and confirmed the notion that there are no significant differences between mPV and overt PV in relation to BM morphology. © 2017 Wiley Periodicals, Inc.

Brief Report: Major Depressive Disorder with Psychotic Features in Williams Syndrome--A Case Series

Science.gov (United States)

Valdes, Francisca; Keary, Christopher J.; Mullett, Jennifer E.; Palumbo, Michelle L.; Waxler, Jessica L.; Pober, Barbara R.; McDougle, Christopher J.

2018-01-01

Descriptions of individuals with Williams syndrome (WS) and co-morbid major depressive disorder (MDD) with psychotic features have not appeared in the literature. In addition to reviewing previous reports of psychotic symptoms in persons with WS, this paper introduces clinical histories and therapeutic management strategies for three previously…

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

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

A Sparsity-Promoted Method Based on Majorization-Minimization for Weak Fault Feature Enhancement.

Science.gov (United States)

Ren, Bangyue; Hao, Yansong; Wang, Huaqing; Song, Liuyang; Tang, Gang; Yuan, Hongfang

2018-03-28

Fault transient impulses induced by faulty components in rotating machinery usually contain substantial interference. Fault features are comparatively weak in the initial fault stage, which renders fault diagnosis more difficult. In this case, a sparse representation method based on the Majorzation-Minimization (MM) algorithm is proposed to enhance weak fault features and extract the features from strong background noise. However, the traditional MM algorithm suffers from two issues, which are the choice of sparse basis and complicated calculations. To address these challenges, a modified MM algorithm is proposed in which a sparse optimization objective function is designed firstly. Inspired by the Basis Pursuit (BP) model, the optimization function integrates an impulsive feature-preserving factor and a penalty function factor. Second, a modified Majorization iterative method is applied to address the convex optimization problem of the designed function. A series of sparse coefficients can be achieved through iterating, which only contain transient components. It is noteworthy that there is no need to select the sparse basis in the proposed iterative method because it is fixed as a unit matrix. Then the reconstruction step is omitted, which can significantly increase detection efficiency. Eventually, envelope analysis of the sparse coefficients is performed to extract weak fault features. Simulated and experimental signals including bearings and gearboxes are employed to validate the effectiveness of the proposed method. In addition, comparisons are made to prove that the proposed method outperforms the traditional MM algorithm in terms of detection results and efficiency.

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.

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

Science.gov (United States)

Yang, Tao; Zhang, Feipeng; Yardımcı, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, Qunhua

2017-11-01

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach. © 2017 Yang et al.; Published by Cold Spring Harbor Laboratory Press.

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?

Risperidone, quetiapine, and olanzapine adjunctive treatments in major depression with psychotic features: a comparative study

Directory of Open Access Journals (Sweden)

Gabriel A

2013-04-01

Full Text Available A Gabriel Departments of Psychiatry and Community Health Sciences, University of Calgary, Calgary, AB, Canada Objectives: The purpose of this study was to compare the effectiveness of novel antipsychotics in the treatment of psychotic depression. Method: Consecutive patients who were admitted (n = 51 with a confirmed diagnosis of major depression with psychotic features (delusions or hallucinations or both participated in this open-label, naturalistic study. All patients were treated with selective serotonin reuptake inhibitors (SSRIs and serotonin–norepinephrine reuptake inhibitors (SNRIs (citalopram or venlafaxine extended release [XR], and atypical antipsychotic agents were added, as tolerated, during the first week of initiating the citalopram or venlafaxine. There were patients (n = 16 who received risperidone, who received quetiapine (n = 20, and who received olanzapine (n = 15, as an adjunctive treatment to either citalopram or venlafaxine for at least 8 weeks. Outcome measures included the Clinical Global Impression-Severity subscale (CGI-S, as the primary outcome measure, as well as the Hamilton Rating Scale for Depression-21 item (HAM-D21 and the Brief Psychiatric Rating Scale (BPRS. Tolerance to treatments and weight changes were monitored over the period of the trial. Results: All patients completed the trial with no drop outs. At 8 weeks, there was a statistically significant (P 0.01 in the olanzapine group. Conclusion: Quetiapine, risperidone, and olanzapine, given as adjunctive treatment with SSRIS or SNRIs can significantly and equally improve depressive and psychotic symptoms, in the short-term treatment of major depression with psychotic features. The author recommends that large controlled trials be conducted to examine the differences in long-term efficacy and tolerance between the atypical antipsychotic agents, in the treatment of major depression with or without psychotic features. Keywords: depression, novels

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.

Sensitivity and specificity of plain radiographic features of peripheral enthesopathy at major sites in psoriatic arthritis

Energy Technology Data Exchange (ETDEWEB)

Helliwell, P.S. [University of Leeds, Academic Unit of Musculoskeletal and Rehabilitation Medicine, Leeds (United Kingdom); Porter, G. [Airedale Hospital NHS Trust, Keighley, West Yorkshire (United Kingdom)

2007-11-15

It has been proposed that the defining difference between rheumatoid arthritis and spondyloarthropathy (including psoriatic arthritis) is the initial pathological lesion where the emphasis in psoriatic arthritis is on the enthesis and in rheumatoid arthritis on the synovium. Classical radiological descriptions of seronegative spondyloarthropathy include enthesopathy at major entheseal insertions characterised by erosions and exuberant new bone formation. In this study, the plain radiographic features of spondyloarthropathy are compared between psoriatic arthritis, other spondyloarthropathies and rheumatoid arthritis. The CASPAR study collected clinical, radiological and laboratory data on 588 patients with physician diagnosed psoriatic arthritis and 525 controls with other inflammatory arthritis, 70% of which had rheumatoid arthritis. Plain radiographs of the pelvis and heels were part of the study protocol, although radiographs of other potential entheseal sites such as the knee, elbow and shoulder, were interpreted if available. All radiographs were read blind by two observers working in tandem. Significant differences in entheseal erosion and entheseal new bone formation were found between psoriatic arthritis, ankylosing spondylitis, undifferentiated spondyloarthropathy, rheumatoid arthritis and other diagnoses (entheseal erosion, chi-squared 20.8, p = 0.008; entheseal new bone formation, chi-squared 24.5, p = 0.001). These differences were mainly due to a higher proportion of these features in ankylosing spondylitis. No differences in the plain radiographic features of enthesopathy were found between psoriatic arthritis and rheumatoid arthritis except in the case of entheseal new bone formation at sites of attachment of inguinal ligament, sartorius and rectus femoris muscles to the ilium (OR 3.01, 95% CI 1.13-8.02). Very few subjects with symptomatic heel involvement had radiographic changes and minimal differences were found between those with and without

Sensitivity and specificity of plain radiographic features of peripheral enthesopathy at major sites in psoriatic arthritis

International Nuclear Information System (INIS)

Helliwell, P.S.; Porter, G.

2007-01-01

It has been proposed that the defining difference between rheumatoid arthritis and spondyloarthropathy (including psoriatic arthritis) is the initial pathological lesion where the emphasis in psoriatic arthritis is on the enthesis and in rheumatoid arthritis on the synovium. Classical radiological descriptions of seronegative spondyloarthropathy include enthesopathy at major entheseal insertions characterised by erosions and exuberant new bone formation. In this study, the plain radiographic features of spondyloarthropathy are compared between psoriatic arthritis, other spondyloarthropathies and rheumatoid arthritis. The CASPAR study collected clinical, radiological and laboratory data on 588 patients with physician diagnosed psoriatic arthritis and 525 controls with other inflammatory arthritis, 70% of which had rheumatoid arthritis. Plain radiographs of the pelvis and heels were part of the study protocol, although radiographs of other potential entheseal sites such as the knee, elbow and shoulder, were interpreted if available. All radiographs were read blind by two observers working in tandem. Significant differences in entheseal erosion and entheseal new bone formation were found between psoriatic arthritis, ankylosing spondylitis, undifferentiated spondyloarthropathy, rheumatoid arthritis and other diagnoses (entheseal erosion, chi-squared 20.8, p = 0.008; entheseal new bone formation, chi-squared 24.5, p = 0.001). These differences were mainly due to a higher proportion of these features in ankylosing spondylitis. No differences in the plain radiographic features of enthesopathy were found between psoriatic arthritis and rheumatoid arthritis except in the case of entheseal new bone formation at sites of attachment of inguinal ligament, sartorius and rectus femoris muscles to the ilium (OR 3.01, 95% CI 1.13-8.02). Very few subjects with symptomatic heel involvement had radiographic changes and minimal differences were found between those with and without

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....

Temporal feature integration for music genre classification

DEFF Research Database (Denmark)

Meng, Anders; Ahrendt, Peter; Larsen, Jan

2007-01-01

, but they capture neither the temporal dynamics nor dependencies among the individual feature dimensions. Here, a multivariate autoregressive feature model is proposed to solve this problem for music genre classification. This model gives two different feature sets, the diagonal autoregressive (DAR......) and multivariate autoregressive (MAR) features which are compared against the baseline mean-variance as well as two other temporal feature integration techniques. Reproducibility in performance ranking of temporal feature integration methods were demonstrated using two data sets with five and eleven music genres...

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

Association of Xerostomia and Ultrasonographic Features of the Major Salivary Glands After Radioactive Iodine Ablation for Papillary Thyroid Carcinoma.

Science.gov (United States)

Soo Roh, Sang; Wook Kim, Dong; Jin Baek, Hye

2016-11-01

The objective of this study is to evaluate the association between xerostomia and sonographic features of the major salivary glands after patients undergo radioactive iodine ablation (RIA) for papillary thyroid carcinoma (PTC). The study included 256 consecutive patients who underwent total thyroidectomy, RIA, and neck ultrasound examinations. Changes in the ultrasound features of the parotid and submandibular glands after RIA were evaluated retrospectively by a single radiologist, on the basis of direct comparison of sonograms obtained before and after RIA. Clinical data, including the presence of xerostomia, were investigated retrospectively by the same radiologist via a review of the electronic medical records. For 111 of the 256 patients (43.4%), ultrasound examination revealed changes in the major salivary glands after RIA. The presence of xerostomia was undetermined in 85 of the 256 patients. Among the remaining 171 patients, the frequency of xerostomia was 36.8% (63/171). When patients with xerostomia were compared with those without xerostomia, no statistically significant differences in patient sex and age, the dose of RIA received, or the number of RIA sessions were noted (p > 0.05). Considering the changes in the ultrasound features of the major salivary glands after RIA, no statistically significant association was found between xerostomia and the number of involved major salivary glands or the presence of an involved submandibular gland (p > 0.05). In this study, ultrasound was unhelpful for evaluating xerostomia after RIA in patients with PTC.

Perfectionistic Self-Presentation and Suicide in a Young Woman with Major Depression and Psychotic Features

Science.gov (United States)

Flett, Gordon L.; Hewitt, Paul L.

2014-01-01

A woman in her midtwenties with a history of major depressive disorder and a recent major depressive episode with mood-congruent psychotic features died by suicide. Two weeks before her death, she demonstrated exceptional elevations on the nondisplay of imperfection factor of Hewitt and Flett's Perfectionistic Self-Presentation Scale. Perfectionism and especially perfectionistic self-presentation have been strongly associated with suicide across several populations, accounting for unique variance in suicidality beyond depression and hopelessness. Yet interpersonal facets of perfectionism are not recognized as clinical risk factors for suicide. There is also a paucity of research on perfectionism in relation to psychotic symptoms. This case account illustrates the role of perfectionistic self-presentation in suicides that occur seemingly without warning and, to our knowledge, this is the first examination of perfectionistic self-presentation and suicide in a case where psychotic features occurred. This study, though single case-based, draws attention to perfectionism and perfectionistic self-presentation and their potential roles in suicide, especially when accompanied by other risk factors. Future research in this area may elucidate the role of perfectionism in suicide, singularly and in the context of a comprehensive clinical risk assessment, demonstrating whether perfectionism confers information about suicide risk beyond known clinical risk factors. PMID:25328746

Perfectionistic Self-Presentation and Suicide in a Young Woman with Major Depression and Psychotic Features

Directory of Open Access Journals (Sweden)

Sabrina Hassan

2014-01-01

Full Text Available A woman in her midtwenties with a history of major depressive disorder and a recent major depressive episode with mood-congruent psychotic features died by suicide. Two weeks before her death, she demonstrated exceptional elevations on the nondisplay of imperfection factor of Hewitt and Flett’s Perfectionistic Self-Presentation Scale. Perfectionism and especially perfectionistic self-presentation have been strongly associated with suicide across several populations, accounting for unique variance in suicidality beyond depression and hopelessness. Yet interpersonal facets of perfectionism are not recognized as clinical risk factors for suicide. There is also a paucity of research on perfectionism in relation to psychotic symptoms. This case account illustrates the role of perfectionistic self-presentation in suicides that occur seemingly without warning and, to our knowledge, this is the first examination of perfectionistic self-presentation and suicide in a case where psychotic features occurred. This study, though single case-based, draws attention to perfectionism and perfectionistic self-presentation and their potential roles in suicide, especially when accompanied by other risk factors. Future research in this area may elucidate the role of perfectionism in suicide, singularly and in the context of a comprehensive clinical risk assessment, demonstrating whether perfectionism confers information about suicide risk beyond known clinical risk factors.

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.

Reproducibility in Research: Systems, Infrastructure, Culture

Directory of Open Access Journals (Sweden)

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.

Mixed features in patients with a major depressive episode: the BRIDGE-II-MIX study.

Science.gov (United States)

Perugi, Giulio; Angst, Jules; Azorin, Jean-Michel; Bowden, Charles L; Mosolov, Sergey; Reis, Joao; Vieta, Eduard; Young, Allan H

2015-03-01

To estimate the frequency of mixed states in patients diagnosed with major depressive episode (MDE) according to conceptually different definitions and to compare their clinical validity. This multicenter, multinational cross-sectional Bipolar Disorders: Improving Diagnosis, Guidance and Education (BRIDGE)-II-MIX study enrolled 2,811 adult patients experiencing an MDE. Data were collected per protocol on sociodemographic variables, current and past psychiatric symptoms, and clinical variables that are risk factors for bipolar disorder. The frequency of mixed features was determined by applying both DSM-5 criteria and a priori described Research-Based Diagnostic Criteria (RBDC). Clinical variables associated with mixed features were assessed using logistic regression. Overall, 212 patients (7.5%) fulfilled DSM-5 criteria for MDE with mixed features (DSM-5-MXS), and 818 patients (29.1%) fulfilled diagnostic criteria for a predefined RBDC depressive mixed state (RBDC-MXS). The most frequent manic/hypomanic symptoms were irritable mood (32.6%), emotional/mood lability (29.8%), distractibility (24.4%), psychomotor agitation (16.1%), impulsivity (14.5%), aggression (14.2%), racing thoughts (11.8%), and pressure to keep talking (11.4%). Euphoria (4.6%), grandiosity (3.7%), and hypersexuality (2.6%) were less represented. In multivariate logistic regression analysis, RBDC-MXS was associated with the largest number of variables including diagnosis of bipolar disorder, family history of mania, lifetime suicide attempts, duration of the current episode > 1 month, atypical features, early onset, history of antidepressant-induced mania/hypomania, and lifetime comorbidity with anxiety, alcohol and substance use disorders, attention-deficit/hyperactivity disorder, and borderline personality disorder. Depressive mixed state, defined as the presence of 3 or more manic/hypomanic features, was present in around one-third of patients experiencing an MDE. The valid symptom, illness

The relationship between uranium distribution and some major crustal features in Canada

International Nuclear Information System (INIS)

Darnley, A.G.

1982-01-01

The availability of reconnaissance scale geochemical maps for large areas of Canada enables spatial associations between major crustal structures and surface uranium content to be identified. Maps of the distribution of uranium for an area greater than 2 million km 2 compiled from airborne gamma-ray spectrometry data are supplemented by maps for uranium, based on stream and lake sediment and some bore hole sampling. These are examined in relation to gravity, aeromagnetic and geological maps. The radioelement distribution can be related in detail to exposed bedrock and surface geology, but in addition there is evidence of the control of uranium distribution by major structural features which are marked by granitoids containing elevated levels of radioelements; several of these granitoids are associated with large negative Bouguer gravity anomalies. The distribution of such granitoids appears to be related to 'megashears', as in the case of the South Mountain batholith in Nova Scotia, or zones of tension. A belt of uranium enrichment, the Athabasca axis which is characterized by uraniferous granitoids with negative Bouguer gravity anomalies and associated tension faulting extends 2500 km northeastward from Edmonton, Alberta to the Melville Peninsula. This structure passes under the Athabasca basin which contains many large uranium deposits. (author)

Melancholic features and hostility are associated with suicidality risk in Asian patients with major depressive disorder.

Science.gov (United States)

Jeon, Hong Jin; Peng, Daihui; Chua, Hong Choon; Srisurapanont, Manit; Fava, Maurizio; Bae, Jae-Nam; Man Chang, Sung; Hong, Jin Pyo

2013-06-01

Suicide rates are higher in East-Asians than other populations, and especially high in Koreans. However, little is known about suicidality risk and melancholic features in Asian patients with major depressive disorder (MDD). Drug-free MDD outpatients were included from 13 centers across five ethnicities consisting of Chinese (n=290), Korean (n=101), Thai (n=102), Indian (n=27), and Malay (n=27). All were interviewed using the Mini-International Neuropsychiatric Interview (M.I.N.I.), the Montgomery-Åsberg Depression Rating Scale (MADRS), and the Symptoms Checklist 90-Revised (SCL-90-R). Of 547 subjects, 177 MDD patients showed melancholic features (32.4%). These melancholic MDD patients revealed significantly higher suicidality risk (pdepression (pdifference in higher hostility. Adjusted odds ratios of melancholic features and hostility for moderate to high suicidality risk were 1.79 (95% CI=1.15-2.79) and 2.45 (95% CI=1.37-4.38), after adjusting for age, sex, education years, and depression severity. Post-hoc analyses showed that suicidality risk was higher in Korean and Chinese than that of Thai, Indian and Malay in MDD subjects with melancholic features, although depression severity showed no significant differences among the ethnicities. Suicidality risk is associated with both melancholic features and hostility and it shows cross-ethnic differences in Asian MDD patients, independent of depression severity. Copyright © 2013 Elsevier B.V. All rights reserved.

The impact of educational status on the clinical features of major depressive disorder among Chinese women

Science.gov (United States)

Gan, Zhaoyu; Li, Yihan; Xie, Dong; Shao, Chunhong; Yang, Fuzhong; Shen, Yuan; Zhang, Ning; Zhang, Guanghua; Tian, Tian; Yin, Aihua; Chen, Ce; Liu, Jun; Tang, Chunling; Zhang, Zhuoqiu; Liu, Jia; Sang, Wenhua; Wang, Xumei; Liu, Tiebang; Wei, Qinling; Xu, Yong; Sun, Ling; Wang, Sisi; Li, Chang; Hu, Chunmei; Cui, Yanping; Liu, Ying; Li, Ying; Zhao, Xiaochuan; Zhang, Lan; Sun, Lixin; Chen, Yunchun; Zhang, Yueying; Ning, Yuping; Shi, Shenxun; Chen, Yiping; Kendler, Kenneth S.; Flint, Jonathan; Zhang, Jinbei

2012-01-01

Background Years of education are inversely related to the prevalence of major depressive disorder (MDD), but the relationship between the clinical features of MDD and educational status is poorly understood. We investigated this in 1970 Chinese women with recurrent MDD identified in a clinical setting. Methods Clinical and demographic features were obtained from 1970 Han Chinese women with DSM-IV major depression between 30 and 60 years of age across China. Analysis of linear, logistic and multiple logistic regression models were used to determine the association between educational level and clinical features of MDD. Results Subjects with more years of education are more likely to have MDD, with an odds ratio of 1.14 for those with more than ten years. Low educational status is not associated with an increase in the number of episodes, nor with increased rates of co-morbidity with anxiety disorders. Education impacts differentially on the symptoms of depression: lower educational attainment is associated with more biological symptoms and increased suicidal ideation and plans to commit suicide. Limitations Findings may not generalize to males or to other patient populations. Since the threshold for treatment seeking differs as a function of education there may an ascertainment bias in the sample. Conclusions The relationship between symptoms of MDD and educational status in Chinese women is unexpectedly complex. Our findings are inconsistent with the simple hypothesis from European and US reports that low levels of educational attainment increase the risk and severity of MDD. PMID:21824664

The impact of educational status on the clinical features of major depressive disorder among Chinese women.

Science.gov (United States)

Gan, Zhaoyu; Li, Yihan; Xie, Dong; Shao, Chunhong; Yang, Fuzhong; Shen, Yuan; Zhang, Ning; Zhang, Guanghua; Tian, Tian; Yin, Aihua; Chen, Ce; Liu, Jun; Tang, Chunling; Zhang, Zhuoqiu; Liu, Jia; Sang, Wenhua; Wang, Xumei; Liu, Tiebang; Wei, Qinling; Xu, Yong; Sun, Ling; Wang, Sisi; Li, Chang; Hu, Chunmei; Cui, Yanping; Liu, Ying; Li, Ying; Zhao, Xiaochuan; Zhang, Lan; Sun, Lixin; Chen, Yunchun; Zhang, Yueying; Ning, Yuping; Shi, Shenxun; Chen, Yiping; Kendler, Kenneth S; Flint, Jonathan; Zhang, Jinbei

2012-02-01

Years of education are inversely related to the prevalence of major depressive disorder (MDD), but the relationship between the clinical features of MDD and educational status is poorly understood. We investigated this in 1970 Chinese women with recurrent MDD identified in a clinical setting. Clinical and demographic features were obtained from 1970 Han Chinese women with DSM-IV major depression between 30 and 60 years of age across China. Analysis of linear, logistic and multiple logistic regression models were used to determine the association between educational level and clinical features of MDD. Subjects with more years of education are more likely to have MDD, with an odds ratio of 1.14 for those with more than ten years. Low educational status is not associated with an increase in the number of episodes, nor with increased rates of co-morbidity with anxiety disorders. Education impacts differentially on the symptoms of depression: lower educational attainment is associated with more biological symptoms and increased suicidal ideation and plans to commit suicide. Findings may not generalize to males or to other patient populations. Since the threshold for treatment seeking differs as a function of education there may an ascertainment bias in the sample. The relationship between symptoms of MDD and educational status in Chinese women is unexpectedly complex. Our findings are inconsistent with the simple hypothesis from European and US reports that low levels of educational attainment increase the risk and severity of MDD. Copyright © 2011 Elsevier B.V. All rights reserved.

Investigation about the thermal features of the ovens used for thermoluminescence

International Nuclear Information System (INIS)

Scarpa, G.; Caporali, C.; Moscati, M.

1991-02-01

The present paper reports the results of an investigation carried out by the PAS-FIBI-DOSIBIO laboratory (ENEA, Casaccia, Roma) about the thermal features of the ovens used for annealing treatments of TL dosemeters. A total number of 45 commercial ovens and muffle furnaces were studied. belonging to 24 Italian Health Physics laboratories. The investigation has shown that the majority of the ovens do not possess a degree of accuracy, stability, uniformity and reproducibility suitable for their use in the field of thermoluminescence dosimetry. Practical suggestions are also given in order to reduce the effects of some of the negative characteristics found in most ovens. (author)

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.

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.

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...

Measures of the DSM-5 mixed-features specifier of major depressive disorder.

Science.gov (United States)

Zimmerman, Mark

2017-04-01

During the past two decades, a number of studies have found that depressed patients frequently have manic symptoms intermixed with depressive symptoms. While the frequency of mixed syndromes are more common in bipolar than in unipolar depressives, mixed states are also common in patients with major depressive disorder. The admixture of symptoms may be evident when depressed patients present for treatment, or they may emerge during ongoing treatment. In some patients, treatment with antidepressant medication might precipitate the emergence of mixed states. It would therefore be useful to systematically inquire into the presence of manic/hypomanic symptoms in depressed patients. We can anticipate that increased attention will likely be given to mixed depression because of changes in the DSM-5. In the present article, I review instruments that have been utilized to assess the presence and severity of manic symptoms and therefore could be potentially used to identify the DSM-5 mixed-features specifier in depressed patients and to evaluate the course and outcome of treatment. In choosing which measure to use, clinicians and researchers should consider whether the measure assesses both depression and mania/hypomania, assesses all or only some of the DSM-5 criteria for the mixed-features specifier, or assesses manic/hypomanic symptoms that are not part of the DSM-5 definition. Feasibility, more so than reliability and validity, will likely determine whether these measures are incorporated into routine clinical practice.

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...

Genetic Association of Major Depression With Atypical Features and Obesity-Related Immunometabolic Dysregulations

DEFF Research Database (Denmark)

Milaneschi, Yuri; Lamers, Femke; Peyrot, Wouter J

2017-01-01

Importance: The association between major depressive disorder (MDD) and obesity may stem from shared immunometabolic mechanisms particularly evident in MDD with atypical features, characterized by increased appetite and/or weight (A/W) during an active episode. Objective: To determine whether...... subgroups of patients with MDD stratified according to the A/W criterion had a different degree of genetic overlap with obesity-related traits (body mass index [BMI] and levels of C-reactive protein [CRP] and leptin). Design, Setting, and Patients: This multicenter study assembled genome-wide genotypic...... between atypical depressive symptoms and obesity-related traits may arise from shared pathophysiologic mechanisms in patients with MDD. Development of treatments effectively targeting immunometabolic dysregulations may benefit patients with depression and obesity, both syndromes with important disability....

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.

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

Extraction of auditory features and elicitation of attributes for the assessment of multichannel reproduced sound

DEFF Research Database (Denmark)

Choisel, Sylvain; Wickelmaier, Florian Maria

2006-01-01

), subjects were asked to directly assign verbal labels to the features when encountering them, and to subsequently rate the sounds on the scales thus obtained. The second method required the subjects to consistently use the perceptually relevant features in triadic comparisons, without having to assign them...

Predictive brain networks for major depression in a semi-multimodal fusion hierarchical feature reduction framework.

Science.gov (United States)

Yang, Jie; Yin, Yingying; Zhang, Zuping; Long, Jun; Dong, Jian; Zhang, Yuqun; Xu, Zhi; Li, Lei; Liu, Jie; Yuan, Yonggui

2018-02-05

Major depressive disorder (MDD) is characterized by dysregulation of distributed structural and functional networks. It is now recognized that structural and functional networks are related at multiple temporal scales. The recent emergence of multimodal fusion methods has made it possible to comprehensively and systematically investigate brain networks and thereby provide essential information for influencing disease diagnosis and prognosis. However, such investigations are hampered by the inconsistent dimensionality features between structural and functional networks. Thus, a semi-multimodal fusion hierarchical feature reduction framework is proposed. Feature reduction is a vital procedure in classification that can be used to eliminate irrelevant and redundant information and thereby improve the accuracy of disease diagnosis. Our proposed framework primarily consists of two steps. The first step considers the connection distances in both structural and functional networks between MDD and healthy control (HC) groups. By adding a constraint based on sparsity regularization, the second step fully utilizes the inter-relationship between the two modalities. However, in contrast to conventional multi-modality multi-task methods, the structural networks were considered to play only a subsidiary role in feature reduction and were not included in the following classification. The proposed method achieved a classification accuracy, specificity, sensitivity, and area under the curve of 84.91%, 88.6%, 81.29%, and 0.91, respectively. Moreover, the frontal-limbic system contributed the most to disease diagnosis. Importantly, by taking full advantage of the complementary information from multimodal neuroimaging data, the selected consensus connections may be highly reliable biomarkers of MDD. Copyright © 2017 Elsevier B.V. All rights reserved.

Impact of SLA assimilation in the Sicily Channel Regional Model: model skills and mesoscale features

Directory of Open Access Journals (Sweden)

A. Olita

2012-07-01

Full Text Available The impact of the assimilation of MyOcean sea level anomalies along-track data on the analyses of the Sicily Channel Regional Model was studied. The numerical model has a resolution of 1/32° degrees and is capable to reproduce mesoscale and sub-mesoscale features. The impact of the SLA assimilation is studied by comparing a simulation (SIM, which does not assimilate data with an analysis (AN assimilating SLA along-track multi-mission data produced in the framework of MyOcean project. The quality of the analysis was evaluated by computing RMSE of the misfits between analysis background and observations (sea level before assimilation. A qualitative evaluation of the ability of the analyses to reproduce mesoscale structures is accomplished by comparing model results with ocean colour and SST satellite data, able to detect such features on the ocean surface. CTD profiles allowed to evaluate the impact of the SLA assimilation along the water column. We found a significant improvement for AN solution in terms of SLA RMSE with respect to SIM (the averaged RMSE of AN SLA misfits over 2 years is about 0.5 cm smaller than SIM. Comparison with CTD data shows a questionable improvement produced by the assimilation process in terms of vertical features: AN is better in temperature while for salinity it gets worse than SIM at the surface. This suggests that a better a-priori description of the vertical error covariances would be desirable. The qualitative comparison of simulation and analyses with synoptic satellite independent data proves that SLA assimilation allows to correctly reproduce some dynamical features (above all the circulation in the Ionian portion of the domain and mesoscale structures otherwise misplaced or neglected by SIM. Such mesoscale changes also infer that the eddy momentum fluxes (i.e. Reynolds stresses show major changes in the Ionian area. Changes in Reynolds stresses reflect a different pumping of eastward momentum from the eddy to

Validity and reproducibility of a food frequency questionnaire for dietary factors related to colorectal cancer

OpenAIRE

Tollosa, Daniel Nigusse; Van Camp, John; Huybrechts, Inge; Huybregts, Lieven; Van Loco, Joris; De Smet, Stefaan; Sterck, Ellen; Rabai, Celine; Van Hecke, Thomas; Vanhaecke, Lynn; Vossen, Els; Peeters, Marc; Lachat, Carl

2017-01-01

Abstract: 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 asses...

Construction of Individual Morphological Brain Networks with Multiple Morphometric Features

Directory of Open Access Journals (Sweden)

Chunlan Yang

2017-04-01

Full Text Available In recent years, researchers have increased attentions to the morphological brain network, which is generally constructed by measuring the mathematical correlation across regions using a certain morphometric feature, such as regional cortical thickness and voxel intensity. However, cerebral structure can be characterized by various factors, such as regional volume, surface area, and curvature. Moreover, most of the morphological brain networks are population-based, which has limitations in the investigations of individual difference and clinical applications. Hence, we have extended previous studies by proposing a novel method for realizing the construction of an individual-based morphological brain network through a combination of multiple morphometric features. In particular, interregional connections are estimated using our newly introduced feature vectors, namely, the Pearson correlation coefficient of the concatenation of seven morphometric features. Experiments were performed on a healthy cohort of 55 subjects (24 males aged from 20 to 29 and 31 females aged from 20 to 28 each scanned twice, and reproducibility was evaluated through test–retest reliability. The robustness of morphometric features was measured firstly to select the more reproducible features to form the connectomes. Then the topological properties were analyzed and compared with previous reports of different modalities. Small-worldness was observed in all the subjects at the range of the entire network sparsity (20–40%, and configurations were comparable with previous findings at the sparsity of 23%. The spatial distributions of the hub were found to be significantly influenced by the individual variances, and the hubs obtained by averaging across subjects and sparsities showed correspondence with previous reports. The intraclass coefficient of graphic properties (clustering coefficient = 0.83, characteristic path length = 0.81, betweenness centrality = 0.78 indicates

Validity and reproducibility of a food frequency questionnaire for dietary factors related to colorectal cancer

OpenAIRE

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

2017-01-01

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 co...

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.

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

High C-Reactive Protein Predicts Delirium Incidence, Duration, and Feature Severity After Major Noncardiac Surgery.

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Vasunilashorn, Sarinnapha M; Dillon, Simon T; Inouye, Sharon K; Ngo, Long H; Fong, Tamara G; Jones, Richard N; Travison, Thomas G; Schmitt, Eva M; Alsop, David C; Freedman, Steven D; Arnold, Steven E; Metzger, Eran D; Libermann, Towia A; Marcantonio, Edward R

2017-08-01

To examine associations between the inflammatory marker C-reactive protein (CRP) measured preoperatively and on postoperative day 2 (POD2) and delirium incidence, duration, and feature severity. Prospective cohort study. Two academic medical centers. Adults aged 70 and older undergoing major noncardiac surgery (N = 560). Plasma CRP was measured using enzyme-linked immunosorbent assay. Delirium was assessed from Confusion Assessment Method (CAM) interviews and chart review. Delirium duration was measured according to number of hospital days with delirium. Delirium feature severity was defined as the sum of CAM-Severity (CAM-S) scores on all postoperative hospital days. Generalized linear models were used to examine independent associations between CRP (preoperatively and POD2 separately) and delirium incidence, duration, and feature severity; prolonged hospital length of stay (LOS, >5 days); and discharge disposition. Postoperative delirium occurred in 24% of participants, 12% had 2 or more delirium days, and the mean ± standard deviation sum CAM-S was 9.3 ± 11.4. After adjusting for age, sex, surgery type, anesthesia route, medical comorbidities, and postoperative infectious complications, participants with preoperative CRP of 3 mg/L or greater had a risk of delirium that was 1.5 times as great (95% confidence interval (CI) = 1.1-2.1) as that of those with CRP less than 3 mg/L, 0.4 more delirium days (P delirium (3.6 CAM-S points higher, P delirium (95% CI = 1.0-2.4) as those in the lowest quartile (≤127.53 mg/L), had 0.2 more delirium days (P delirium (4.5 CAM-S points higher, P delirium incidence, duration, and feature severity. CRP may be useful to identify individuals who are at risk of developing delirium. © 2017, Copyright the Authors Journal compilation © 2017, The American Geriatrics Society.

Extraction of auditory features and elicitation of attributes for the assessment of multi-channel reproduced sound

DEFF Research Database (Denmark)

Choisel, Sylvain; Wickelmaier, Florian Maria

2005-01-01

), subjects were asked to directly assign verbal labels to the features when encountering them and to subsequently rate the sounds on the scales thus obtained. The second method requires the subjects to consistently identify the perceptually relevant features before assigning them a verbal label. Under...

Extraction of auditory features and elicitation of attributes for the assessment of multi-channel reproduced sound

DEFF Research Database (Denmark)

Choisel, Sylvain; Wickelmaier, Florian

2005-01-01

), subjects were asked to directly assign verbal labels to the features when encountering them, and to subsequently rate the sounds on the scales thus obtained. The second method requires the subjects to consistently identify the perceptually relevant features before assigning them a verbal label. Under...

White matter abnormalities in major depressive disorder with melancholic and atypical features: A diffusion tensor imaging study.

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Ota, Miho; Noda, Takamasa; Sato, Noriko; Hattori, Kotaro; Hori, Hiroaki; Sasayama, Daimei; Teraishi, Toshiya; Nagashima, Anna; Obu, Satoko; Higuchi, Teruhiko; Kunugi, Hiroshi

2015-06-01

The DSM-IV recognizes some subtypes of major depressive disorder (MDD). It is known that the effectiveness of antidepressants differs among the MDD subtypes, and thus the differentiation of the subtypes is important. However, little is known as to structural brain changes in MDD with atypical features (aMDD) in comparison with MDD with melancholic features (mMDD), which prompted us to examine possible differences in white matter integrity assessed with diffusion tensor imaging (DTI) between these two subtypes. Subjects were 21 patients with mMDD, 24 with aMDD, and 37 age- and sex-matched healthy volunteers whose DTI data were obtained by 1.5 tesla magnetic resonance imaging. We compared fractional anisotropy and mean diffusivity value derived from DTI data on a voxel-by-voxel basis among the two diagnostic groups and healthy subjects. There were significant decreases of fractional anisotropy and increases of mean diffusivity in patients with MDD compared with healthy subjects in the corpus callosum, inferior fronto-occipital fasciculus, and left superior longitudinal fasciculus. However, we detected no significant difference in any brain region between mMDD and aMDD. Our results suggest that patients with MDD had reduced white matter integrity in some regions; however, there was no major difference between aMDD and mMDD. © 2014 The Authors. Psychiatry and Clinical Neurosciences © 2014 Japanese Society of Psychiatry and Neurology.

Dark blood versus bright blood T2* acquisition in cardiovascular magnetic resonance (CMR) for thalassaemia major (TM) patients: Evaluation of feasibility, reproducibility and image quality

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Liguori, Carlo, E-mail: c.liguori@unicampus.it [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Di Giampietro, Ilenia; Pitocco, Francesca; De Vivo, Aldo Eros [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Schena, Emiliano [Unit of Measurements and Biomedical Instrumentation, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Mortato, Luca [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy); Pirro, Federica [Department of Biomaging and Radiological Sciences, Catholic University of Sacred Herart, Largo A. Gemelli 1, 00135 Rome (Italy); Cianciulli, Paolo [Thalassemia Unit, Ospedale Sant Eugenio, Piazzale dell’Umanesimo 10, 00143 Rome (Italy); Zobel, Bruno Beomonte [Department of Diagnostic Imaging, Campus Bio Medico University, via Alvaro del Portillo 200, 00128 Rome (Italy)

2014-01-15

Objectives: To compare the effectiveness of dark blood (DB) versus bright blood (BB) sequences. To assess the intra and inter-observer variability and inter-study reproducibility between BB versus DB. To evaluate image quality level in the two sequences. Methods: In a setting of 138 patients we performed CMR using cardiac gated Gradient-multiecho single breath-hold BB and DB sequences in the middle ventricular septum. Each acquisition was repeated during the same exam. Truncation method was used to account for background noise. Image quality (IQ) was assessed using a 5 point grading scale and image analysis was conducted by 2 experienced observers. Results: Compared with the conventional BB acquisition, the coefficient of correlation and significance of the DB technique was superior for intra-observer reproducibility (p < 0.001), inter-observer reproducibility (p < 0.001) and inter-study reproducibility (p < 0.001). The variability is also lower for DB sequences for T2* values <14 ms. Assessment of artifacts showed a superior score for DB versus BB scans (4 versus 3, p < 0.001). Conclusions: Improvement in terms of inter observer and inter study variability using DB sequences was obtained. The greatest disparity between them was seen in inter-study reproducibility and higher IQ in DB was seen. Study demonstrates better performance of DB imaging compared to BB in presence of comparable effectiveness.

Reproducing Epidemiologic Research and Ensuring Transparency.

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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.

Feature Import Vector Machine: A General Classifier with Flexible Feature Selection.

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Ghosh, Samiran; Wang, Yazhen

2015-02-01

The support vector machine (SVM) and other reproducing kernel Hilbert space (RKHS) based classifier systems are drawing much attention recently due to its robustness and generalization capability. General theme here is to construct classifiers based on the training data in a high dimensional space by using all available dimensions. The SVM achieves huge data compression by selecting only few observations which lie close to the boundary of the classifier function. However when the number of observations are not very large (small n ) but the number of dimensions/features are large (large p ), then it is not necessary that all available features are of equal importance in the classification context. Possible selection of an useful fraction of the available features may result in huge data compression. In this paper we propose an algorithmic approach by means of which such an optimal set of features could be selected. In short, we reverse the traditional sequential observation selection strategy of SVM to that of sequential feature selection. To achieve this we have modified the solution proposed by Zhu and Hastie (2005) in the context of import vector machine (IVM), to select an optimal sub-dimensional model to build the final classifier with sufficient accuracy.

Main modelling features of the ASTEC V2.1 major version

International Nuclear Information System (INIS)

Chatelard, P.; Belon, S.; Bosland, L.; Carénini, L.; Coindreau, O.; Cousin, F.; Marchetto, C.; Nowack, H.; Piar, L.; Chailan, L.

2016-01-01

Highlights: • Recent modelling improvements of the ASTEC European severe accident code are outlined. • Key new physical models now available in the ASTEC V2.1 major version are described. • ASTEC progress towards a multi-design reactor code is illustrated for BWR and PHWR. • ASTEC strong link with the on-going EC CESAM FP7 project is emphasized. • Main remaining modelling issues (on which IRSN efforts are now directing) are given. - Abstract: A new major version of the European severe accident integral code ASTEC, developed by IRSN with some GRS support, was delivered in November 2015 to the ASTEC worldwide community. Main modelling features of this V2.1 version are summarised in this paper. In particular, the in-vessel coupling technique between the reactor coolant system thermal-hydraulics module and the core degradation module has been strongly re-engineered to remove some well-known weaknesses of the former V2.0 series. The V2.1 version also includes new core degradation models specifically addressing BWR and PHWR reactor types, as well as several other physical modelling improvements, notably on reflooding of severely damaged cores, Zircaloy oxidation under air atmosphere, corium coolability during corium concrete interaction and source term evaluation. Moreover, this V2.1 version constitutes the back-bone of the CESAM FP7 project, which final objective is to further improve ASTEC for use in Severe Accident Management analysis of the Gen.II–III nuclear power plants presently under operation or foreseen in near future in Europe. As part of this European project, IRSN efforts to continuously improve both code numerical robustness and computing performances at plant scale as well as users’ tools are being intensified. Besides, ASTEC will continue capitalising the whole knowledge on severe accidents phenomenology by progressively keeping physical models at the state of the art through a regular feed-back from the interpretation of the current and

Enacting the International/Reproducing Eurocentrism

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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 of somatosensory spatial perceptual maps.

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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.

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 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

Prescribing patterns of psychotropic medications and clinical features in patients with major depressive disorder with and without comorbid dysthymia in China.

Science.gov (United States)

Feng, Yuan; Sha, Sha; Hu, Chen; Wang, Gang; Ungvari, Gabor S; Chiu, Helen F K; Ng, Chee H; Si, Tian-Mei; Chen, Da-Fang; Fang, Yi-Ru; Lu, Zheng; Yang, Hai-Chen; Hu, Jian; Chen, Zhi-Yu; Huang, Yi; Sun, Jing; Wang, Xiao-Ping; Li, Hui-Chun; Zhang, Jin-Bei; Xiang, Yu-Tao

2017-03-01

Little has been reported about the demographic and clinical features of major depressive disorder (MDD) with comorbid dysthymia in Chinese patients. This study examined the frequency of comorbid dysthymia in Chinese MDD patients together with the demographic and clinical correlates and prescribing patterns of psychotropic drugs. Consecutively collected sample of 1178 patients with MDD were examined in 13 major psychiatric hospitals in China. Patients' demographic and clinical characteristics and psychotropic drugs prescriptions were recorded using a standardized protocol and data collection procedure. The diagnosis of dysthymia was established using the Mini International Neuropsychiatric Interview. Medications ascertained included antidepressants, antipsychotics, benzodiazepines, and mood stabilizers. One hundred and three (8.7%) patients fulfilled criteria for dysthymia. In multiple logistic regression analyses, compared to non-dysthymia counterparts, MDD patients with dysthymia had more depressive episodes with atypical features including increased appetite, sleep, and weight gain, more frequent lifetime depressive episodes, and less likelihood of family history of psychiatric disorders. There was no significant difference in the pattern of psychotropic prescription between the 2 groups. There are important differences in the demographic and clinical features of comorbid dysthymia in Chinese MDD patients compared with previous reports. The clinical profile found in this study has implications for treatment decisions. © 2016 John Wiley & Sons Australia, Ltd.

Extensible, Reusable, and Reproducible Computing: A Case Study of PySPH

International Nuclear Information System (INIS)

Ramachandran, Prabhu

2016-01-01

In this work, the Smoothed Particle Hydrodynamics (SPH) technique is considered as an example of a typical computational research area. PySPH is an open source framework for SPH computations. PySPH is designed to be easy to use. The framework allows a user to implement an entire simulation in pure Python. It is designed to make it easy for scientists to reuse their code and extend the work of others. These important features allow PySPH to facilitate reproducible computational research. Based on the experience with PySPH, general recommendations are suggested for other computational researchers. (paper)

Assessing the contribution of borderline personality disorder and features to suicide risk in psychiatric inpatients with bipolar disorder, major depression and schizoaffective disorder.

Science.gov (United States)

Zeng, Ruifan; Cohen, Lisa J; Tanis, Thachell; Qizilbash, Azra; Lopatyuk, Yana; Yaseen, Zimri S; Galynker, Igor

2015-03-30

Suicidal behavior often accompanies both borderline personality disorder (BPD) and severe mood disorders, and comorbidity between the two appears to further increase suicide risk. The current study aims to quantify the risk of suicidality conferred by comorbid BPD diagnosis or features in three affective disorders: major depressive disorder (MDD), bipolar disorder (BP) and schizoaffective disorder. One hundred forty-nine (149) psychiatric inpatients were assessed by SCID I and II, and the Columbia Suicide Severity Rating Scale. Logistic regression analyses investigated the associations between previous suicide attempt and BPD diagnosis or features in patients with MDD, BP, and schizoaffective disorder, as well as a history of manic or major depressive episodes, and psychotic symptoms. Comorbid BPD diagnosis significantly increased suicide risk in the whole sample, and in those with MDD, BP, and history of depressive episode or psychotic symptoms. Each additional borderline feature also increased risk of past suicide attempt in these same groups (excepting BP) and in those with a previous manic episode. Of the BPD criteria, only unstable relationships and impulsivity independently predicted past suicide attempt. Overall, among patients with severe mood disorders, the presence of comorbid BPD features or disorder appears to substantially increase the risk of suicide attempts. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Reproducibility of mean nuclear volume and correlation with mean nuclear area in breast cancer

DEFF Research Database (Denmark)

Baak, J P; Ladekarl, M; Sørensen, Flemming Brandt

1994-01-01

reproducible and strongly correlated with nuclear vv assessed in the TOTAL. In invasive breast cancer assessments in the whole tumor section can be used if delineation of the measurement area cannot be done easily. In small areas with a limited number of nuclei (eg, microinvasive parts) MNA can be easier......Previous studies have shown that quantitative, histopathologic features obtained from a carefully selected area in the tumor section ("selective" approach) have a strong prognostic value in breast cancer. On the other hand, it was found that mean nuclear volume estimation in the whole area...... as to their intraobserver and interobserver reproducibility in 22 invasive breast cancer cases. The mean nuclear volume (nuclear vv) was assessed both in the most atypical area (AREA) (selected on morphologic criteria) and in the whole tumor section (TOTAL). Furthermore, the correlation with mean nuclear (profile) area...

Market mechanism based on the endogenous changing of game types such as Minority-Majority games

Science.gov (United States)

Ahn, Sanghyun; Lim, Gyuchang; Kim, Sooyong; Kim, Kyungsik

2010-03-01

In many social and biological systems agents simultaneously and adaptively compete for limited resources, thereby altering their environment. We propose a evolution function extending Minority-Majority Games that captures the competition between agents to make money. The dynamics changes the ratio of two types of boundedly rational traders, fundamentalists and chartists with the payoff function endogenously. In the previous game theories, the best strategies are not always targeting the minority but are shifting opportunistically between the minority and the majority. And using a mixture of local bifurcation theory and numerical methods, there are possible bifurcation routes to complicated asset price dynamics, chaotic attractors. Hereby we improve the thinking logic of the atoms for attaching the dynamics to the market. This working shows that removing unrealistic features of the game theories leads to models which reproduce a behavior close to what is observed in real markets.

Is Early-onset in Major Depression a Predictor of Specific Clinical Features with More Impaired Social Function?

Institute of Scientific and Technical Information of China (English)

Yan-Hong Liu; Lin Chen; Yun-Ai Su; Yi-Ru Fang; Manit Srisurapanont; Jin Pyo Hong; Ahmad Hatim

2015-01-01

Background:Early-onset major depressive disorder (MDD) (EOD) is often particularly malignant due to its special clinical features,accompanying impaired social function,protracted recovery time,and frequent recurrence.This study aimed to observe the effects of age onset on clinical characteristics and social function in MDD patients in Asia.Methods:In total,547 out-patients aged 18-65 years who were from 13 study sites in five Asian countries were included.These patients had MDD diagnose according to the Diagnostic and Statistical Manual of Mental Disorders,4th Edition criteria.Clinical features and social function were assessed using Symptom Checklist-90-revised (SCL-90-R) and Sheehan Disability Scale (SDS).Quality of life was assessed by a 36-item Short-form Health Survey (SF-36).Analyses were performed using a continuous or dichotomous (cut-off:30 years)age-of-onset indicator.Results:Early-onset MDD (EOD,＜30 years) was associated with longer illness (P =0.003),unmarried status (P ＜ 0.001),higher neuroticism (P ≤ 0.002) based on the SCL-90-R,and more limited social function and mental health (P =0.006,P =0.007) based on the SF-36 and SDS.The impairment of social function and clinical severity were more prominent at in-patients with younger onset ages.Special clinical features and more impaired social function and quality of life were associated with EOD,as in western studies.Conclusions:EOD often follows higher levels of neuroticism.Age of onset of MDD may be a predictor of clinical features and impaired social function,allowing earlier diagnosis and treatment.

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

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.

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

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.

A technique for reproducible roentgenprograms of the intercondylar sulcus for the study of the femoropatellar

International Nuclear Information System (INIS)

Koelbel, R.; Bergmann, G.; Rohlmann, A.

1979-01-01

Roentgenographic documentation of certain features of FP-joint geometry and orientation may serve as guideline in deciding on the form of treatment for chondromalacia or recurrent patellar dislocation. Reproducible conditions for taking roentgen films are equally important for this purpose as well as for quantitative measurements and possible statistical work. A new positioning device for the patient's legs has been designed utilizing a parallellogram frame. The roentgenographic technique for skyline views at 30 0 , 60 0 and 90 0 inclination of the central beam relative to the femoral axis is described. The advantages over previous techniques are the ease of handling the positioning frame, the need for only vertical and horizontal adjustment of the roentgen tube, independence of the type of tube or table, reproducibility of cassette and patient positioning. (orig.) [de

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

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

Science.gov (United States)

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

In utero diffusion tensor imaging of the fetal brain: A reproducibility study.

Science.gov (United States)

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.

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...

Characterization of the major histopathological components of thyroid nodules using sonographic textural features for clinical diagnosis and management.

Science.gov (United States)

Chen, Shao-Jer; Yu, Sung-Nien; Tzeng, Jeh-En; Chen, Yen-Ting; Chang, Ku-Yaw; Cheng, Kuo-Sheng; Hsiao, Fu-Tsung; Wei, Chang-Kuo

2009-02-01

In this study, the characteristic sonographic textural feature that represents the major histopathologic components of the thyroid nodules was objectively quantified to facilitate clinical diagnosis and management. A total of 157 regions-of-interest thyroid ultrasound image was recruited in the study. The sonographic system used was the GE LOGIQ 700), (General Electric Healthcare, Chalfant St. Giles, UK). The parameters affecting image acquisition were kept in the same condition for all lesions. Commonly used texture analysis methods were applied to characterize thyroid ultrasound images. Image features were classified according to the corresponding pathologic findings. To estimate their relevance and performance to classification, ReliefF was used as a feature selector. Among the various textural features, the sum average value derived from co-occurrence matrix can well reflect echogenicity and can effectively differentiate between follicles and fibrosis base thyroid nodules. Fibrosis shows lowest echogenicity and lowest difference sum average value. Enlarged follicles show highest echogenicity and difference sum average values. Papillary cancer or follicular tumors show the difference sum average values and echogenicity between. The rule of thumb for the echogenicity is that the more follicles are mixed in, the higher the echo of the follicular tumor and papillary cancer will be and vice versa for fibrosis mixed. Areas with intermediate and lower echo should address the possibility of follicular or papillary neoplasm mixed with either follicles or fibrosis. These areas provide more cellular information for ultrasound guided aspiration

Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II.

Science.gov (United States)

Kury, Fabrício S P; Huser, Vojtech; Cimino, James J

2015-01-01

In this paper we sought to reproduce, as a computational retrospective study in an EHR database (MIMIC-II), a recent large prospective clinical study: the 2013 publication, by the Japanese Association for Acute Medicine (JAAM), about disseminated intravascular coagulation, in the journal Critical Care (PMID: 23787004). We designed in SQL and Java a set of electronic phenotypes that reproduced the study's data sampling, and used R to perform the same statistical inference procedures. All produced source code is available online at https://github.com/fabkury/paamia2015. Our program identified 2,257 eligible patients in MIMIC-II, and the results remarkably agreed with the prospective study. A minority of the needed data elements was not found in MIMIC-II, and statistically significant inferences were possible in the majority of the cases.

NetProt: Complex-based Feature Selection.

Science.gov (United States)

Goh, Wilson Wen Bin; Wong, Limsoon

2017-08-04

Protein complex-based feature selection (PCBFS) provides unparalleled reproducibility with high phenotypic relevance on proteomics data. Currently, there are five PCBFS paradigms, but not all representative methods have been implemented or made readily available. To allow general users to take advantage of these methods, we developed the R-package NetProt, which provides implementations of representative feature-selection methods. NetProt also provides methods for generating simulated differential data and generating pseudocomplexes for complex-based performance benchmarking. The NetProt open source R package is available for download from https://github.com/gohwils/NetProt/releases/ , and online documentation is available at http://rpubs.com/gohwils/204259 .

Is Early-onset in Major Depression a Predictor of Specific Clinical Features with More Impaired Social Function?

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Liu, Yan-Hong; Chen, Lin; Su, Yun-Ai; Fang, Yi-Ru; Srisurapanont, Manit; Hong, Jin Pyo; Hatim, Ahmad; Chua, Hong Choon; Bautista, Dianne; Si, Tian-Mei

2015-01-01

Background: Early-onset major depressive disorder (MDD) (EOD) is often particularly malignant due to its special clinical features, accompanying impaired social function, protracted recovery time, and frequent recurrence. This study aimed to observe the effects of age onset on clinical characteristics and social function in MDD patients in Asia. Methods: In total, 547 out-patients aged 18–65 years who were from 13 study sites in five Asian countries were included. These patients had MDD diagnose according to the Diagnostic and Statistical Manual of Mental Disorders, 4th Edition criteria. Clinical features and social function were assessed using Symptom Checklist-90-revised (SCL-90-R) and Sheehan Disability Scale (SDS). Quality of life was assessed by a 36-item Short-form Health Survey (SF-36). Analyses were performed using a continuous or dichotomous (cut-off: 30 years) age-of-onset indicator. Results: Early-onset MDD (EOD, <30 years) was associated with longer illness (P = 0.003), unmarried status (P < 0.001), higher neuroticism (P ≤ 0.002) based on the SCL-90-R, and more limited social function and mental health (P = 0.006, P = 0.007) based on the SF-36 and SDS. The impairment of social function and clinical severity were more prominent at in-patients with younger onset ages. Special clinical features and more impaired social function and quality of life were associated with EOD, as in western studies. Conclusions: EOD often follows higher levels of neuroticism. Age of onset of MDD may be a predictor of clinical features and impaired social function, allowing earlier diagnosis and treatment. PMID:25758278

Guidelines for Reproducibly Building and Simulating Systems Biology Models.

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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.

Age at onset of major depressive disorder in Han Chinese women: Relationship with clinical features and family history☆

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Yang, Fuzhong; Li, Yihan; Xie, Dong; Shao, Chunhong; Ren, Jianer; Wu, Wenyuan; Zhang, Ning; Zhang, Zhen; Zou, Ying; Zhang, Jiulong; Qiao, Dongdong; Gao, Chengge; Li, Youhui; Hu, Jian; Deng, Hong; Wang, Gang; Du, Bo; Wang, Xumei; Liu, Tiebang; Gan, Zhaoyu; Peng, Juyi; Wei, Bo; Pan, Jiyang; Chen, Honghui; Sun, Shufan; Jia, Hong; Liu, Ying; Chen, Qiaoling; Wang, Xueyi; Cao, Juling; Lv, Luxian; Chen, Yunchun; Ha, Baowei; Ning, Yuping; Chen, YiPing; Kendler, Kenneth S.; Flint, Jonathan; Shi, Shenxun

2011-01-01

Background Individuals with early-onset depression may be a clinically distinct group with particular symptom patterns, illness course, comorbidity and family history. This question has not been previously investigated in a Han Chinese population. Methods We examined the clinical features of 1970 Han Chinese women with DSM-IV major depressive disorder (MDD) between 30 and 60 years of age across China. Analysis of linear, logistic and multiple logistic regression models was used to determine the association between age at onset (AAO) with continuous, binary and discrete characteristic clinical features of MDD. Results Earlier AAO was associated with more suicidal ideation and attempts and higher neuroticism, but fewer sleep, appetite and weight changes. Patients with an earlier AAO were more likely to suffer a chronic course (longer illness duration, more MDD episodes and longer index episode), increased rates of MDD in their parents and a lower likelihood of marriage. They tend to have higher comorbidity with anxiety disorders (general anxiety disorder, social phobia and agoraphobia) and dysthymia. Conclusions Early AAO in MDD may be an index of a more severe, highly comorbid and familial disorder. Our findings indicate that the features of MDD in China are similar to those reported elsewhere in the world. PMID:21782247

Age at onset of major depressive disorder in Han Chinese women: relationship with clinical features and family history.

Science.gov (United States)

Yang, Fuzhong; Li, Yihan; Xie, Dong; Shao, Chunhong; Ren, Jianer; Wu, Wenyuan; Zhang, Ning; Zhang, Zhen; Zou, Ying; Zhang, Jiulong; Qiao, Dongdong; Gao, Chengge; Li, Youhui; Hu, Jian; Deng, Hong; Wang, Gang; Du, Bo; Wang, Xumei; Liu, Tiebang; Gan, Zhaoyu; Peng, Juyi; Wei, Bo; Pan, Jiyang; Chen, Honghui; Sun, Shufan; Jia, Hong; Liu, Ying; Chen, Qiaoling; Wang, Xueyi; Cao, Juling; Lv, Luxian; Chen, Yunchun; Ha, Baowei; Ning, Yuping; Chen, Yiping; Kendler, Kenneth S; Flint, Jonathan; Shi, Shenxun

2011-12-01

Individuals with early-onset depression may be a clinically distinct group with particular symptom patterns, illness course, comorbidity and family history. This question has not been previously investigated in a Han Chinese population. We examined the clinical features of 1970 Han Chinese women with DSM-IV major depressive disorder (MDD) between 30 and 60 years of age across China. Analysis of linear, logistic and multiple logistic regression models was used to determine the association between age at onset (AAO) with continuous, binary and discrete characteristic clinical features of MDD. Earlier AAO was associated with more suicidal ideation and attempts and higher neuroticism, but fewer sleep, appetite and weight changes. Patients with an earlier AAO were more likely to suffer a chronic course (longer illness duration, more MDD episodes and longer index episode), increased rates of MDD in their parents and a lower likelihood of marriage. They tend to have higher comorbidity with anxiety disorders (general anxiety disorder, social phobia and agoraphobia) and dysthymia. Early AAO in MDD may be an index of a more severe, highly comorbid and familial disorder. Our findings indicate that the features of MDD in China are similar to those reported elsewhere in the world. Copyright © 2011 Elsevier B.V. All rights reserved.

Comment on "Most computational hydrology is not reproducible, so is it really science?" by Christopher Hutton et al.

Science.gov (United States)

Añel, Juan A.

2017-03-01

Nowadays, the majority of the scientific community is not aware of the risks and problems associated with an inadequate use of computer systems for research, mostly for reproducibility of scientific results. Such reproducibility can be compromised by the lack of clear standards and insufficient methodological description of the computational details involved in an experiment. In addition, the inappropriate application or ignorance of copyright laws can have undesirable effects on access to aspects of great importance of the design of experiments and therefore to the interpretation of results.Plain Language SummaryThis article highlights several important issues to ensure the scientific reproducibility of results within the current scientific framework, going beyond simple documentation. Several specific examples are discussed in the field of hydrological modeling.

A clinically useful self-report measure of the DSM-5 mixed features specifier of major depressive disorder.

Science.gov (United States)

Zimmerman, Mark; Chelminski, Iwona; Young, Diane; Dalrymple, Kristy; Martinez, Jennifer H

2014-10-01

To acknowledge the clinical significance of manic features in depressed patients, DSM-5 included criteria for a mixed features specifier for major depressive disorder (MDD). In the present report from the Rhode Island Methods to Improve Diagnostic Assessment and Services (MIDAS) project we modified our previously published depression scale to include a subscale assessing the DSM-5 mixed features specifier. More than 1100 psychiatric outpatients with MDD or bipolar disorder completed the Clinically Useful Depression Outcome Scale (CUDOS) supplemented with questions for the DSM-5 mixed features specifier (CUDOS-M). To examine discriminant and convergent validity the patients were rated on clinician severity indices of depression, anxiety, agitation, and irritability. Discriminant and convergent validity was further examined in a subset of patients who completed other self-report symptom severity scales. Test-retest reliability was examined in a subset who completed the CUDOS-M twice. We compared CUDOS-M scores in patients with MDD, bipolar depression, and hypomania. The CUDOS-M subscale had high internal consistency and test-retest reliability, was more highly correlated with another self-report measure of mania than with measures of depression, anxiety, substance use problems, eating disorders, and anger, and was more highly correlated with clinician severity ratings of agitation and irritability than anxiety and depression. CUDOS-M scores were significantly higher in hypomanic patients than depressed patients, and patients with bipolar depression than patients with MDD. The study was cross-sectional, thus we did not examine whether the CUDOS-M detects emerging mixed symptoms when depressed patients are followed over time. Also, while we examined the correlation between the CUDOS-M and clinician ratings of agitation and irritability, we did not examine the association with a clinician measure of manic symptomatology such as the Young Mania Rating Scale In the

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

.5 mm, and 0.2 mm in the CC, AP, and medial-lateral (ML) directions, with a standard deviation of 1.5 mm, 1.5 mm, and 1.5 mm, respectively. Ninety-five percent of the liver surface had an absolute differences in position between repeat ABC CT scans of less than 4.1 mm, 3.3 mm, and 3.3 mm in the CC, AP, and ML directions, respectively. Analysis of 257 MV AP images from patients treated using ABC revealed an average intrafraction CC reproducibility (σ) of diaphragm relative to vertebral bodies of 1.5 mm (range, 0.6-3.9 mm). The average interfraction CC reproducibility (σ) was 3.4 mm (range, 1.5-7.9 mm), indicating less day-to-day reproducibility of diaphragm position relative to vertebral bodies. The average absolute intra and interfraction CC offset in diaphragm position relative to vertebral bodies was 1.7 and 3.7 mm, respectively, with 86% of intrafraction and 54% of interfraction absolute offsets 3.0 mm or less. Conclusions: Intrafraction reproducibility of liver position using ABC is good in the majority of screened patients. However, interfraction reproducibility is worse, suggesting a need for image guidance

Reproducibility and Practical Adoption of GEOBIA with Open-Source Software in Docker Containers

Directory of Open Access Journals (Sweden)

Christian Knoth

2017-03-01

Full Text Available Geographic Object-Based Image Analysis (GEOBIA mostly uses proprietary software,but the interest in Free and Open-Source Software (FOSS for GEOBIA is growing. This interest stems not only from cost savings, but also from benefits concerning reproducibility and collaboration. Technical challenges hamper practical reproducibility, especially when multiple software packages are required to conduct an analysis. In this study, we use containerization to package a GEOBIA workflow in a well-defined FOSS environment. We explore the approach using two software stacks to perform an exemplary analysis detecting destruction of buildings in bi-temporal images of a conflict area. The analysis combines feature extraction techniques with segmentation and object-based analysis to detect changes using automatically-defined local reference values and to distinguish disappeared buildings from non-target structures. The resulting workflow is published as FOSS comprising both the model and data in a ready to use Docker image and a user interface for interaction with the containerized workflow. The presented solution advances GEOBIA in the following aspects: higher transparency of methodology; easier reuse and adaption of workflows; better transferability between operating systems; complete description of the software environment; and easy application of workflows by image analysis experts and non-experts. As a result, it promotes not only the reproducibility of GEOBIA, but also its practical adoption.

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

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.

Major depressive disorder with subthreshold hypomanic (mixed) features: A real-world assessment of treatment patterns and economic burden.

Science.gov (United States)

McIntyre, Roger S; Ng-Mak, Daisy; Chuang, Chien-Chia; Halpern, Rachel; Patel, Pankaj A; Rajagopalan, Krithika; Loebel, Antony

2017-03-01

To compare outcomes for individuals with major depressive disorder (MDD) with or without subthreshold hypomania (mixed features) in naturalistic settings. Using the Optum Research Database (1/1/2009─10/31/2014), a retrospective analysis of individuals newly diagnosed with MDD was conducted. Continuous enrollment for 12-months before and after the initial MDD diagnosis was required. MDD with subthreshold hypomania (mixed features) (MDD-MF) was defined based on ≥1 hypomania diagnosis within 30 days after an MDD diagnosis during the one-year follow-up period, in the absence of bipolar I diagnoses. Psychiatric medication use, healthcare utilization, and costs during the one-year follow-up period were compared using multivariate logistic and gamma regressions, controlling for baseline differences. Of 130,626 MDD individuals, 652 (0.5%) met the operational definition of MDD-MF. Compared to the MDD-only group, the MDD-MF group had more suicidality (2.0% vs. 0.5%), anxiety disorders (46.8% vs. 34.0%), and substance use disorders (15.5% vs. 6.1%, all P<0.001). More individuals with MDD-MF were treated with antidepressants (83.6% vs. 71.6%), mood stabilizers (50.5% vs. 2.7%), atypical antipsychotics (39.0% vs. 5.5%), and polypharmacy with multiple drug classes (72.1% vs. 22.7%, all P<0.001). Individuals with MDD-MF had higher hospitalizations rates (24.2% vs. 10.5%) and total healthcare costs (mean: $15,660 vs. $10,744, all P<0.001). The commercial claims data used were not collected for research purposes and may over- or under-represent certain populations. No specific claims-based diagnostic code for MDD with mixed features exists. Greater use of mood stabilizers, atypical antipsychotics, polypharmacy, and healthcare resources provides evidence of the complexity and severity of MDD-MF. Identifying optimal treatment regimens for this population represents a major unmet medical need. Copyright © 2016 Elsevier B.V. All rights reserved.

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

Morphological features of the major duodenal papilla in patients with cholelithiasis

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V. M. Klymenko

2017-12-01

Full Text Available The high prevalence of the pathology of major duodenal papilla in patients with gallstone disease, the difficulties of diagnosis and treatment determine the relevance of the study. The purpose is to study the morphological features of the major duodenal papilla in patients with cholelithiasis. Material and methods. During autopsies, selection of fragments of major duodenal papilla from 30 dead was performed. The main group consisted of autopsy specimens (n = 15 from the dead, which had stones in the gallbladder in the absence of signs of inflammation of the walls of the gallbladder and bile ducts. Biomaterial samples (n = 15 from the dead, which had no stones and signs of inflammation of the biliary system, were included in the control group. To study the severity of the stromal component, the Mason’s trichrome and the Van Gieson’s stains were used. Light microscopy was carried out using a light microscope Axioplan 2 (Carl Zeiss - Germany using x10, x20, x40, x100 lenses and x10 eyepiece. For a quantitative assessment of the severity of sclerotic changes, we conducted a morphometric study of preparations stained with picrofuchsin accordimg to Van Gieson. The area of the stromal component was calculated in the resulted images in 5 fields of view under magnification of x200 using the medical software for analysis and processing of digital images ImageJ, initiated by W. Rasband (1997-2012. The expression area was the percentage ratio of the number of pixels of the digital image of the zones of expression of the connective tissue component to the total number of pixels in the image. Results. The quantitative analysis of the severity of sclerotic changes in the periductal tissue in both studied groups showed that in the control observations the expression area of the connective tissue component was 18.84 ± 3.14%, and in the main group (cases of gallstone disease – 78.06 ± 15.12% (p = 0.0031. Conclusions. 1. In patients with gallstone disease

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.

Clinical Features of Anthroponotic Cutaneous Leishmaniasis in a Major Focus, Southeastern Iran, 1994-2014

Directory of Open Access Journals (Sweden)

Ahmad KHOSRAVI

2017-12-01

Full Text Available AbstractBackground: Cutaneous leishmaniasis (CL is associated with a broad and complex clinical spectrum of diseases. The objectives of this study were to assess the clinical features and identification of the causative agents of CL in a well-known focus of anthroponotic CL (ACL caused by Leishmania tropica, southeast Iran.Methods: This study was performed randomly as a descriptive cross-sectional survey to evaluate 2000 CL patients by active and passive case-detection approaches in Kerman Province from 1994 to 2014. The ACL patients were confirmed by direct smear and 600 cases by one or a combination of intrinsic methods.Results: Children aged <10 yr old were the most infected patients (P<0.001. The majority of the CL lesions were located in hands (46.3%, face (34.1%, legs (14.3%, and other parts of the body (5.3%. The mean number of lesions was 1.5 and most of the patients had single lesion (65%.Typical clinical lesions included papule (36.8%, followed by ulcerated nodule (20.7%, plaque (18.4%, and ulcerated plaque (18.5%. While among atypical clinical features, leishmaniasis recidivans (LR (4.7% and leishmanid (0.3% were the dominant forms, followed by diffuse, disseminated, sporotrichoid, and erysipeloid types, 0.1% each, and then lymphedematous, lymphadenic, hyperkeratotic, paronychial, and mutilating types, 0.05% each. Based on various intrinsic methods the parasites isolated from the lesions were characterized as L. tropica.Conclusion: ACL due to L. tropica presents numerous cases of localized form and diverse uncommon clinical presentations, which mimic other disease conditions. Therefore, physicians should be aware of such manifestations for selecting appropriate treatment modality.

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.

Mid-Infrared Emission Features in the ISM: Feature-to-Features Flux Ratios

Science.gov (United States)

Lu, N. Y.

1998-01-01

Using a limited, but representative sample of sources in the ISM of our Galaxy with published spectra from the Infrared Space Observatory, we analyze flux ratios between the major mid-IR emission features (EFs) centered around 6.2, 7.7, 8.6 and 11.3 mu, respectively.

The pancreas in {beta}-thalassemia major: MR imaging features and correlation with iron stores and glucose disturbunces

Energy Technology Data Exchange (ETDEWEB)

Papakonstantinou, Olympia [University Hospital of Heraklion, Medical School of Crete, Department of Radiology, Heraklion, Crete (Greece); Attikon Hospital, 2nd Department of Radiology, Athens (Greece); Ladis, Vasilios; Kostaridou, Stavroula; Berdousi, Helen; Kattamis, Christos [Thalassemia Unit, University of Athens, ' ' Aghia Sophia' ' Children' s Hospital, Athens (Greece); Maris, Thomas; Gourtsoyiannis, Nicholas [University Hospital of Heraklion, Medical School of Crete, Department of Radiology, Heraklion, Crete (Greece)

2007-06-15

The study aims at describing the MR features of pancreas in beta-thalassemia major, investigating the relations between MR findings and glucose disturbances and between hepatic and pancreatic siderosis. Signal intensity ratios of the pancreas and liver to right paraspinous muscle (P/M, L/M) were retrospectively assessed on abdominal MR imaging studies of 31 transfusion-dependent patients with beta-thalassemia major undergoing quantification of hepatic siderosis and 10 healthy controls, using T1- (120/4/90), intermediate in and out of phase - (120/2.7, 4/20), and T2*-(120/15/20) weighted GRE sequences. Using the signal drop of the liver and pancreas on opposed phase images, we recorded serum ferritin and results of oral glucose tolerance test (OGTT). Decreased L/M and P/M on at least the T2* sequence were noticed in 31/31 and 30/31 patients, respectively, but no correlation between P/M and L/M was found. Patients with pathologic OGTT displayed a higher degree of hepatic siderosis (p < 0.04) and signal drop of pancreas on opposed phase imaging (p < 0.025), implying fatty replacement of pancreas. P/M was neither correlated with glucose disturbances nor serum ferritin. Iron deposition in the pancreas cannot be predicted by the degree of hepatic siderosis in beta-thalassemia major. Fatty replacement of the pancreas is common and may be associated with glucose disturbances. (orig.)

The pancreas in β-thalassemia major: MR imaging features and correlation with iron stores and glucose disturbunces

International Nuclear Information System (INIS)

Papakonstantinou, Olympia; Ladis, Vasilios; Kostaridou, Stavroula; Berdousi, Helen; Kattamis, Christos; Maris, Thomas; Gourtsoyiannis, Nicholas

2007-01-01

The study aims at describing the MR features of pancreas in beta-thalassemia major, investigating the relations between MR findings and glucose disturbances and between hepatic and pancreatic siderosis. Signal intensity ratios of the pancreas and liver to right paraspinous muscle (P/M, L/M) were retrospectively assessed on abdominal MR imaging studies of 31 transfusion-dependent patients with beta-thalassemia major undergoing quantification of hepatic siderosis and 10 healthy controls, using T1- (120/4/90), intermediate in and out of phase - (120/2.7, 4/20), and T2*-(120/15/20) weighted GRE sequences. Using the signal drop of the liver and pancreas on opposed phase images, we recorded serum ferritin and results of oral glucose tolerance test (OGTT). Decreased L/M and P/M on at least the T2* sequence were noticed in 31/31 and 30/31 patients, respectively, but no correlation between P/M and L/M was found. Patients with pathologic OGTT displayed a higher degree of hepatic siderosis (p < 0.04) and signal drop of pancreas on opposed phase imaging (p < 0.025), implying fatty replacement of pancreas. P/M was neither correlated with glucose disturbances nor serum ferritin. Iron deposition in the pancreas cannot be predicted by the degree of hepatic siderosis in beta-thalassemia major. Fatty replacement of the pancreas is common and may be associated with glucose disturbances. (orig.)

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

Intra-observer reproducibility and interobserver reliability of the radiographic parameters in the Spinal Deformity Study Group's AIS Radiographic Measurement Manual.

Science.gov (United States)

Dang, Natasha Radhika; Moreau, Marc J; Hill, Douglas L; Mahood, James K; Raso, James

2005-05-01

Retrospective cross-sectional assessment of the reproducibility and reliability of radiographic parameters. To measure the intra-examiner and interexaminer reproducibility and reliability of salient radiographic features. The management and treatment of adolescent idiopathic scoliosis (AIS) depends on accurate and reproducible radiographic measurements of the deformity. Ten sets of radiographs were randomly selected from a sample of patients with AIS, with initial curves between 20 degrees and 45 degrees. Fourteen measures of the deformity were measured from posteroanterior and lateral radiographs by 2 examiners, and were repeated 5 times at intervals of 3-5 days. Intra-examiner and interexaminer differences were examined. The parameters include measures of curve size, spinal imbalance, sagittal kyphosis and alignment, maximum apical vertebral rotation, T1 tilt, spondylolysis/spondylolisthesis, and skeletal age. Intra-examiner reproducibility was generally excellent for parameters measured from the posteroanterior radiographs but only fair to good for parameters from the lateral radiographs, in which some landmarks were not clearly visible. Of the 13 parameters observed, 7 had excellent interobserver reliability. The measurements from the lateral radiograph were less reproducible and reliable and, thus, may not add value to the assessment of AIS. Taking additional measures encourages a systematic and comprehensive assessment of spinal radiographs.

Bile Routing Modification Reproduces Key Features of Gastric Bypass in Rat.

Science.gov (United States)

Goncalves, Daisy; Barataud, Aude; De Vadder, Filipe; Vinera, Jennifer; Zitoun, Carine; Duchampt, Adeline; Mithieux, Gilles

2015-12-01

To evaluate the role of bile routing modification on the beneficial effects of gastric bypass surgery on glucose and energy metabolism. Gastric bypass surgery (GBP) promotes early improvements in glucose and energy homeostasis in obese diabetic patients. A suggested mechanism associates a decrease in hepatic glucose production to an enhanced intestinal gluconeogenesis. Moreover, plasma bile acids are elevated after GBP and bile acids are inhibitors of gluconeogenesis. In male Sprague-Dawley rats, we performed bile diversions from the bile duct to the midjejunum or the mid-ileum to match the modified bile delivery in the gut occurring in GBP. Body weight, food intake, glucose tolerance, insulin sensitivity, and food preference were analyzed. The expression of gluconeogenesis genes was evaluated in both the liver and the intestine. Bile diversions mimicking GBP promote an increase in plasma bile acids and a marked improvement in glucose control. Bile bioavailability modification is causal because a bile acid sequestrant suppresses the beneficial effects of bile diversions on glucose control. In agreement with the inhibitory role of bile acids on gluconeogenesis, bile diversions promote a blunting in hepatic glucose production, whereas intestinal gluconeogenesis is increased in the gut segments devoid of bile. In rats fed a high-fat-high-sucrose diet, bile diversions improve glucose control and dramatically decrease food intake because of an acquired disinterest in fatty food. This study shows that bile routing modification is a key mechanistic feature in the beneficial outcomes of GBP.

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

Online Distributed Learning Over Networks in RKH Spaces Using Random Fourier Features

Science.gov (United States)

Bouboulis, Pantelis; Chouvardas, Symeon; Theodoridis, Sergios

2018-04-01

We present a novel diffusion scheme for online kernel-based learning over networks. So far, a major drawback of any online learning algorithm, operating in a reproducing kernel Hilbert space (RKHS), is the need for updating a growing number of parameters as time iterations evolve. Besides complexity, this leads to an increased need of communication resources, in a distributed setting. In contrast, the proposed method approximates the solution as a fixed-size vector (of larger dimension than the input space) using Random Fourier Features. This paves the way to use standard linear combine-then-adapt techniques. To the best of our knowledge, this is the first time that a complete protocol for distributed online learning in RKHS is presented. Conditions for asymptotic convergence and boundness of the networkwise regret are also provided. The simulated tests illustrate the performance of the proposed scheme.

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

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 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.

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

Comparison of laminite fracture features at different scales

OpenAIRE

Zihms, Stephanie; Miranda, Tiago; Lewis, Helen; Hall, Stephen

2017-01-01

Laminites (NE Brazil) are well laminated carbonates that provide insight into the geomechanical behaviour of layered systems, especially when comparing deformation characteristics observed in the laboratory with outcrop / field scale deformations. This is useful in order to a)  validate where laboratory experiments can reproduce field scale deformation types b)  understand which feature characteristics can or cannot be scaled

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....

Major depressive disorder with psychotic features may lead to misdiagnosis of dementia: a case report and review of the literature.

Science.gov (United States)

Wagner, Gerhardt S; McClintock, Shawn M; Rosenquist, Peter B; McCall, W Vaughn; Kahn, David A

2011-11-01

Major depressive disorder (MDD) with psychotic features is relatively frequent in patients with greater depressive symptom severity and is associated with a poorer course of illness and greater functional impairment than MDD without psychotic features. Multiple studies have found that patients with psychotic mood disorders demonstrate significantly poorer cognitive performance in a variety of areas than those with nonpsychotic mood disorders. The Mini Mental State Examination (MMSE) and the Dementia Rating Scale, Second Edition (DRS-2) are widely used to measure cognitive functions in research on MDD with psychotic features. Established total raw score cut-offs of 24 on the MMSE and 137 on the DRS-2 in published manuals suggest possible global cognitive impairment and dementia, respectively. Limited research is available on these suggested cut-offs for patients with MDD with psychotic features. We document the therapeutic benefit of electroconvulsive therapy (ECT), which is usually associated with short-term cognitive impairment, in a 68-year-old woman with psychotic depression whose MMSE and DRS-2 scores initially suggested possible global cognitive impairment and dementia. Over the course of four ECT treatments, the patient's MMSE scores progressively increased. After the second ECT treatment, the patient no longer met criteria for global cognitive impairment. With each treatment, depression severity, measured by the 24-item Hamilton Rating Scale for Depression, improved sequentially. Thus, the suggested cut-off scores for the MMSE and the DRS-2 in patients with MDD with psychotic features may in some cases produce false-positive indications of dementia.

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

Participant Nonnaiveté and the reproducibility of cognitive psychology.

Science.gov (United States)

Zwaan, Rolf A; Pecher, Diane; Paolacci, Gabriele; Bouwmeester, Samantha; Verkoeijen, Peter; Dijkstra, Katinka; Zeelenberg, René

2017-07-25

Many 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 they be reproduced in online environments, but they also can be reproduced with nonnaïve participants with no reduction of effect size. Apparently, some cognitive tasks are so constraining that they encapsulate behavior from external influences, such as testing situation and prior recent experience with the experiment to yield highly robust effects.

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.

Clinical, immunological and genetic features in eleven Algerian patients with major histocompatibility complex class II expression deficiency

Directory of Open Access Journals (Sweden)

Djidjik Réda

2012-08-01

Full Text Available Abstract Presenting processed antigens to CD4+ lymphocytes during the immune response involves major histocompatibility complex class II molecules. MHC class II genes transcription is regulated by four transcription factors: CIITA, RFXANK, RFX5 and RFXAP. Defects in these factors result in major histocompatibility complex class II expression deficiency, a primary combined immunodeficiency frequent in North Africa. Autosomal recessive mutations in the RFXANK gene have been reported as being the principal defect found in North African patients with this disorder. In this paper, we describe clinical, immunological and genetic features of 11 unrelated Algerian patients whose monocytes display a total absence of MHC class II molecules. They shared mainly the same clinical picture which included protracted diarrhoea and respiratory tract recurrent infections. Genetic analysis revealed that 9 of the 11 patients had the same RFXANK founder mutation, a 26 bp deletion (named I5E6-25_I5E6+1, also known as 752delG26. Immunological and genetic findings in our series may facilitate genetic counselling implementation for Algerian consanguineous families. Further studies need to be conducted to determine 752delG26 heterozygous mutation frequency in Algerian population.

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....

MO-DE-207B-07: Assessment of Reproducibility Of FDG-PET-Based Radiomics Features Across Scanners Using Phantom Imaging

Energy Technology Data Exchange (ETDEWEB)

Fried, D [University of North Carolina at Chapel Hill, Chapel Hill, NC (United States); Meier, J; Mawlawi, O; Zhou, S; Ibbott, G; Liao, Z; Court, L [UT MD Anderson Cancer Center, Houston, TX (United States)

2016-06-15

Purpose: Use a NEMA-IEC PET phantom to assess the robustness of FDG-PET-based radiomics features to changes in reconstruction parameters across different scanners. Methods: We scanned a NEMA-IEC PET phantom on 3 different scanners (GE Discovery VCT, GE Discovery 710, and Siemens mCT) using a FDG source-to-background ratio of 10:1. Images were retrospectively reconstructed using different iterations (2–3), subsets (21–24), Gaussian filter widths (2, 4, 6mm), and matrix sizes (128,192,256). The 710 and mCT used time-of-flight and point-spread-functions in reconstruction. The axial-image through the center of the 6 active spheres was used for analysis. A region-of-interest containing all spheres was able to simulate a heterogeneous lesion due to partial volume effects. Maximum voxel deviations from all retrospectively reconstructed images (18 per scanner) was compared to our standard clinical protocol. PET Images from 195 non-small cell lung cancer patients were used to compare feature variation. The ratio of a feature’s standard deviation from the patient cohort versus the phantom images was calculated to assess for feature robustness. Results: Across all images, the percentage of voxels differing by <1SUV and <2SUV ranged from 61–92% and 88–99%, respectively. Voxel-voxel similarity decreased when using higher resolution image matrices (192/256 versus 128) and was comparable across scanners. Taking the ratio of patient and phantom feature standard deviation was able to identify features that were not robust to changes in reconstruction parameters (e.g. co-occurrence correlation). Metrics found to be reasonably robust (standard deviation ratios > 3) were observed for routinely used SUV metrics (e.g. SUVmean and SUVmax) as well as some radiomics features (e.g. co-occurrence contrast, co-occurrence energy, standard deviation, and uniformity). Similar standard deviation ratios were observed across scanners. Conclusions: Our method enabled a comparison of

Reproducibility of ZrO2-based freeze casting for biomaterials.

Science.gov (United States)

Naleway, Steven E; Fickas, Kate C; Maker, Yajur N; Meyers, Marc A; McKittrick, Joanna

2016-04-01

The processing technique of freeze casting has been intensely researched for its potential to create porous scaffold and infiltrated composite materials for biomedical implants and structural materials. However, in order for this technique to be employed medically or commercially, it must be able to reliably produce materials in great quantities with similar microstructures and properties. Here we investigate the reproducibility of the freeze casting process by independently fabricating three sets of eight ZrO2-epoxy composite scaffolds with the same processing conditions but varying solid loading (10, 15 and 20 vol.%). Statistical analyses (One-way ANOVA and Tukey's HSD tests) run upon measurements of the microstructural dimensions of these composite scaffold sets show that, while the majority of microstructures are similar, in all cases the composite scaffolds display statistically significant variability. In addition, composite scaffolds where mechanically compressed and statistically analyzed. Similar to the microstructures, almost all of their resultant properties displayed significant variability though most composite scaffolds were similar. These results suggest that additional research to improve control of the freeze casting technique is required before scaffolds and composite scaffolds can reliably be reproduced for commercial or medical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Reproducibility of in-vivo diffusion tensor cardiovascular magnetic resonance in hypertrophic cardiomyopathy

Directory of Open Access Journals (Sweden)

McGill Laura-Ann

2012-12-01

Full Text Available Abstract Background Myocardial disarray is an important histological feature of hypertrophic cardiomyopathy (HCM which has been studied post-mortem, but its in-vivo prevalence and extent is unknown. Cardiac Diffusion Tensor Imaging (cDTI provides information on mean intravoxel myocyte orientation and potentially myocardial disarray. Recent technical advances have improved in-vivo cDTI, and the aim of this study was to assess the interstudy reproducibility of quantitative in-vivo cDTI in patients with HCM. Methods and results A stimulated-echo single-shot-EPI sequence with zonal excitation and parallel imaging was implemented. Ten patients with HCM were each scanned on 2 different days. For each scan 3 short axis mid-ventricular slices were acquired with cDTI at end systole. Fractional anisotropy (FA, mean diffusivity (MD, and helix angle (HA maps were created using a cDTI post-processing platform developed in-house. The mean ± SD global FA was 0.613 ± 0.044, MD was 0.750 ± 0.154 × 10-3 mm2/s and HA was epicardium −34.3 ± 7.6°, mesocardium 3.5 ± 6.9° and endocardium 38.9 ± 8.1°. Comparison of initial and repeat studies showed global interstudy reproducibility for FA (SD = ± 0.045, Coefficient of Variation (CoV = 7.2%, MD (SD = ± 0.135 × 10-3 mm2/s, CoV = 18.6% and HA (epicardium SD = ± 4.8°; mesocardium SD = ± 3.4°; endocardium SD = ± 2.9°. Reproducibility of FA was superior to MD (p = 0.003. Global MD was significantly higher in the septum than the reference lateral wall (0.784 ± 0.188 vs 0.750 ± 0.154 x10-3 mm2/s, p  Conclusions To the best of our knowledge, this is the first study to assess the interstudy reproducibility of DTI in the human HCM heart in-vivo and the largest cDTI study in HCM to date. Our results show good reproducibility of FA, MD and HA which indicates that current technology yields robust in-vivo measurements that have potential clinical value. The

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

Crystallization features of ternary reversible reciprocal systems

International Nuclear Information System (INIS)

Tomashik, V.N.; Shcherbak, L.P.; Fejchuk, P.I.; Grytsiv, V.I.

2006-01-01

Some features of the primary crystallization of phases in ternary reversible reciprocal system are considered and discussed. The diagonal join CdTe-GeSe of the CdTe + GeSe = CdSe + GeTe ternary reciprocal system is studied to show that the features in primary and secondary heating and cooling curves in such systems under fully equilibrium conditions are not reproduced upon consecutive heating and cooling sessions, because of the existence of different amounts of the reagents and the reaction products in the mixture; the temperatures of each transformation lie in a range. Those who experimentally investigate other ternary and more complex reversible reciprocal systems should take this fact into account [ru

Reproducibility of graph metrics in fMRI networks

Directory of Open Access Journals (Sweden)

Qawi K Telesford

2010-12-01

Full Text Available The reliability of graph metrics calculated in network analysis is essential to the interpretation of complex network organization. These graph metrics are used to deduce the small-world properties in networks. In this study, we investigated the test-retest reliability of graph metrics from functional magnetic resonance imaging (fMRI data collected for two runs in 45 healthy older adults. Graph metrics were calculated on data for both runs and compared using intraclass correlation coefficient (ICC statistics and Bland-Altman (BA plots. ICC scores describe the level of absolute agreement between two measurements and provide a measure of reproducibility. For mean graph metrics, ICC scores were high for clustering coefficient (ICC=0.86, global efficiency (ICC=0.83, path length (ICC=0.79, and local efficiency (ICC=0.75; the ICC score for degree was found to be low (ICC=0.29. ICC scores were also used to generate reproducibility maps in brain space to test voxel-wise reproducibility for unsmoothed and smoothed data. Reproducibility was uniform across the brain for global efficiency and path length, but was only high in network hubs for clustering coefficient, local efficiency and degree. BA plots were used to test the measurement repeatability of all graph metrics. All graph metrics fell within the limits for repeatability. Together, these results suggest that with exception of degree, mean graph metrics are reproducible and suitable for clinical studies. Further exploration is warranted to better understand reproducibility across the brain on a voxel-wise basis.

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.

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...

[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

Radial gradient and radial deviation radiomic features from pre-surgical CT scans are associated with survival among lung adenocarcinoma patients.

Science.gov (United States)

Tunali, Ilke; Stringfield, Olya; Guvenis, Albert; Wang, Hua; Liu, Ying; Balagurunathan, Yoganand; Lambin, Philippe; Gillies, Robert J; Schabath, Matthew B

2017-11-10

The goal of this study was to extract features from radial deviation and radial gradient maps which were derived from thoracic CT scans of patients diagnosed with lung adenocarcinoma and assess whether these features are associated with overall survival. We used two independent cohorts from different institutions for training (n= 61) and test (n= 47) and focused our analyses on features that were non-redundant and highly reproducible. To reduce the number of features and covariates into a single parsimonious model, a backward elimination approach was applied. Out of 48 features that were extracted, 31 were eliminated because they were not reproducible or were redundant. We considered 17 features for statistical analysis and identified a final model containing the two most highly informative features that were associated with lung cancer survival. One of the two features, radial deviation outside-border separation standard deviation, was replicated in a test cohort exhibiting a statistically significant association with lung cancer survival (multivariable hazard ratio = 0.40; 95% confidence interval 0.17-0.97). Additionally, we explored the biological underpinnings of these features and found radial gradient and radial deviation image features were significantly associated with semantic radiological features.

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

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).

Quark/gluon jet discrimination: a reproducible analysis using R

CERN Multimedia

CERN. Geneva

2017-01-01

The power to discriminate between light-quark jets and gluon jets would have a huge impact on many searches for new physics at CERN and beyond. This talk will present a walk-through of the development of a prototype machine learning classifier for differentiating between quark and gluon jets at experiments like those at the Large Hadron Collider at CERN. A new fast feature selection method that combines information theory and graph analytics will be outlined. This method has found new variables that promise significant improvements in discrimination power. The prototype jet tagger is simple, interpretable, parsimonious, and computationally extremely cheap, and therefore might be suitable for use in trigger systems for real-time data processing. Nested stratified k-fold cross validation was used to generate robust estimates of model performance. The data analysis was performed entirely in the R statistical programming language, and is fully reproducible. The entire analysis workflow is data-driven, automated a...

Do You Have Major Depression?

Science.gov (United States)

... of this page please turn Javascript on. Feature: Depression Do You Have Major Depression? Past Issues / Fall 2009 Table of Contents Simple ... member may have major depression. —NIMH Types of Depression Just like other illnesses, such as heart disease, ...

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.

Meiotic faults as a major cause of offspring inviability

DEFF Research Database (Denmark)

Levitis, Daniel; Zimmerman, Kolea; Pringle, Anne

2014-01-01

, this result demonstrates that failures associated with meiosis are a major cause of offspring inviability not only for meiotic parthenogenesis, but for sexual reproducers such as humans. Meiosis is necessary for genetic recombination in eukaryotes, but is vestigial, and costly, in parthenogens. The question...... range of organisms....

Age and binding within-dimension features in visual short-term memory

OpenAIRE

Parra, Mario; Abrahams, S.; Logie, R. H.; Della Sala, S.

2009-01-01

Older adults have difficulties in binding information in long-term memory (e.g. objects with colours). The effect of age on visual short-term memory (VSTM) binding is less well understood. Recent evidence has suggested that older adults' VSTM for colours bound to shapes or for locations bound in configural representations may be preserved. In two experiments we investigated whether this lack of an age effect on VSTM for bound features can be reproduced when features are drawn from the same di...

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

MO-DE-207B-07: Assessment of Reproducibility Of FDG-PET-Based Radiomics Features Across Scanners Using Phantom Imaging

International Nuclear Information System (INIS)

Fried, D; Meier, J; Mawlawi, O; Zhou, S; Ibbott, G; Liao, Z; Court, L

2016-01-01

Purpose: Use a NEMA-IEC PET phantom to assess the robustness of FDG-PET-based radiomics features to changes in reconstruction parameters across different scanners. Methods: We scanned a NEMA-IEC PET phantom on 3 different scanners (GE Discovery VCT, GE Discovery 710, and Siemens mCT) using a FDG source-to-background ratio of 10:1. Images were retrospectively reconstructed using different iterations (2–3), subsets (21–24), Gaussian filter widths (2, 4, 6mm), and matrix sizes (128,192,256). The 710 and mCT used time-of-flight and point-spread-functions in reconstruction. The axial-image through the center of the 6 active spheres was used for analysis. A region-of-interest containing all spheres was able to simulate a heterogeneous lesion due to partial volume effects. Maximum voxel deviations from all retrospectively reconstructed images (18 per scanner) was compared to our standard clinical protocol. PET Images from 195 non-small cell lung cancer patients were used to compare feature variation. The ratio of a feature’s standard deviation from the patient cohort versus the phantom images was calculated to assess for feature robustness. Results: Across all images, the percentage of voxels differing by 3) were observed for routinely used SUV metrics (e.g. SUVmean and SUVmax) as well as some radiomics features (e.g. co-occurrence contrast, co-occurrence energy, standard deviation, and uniformity). Similar standard deviation ratios were observed across scanners. Conclusions: Our method enabled a comparison of feature variability across scanners and was able to identify features that were not robust to changes in reconstruction parameters.

Major Highway Lines, US, 2015, NAVTEQ

Data.gov (United States)

U.S. Environmental Protection Agency — NAVTEQ Major Highways for the United States. The Major Highways layer contains Road Network features based on the Functional Class attribute value on each link...

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.

Highly reproducible polyol synthesis for silver nanocubes

Science.gov (United States)

Han, Hye Ji; Yu, Taekyung; Kim, Woo-Sik; Im, Sang Hyuk

2017-07-01

We could synthesize the Ag nanocubes highly reproducibly by conducting the polyol synthesis using HCl etchant in dark condition because the photodecomposition/photoreduction of AgCl nanoparticles formed at initial reaction stage were greatly depressed and consequently the selective self-nucleation of Ag single crystals and their selective growth reaction could be promoted. Whereas the reproducibility of the formation of Ag nanocubes were very poor when we synthesize the Ag nanocubes in light condition due to the photoreduction of AgCl to Ag.

Improving mass candidate detection in mammograms via feature maxima propagation and local feature selection.

Science.gov (United States)

Melendez, Jaime; Sánchez, Clara I; van Ginneken, Bram; Karssemeijer, Nico

2014-08-01

Mass candidate detection is a crucial component of multistep computer-aided detection (CAD) systems. It is usually performed by combining several local features by means of a classifier. When these features are processed on a per-image-location basis (e.g., for each pixel), mismatching problems may arise while constructing feature vectors for classification, which is especially true when the behavior expected from the evaluated features is a peaked response due to the presence of a mass. In this study, two of these problems, consisting of maxima misalignment and differences of maxima spread, are identified and two solutions are proposed. The first proposed method, feature maxima propagation, reproduces feature maxima through their neighboring locations. The second method, local feature selection, combines different subsets of features for different feature vectors associated with image locations. Both methods are applied independently and together. The proposed methods are included in a mammogram-based CAD system intended for mass detection in screening. Experiments are carried out with a database of 382 digital cases. Sensitivity is assessed at two sets of operating points. The first one is the interval of 3.5-15 false positives per image (FPs/image), which is typical for mass candidate detection. The second one is 1 FP/image, which allows to estimate the quality of the mass candidate detector's output for use in subsequent steps of the CAD system. The best results are obtained when the proposed methods are applied together. In that case, the mean sensitivity in the interval of 3.5-15 FPs/image significantly increases from 0.926 to 0.958 (p < 0.0002). At the lower rate of 1 FP/image, the mean sensitivity improves from 0.628 to 0.734 (p < 0.0002). Given the improved detection performance, the authors believe that the strategies proposed in this paper can render mass candidate detection approaches based on image location classification more robust to feature

Influence of family history of major depression, bipolar disorder, and suicide on clinical features in patients with major depression and bipolar disorder.

Science.gov (United States)

Serretti, Alessandro; Chiesa, Alberto; Calati, Raffaella; Linotte, Sylvie; Sentissi, Othman; Papageorgiou, Konstantinos; Kasper, Siegfried; Zohar, Joseph; De Ronchi, Diana; Mendlewicz, Julien; Amital, Daniela; Montgomery, Stuart; Souery, Daniel

2013-03-01

The extent to which a family history of mood disorders and suicide could impact on clinical features of patients suffering from major depression (MD) and bipolar disorder (BD) has received relatively little attention so far. The aim of the present work is, therefore, to assess the clinical implications of the presence of at least one first- and/or second-degree relative with a history of MD, BD and suicide in a large sample of patients with MD or BD. One thousand one hundred and fifty-seven subjects with MD and 686 subjects with BD were recruited within the context of two large projects. The impact of a family history of MD, BD, and suicide-considered both separately and together-on clinical and socio-demographic variables was investigated. A family history of MD, BD, and suicide was more common in BD patients than in MD patients. A positive family history of mood disorders and/or suicide as well as a positive family history of MD and BD separately considered, but not a positive history of suicide alone, were significantly associated with a comorbidity with several anxiety disorders and inversely associated with age of onset. The clinical implications as well as the limitations of our findings are discussed.

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

Machine learning spatial geometry from entanglement features

Science.gov (United States)

You, Yi-Zhuang; Yang, Zhao; Qi, Xiao-Liang

2018-02-01

Motivated by the close relations of the renormalization group with both the holography duality and the deep learning, we propose that the holographic geometry can emerge from deep learning the entanglement feature of a quantum many-body state. We develop a concrete algorithm, call the entanglement feature learning (EFL), based on the random tensor network (RTN) model for the tensor network holography. We show that each RTN can be mapped to a Boltzmann machine, trained by the entanglement entropies over all subregions of a given quantum many-body state. The goal is to construct the optimal RTN that best reproduce the entanglement feature. The RTN geometry can then be interpreted as the emergent holographic geometry. We demonstrate the EFL algorithm on a 1D free fermion system and observe the emergence of the hyperbolic geometry (AdS3 spatial geometry) as we tune the fermion system towards the gapless critical point (CFT2 point).

BioModels: Content, Features, Functionality, and Use

Science.gov (United States)

Juty, N; Ali, R; Glont, M; Keating, S; Rodriguez, N; Swat, MJ; Wimalaratne, SM; Hermjakob, H; Le Novère, N; Laibe, C; Chelliah, V

2015-01-01

BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales. The resource provides access to over 1,200 models described in literature and over 140,000 models automatically generated from pathway resources. Most model components are cross-linked with external resources to facilitate interoperability. A large proportion of models are manually curated to ensure reproducibility of simulation results. This tutorial presents BioModels' content, features, functionality, and usage. PMID:26225232

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

In vivo quantification of intracerebral GABA by single-voxel 1H-MRS-How reproducible are the results?

International Nuclear Information System (INIS)

Bogner, W.; Gruber, S.; Doelken, M.; Stadlbauer, A.; Ganslandt, O.; Boettcher, U.; Trattnig, S.; Doerfler, A.; Stefan, H.; Hammen, T.

2010-01-01

Gamma aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the human brain. It plays a decisive role in a variety of nervous system disorders, such as anxiety disorders, epilepsy, schizophrenia, insomnia, and many others. The reproducibility of GABA quantification results obtained with a single-voxel spectroscopy J-difference editing sequence with Point Resolved Spectroscopy localization (MEGA-PRESS) was determined on a 3.0 Tesla MR scanner in healthy adults. Eleven volunteers were measured in long- and short-term intervals. Intra- and inter-subject reproducibility were evaluated. Internal referencing of GABA+ to total creatine (tCr) and water (H 2 O), as well as two different post-processing methods for the evaluation (signal integration and time-domain fitting) were compared. In all subjects lower coefficient of variation and therefore higher reproducibility can be observed for fitting compared to integration. The GABA+/tCr ratio performs better than the GABA+/H 2 O ratio or GABA+ without internal referencing for both fitting and integration (GABA+/tCr: 13.3% and 17.0%; GABA+/H 2 O: 15.0% and 17.8%; GABA+: 19.2% and 21.7%). Four-day measurements on three subjects showed higher intra- than inter-subject reproducibility (GABA+/tCr ∼10-12%). With a coefficient of variation of about 13% for inter-subject and 10-12% for intra-subject variability of GABA+/tCr, this technique seems to be a precise tool that can detect GABA confidently. The results of this study show the reproducibility limitations of GABA quantification in vivo, which are necessary for further clinical studies.

Evolvix BEST Names for semantic reproducibility across code2brain interfaces.

Science.gov (United States)

Loewe, Laurence; Scheuer, Katherine S; Keel, Seth A; Vyas, Vaibhav; Liblit, Ben; Hanlon, Bret; Ferris, Michael C; Yin, John; Dutra, Inês; Pietsch, Anthony; Javid, Christine G; Moog, Cecilia L; Meyer, Jocelyn; Dresel, Jerdon; McLoone, Brian; Loberger, Sonya; Movaghar, Arezoo; Gilchrist-Scott, Morgaine; Sabri, Yazeed; Sescleifer, Dave; Pereda-Zorrilla, Ivan; Zietlow, Andrew; Smith, Rodrigo; Pietenpol, Samantha; Goldfinger, Jacob; Atzen, Sarah L; Freiberg, Erika; Waters, Noah P; Nusbaum, Claire; Nolan, Erik; Hotz, Alyssa; Kliman, Richard M; Mentewab, Ayalew; Fregien, Nathan; Loewe, Martha

2017-01-01

Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general-purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long-term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder-brains to reader-brains by code alone). Semantic reproducibility is often assumed until confusing synonyms degrade modeling in biology to deciphering exercises. We highlight empirical naming priorities from diverse individuals and roles of names in different modes of computing to show how naming easily becomes impossibly difficult. We present the Evolvix BEST (Brief, Explicit, Summarizing, Technical) Names concept for reducing naming priority conflicts, test it on a real challenge by naming subfolders for the Project Organization Stabilizing Tool system, and provide naming questionnaires designed to facilitate C2B debugging by improving names used as keywords in a stabilizing programming language. Our experiences inspired us to develop Evolvix using a flipped programming language design approach with some unexpected features and BEST Names at its core. © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

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...

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

[Inter-laboratory reproducibility of pulsed-field electrophoresis for the study of 12 types of Pseudomonas aeruginosa].

Science.gov (United States)

Foissaud, V; Puyhardy, J M; Chapalain, J C; Salord, H; Depina, J J; Morillon, M; Nicolas, P; Perrier-Gros-Claude, J D

1999-12-01

The increasing hospital-to-hospital transmission of multiple drug-resistant bacteria is a major concern for bacteriology laboratories involved in nosocomial infection control. The interlaboratory reproducibility of pulsed-field gel electrophoresis (PFGE) for Pseudomonas aeruginosa typing was evaluated by asking four hospital laboratories (two in Lyon, one in Brest, and one in Marseille) to study 11 P. aeruginosa isolates, some of which were epidemiologically related, and the reference strain ATCC 27853. Two laboratories used the Genepath system, one the Chef DR II, system, and one the Chef Mapper system, Bio-Rad, restriction/Spe I. Profiles were read visually and by computerized comparison of restriction band molecular weights (Taxotron, software, PAD Grimont, Pasteur Institute, Paris, France). These two methods led to similar epidemiological conclusions. However, centralization of the data showed poor center-to-center reproducibility due to inadequate standardization of the procedure.

Production process reproducibility and product quality consistency of transient gene expression in HEK293 cells with anti-PD1 antibody as the model protein.

Science.gov (United States)

Ding, Kai; Han, Lei; Zong, Huifang; Chen, Junsheng; Zhang, Baohong; Zhu, Jianwei

2017-03-01

Demonstration of reproducibility and consistency of process and product quality is one of the most crucial issues in using transient gene expression (TGE) technology for biopharmaceutical development. In this study, we challenged the production consistency of TGE by expressing nine batches of recombinant IgG antibody in human embryonic kidney 293 cells to evaluate reproducibility including viable cell density, viability, apoptotic status, and antibody yield in cell culture supernatant. Product quality including isoelectric point, binding affinity, secondary structure, and thermal stability was assessed as well. In addition, major glycan forms of antibody from different batches of production were compared to demonstrate glycosylation consistency. Glycan compositions of the antibody harvested at different time periods were also measured to illustrate N-glycan distribution over the culture time. From the results, it has been demonstrated that different TGE batches are reproducible from lot to lot in overall cell growth, product yield, and product qualities including isoelectric point, binding affinity, secondary structure, and thermal stability. Furthermore, major N-glycan compositions are consistent among different TGE batches and conserved during cell culture time.

Emergent interfaces for feature modularization

CERN Document Server

Ribeiro, Márcio; Brabrand, Claus

2014-01-01

Developers frequently introduce errors into software systems when they fail to recognise module dependencies. Using forty-three software families and Software Product Lines (SPLs), where the majority are commonly used in industrial practice, the authors reports on the feature modularization problem and provides a study of how often it may occur in practice. To solve the problem they present the concept of emergent feature modularization which aims to establish contracts between features to prevent developers from breaking other features when performing a maintenance task.

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.

Discriminative topological features reveal biological network mechanisms

Directory of Open Access Journals (Sweden)

Levovitz Chaya

2004-11-01

Full Text Available Abstract Background Recent genomic and bioinformatic advances have motivated the development of numerous network models intending to describe graphs of biological, technological, and sociological origin. In most cases the success of a model has been evaluated by how well it reproduces a few key features of the real-world data, such as degree distributions, mean geodesic lengths, and clustering coefficients. Often pairs of models can reproduce these features with indistinguishable fidelity despite being generated by vastly different mechanisms. In such cases, these few target features are insufficient to distinguish which of the different models best describes real world networks of interest; moreover, it is not clear a priori that any of the presently-existing algorithms for network generation offers a predictive description of the networks inspiring them. Results We present a method to assess systematically which of a set of proposed network generation algorithms gives the most accurate description of a given biological network. To derive discriminative classifiers, we construct a mapping from the set of all graphs to a high-dimensional (in principle infinite-dimensional "word space". This map defines an input space for classification schemes which allow us to state unambiguously which models are most descriptive of a given network of interest. Our training sets include networks generated from 17 models either drawn from the literature or introduced in this work. We show that different duplication-mutation schemes best describe the E. coli genetic network, the S. cerevisiae protein interaction network, and the C. elegans neuronal network, out of a set of network models including a linear preferential attachment model and a small-world model. Conclusions Our method is a first step towards systematizing network models and assessing their predictability, and we anticipate its usefulness for a number of communities.

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

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.

Clinical features of and risk factors for major depression with history of postpartum episodes in Han Chinese women: A retrospective study.

Science.gov (United States)

Yang, Fuzhong; Gardner, Charles O; Bigdeli, Tim; Gao, Jingfang; Zhang, Zhen; Tao, Ming; Liu, Ying; Li, Youhui; Wang, Gang; Shi, Jianguo; Gao, Chengge; Zhang, Kerang; Li, Kan; Wang, Xumei; Liu, Lanfen; Sun, Jing; Du, Bo; Shi, Shenxun; Zhang, Jingbei; Wu, Wenyuan; Wang, Xueyi; Shen, Jianhua; Liu, Tiebang; Gu, Danhua; Liang, Wei; Deng, Hong; Pan, Jiyang; Yang, Lijun; Jian, Hu; Jiang, Guoqin; Meng, Huaqing; Miao, Guodong; Li, Yi; Hu, Chunmei; Huang, Guoping; Zhang, Yutang; Chen, Yunchun; Ha, Baowei; Gao, Shu; Fang, Xiang; Mei, Qiyi; Hong, Xiaohong; Yang, Donglin; Liu, Tieqiao; Fengyu, Yu; Zhong, Hui; Sang, Hong; Chen, Guibing; Cai, Min; Song, Yan; Dong, Jicheng; Shen, Zhenmin; Zhang, Wei; Wang, Xiaoping; Pan, Runde; Liu, Xiaojuan; Li, Yi; Liu, Zhengrong; Zhang, Qiwen; Li, Gongying; Flint, Jonathan; Kendler, Kenneth S

2015-09-01

We sought to investigate the clinical features of and risk factors for recurrent major depression (MD) with history of postpartum episodes (PPD) in Han Chinese women and the differences between first-onset postpartum MD (MD that has its first lifetime depressive episode in the postpartum period) and first-onset non-postpartum MD (MD with history of PPD and has its first lifetime depressive episode in a period other than postpartum). Data were derived from the China, Oxford and Virginia Commonwealth University Experimental Research on Genetic Epidemiology (CONVERGE) study (N=6017 cases) and analyzed in two steps. We first examined the clinical features of and risk factors for MD patients with (N=981) or without (N=4410) a history of PPD. We then compared the differences between first-onset postpartum MD (N=583) and first-onset non-postpartum MD (N=398) in those with a history of PPD. Linear, logistic and multinomial logistic models were employed to measure the associations. A history of PPD was associated with more guilt feelings, greater psychiatric comorbidity, higher neuroticism, earlier onset and more chronicity (OR 0.2-2.8). Severe premenstrual symptoms (PMS) and more childbirths increased the risk of PPD, as did a family history of MD, childhood sexual abuse, stressful life events and lack of social support (OR 1.1-1.3). In the MD with history of PPD subsample, first-onset postpartum MD was associated with fewer recurrent major depressive episodes, less psychiatric comorbidity, lower neuroticism, less severe PMS and fewer disagreements with their husbands (OR 0.5-0.8), but more childbirths (OR 1.2). Data were obtained retrospectively through interview and recall bias may have affected the results. MD with history of PPD in Han Chinese women is typically chronic and severe, with particular risk factors including severe PMS and more childbirths. First-onset postpartum MD and first-onset non-postpartum MD can be partly differentiated by their clinical features

Peptides reproducibly released by in vivo digestion of beef meat and trout flesh in pigs.

Science.gov (United States)

Bauchart, Caroline; Morzel, Martine; Chambon, Christophe; Mirand, Philippe Patureau; Reynès, Christelle; Buffière, Caroline; Rémond, Didier

2007-12-01

Characterisation and identification of peptides (800 to 5000 Da) generated by intestinal digestion of fish or meat were performed using MS analyses (matrix-assisted laser desorption ionisation time of flight and nano-liquid chromatography electrospray-ionisation ion trap MS/MS). Four pigs fitted with cannulas at the duodenum and jejunum received a meal exclusively made of cooked Pectoralis profundus beef meat or cooked trout fillets. A protein-free meal, made of free amino acids, starch and fat, was used to identify peptides of endogenous origin. Peptides reproducibly detected in digesta (i.e. from at least three pigs) were evidenced predominantly in the first 3 h after the meal. In the duodenum, most of the fish- and meat-derived peptides were characteristic of a peptic digestion. In the jejunum, the majority of peptides appeared to result from digestion by chymotrypsin and trypsin. Despite slight differences in gastric emptying kinetics and overall peptide production, possibly in relation to food structure and texture, six and four similar peptides were released after ingestion of fish or meat in the duodenum and jejunum. A total of twenty-six different peptides were identified in digesta. All were fragments of major structural (actin, myosin) or sarcoplasmic (creatine kinase, glyceraldehyde-3-phosphate dehydrogenase and myoglobin) muscle proteins. Peptides were short ( digestion, some of them can be reproducibly observed in intestinal digesta.

Discrete Feature Model (DFM) User Documentation

Energy Technology Data Exchange (ETDEWEB)

Geier, Joel (Clearwater Hardrock Consulting, Corvallis, OR (United States))

2008-06-15

This manual describes the Discrete-Feature Model (DFM) software package for modelling groundwater flow and solute transport in networks of discrete features. A discrete-feature conceptual model represents fractures and other water-conducting features around a repository as discrete conductors surrounded by a rock matrix which is usually treated as impermeable. This approximation may be valid for crystalline rocks such as granite or basalt, which have very low permeability if macroscopic fractures are excluded. A discrete feature is any entity that can conduct water and permit solute transport through bedrock, and can be reasonably represented as a piecewise-planar conductor. Examples of such entities may include individual natural fractures (joints or faults), fracture zones, and disturbed-zone features around tunnels (e.g. blasting-induced fractures or stress-concentration induced 'onion skin' fractures around underground openings). In a more abstract sense, the effectively discontinuous nature of pathways through fractured crystalline bedrock may be idealized as discrete, equivalent transmissive features that reproduce large-scale observations, even if the details of connective paths (and unconnected domains) are not precisely known. A discrete-feature model explicitly represents the fundamentally discontinuous and irregularly connected nature of systems of such systems, by constraining flow and transport to occur only within such features and their intersections. Pathways for flow and solute transport in this conceptualization are a consequence not just of the boundary conditions and hydrologic properties (as with continuum models), but also the irregularity of connections between conductive/transmissive features. The DFM software package described here is an extensible code for investigating problems of flow and transport in geological (natural or human-altered) systems that can be characterized effectively in terms of discrete features. With this

Discrete Feature Model (DFM) User Documentation

International Nuclear Information System (INIS)

Geier, Joel

2008-06-01

This manual describes the Discrete-Feature Model (DFM) software package for modelling groundwater flow and solute transport in networks of discrete features. A discrete-feature conceptual model represents fractures and other water-conducting features around a repository as discrete conductors surrounded by a rock matrix which is usually treated as impermeable. This approximation may be valid for crystalline rocks such as granite or basalt, which have very low permeability if macroscopic fractures are excluded. A discrete feature is any entity that can conduct water and permit solute transport through bedrock, and can be reasonably represented as a piecewise-planar conductor. Examples of such entities may include individual natural fractures (joints or faults), fracture zones, and disturbed-zone features around tunnels (e.g. blasting-induced fractures or stress-concentration induced 'onion skin' fractures around underground openings). In a more abstract sense, the effectively discontinuous nature of pathways through fractured crystalline bedrock may be idealized as discrete, equivalent transmissive features that reproduce large-scale observations, even if the details of connective paths (and unconnected domains) are not precisely known. A discrete-feature model explicitly represents the fundamentally discontinuous and irregularly connected nature of systems of such systems, by constraining flow and transport to occur only within such features and their intersections. Pathways for flow and solute transport in this conceptualization are a consequence not just of the boundary conditions and hydrologic properties (as with continuum models), but also the irregularity of connections between conductive/transmissive features. The DFM software package described here is an extensible code for investigating problems of flow and transport in geological (natural or human-altered) systems that can be characterized effectively in terms of discrete features. With this software, the

ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments

Science.gov (United States)

Mavelli, Fabio; Ruiz-Mirazo, Kepa

2010-09-01

'ENVIRONMENT' is a computational platform that has been developed in the last few years with the aim to simulate stochastically the dynamics and stability of chemically reacting protocellular systems. Here we present and describe some of its main features, showing how the stochastic kinetics approach can be applied to study the time evolution of reaction networks in heterogeneous conditions, particularly when supramolecular lipid structures (micelles, vesicles, etc) coexist with aqueous domains. These conditions are of special relevance to understand the origins of cellular, self-reproducing compartments, in the context of prebiotic chemistry and evolution. We contrast our simulation results with real lab experiments, with the aim to bring together theoretical and experimental research on protocell and minimal artificial cell systems.

Simulation of Synoptic Scale Circulation Features over Southern Africa Using GCMS

International Nuclear Information System (INIS)

Browne, Nana Ama Kum; Abiodun, Babatunde Joseph; Tadross, Mark; Hewitson, Bruce

2009-11-01

Two global models (HadAM3: The Hadley Centre Atmospheric Model version 3 and CAM3: The Community Atmospheric model version 3) have been studied regarding their capabilities in reproducing the small scale features over southern Africa compared with the NCEP reanalysis. In this study, geopotential height at 500hPa and 850hPa pressure levels are used to investigate the variability of small scale circulation features over southern Africa. The investigation took into consideration the magnitude of the models standard deviations. Most of the results were linked with rainfall and temperature over the region. It was found that the standardized anomalies in the geopotential height at the 500hPa pressure level are in phase with that of rainfall. In contrast, the standardized anomalies of 850hPa pressure level geopotential height are out of phase with the standardized anomalies of rainfall and temperature. In addition, the models are able to capture the variation in the mean cut-off lows, number of days with deep tropical lows and number of days with Tropical Temperate Troughs (TTTs) quite well. However, the models could not capture the number of days with temperate lows very well. Generally, the models are able to reproduce the synoptic scale circulation features which are crucial for reliable seasonal forecast over southern Africa. (author)

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.

Roles of different IRES-dependent FGF2 isoforms in the acquisition of the major aggressive features of human metastatic melanoma.

Science.gov (United States)

Andreucci, Elena; Bianchini, Francesca; Biagioni, Alessio; Del Rosso, Mario; Papucci, Laura; Schiavone, Nicola; Magnelli, Lucia

2017-01-01

Fibroblast growth factor 2 (FGF2) is involved in many physiological and pathological processes. Fgf2 deregulation contributes to the acquisition of malignant features of melanoma and other cancers. FGF2 is an alternative translation product expressed as five isoforms, a low-molecular-weight (18 KDa) and four high-molecular-weight (22, 22.5, 24, 34 KDa) isoforms, with different subcellular distributions. An internal ribosomal entry site (IRES) in its mRNA controls the translation of all the isoforms with the exception for the cap-dependent 34 KDa. The 18-KDa isoform has been extensively studied, while very few is known about the roles of high molecular weight isoforms. FGF2 is known to promote melanoma development and progression. To disclose the differential contribution of FGF2 isoforms in melanoma, we forced the expression of IRES-dependent low-molecular-weight (LMW, 18 KDa) and high-molecular-weight (HMW, 22, 22.5, 24 KDa) isoforms in a human metastatic melanoma cell line. This comparative study highlights that, while LMW isoform confers stem-like features to melanoma cells and promotes angiogenesis, HMW isoforms induce higher migratory ability and contribute to tumor perfusion by promoting vasculogenic mimicry (VM) when endothelial cell-driven angiogenesis is lacking. To conclude, FGF2 isoforms mainly behave in specific, antithetical manners, but can cooperate in different steps of tumor progression, providing melanoma cells with major malignant features. FGF2 is an alternative translation product expressed as different isoforms termed LMW and HMW. FGF2 is involved in melanoma development and progression. HMW FGF2 isoforms enhance in vitro motility of melanoma cells. LMW FGF2 confers stem-like features and increases in vivo metastasization. LMW FGF2 promotes angiogenesis while HMW FGF2 induces vasculogenic mimicry.

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)

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.

Investigation about the thermal features of the ovens used for thermoluminescence; Indagine sulle specifiche dei forni usati per i trattamenti termici dei rilevatori a termoluminescenza

Energy Technology Data Exchange (ETDEWEB)

Scarpa, G; Caporali, C; Moscati, M [ENEA - Area Energia, Ambiente e Salute, Centro Ricerche Energia, Casaccia, Rome (Italy)

1991-02-15

The present paper reports the results of an investigation carried out by the PAS-FIBI-DOSIBIO laboratory (ENEA, Casaccia, Roma) about the thermal features of the ovens used for annealing treatments of TL dosemeters. A total number of 45 commercial ovens and muffle furnaces were studied. belonging to 24 Italian Health Physics laboratories. The investigation has shown that the majority of the ovens do not possess a degree of accuracy, stability, uniformity and reproducibility suitable for their use in the field of thermoluminescence dosimetry. Practical suggestions are also given in order to reduce the effects of some of the negative characteristics found in most ovens. (author)

Measurement of Trabecular Bone Parameters in Porcine Vertebral Bodies Using Multidetector CT: Evaluation of Reproducibility of 3-Dimensional CT Histomorphometry

Energy Technology Data Exchange (ETDEWEB)

Hong, Sung Hwan; Goo, Jin Mo [Dept. of Radiology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul (Korea, Republic of); Moon Kyung Chul [Dept. of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul (Korea, Republic of); An, Sang Bu [Dept. of radiology, National Cancer Center, Goyang (Korea, Republic of); Kim, Kwang Gi [Dept. of Biomedical Engineering, Division of Basic and Applied Sciences, National Cancer Center, Goyang (Korea, Republic of)

2011-05-15

To evaluate the reproducibility of 3-dimensional histomorphometry for the microarchitecture analysis of trabecular bone parameters using multidetector computed tomography (MDCT). Thirty-six specimens from porcine vertebral bodies were imaged five times with a 64- detector row MDCT system using the same scan protocols. Locations of the specimens were nearly identical through the scans. Three-dimensional structural parameters of trabecular bone were derived from the five data sets using image analyzing software. The features measured by the analysis programs were trabecular bone volume, trabecular bone volume/tissue volume, trabecular thickness, trabecular separation, trabecular number, trabecular bone pattern factor, structural model index. The structural trabecular parameters showed excellent reproducibility through repeated scanning. Intraclass correlation coefficients of all seven structural parameters were in the range of 0.998 to 1.000. Coefficients of variation of the six structural parameters, excluding structural model index, were not over 1.6%. The measurement of the trabecular structural parameters using multidetector CT and three-dimensional histomophometry analysis program was validated and showed excellent reproducibility. This method could be used as a noninvasive and easily available test in a clinical setting.

Ultrasound characteristics of gouty tophi in the olecranon bursa and evaluation of their reproducibility

International Nuclear Information System (INIS)

Fernandes, Eloy A.; Lopes, Matheus G.; Mitraud, Sônia A.V.; Ferrari, Antonio J.L.; Fernandes, Artur R.C.

2012-01-01

Objectives: To describe the ultrasound characteristics of gouty tophi in the olecranon bursa and to evaluate their reproducibility. Methods: A prospective study of the ultrasound features of 35 sites of tophi nodulations in the elbows of 31 men (mean 54.6 years). The findings were evaluated dynamically following pre-established standards. The static images were evaluated by another radiologist and were reviewed by the first examiner. Results: The most frequent characteristics of tophi are: hyperechogenicity (91.7%), poorly defined contours (88.6%), multiple grouped nodules (85.6%) and heterogeneity (68.6%). Intra-observer agreement is almost perfect for echogenicity (K = 1.0), moderate for the involvement of the olecranon bursa (K = 0.47) and fair for other characteristics. Inter-observer agreement is substantial for the echogenicity (K = 0.65), fair for the echotexture (K = 0.27) and the presence of a perilesional hypoechoic halo (K = 0.34) and slight for other characteristics. Conclusions: The most frequent characteristic of tophi is hyperechogenicity. The intra-observer and inter-observer concordance for echogenicity are almost perfect and substantial, respectively. Knowledge of characteristics of the tophi in the elbow and their intra and inter-observer reproducibility may assist in establishing parameters for monitoring treatment and setting up criteria for differential diagnosis of processes involving the olecraneon bursa.

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....

Major life events and development of major depression in Parkinson's disease patients

DEFF Research Database (Denmark)

Rod, Naja Hulvej; Bordelon, Y; Thompson, A

2012-01-01

BACKGROUND AND PURPOSE: Non-motor symptoms including depression are important features of Parkinson's disease (PD). We aim to address the relationship between major life events and depression amongst PD patients free of depressive symptoms at baseline. METHODS: New-onset PD patients from California...... were recruited in 2001-2007 and followed up for 3-4 years. The participants (n = 221) were examined by neurologists and responded to comprehensive interviews that included major life events, social support, and coping measures from validated scales. Major depression was assessed using the Structured...... Clinical Interview for the DSM-IV depression module (SCID). RESULTS: More than half of all patients had experienced major life events since diagnosed with PD, and 22 patients developed a major depression. The number of life events was associated with risk of depression in an exposure-dependent manner...

Rapid Quantification of Major Volatile Metabolites in Fermented Food and Beverages Using Gas Chromatography-Mass Spectrometry.

Science.gov (United States)

Pinu, Farhana R; Villas-Boas, Silas G

2017-07-26

Here we present a method for the accurate quantification of major volatile metabolites found in different food and beverages, including ethanol, acetic acid and other aroma compounds, using gas chromatography coupled to mass spectrometry (GC-MS). The method is combined with a simple sample preparation procedure using sodium chloride and anhydrous ethyl acetate. The GC-MS analysis was accomplished within 4.75 min, and over 80 features were detected, of which 40 were positively identified using an in-house and a commercialmass spectrometry (MS) library. We determined different analytical parameters of these metabolites including the limit of detection (LOD), limit of quantitation (LOQ) and range of quantification. In order to validate the method, we also determined detailed analytical characteristics of five major fermentation end products including ethanol, acetic acid, isoamyl alcohol, ethyl-L-lactate and, acetoin. The method showed very low technical variability for the measurements of these metabolites in different matrices (<3%) with an excellent accuracy (100% ± 5%), recovery (100% ± 10%), reproducibility and repeatability [Coefficient of variation (CV) 1-10%)]. To demonstrate the applicability of the method, we analysed different fermented products including balsamic vinegars, sourdough, distilled (whisky) and non-distilled beverages (wine and beer).

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.)

In vivo quantification of intracerebral GABA by single-voxel {sup 1}H-MRS-How reproducible are the results?

Energy Technology Data Exchange (ETDEWEB)

Bogner, W. [MR Centre of Excellence, Department of Radiology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna (Austria)], E-mail: wolfgang@nmr.at; Gruber, S. [MR Centre of Excellence, Department of Radiology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna (Austria)], E-mail: stephan@nmr.at; Doelken, M. [Department of Neuroradiology, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Austria)], E-mail: marc.doelken@uk-erlangen.de; Stadlbauer, A. [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Austria)], E-mail: andi@nmr.at; Ganslandt, O. [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Austria)], E-mail: oliver.ganslandt@uk-erlangen.de; Boettcher, U. [Siemens Medical Solution, Karl-Schall Str. 6, D-91052 Erlangen (Germany)], E-mail: uwe.boettcher@siemens.com; Trattnig, S. [MR Centre of Excellence, Department of Radiology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna (Austria)], E-mail: siegfried.trattnig@meduniwien.ac.at; Doerfler, A. [Department of Neuroradiology, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Austria)], E-mail: a.doerfler@nrad.imed.uni-erlangen.de; Stefan, H. [Center Epilepsy Erlangen (ZEE), Department of Neurology, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Germany)], E-mail: Hermann.Stefan@uk-erlangen.de; Hammen, T. [Center Epilepsy Erlangen (ZEE), Department of Neurology, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Germany)], E-mail: thilo.hammen@uk-erlangen.de

2010-03-15

Gamma aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the human brain. It plays a decisive role in a variety of nervous system disorders, such as anxiety disorders, epilepsy, schizophrenia, insomnia, and many others. The reproducibility of GABA quantification results obtained with a single-voxel spectroscopy J-difference editing sequence with Point Resolved Spectroscopy localization (MEGA-PRESS) was determined on a 3.0 Tesla MR scanner in healthy adults. Eleven volunteers were measured in long- and short-term intervals. Intra- and inter-subject reproducibility were evaluated. Internal referencing of GABA+ to total creatine (tCr) and water (H{sub 2}O), as well as two different post-processing methods for the evaluation (signal integration and time-domain fitting) were compared. In all subjects lower coefficient of variation and therefore higher reproducibility can be observed for fitting compared to integration. The GABA+/tCr ratio performs better than the GABA+/H{sub 2}O ratio or GABA+ without internal referencing for both fitting and integration (GABA+/tCr: 13.3% and 17.0%; GABA+/H{sub 2}O: 15.0% and 17.8%; GABA+: 19.2% and 21.7%). Four-day measurements on three subjects showed higher intra- than inter-subject reproducibility (GABA+/tCr {approx}10-12%). With a coefficient of variation of about 13% for inter-subject and 10-12% for intra-subject variability of GABA+/tCr, this technique seems to be a precise tool that can detect GABA confidently. The results of this study show the reproducibility limitations of GABA quantification in vivo, which are necessary for further clinical studies.

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 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

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.

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.

Using thermodynamic data to reproduce main seismic features of transition zone

Science.gov (United States)

Fomin, Ilya; Saukko, Anna; Edwards, Paul; Schiffer, Christian

2016-04-01

Most of the seismic tomography studies nowadays are based on comprehensive models with optimization of lots of parameters. These models are able to resolve very subtle features of the Earth's mantle, but the influence of each specific parameter is not seen directly. In our research we try to minimize the number of processed parameters to produce simple synthetic cases. The main goals of our model are to see how water content influences the depth of the transition zone, and if melting at the transition zone is plausible. We also attempt to see how water content and the presence of melts influence the signal strength of the transition zone in receiver functions. Our MATLAB-code calculates phase assemblage according to specific temperature and pressure within 2D numerical domain (e.g. 300x700 km). Phase properties are calculated with database of Stixrude and Lithgow-Bertelloni [2011], with corrections for water impact on elastic constants according to Liu et al., [2012]. We use the mantle phase composition 55% garnet and 45% olivine-polymorph, soliduses by Ohtani et al. [2004] and melt properties by Sakamaki et al. [2006]. These data are used to calculate seismic velocities and, furthermore, receiver functions with standard routines (e.g.[Schiffer et al., 2012]). Model predicts Vs within 5 to 5.5 km/s and Vp around 9.5-10 km/s within transition zone (Vp/Vs = 1.84-1.87), which is close to standard values. The presence of water enlarges the wadsleyite region, but also dampens the peak of receiver functions down to background level. Increase in water content causes melting at much shallower depths. Using a normal thermal gradient, we can get up to 10% of melt at depths around 390 km with 80% of water saturation, shown by a negative anomaly on receiver functions. This result is similar to data obtained for Afar Plateau [Thompson et al., 2015]. With cratonic thermal gradient, the olivine-wadsleyite transition and corresponding melt layer appear at depths around 350 km

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)

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.

Bone marrow edema-like lesions change in volume in the majority of patients with osteoarthritis; associations with clinical features

Energy Technology Data Exchange (ETDEWEB)

Kornaat, Peter R.; Sharma, Ruby; Bloem, Johan L.; Watt, Iain [Leiden University Medical Center, Department of Radiology, Leiden (Netherlands); Kloppenburg, Margreet; Botha-Scheepers, Stella A. [Leiden University Medical Center, Department of Rheumatology, Leiden (Netherlands); Hellio le Graverand, Marie-Pierre [Pfizer Groton, Groton, CT (United States); Coene, L.N.J.E.M. [Haga Hospital, Department of Orthopaedic Surgery, The Hague (Netherlands)

2007-12-15

It has been suggested that bone marrow edema-like (BME) lesions in the knee are associated with progression of osteoarthritis (OA). The purpose of our study in patients with OA was to evaluate prospectively changes of BME lesions over 2 years and their relationship with clinical features. Magnetic resonance (MR) images of the knee were obtained from 182 patients (20% male; aged 43-76 years; mean age 59 years) who had been diagnosed with familial symptomatic OA at multiple joint sites. MR images were made at baseline and at 2 years follow-up. BME lesions in 2 years were associated with clinical features assessed by Western Ontario and McMaster Universities Osteoarthritis (WOMAC) scores. A total of 327 BME lesions were recorded. Total size of BME lesions changed in 90 patients (66%). Size of individual lesions changed in 147 foci (45%): new lesions appeared in 69 (21%), existing lesions disappeared in 32 (10%), increased in size in 26 (8%) and decreased in size in 20 (6%) lesions. Increase or decrease of BME lesions, over a 2-year time period, was not associated with severity of WOMAC scores. BME lesions fluctuated in the majority of patients with OA over a 2-year time period. These changes were not associated with severity of WOMAC scores at the study end point. (orig.)

Bone marrow edema-like lesions change in volume in the majority of patients with osteoarthritis; associations with clinical features

International Nuclear Information System (INIS)

Kornaat, Peter R.; Sharma, Ruby; Bloem, Johan L.; Watt, Iain; Kloppenburg, Margreet; Botha-Scheepers, Stella A.; Hellio le Graverand, Marie-Pierre; Coene, L.N.J.E.M.

2007-01-01

It has been suggested that bone marrow edema-like (BME) lesions in the knee are associated with progression of osteoarthritis (OA). The purpose of our study in patients with OA was to evaluate prospectively changes of BME lesions over 2 years and their relationship with clinical features. Magnetic resonance (MR) images of the knee were obtained from 182 patients (20% male; aged 43-76 years; mean age 59 years) who had been diagnosed with familial symptomatic OA at multiple joint sites. MR images were made at baseline and at 2 years follow-up. BME lesions in 2 years were associated with clinical features assessed by Western Ontario and McMaster Universities Osteoarthritis (WOMAC) scores. A total of 327 BME lesions were recorded. Total size of BME lesions changed in 90 patients (66%). Size of individual lesions changed in 147 foci (45%): new lesions appeared in 69 (21%), existing lesions disappeared in 32 (10%), increased in size in 26 (8%) and decreased in size in 20 (6%) lesions. Increase or decrease of BME lesions, over a 2-year time period, was not associated with severity of WOMAC scores. BME lesions fluctuated in the majority of patients with OA over a 2-year time period. These changes were not associated with severity of WOMAC scores at the study end point. (orig.)

Reproducibility of quantitative susceptibility mapping in the brain at two field strengths from two vendors.

Science.gov (United States)

Deh, Kofi; Nguyen, Thanh D; Eskreis-Winkler, Sarah; Prince, Martin R; Spincemaille, Pascal; Gauthier, Susan; Kovanlikaya, Ilhami; Zhang, Yan; Wang, Yi

2015-12-01

To assess the reproducibility of brain quantitative susceptibility mapping (QSM) in healthy subjects and in patients with multiple sclerosis (MS) on 1.5 and 3T scanners from two vendors. Ten healthy volunteers and 10 patients were scanned twice on a 3T scanner from one vendor. The healthy volunteers were also scanned on a 1.5T scanner from the same vendor and on a 3T scanner from a second vendor. Similar imaging parameters were used for all scans. QSM images were reconstructed using a recently developed nonlinear morphology-enabled dipole inversion (MEDI) algorithm with L1 regularization. Region-of-interest (ROI) measurements were obtained for 20 major brain structures. Reproducibility was evaluated with voxel-wise and ROI-based Bland-Altman plots and linear correlation analysis. ROI-based QSM measurements showed excellent correlation between all repeated scans (correlation coefficient R ≥ 0.97), with a mean difference of less than 1.24 ppb (healthy subjects) and 4.15 ppb (patients), and 95% limits of agreements of within -25.5 to 25.0 ppb (healthy subjects) and -35.8 to 27.6 ppb (patients). Voxel-based QSM measurements had a good correlation (0.64 ≤ R ≤ 0.88) and limits of agreements of -60 to 60 ppb or less. Brain QSM measurements have good interscanner and same-scanner reproducibility for healthy and MS subjects, respectively, on the systems evaluated in this study. © 2015 Wiley Periodicals, Inc.

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.

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.

A Closer Look at Deep Learning Neural Networks with Low-level Spectral Periodicity Features

DEFF Research Database (Denmark)

Sturm, Bob L.; Kereliuk, Corey; Pikrakis, Aggelos

2014-01-01

Systems built using deep learning neural networks trained on low-level spectral periodicity features (DeSPerF) reproduced the most “ground truth” of the systems submitted to the MIREX 2013 task, “Audio Latin Genre Classification.” To answer why this was the case, we take a closer look...

First Report on Isolation and Characterization of Leishmania major from Meriones hurrianae (Rodentia: Gerbillidae) of A Rural Cutaneous leishmaniasis Focus in South-Eastern Iran.

Science.gov (United States)

Kassiri, Hamid; Naddaf, Saied Reza; Javadian, Ezat-Aldin; Mohebali, Mehdi

2013-09-01

Zoonotic Cutaneous Leishmaniasis (ZCL) is an endemic health problem in many rural areas of Iran, with doubled number of incidences over the last decade. Different species of rodents serve as natural reservoir host for ZCL. The disease is considered as a major health problem in rural areas of Mirjaveh, Chabahar, and Konarak Counties of Sistan va Baluchistan Province. This study describes the identity of Leishmania species, isolated from Meriones hurrianae from Chabahar County using RAPD-PCR methodology. Rodents were entrapped by live traps baited with roasted walnut, tomato, and cucumber during spring and summer. All rodents were identified based on external features including fur color, ears characteristics, tail length, hind feet, body measurements, and internal features of teeth and cranium. Giemsa-stained impressions from rodents' ears were examined for amastigotes microscopically. The samples from infected rodents were cultured in NNN+LIT medium and then the harvested parasites at the stationary phase were subjected to DNA extraction followed by amplification with RAPD-PCR. All the 28 entrapped animals were identified as M. hurrianae. Five animals showed to harbor Leishmania parasite by microscopy. Leishmania DNA isolated from five M. hurrianae produced distinctive bands of L. major with four primers. However, the products that were amplified with primers AB1-07, 327, and 329 were stable and reproducible. This is the first report on the isolation and identification of L. major from M. hurrianae from Iran. Regarding infection rate of 17.8%, M. hurrianae seems to play the major role in the maintenance and transmission of disease to humans in this area.

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.

Bipolar polygenic loading and bipolar spectrum features in major depressive disorder

NARCIS (Netherlands)

Wiste, Anna; Robinson, Elise B.; Milaneschi, Yuri; Meier, Sandra; Ripke, Stephan; Clements, Caitlin C.; Fitzmaurice, Garrett M.; Rietschel, Marcella; Penninx, Brenda W.; Smoller, Jordan W.; Perlis, Roy H.

Objectives Family and genetic studies indicate overlapping liability for major depressive disorder and bipolar disorder. The purpose of the present study was to determine whether this shared genetic liability influences clinical presentation. Methods A polygenic risk score for bipolar disorder,

Urethral pressure reflectometry in women with pelvic organ prolapse: a study of reproducibility.

Science.gov (United States)

Khayyami, Yasmine; Lose, Gunnar; Klarskov, Niels

2017-05-01

The mechanism of continence in women with pelvic organ prolapse (POP) before and after surgery remains unknown. Urethral pressure reflectometry (UPR) separates women with stress urinary incontinence (SUI) from continent women by measuring urethral opening pressure at an abdominal pressure of 50 cmH 2 O (P O-Abd 50 ). UPR can help identify women with POP at risk of postoperative de novo SUI. The aim of this study was to investigate the reproducibility of UPR in women with POP. Women with anterior or posterior vaginal wall prolapse were recruited for this prospective, observational study from our outpatient clinic. The women were examined with UPR on two occasions. Measurements were done at rest, and during squeezing and straining. Statistical analyses were performed using SAS 9.4. A Bland-Altman analysis with limits of agreement and coefficients of variation was used to determine the level of agreement between measurements. Paired t tests were used to estimate the difference; a two-tailed P value of rest or during squeezing or in the values of P O-Abd 50 . P O-Abd 50 showed limits of agreement of 15.3 cmH 2 O and a coefficient of variation of 9.9 %. UPR was found to be a highly reproducible method in women with POP. UPR may be used in future studies to help reveal urodynamic features predictive of postoperative de novo SUI in women with POP.

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.

Depth estimation of features in video frames with improved feature matching technique using Kinect sensor

Science.gov (United States)

Sharma, Kajal; Moon, Inkyu; Kim, Sung Gaun

2012-10-01

Estimating depth has long been a major issue in the field of computer vision and robotics. The Kinect sensor's active sensing strategy provides high-frame-rate depth maps and can recognize user gestures and human pose. This paper presents a technique to estimate the depth of features extracted from video frames, along with an improved feature-matching method. In this paper, we used the Kinect camera developed by Microsoft, which captured color and depth images for further processing. Feature detection and selection is an important task for robot navigation. Many feature-matching techniques have been proposed earlier, and this paper proposes an improved feature matching between successive video frames with the use of neural network methodology in order to reduce the computation time of feature matching. The features extracted are invariant to image scale and rotation, and different experiments were conducted to evaluate the performance of feature matching between successive video frames. The extracted features are assigned distance based on the Kinect technology that can be used by the robot in order to determine the path of navigation, along with obstacle detection applications.

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.

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 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.

Anterograde Amnesia during Electroconvulsive Therapy: A Prospective Pilot-Study in Patients with Major Depressive Disorder.

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Elvira Boere

Full Text Available Electroconvulsive therapy (ECT is considered an effective treatment for major depression with melancholic features. However, neurocognitive side-effects such as anterograde amnesia still regularly occur. The present study aims to evaluate the severity and course of anterograde amnesia in severely depressed patients undergoing ECT. In a prospective naturalistic study, anterograde memory function was assessed among inpatients who underwent ECT (n = 11. Subjects met DSM-IV criteria for major depressive disorder. Recruitment took place between March 2010-March 2011 and March 2012-March 2013. Controls treated with antidepressants (n = 9 were matched for age, gender and depression severity. Primary outcome measure was immediate recall; secondary outcome measures were delayed recall, recognition, and visual association. Differences were tested using repeated measures ANOVA and paired t-tests. Correlations with hypothesized covariates were calculated. In patients with major depressive disorder, ECT had a significant effect on delayed memory function (p<0.01 with large effect sizes. Findings on immediate recall were less consistent. Four weeks after treatment discontinuation, these memory functions had recovered. Age was identified as a very important covariate. The main limitations of our study are its naturalistic design, possibly compromising internal validity, and its small sample size. However, if these findings can be reproduced in a more comprehensive study group, then the possible induction of anterograde amnesia is not a justifiable reason for clinicians to disregard ECT as a treatment option.

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

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.

Reproducibility of the Portuguese version of the PEDro Scale

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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.

Relative validity and reproducibility of a food frequency questionnaire to assess dietary fiber intake in Danish adults.

Science.gov (United States)

Vuholm, Stine; Lorenzen, Janne K; Kristensen, Mette

2014-01-01

Differences in habitual dietary fiber intake may modify effects of dietary fiber interventions, thus measurement of habitual dietary fiber intake is relevant to apply in intervention studies on fiber-rich foods, and food frequency questionnaire (FFQ) is a commonly used method. Rye bread is the major contributor of dietary fiber in the Danish population, and a nation-specific FFQ is therefore needed. The aim of this study was to assess the relative validity and reproducibility of a self-administered quantitative FFQ designed to assess total dietary fiber intake among Danish adults. In order to assess the relative validity of the FFQ, a total of 125 participants completed both a 7-day weighed dietary recording (DR) and an FFQ consisting of 60 questions. To evaluate the reproducibility of the FFQ, a sub-group of 12 participants subsequently completed an FFQ approximately 6 months later. Estimates of mean dietary fiber intake were 24.9±9.8 and 28.1±9.4 g/day when applying the FFQ and DR, respectively, where FFQ estimates were ~12% lower (pfiber intake of the two methods was r=0.63 (pfiber intake (g/day), adequate ranking of subjects according to their dietary fiber intake, and good reproducibility. The FFQ is therefore believed to be a valuable tool for epidemiology and screening in human interventions, where intake of dietary fibers is of specific interest.

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.

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.

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

Obesity in patients with major depression is related to bipolarity and mixed features: evidence from the BRIDGE-II-Mix study.

Science.gov (United States)

Petri, Eleonora; Bacci, Olivia; Barbuti, Margherita; Pacchiarotti, Isabella; Azorin, Jean-Michel; Angst, Jules; Bowden, Charles L; Mosolov, Sergey; Vieta, Eduard; Young, Allan H; Perugi, Giulio

2017-09-01

The Bipolar Disorders: Improving Diagnosis, Guidance and Education (BRIDGE)-II-Mix study aimed to estimate the frequency of mixed states in patients with a major depressive episode (MDE) according to different definitions. The present post-hoc analysis evaluated the association between obesity and the presence of mixed features and bipolarity. A total of 2811 MDE subjects were enrolled in a multicenter cross-sectional study. In 2744 patients, the body mass index (BMI) was evaluated. Psychiatric symptoms, and sociodemographic and clinical variables were collected, comparing the characteristics of MDE patients with (MDE-OB) and without (MDE-NOB) obesity. Obesity (BMI ≥30) was registered in 493 patients (18%). In the MDE-OB group, 90 patients (20%) fulfilled the DSM-IV-TR criteria for bipolar disease (BD), 225 patients (50%) fulfilled the bipolarity specifier criteria, 59 patients (13%) fulfilled DSM-5 criteria for MDEs with mixed features, and 226 patients (50%) fulfilled Research-Based Diagnostic Criteria for an MDE. Older age, history of (hypo)manic switches during antidepressant treatment, the occurrence of three or more MDEs, atypical depressive features, antipsychotic treatment, female gender, depressive mixed state according to DSM-5 criteria, comorbid eating disorders, and anxiety disorders were significantly associated with the MDE-OB group. Among (hypo)manic symptoms during the current MDE, psychomotor agitation, distractibility, increased energy, and risky behaviors were the variables most frequently associated with MDE-OB group. In our sample, the presence of obesity in patients with an MDE seemed to be associated with higher rates of bipolar spectrum disorders. These findings suggest that obesity in patients with an MDE could be considered as a possible marker of bipolarity. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Rapid Quantification of Major Volatile Metabolites in Fermented Food and Beverages Using Gas Chromatography-Mass Spectrometry

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Farhana R. Pinu

2017-07-01

Full Text Available Here we present a method for the accurate quantification of major volatile metabolites found in different food and beverages, including ethanol, acetic acid and other aroma compounds, using gas chromatography coupled to mass spectrometry (GC-MS. The method is combined with a simple sample preparation procedure using sodium chloride and anhydrous ethyl acetate. The GC-MS analysis was accomplished within 4.75 min, and over 80 features were detected, of which 40 were positively identified using an in-house and a commercialmass spectrometry (MS library. We determined different analytical parameters of these metabolites including the limit of detection (LOD, limit of quantitation (LOQ and range of quantification. In order to validate the method, we also determined detailed analytical characteristics of five major fermentation end products including ethanol, acetic acid, isoamyl alcohol, ethyl-L-lactate and, acetoin. The method showed very low technical variability for the measurements of these metabolites in different matrices (<3% with an excellent accuracy (100% ± 5%, recovery (100% ± 10%, reproducibility and repeatability [Coefficient of variation (CV 1–10%]. To demonstrate the applicability of the method, we analysed different fermented products including balsamic vinegars, sourdough, distilled (whisky and non-distilled beverages (wine and beer.

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...

Demographic and clinical features and prescribing patterns of psychotropic medications in patients with the melancholic subtype of major depressive disorder in China.

Directory of Open Access Journals (Sweden)

Yu-Tao Xiang

Full Text Available BACKGROUND: Little has been known about the demographic and clinical features of the melancholic subtype of major depressive disorder (MDD in Chinese patients. This study examined the frequency of melancholia in Chinese MDD patients and explored its demographic and clinical correlates and prescribing patterns of psychotropic drugs. METHODS: A consecutively collected sample of 1,178 patients with MDD were examined in 13 psychiatric hospitals or psychiatric units of general hospitals in China nationwide. The cross-sectional data of patients' demographic and clinical characteristics and prescriptions of psychotropic drugs were recorded using a standardized protocol and data collection procedure. The diagnosis of the melancholic subtype was established using the Mini International Neuropsychiatric Interview (MINI. Medications ascertained included antidepressants, mood stabilizers, antipsychotics and benzodiazepines. RESULTS: Six hundred and twenty nine (53.4% of the 1,178 patients fulfilled criteria for melancholia. In multiple logistic regression analyses, compared to non-melancholic counterparts, melancholic MDD patients were more likely to be male and receive benzodiazepines, had more frequent suicide ideations and attempts and seasonal depressive episodes, while they were less likely to be employed and receive antidepressants and had less family history of psychiatric disorders and lifetime depressive episodes. CONCLUSIONS: The demographic and clinical features of melancholic MDD in Chinese patients were not entirely consistent with those found in Western populations. Compared to non-melancholic MDD patients, melancholic patients presented with different demographic and clinical features, which have implications for treatment decisions.

MO-DE-207B-08: Radiomic CT Features Complement Semantic Annotations to Predict EGFR Mutations in Lung Adenocarcinomas

Energy Technology Data Exchange (ETDEWEB)

Rios Velazquez, E; Parmar, C; Narayan, V; Aerts, H [Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts (United States); Liu, Y; Gillies, R [H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL (United States)

2016-06-15

Purpose: To compare the complementary value of quantitative radiomic features to that of radiologist-annotated semantic features in predicting EGFR mutations in lung adenocarcinomas. Methods: Pre-operative CT images of 258 lung adenocarcinoma patients were available. Tumors were segmented using the sing-click ensemble segmentation algorithm. A set of radiomic features was extracted using 3D-Slicer. Test-retest reproducibility and unsupervised dimensionality reduction were applied to select a subset of reproducible and independent radiomic features. Twenty semantic annotations were scored by an expert radiologist, describing the tumor, surrounding tissue and associated findings. Minimum-redundancy-maximum-relevance (MRMR) was used to identify the most informative radiomic and semantic features in 172 patients (training-set, temporal split). Radiomic, semantic and combined radiomic-semantic logistic regression models to predict EGFR mutations were evaluated in and independent validation dataset of 86 patients using the area under the receiver operating curve (AUC). Results: EGFR mutations were found in 77/172 (45%) and 39/86 (45%) of the training and validation sets, respectively. Univariate AUCs showed a similar range for both feature types: radiomics median AUC = 0.57 (range: 0.50 – 0.62); semantic median AUC = 0.53 (range: 0.50 – 0.64, Wilcoxon p = 0.55). After MRMR feature selection, the best-performing radiomic, semantic, and radiomic-semantic logistic regression models, for EGFR mutations, showed a validation AUC of 0.56 (p = 0.29), 0.63 (p = 0.063) and 0.67 (p = 0.004), respectively. Conclusion: Quantitative volumetric and textural Radiomic features complement the qualitative and semi-quantitative radiologist annotations. The prognostic value of informative qualitative semantic features such as cavitation and lobulation is increased with the addition of quantitative textural features from the tumor region.

MO-DE-207B-08: Radiomic CT Features Complement Semantic Annotations to Predict EGFR Mutations in Lung Adenocarcinomas

International Nuclear Information System (INIS)

Rios Velazquez, E; Parmar, C; Narayan, V; Aerts, H; Liu, Y; Gillies, R

2016-01-01

Purpose: To compare the complementary value of quantitative radiomic features to that of radiologist-annotated semantic features in predicting EGFR mutations in lung adenocarcinomas. Methods: Pre-operative CT images of 258 lung adenocarcinoma patients were available. Tumors were segmented using the sing-click ensemble segmentation algorithm. A set of radiomic features was extracted using 3D-Slicer. Test-retest reproducibility and unsupervised dimensionality reduction were applied to select a subset of reproducible and independent radiomic features. Twenty semantic annotations were scored by an expert radiologist, describing the tumor, surrounding tissue and associated findings. Minimum-redundancy-maximum-relevance (MRMR) was used to identify the most informative radiomic and semantic features in 172 patients (training-set, temporal split). Radiomic, semantic and combined radiomic-semantic logistic regression models to predict EGFR mutations were evaluated in and independent validation dataset of 86 patients using the area under the receiver operating curve (AUC). Results: EGFR mutations were found in 77/172 (45%) and 39/86 (45%) of the training and validation sets, respectively. Univariate AUCs showed a similar range for both feature types: radiomics median AUC = 0.57 (range: 0.50 – 0.62); semantic median AUC = 0.53 (range: 0.50 – 0.64, Wilcoxon p = 0.55). After MRMR feature selection, the best-performing radiomic, semantic, and radiomic-semantic logistic regression models, for EGFR mutations, showed a validation AUC of 0.56 (p = 0.29), 0.63 (p = 0.063) and 0.67 (p = 0.004), respectively. Conclusion: Quantitative volumetric and textural Radiomic features complement the qualitative and semi-quantitative radiologist annotations. The prognostic value of informative qualitative semantic features such as cavitation and lobulation is increased with the addition of quantitative textural features from the tumor region.

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

Feature confirmation in object perception: Feature integration theory 26 years on from the Treisman Bartlett lecture.

Science.gov (United States)

Humphreys, Glyn W

2016-10-01

The Treisman Bartlett lecture, reported in the Quarterly Journal of Experimental Psychology in 1988, provided a major overview of the feature integration theory of attention. This has continued to be a dominant account of human visual attention to this day. The current paper provides a summary of the work reported in the lecture and an update on critical aspects of the theory as applied to visual object perception. The paper highlights the emergence of findings that pose significant challenges to the theory and which suggest that revisions are required that allow for (a) several rather than a single form of feature integration, (b) some forms of feature integration to operate preattentively, (c) stored knowledge about single objects and interactions between objects to modulate perceptual integration, (d) the application of feature-based inhibition to object files where visual features are specified, which generates feature-based spreading suppression and scene segmentation, and (e) a role for attention in feature confirmation rather than feature integration in visual selection. A feature confirmation account of attention in object perception is outlined.

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

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.

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

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

Quantized correlation coefficient for measuring reproducibility of ChIP-chip data

Directory of Open Access Journals (Sweden)

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.

Fully automatic GBM segmentation in the TCGA-GBM dataset: Prognosis and correlation with VASARI features.

Science.gov (United States)

Rios Velazquez, Emmanuel; Meier, Raphael; Dunn, William D; Alexander, Brian; Wiest, Roland; Bauer, Stefan; Gutman, David A; Reyes, Mauricio; Aerts, Hugo J W L

2015-11-18

Reproducible definition and quantification of imaging biomarkers is essential. We evaluated a fully automatic MR-based segmentation method by comparing it to manually defined sub-volumes by experienced radiologists in the TCGA-GBM dataset, in terms of sub-volume prognosis and association with VASARI features. MRI sets of 109 GBM patients were downloaded from the Cancer Imaging archive. GBM sub-compartments were defined manually and automatically using the Brain Tumor Image Analysis (BraTumIA). Spearman's correlation was used to evaluate the agreement with VASARI features. Prognostic significance was assessed using the C-index. Auto-segmented sub-volumes showed moderate to high agreement with manually delineated volumes (range (r): 0.4 - 0.86). Also, the auto and manual volumes showed similar correlation with VASARI features (auto r = 0.35, 0.43 and 0.36; manual r = 0.17, 0.67, 0.41, for contrast-enhancing, necrosis and edema, respectively). The auto-segmented contrast-enhancing volume and post-contrast abnormal volume showed the highest AUC (0.66, CI: 0.55-0.77 and 0.65, CI: 0.54-0.76), comparable to manually defined volumes (0.64, CI: 0.53-0.75 and 0.63, CI: 0.52-0.74, respectively). BraTumIA and manual tumor sub-compartments showed comparable performance in terms of prognosis and correlation with VASARI features. This method can enable more reproducible definition and quantification of imaging based biomarkers and has potential in high-throughput medical imaging research.

PROBLEMATIC FEATURES OF THE POLITICAL DECISION MAKERS

OpenAIRE

Aleksey Sergeevih Voynov

2014-01-01

Purpose: identify the most important features in the process of making political decisions that affect the effectiveness of problem-solving situationsScientific novelty: as a result of the analysis identified the problematic features of major importance for the efficiency of the development and adoption of the most rational solution to a problem situation.Results: the analysis of the most significant features affecting the quality of decisions among them the interest of the person making deci...

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.

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

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.

Application of eigen value expansion to feature extraction from MRI images

International Nuclear Information System (INIS)

Kinosada, Yasutomi; Takeda, Kan; Nakagawa, Tsuyoshi

1991-01-01

The eigen value expansion technique was utilized for feature extraction of magnetic resonance (MR) images. The eigen value expansion is an orthonormal transformation method which decomposes a set of images into some statistically uncorrelated images. The technique was applied to MR images obtained with various imaging parameters at the same anatomical site. It generated one mean image and another set of images called bases for the images. Each basis corresponds to a feature in the images. A basis is, therefore, utilized for the feature extraction from MR images and a weighted sum of bases is also used for the feature enhancement. Furthermore, any MR image with specific feature can be obtained from a linear combination of the mean image and all of the bases. Images of hemorrhaged brain with a spin echo sequence and a series of cinematic cerebro spinal fluid flow images with ECG gated gradient refocused echo sequence were employed to estimate the ability of the feature extraction and the contrast enhancement. Results showed us that proposed application of an eigen value expansion technique to the feature extraction of MR images is good enough to clinical use and superior to other feature extraction methods such as producing a calculated MR image with a given TR and TE or the matched-filter method in processing speed and reproducibility of results. (author)

Reproducibility of abdominal fat assessment by ultrasound and computed tomography

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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)

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.

An adaptation study of internal and external features in facial representations.

Science.gov (United States)

Hills, Charlotte; Romano, Kali; Davies-Thompson, Jodie; Barton, Jason J S

2014-07-01

Prior work suggests that internal features contribute more than external features to face processing. Whether this asymmetry is also true of the mental representations of faces is not known. We used face adaptation to determine whether the internal and external features of faces contribute differently to the representation of facial identity, whether this was affected by familiarity, and whether the results differed if the features were presented in isolation or as part of a whole face. In a first experiment, subjects performed a study of identity adaptation for famous and novel faces, in which the adapting stimuli were whole faces, the internal features alone, or the external features alone. In a second experiment, the same faces were used, but the adapting internal and external features were superimposed on whole faces that were ambiguous to identity. The first experiment showed larger aftereffects for unfamiliar faces, and greater aftereffects from internal than from external features, and the latter was true for both familiar and unfamiliar faces. When internal and external features were presented in a whole-face context in the second experiment, aftereffects from either internal or external features was less than that from the whole face, and did not differ from each other. While we reproduce the greater importance of internal features when presented in isolation, we find this is equally true for familiar and unfamiliar faces. The dominant influence of internal features is reduced when integrated into a whole-face context, suggesting another facet of expert face processing. Copyright © 2014 Elsevier B.V. All rights reserved.

Adrenal glands in beta-thalassemia major: magnetic resonance (MR) imaging features and correlation with iron stores

International Nuclear Information System (INIS)

Drakonaki, Eleni; Papakonstantinou, Olympia; Maris, Thomas; Gourtsoyiannis, Nicholas; Vasiliadou, Artemis; Papadakis, Alex

2005-01-01

This study aimed at describing the magnetic resonance (MR) imaging features of the adrenal glands in beta-thalassemic patients and at investigating the relation between adrenal and hepatic siderosis. Adrenal signal intensity (SI) was retrospectively assessed on abdominal MR studies of 35 patients with beta-thalassemia major undergoing quantification of hepatic siderosis and 12 healthy controls, using T1- (120/4/90), intermediate - (120/4/20), and T2*- (120/15/20) weighted GRE sequences. Adrenal SI was graded as grade 0 (normal SI on all sequences), grade 1 (hypointensity on T2* alone), or grade 2 (hypointensity on at least T2*). Adrenal size was measured in the thalassemic patients and compared with normative data. Liver-to-muscle (L/M) SI ratios, expressing hepatic siderosis, were estimated on each sequence. Serum ferritin levels were recorded. Adrenal hypointensity (grades 1 and 2) was noted in 24/35 (68.6%) patients. L/M ratios correlated significantly with adrenal SI in all sequences. Patients with grade 1 and grade 2 adrenal SI had significantly decreased L/M ratios compared with grade 0. Serum ferritin correlated significantly with L/M values but not with adrenal SI. Adrenal size was within normal limits. Diffuse hypointensity in normal-sized adrenals is a common MR finding in beta-thalassemic patients and correlates with the degree of hepatic siderosis. (orig.)

Adrenal glands in beta-thalassemia major: magnetic resonance (MR) imaging features and correlation with iron stores

Energy Technology Data Exchange (ETDEWEB)

Drakonaki, Eleni; Papakonstantinou, Olympia; Maris, Thomas; Gourtsoyiannis, Nicholas [University Hospital of Heraklion, Department of Radiology, Heraklion (Greece); Vasiliadou, Artemis [Aghios Georgios Hospital of Chania, Thalassemia Unit, Chania (Greece); Papadakis, Alex [Venizelion Hospital of Heraklion, Thalassemia Unit, Heraklion (Greece)

2005-12-01

This study aimed at describing the magnetic resonance (MR) imaging features of the adrenal glands in beta-thalassemic patients and at investigating the relation between adrenal and hepatic siderosis. Adrenal signal intensity (SI) was retrospectively assessed on abdominal MR studies of 35 patients with beta-thalassemia major undergoing quantification of hepatic siderosis and 12 healthy controls, using T1- (120/4/90), intermediate - (120/4/20), and T2*- (120/15/20) weighted GRE sequences. Adrenal SI was graded as grade 0 (normal SI on all sequences), grade 1 (hypointensity on T2* alone), or grade 2 (hypointensity on at least T2*). Adrenal size was measured in the thalassemic patients and compared with normative data. Liver-to-muscle (L/M) SI ratios, expressing hepatic siderosis, were estimated on each sequence. Serum ferritin levels were recorded. Adrenal hypointensity (grades 1 and 2) was noted in 24/35 (68.6%) patients. L/M ratios correlated significantly with adrenal SI in all sequences. Patients with grade 1 and grade 2 adrenal SI had significantly decreased L/M ratios compared with grade 0. Serum ferritin correlated significantly with L/M values but not with adrenal SI. Adrenal size was within normal limits. Diffuse hypointensity in normal-sized adrenals is a common MR finding in beta-thalassemic patients and correlates with the degree of hepatic siderosis. (orig.)

Feature Selection based on Machine Learning in MRIs for Hippocampal Segmentation

Science.gov (United States)

Tangaro, Sabina; Amoroso, Nicola; Brescia, Massimo; Cavuoti, Stefano; Chincarini, Andrea; Errico, Rosangela; Paolo, Inglese; Longo, Giuseppe; Maglietta, Rosalia; Tateo, Andrea; Riccio, Giuseppe; Bellotti, Roberto

2015-01-01

Neurodegenerative diseases are frequently associated with structural changes in the brain. Magnetic resonance imaging (MRI) scans can show these variations and therefore can be used as a supportive feature for a number of neurodegenerative diseases. The hippocampus has been known to be a biomarker for Alzheimer disease and other neurological and psychiatric diseases. However, it requires accurate, robust, and reproducible delineation of hippocampal structures. Fully automatic methods are usually the voxel based approach; for each voxel a number of local features were calculated. In this paper, we compared four different techniques for feature selection from a set of 315 features extracted for each voxel: (i) filter method based on the Kolmogorov-Smirnov test; two wrapper methods, respectively, (ii) sequential forward selection and (iii) sequential backward elimination; and (iv) embedded method based on the Random Forest Classifier on a set of 10 T1-weighted brain MRIs and tested on an independent set of 25 subjects. The resulting segmentations were compared with manual reference labelling. By using only 23 feature for each voxel (sequential backward elimination) we obtained comparable state-of-the-art performances with respect to the standard tool FreeSurfer.

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.

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

Science.gov (United States)

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

Science.gov (United States)

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.

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

Genetic basis of early-onset, MODY-like diabetes in Japan and features of patients without mutations in the major MODY genes: dominance of maternal inheritance.

Science.gov (United States)

Yorifuji, Tohru; Higuchi, Shinji; Kawakita, Rie; Hosokawa, Yuki; Aoyama, Takane; Murakami, Akiko; Kawae, Yoshiko; Hatake, Kazue; Nagasaka, Hironori; Tamagawa, Nobuyoshi

2018-06-21

Causative mutations cannot be identified in the majority of Asian patients with suspected maturity-onset diabetes of the young (MODY). To elucidate the genetic basis of Japanese patients with MODY-like diabetes and gain insight into the etiology of patients without mutations in the major MODY genes. 263 Japanese patients with early-onset, nonobese, MODY-like diabetes mellitus referred to Osaka City General Hospital for diagnosis. Mutational analysis of the four major MODY genes (GCK, HNF1A, HNF4A, HNF1B) by Sanger sequencing. Mutation-positive and mutation-negative patients were further analyzed for clinical features. Mutations were identified in 103 (39.2%) patients; 57 mutations in GCK; 29, HNF1A; 7, HNF4A; and 10, HNF1B. Contrary to conventional diagnostic criteria, 18.4% of mutation-positive patients did not have affected parents and 8.2% were in the overweight range (BMI >85 th percentile). HOMA-IR at diagnosis was elevated (>2) in 15 of 66 (22.7%) mutation-positive patients. Compared with mutation-positive patients, mutation-negative patients were significantly older (p = 0.003), and had higher BMI percentile at diagnosis (p = 0.0006). Interestingly, maternal inheritance of diabetes was significantly more common in mutation-negative patients (p = 0.0332) and these patients had significantly higher BMI percentile as compared with mutation-negative patients with paternal inheritance (p = 0.0106). Contrary to the conventional diagnostic criteria, de novo diabetes, overweight, and insulin-resistance are common in Japanese patients with mutation-positive MODY. A significant fraction of mutation-negative patients had features of early-onset type 2 diabetes common in Japanese, and non-Mendelian inheritance needs to be considered for these patients. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Relevant principal factors affecting the reproducibility of insect primary culture.

Science.gov (United States)

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...

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.

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

Pulmonary nodule characterization, including computer analysis and quantitative features.

Science.gov (United States)

Bartholmai, Brian J; Koo, Chi Wan; Johnson, Geoffrey B; White, Darin B; Raghunath, Sushravya M; Rajagopalan, Srinivasan; Moynagh, Michael R; Lindell, Rebecca M; Hartman, Thomas E

2015-03-01

Pulmonary nodules are commonly detected in computed tomography (CT) chest screening of a high-risk population. The specific visual or quantitative features on CT or other modalities can be used to characterize the likelihood that a nodule is benign or malignant. Visual features on CT such as size, attenuation, location, morphology, edge characteristics, and other distinctive "signs" can be highly suggestive of a specific diagnosis and, in general, be used to determine the probability that a specific nodule is benign or malignant. Change in size, attenuation, and morphology on serial follow-up CT, or features on other modalities such as nuclear medicine studies or MRI, can also contribute to the characterization of lung nodules. Imaging analytics can objectively and reproducibly quantify nodule features on CT, nuclear medicine, and magnetic resonance imaging. Some quantitative techniques show great promise in helping to differentiate benign from malignant lesions or to stratify the risk of aggressive versus indolent neoplasm. In this article, we (1) summarize the visual characteristics, descriptors, and signs that may be helpful in management of nodules identified on screening CT, (2) discuss current quantitative and multimodality techniques that aid in the differentiation of nodules, and (3) highlight the power, pitfalls, and limitations of these various techniques.

Reproducibility of Manual Platelet Estimation Following Automated Low Platelet Counts

Directory of Open Access Journals (Sweden)

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)

Inter-examiner reproducibility of tests for lumbar motor control

Directory of Open Access Journals (Sweden)

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

Temperament and character profiles in bipolar I, bipolar II and major depressive disorder: Impact over illness course, comorbidity pattern and psychopathological features of depression.

Science.gov (United States)

Zaninotto, Leonardo; Souery, Daniel; Calati, Raffaella; Di Nicola, Marco; Montgomery, Stuart; Kasper, Siegfried; Zohar, Joseph; Mendlewicz, Julien; Robert Cloninger, C; Serretti, Alessandro; Janiri, Luigi

2015-09-15

Studies comparing temperament and character traits between patients with mood disorders and healthy individuals have yielded variable results. The Temperament and Character Inventory (TCI) was administered to 101 bipolar I (BP-I), 96 bipolar II (BP-II), 123 major depressive disorder (MDD) patients, and 125 HS. A series of generalized linear models were performed in order to: (a) compare the TCI dimensions across groups; (b) test any effect of the TCI dimensions on clinical features of mood disorders; and (c) detect any association between TCI dimensions and the psychopathological features of a major depressive episode. Demographic and clinical variables were also included in the models as independent variables. Higher Harm Avoidance was found in BP-II and MDD, but not in BP-I. Higher Self-Transcendence was found in BP-I. Our models also showed higher Self-Directedness in HS, either vs MDD or BP-II. No association was found between any TCI dimension and the severity of symptoms. Conversely, a positive association was found between Harm Avoidance and the overall burden of depressive episodes during lifetime. The cross-sectional design and the heterogeneity of the sample may be the main limitations of our study. In general, our sample seems to support the view of a similar profile of temperament and character between MDD and BP-II, characterized by high Harm Avoidance and low Self-Directedness. In contrast, patients with BP-I only exhibit high Self-Transcendence, having a near-normal profile in terms of Harm Avoidance or Self-Directedness. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of Gradient Coil Noise and Gradient Coil Replacement on the Reproducibility of Resting State Networks.

Science.gov (United States)

Bagarinao, Epifanio; Tsuzuki, Erina; Yoshida, Yukina; Ozawa, Yohei; Kuzuya, Maki; Otani, Takashi; Koyama, Shuji; Isoda, Haruo; Watanabe, Hirohisa; Maesawa, Satoshi; Naganawa, Shinji; Sobue, Gen

2018-01-01

The stability of the MRI scanner throughout a given study is critical in minimizing hardware-induced variability in the acquired imaging data set. However, MRI scanners do malfunction at times, which could generate image artifacts and would require the replacement of a major component such as its gradient coil. In this article, we examined the effect of low intensity, randomly occurring hardware-related noise due to a faulty gradient coil on brain morphometric measures derived from T1-weighted images and resting state networks (RSNs) constructed from resting state functional MRI. We also introduced a method to detect and minimize the effect of the noise associated with a faulty gradient coil. Finally, we assessed the reproducibility of these morphometric measures and RSNs before and after gradient coil replacement. Our results showed that gradient coil noise, even at relatively low intensities, could introduce a large number of voxels exhibiting spurious significant connectivity changes in several RSNs. However, censoring the affected volumes during the analysis could minimize, if not completely eliminate, these spurious connectivity changes and could lead to reproducible RSNs even after gradient coil replacement.

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)

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

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, ...

Performance profiles of major energy producers 1979

International Nuclear Information System (INIS)

1981-07-01

The purpose of this report is to examine year-to-year developments in the operations of 26 major US energy companies on a corporate level and also by major line of energy business and by major functions within each line of business. The period covered is 1977 to 1979. Comparisons of income and investment flow are featured and related to functionally allocated net investment in place. The presentation seeks to identify similarities and dissimilarities in results across lines-of-business activity or by firm size

Nonmotor Features in Atypical Parkinsonism.

Science.gov (United States)

Bhatia, Kailash P; Stamelou, Maria

2017-01-01

Atypical parkinsonism (AP) comprises mainly multiple system atrophy (MSA), progressive supranuclear palsy (PSP), and corticobasal degeneration (CBD), which are distinct pathological entities, presenting with a wide phenotypic spectrum. The classic syndromes are now called MSA-parkinsonism (MSA-P), MSA-cerebellar type (MSA-C), Richardson's syndrome, and corticobasal syndrome. Nonmotor features in AP have been recognized almost since the initial description of these disorders; however, research has been limited. Autonomic dysfunction is the most prominent nonmotor feature of MSA, but also gastrointestinal symptoms, sleep dysfunction, and pain, can be a feature. In PSP and CBD, the most prominent nonmotor symptoms comprise those deriving from the cognitive/neuropsychiatric domain. Apart from assisting the clinician in the differential diagnosis with Parkinson's disease, nonmotor features in AP have a big impact on quality of life and prognosis of AP and their treatment poses a major challenge for clinicians. © 2017 Elsevier Inc. All rights reserved.

Reproducible automated breast density measure with no ionizing radiation using fat-water decomposition MRI.

Science.gov (United States)

Ding, Jie; Stopeck, Alison T; Gao, Yi; Marron, Marilyn T; Wertheim, Betsy C; Altbach, Maria I; Galons, Jean-Philippe; Roe, Denise J; Wang, Fang; Maskarinec, Gertraud; Thomson, Cynthia A; Thompson, Patricia A; Huang, Chuan

2018-04-06

Increased breast density is a significant independent risk factor for breast cancer, and recent studies show that this risk is modifiable. Hence, breast density measures sensitive to small changes are desired. Utilizing fat-water decomposition MRI, we propose an automated, reproducible breast density measurement, which is nonionizing and directly comparable to mammographic density (MD). Retrospective study. The study included two sample sets of breast cancer patients enrolled in a clinical trial, for concordance analysis with MD (40 patients) and reproducibility analysis (10 patients). The majority of MRI scans (59 scans) were performed with a 1.5T GE Signa scanner using radial IDEAL-GRASE sequence, while the remaining (seven scans) were performed with a 3T Siemens Skyra using 3D Cartesian 6-echo GRE sequence with a similar fat-water separation technique. After automated breast segmentation, breast density was calculated using FraGW, a new measure developed to reliably reflect the amount of fibroglandular tissue and total water content in the entire breast. Based on its concordance with MD, FraGW was calibrated to MR-based breast density (MRD) to be comparable to MD. A previous breast density measurement, Fra80-the ratio of breast voxels with density changes and treatment response. 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2018. © 2018 International Society for Magnetic Resonance in Medicine.

Critical feature analysis of a radiotherapy machine

International Nuclear Information System (INIS)

Rae, Andrew; Jackson, Daniel; Ramanan, Prasad; Flanz, Jay; Leyman, Didier

2005-01-01

The software implementation of the emergency shutdown feature in a major radiotherapy system was analyzed, using a directed form of code review based on module dependences. Dependences between modules are labelled by particular assumptions; this allows one to trace through the code, and identify those fragments responsible for critical features. An 'assumption tree' is constructed in parallel, showing the assumptions which each module makes about others. The root of the assumption tree is the critical feature of interest, and its leaves represent assumptions which, if not valid, might cause the critical feature to fail. The analysis revealed some unexpected assumptions that motivated improvements to the code

A database for reproducible manipulation research: CapriDB – Capture, Print, Innovate

Directory of Open Access Journals (Sweden)

Florian T. Pokorny

2017-04-01

Full Text Available We present a novel approach and database which combines the inexpensive generation of 3D object models via monocular or RGB-D camera images with 3D printing and a state of the art object tracking algorithm. Unlike recent efforts towards the creation of 3D object databases for robotics, our approach does not require expensive and controlled 3D scanning setups and aims to enable anyone with a camera to scan, print and track complex objects for manipulation research. The proposed approach results in detailed textured mesh models whose 3D printed replicas provide close approximations of the originals. A key motivation for utilizing 3D printed objects is the ability to precisely control and vary object properties such as the size, material properties and mass distribution in the 3D printing process to obtain reproducible conditions for robotic manipulation research. We present CapriDB – an extensible database resulting from this approach containing initially 40 textured and 3D printable mesh models together with tracking features to facilitate the adoption of the proposed approach.

ClusTrack: feature extraction and similarity measures for clustering of genome-wide data sets.

Directory of Open Access Journals (Sweden)

Halfdan Rydbeck

Full Text Available Clustering is a popular technique for explorative analysis of data, as it can reveal subgroupings and similarities between data in an unsupervised manner. While clustering is routinely applied to gene expression data, there is a lack of appropriate general methodology for clustering of sequence-level genomic and epigenomic data, e.g. ChIP-based data. We here introduce a general methodology for clustering data sets of coordinates relative to a genome assembly, i.e. genomic tracks. By defining appropriate feature extraction approaches and similarity measures, we allow biologically meaningful clustering to be performed for genomic tracks using standard clustering algorithms. An implementation of the methodology is provided through a tool, ClusTrack, which allows fine-tuned clustering analyses to be specified through a web-based interface. We apply our methods to the clustering of occupancy of the H3K4me1 histone modification in samples from a range of different cell types. The majority of samples form meaningful subclusters, confirming that the definitions of features and similarity capture biological, rather than technical, variation between the genomic tracks. Input data and results are available, and can be reproduced, through a Galaxy Pages document at http://hyperbrowser.uio.no/hb/u/hb-superuser/p/clustrack. The clustering functionality is available as a Galaxy tool, under the menu option "Specialized analyzis of tracks", and the submenu option "Cluster tracks based on genome level similarity", at the Genomic HyperBrowser server: http://hyperbrowser.uio.no/hb/.

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.

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

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

Quantitative imaging features: extension of the oncology medical image database

Science.gov (United States)

Patel, M. N.; Looney, P. T.; Young, K. C.; Halling-Brown, M. D.

2015-03-01

Radiological imaging is fundamental within the healthcare industry and has become routinely adopted for diagnosis, disease monitoring and treatment planning. With the advent of digital imaging modalities and the rapid growth in both diagnostic and therapeutic imaging, the ability to be able to harness this large influx of data is of paramount importance. The Oncology Medical Image Database (OMI-DB) was created to provide a centralized, fully annotated dataset for research. The database contains both processed and unprocessed images, associated data, and annotations and where applicable expert determined ground truths describing features of interest. Medical imaging provides the ability to detect and localize many changes that are important to determine whether a disease is present or a therapy is effective by depicting alterations in anatomic, physiologic, biochemical or molecular processes. Quantitative imaging features are sensitive, specific, accurate and reproducible imaging measures of these changes. Here, we describe an extension to the OMI-DB whereby a range of imaging features and descriptors are pre-calculated using a high throughput approach. The ability to calculate multiple imaging features and data from the acquired images would be valuable and facilitate further research applications investigating detection, prognosis, and classification. The resultant data store contains more than 10 million quantitative features as well as features derived from CAD predictions. Theses data can be used to build predictive models to aid image classification, treatment response assessment as well as to identify prognostic imaging biomarkers.

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...

Influences of High-Level Features, Gaze, and Scene Transitions on the Reliability of BOLD Responses to Natural Movie Stimuli

Science.gov (United States)

Lu, Kun-Han; Hung, Shao-Chin; Wen, Haiguang; Marussich, Lauren; Liu, Zhongming

2016-01-01

Complex, sustained, dynamic, and naturalistic visual stimulation can evoke distributed brain activities that are highly reproducible within and across individuals. However, the precise origins of such reproducible responses remain incompletely understood. Here, we employed concurrent functional magnetic resonance imaging (fMRI) and eye tracking to investigate the experimental and behavioral factors that influence fMRI activity and its intra- and inter-subject reproducibility during repeated movie stimuli. We found that widely distributed and highly reproducible fMRI responses were attributed primarily to the high-level natural content in the movie. In the absence of such natural content, low-level visual features alone in a spatiotemporally scrambled control stimulus evoked significantly reduced degree and extent of reproducible responses, which were mostly confined to the primary visual cortex (V1). We also found that the varying gaze behavior affected the cortical response at the peripheral part of V1 and in the oculomotor network, with minor effects on the response reproducibility over the extrastriate visual areas. Lastly, scene transitions in the movie stimulus due to film editing partly caused the reproducible fMRI responses at widespread cortical areas, especially along the ventral visual pathway. Therefore, the naturalistic nature of a movie stimulus is necessary for driving highly reliable visual activations. In a movie-stimulation paradigm, scene transitions and individuals’ gaze behavior should be taken as potential confounding factors in order to properly interpret cortical activity that supports natural vision. PMID:27564573

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)

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.

ROMANCE: A new software tool to improve data robustness and feature identification in CE-MS metabolomics.

Science.gov (United States)

González-Ruiz, Víctor; Gagnebin, Yoric; Drouin, Nicolas; Codesido, Santiago; Rudaz, Serge; Schappler, Julie

2018-05-01

The use of capillary electrophoresis coupled to mass spectrometry (CE-MS) in metabolomics remains an oddity compared to the widely adopted use of liquid chromatography. This technique is traditionally regarded as lacking the reproducibility to adequately identify metabolites by their migration times. The major reason is the variability of the velocity of the background electrolyte, mainly coming from shifts in the magnitude of the electroosmotic flow and from the suction caused by electrospray interfaces. The use of the effective electrophoretic mobility is one solution to overcome this issue as it is a characteristic feature of each compound. To date, such an approach has not been applied to metabolomics due to the complexity and size of CE-MS data obtained in such studies. In this paper, ROMANCE (RObust Metabolomic Analysis with Normalized CE) is introduced as a new software for CE-MS-based metabolomics. It allows the automated conversion of batches of CE-MS files with minimal user intervention. ROMANCE converts the x-axis of each MS file from the time into the effective mobility scale and the resulting files are already pseudo-aligned, present normalized peak areas and improved reproducibility, and can eventually follow existing metabolomic workflows. The software was developed in Scala, so it is multi-platform and computationally-efficient. It is available for download under a CC license. In this work, the versatility of ROMANCE was demonstrated by using data obtained in the same and in different laboratories, as well as its application to the analysis of human plasma samples. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Non-genetic polymorphisms in rotifers: environmental and endogenous controls, development, and features for predictable or unpredictable environments.

Science.gov (United States)

Gilbert, John J

2017-05-01

Pronounced non-genetic polymorphisms, or polyphenisms, occur in some monogonont rotifers reproducing by diploid, female parthenogenesis. In many brachionids, there is great variation in spine length. In trimorphic species of Asplanchna, females can vary in size and shape, from a small saccate morph to giant cruciform and campanulate morphs. In species that also reproduce sexually, diploid eggs can develop into two types of females. Amictic females produce diploid eggs that develop parthenogenetically into females; mictic females produce haploid eggs that develop parthenogenetically into males or, if fertilized, into resting eggs. In a species of Synchaeta, amictic females produce diploid eggs that can be either thin-shelled and subitaneous or thicker-shelled and diapausing. In all cases, morph determination occurs during the oogenesis or embryological development of diploid eggs in the maternal body cavity. For the first time, these polymorphisms are reviewed together and compared regarding a number of features associated with transitions from default to induced morphs: (i) type of variation (morphological, physiological, or both; continuous or discrete); (ii) inducing signal (environmental, endogenous, or both); (iii) universality of response to that signal (all or only some individuals); (iv) fitness cost; (v) reversibility; and (vi) ecological significance. Most of the polymorphisms fall into two major categories regarding these features. Transitions suitable for predictable environments involve: universal responses to environmental signals; continuous morphological variation; low reproductive cost; rapid reversibility; and adaptations for defence, hydrodynamics or prey ingestion. Transitions suitable for unpredictable environments are bet-hedging strategies and usually involve: partial (stochastic) responses to environmental or endogenous signals; discontinuous physiological variation; initiation of diapause, and thus high reproductive cost and slow

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.

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

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.

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...

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...

SU-E-J-227: Breathing Pattern Consistency and Reproducibility: Comparative Analysis for Supine and Prone Body Positioning

International Nuclear Information System (INIS)

Laugeman, E; Weiss, E; Chen, S; Hugo, G; Rosu, M

2014-01-01

Purpose: Evaluate and compare the cycle-to-cycle consistency of breathing patterns and their reproducibility over the course of treatment, for supine and prone positioning. Methods: Respiratory traces from 25 patients were recorded for sequential supine/prone 4DCT scans acquired prior to treatment, and during the course of the treatment (weekly or bi-weekly). For each breathing cycle, the average(AVE), end-of-exhale(EoE) and end-of-inhale( EoI) locations were identified using in-house developed software. In addition, the mean values and variations for the above quantities were computed for each breathing trace. F-tests were used to compare the cycle-to-cycle consistency of all pairs of sequential supine and prone scans. Analysis of variances was also performed using population means for AVE, EoE and EoI to quantify differences between the reproducibility of prone and supine respiration traces over the treatment course. Results: Consistency: Cycle-to-cycle variations are less in prone than supine in the pre-treatment and during-treatment scans for AVE, EoE and EoI points, for the majority of patients (differences significant at p<0.05). The few cases where the respiratory pattern had more variability in prone appeared to be random events. Reproducibility: The reproducibility of breathing patterns (supine and prone) improved as treatment progressed, perhaps due to patients becoming more comfortable with the procedure. However, variability in supine position continued to remain significantly larger than in prone (p<0.05), as indicated by the variance analysis of population means for the pretreatment and subsequent during-treatment scans. Conclusions: Prone positioning stabilizes breathing patterns in most subjects investigated in this study. Importantly, a parallel analysis of the same group of patients revealed a tendency towards increasing motion amplitude of tumor targets in prone position regardless of their size or location; thus, the choice for body positioning

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

Opinion mining feature-level using Naive Bayes and feature extraction based analysis dependencies

Science.gov (United States)

Sanda, Regi; Baizal, Z. K. Abdurahman; Nhita, Fhira

2015-12-01

Development of internet and technology, has major impact and providing new business called e-commerce. Many e-commerce sites that provide convenience in transaction, and consumers can also provide reviews or opinions on products that purchased. These opinions can be used by consumers and producers. Consumers to know the advantages and disadvantages of particular feature of the product. Procuders can analyse own strengths and weaknesses as well as it's competitors products. Many opinions need a method that the reader can know the point of whole opinion. The idea emerged from review summarization that summarizes the overall opinion based on sentiment and features contain. In this study, the domain that become the main focus is about the digital camera. This research consisted of four steps 1) giving the knowledge to the system to recognize the semantic orientation of an opinion 2) indentify the features of product 3) indentify whether the opinion gives a positive or negative 4) summarizing the result. In this research discussed the methods such as Naï;ve Bayes for sentiment classification, and feature extraction algorithm based on Dependencies Analysis, which is one of the tools in Natural Language Processing (NLP) and knowledge based dictionary which is useful for handling implicit features. The end result of research is a summary that contains a bunch of reviews from consumers on the features and sentiment. With proposed method, accuration for sentiment classification giving 81.2 % for positive test data, 80.2 % for negative test data, and accuration for feature extraction reach 90.3 %.

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.

New features of the Helioviewer Project

Science.gov (United States)

Ireland, J.; Zahniy, S.; Nicula, B.; Mueller, D.; Felix, S.; Verstringe, F.; Bourgoignie, B.

2016-12-01

This year saw the release of major new upgrades to the capabilities of helioviewer.org and JHelioviewer. The helioviewer.org interface was completely re-designed, and now provides image and feature/event time-lines and data download capabilities. JHelioviewer introduced interactive time-series, the ability to query different servers for different data, and image reprojection. We introduce the new features of these software releases and give use cases. We will summarize our latest usage statistics, and discuss what's coming up next for the Helioviewer Project. We will also be soliciting bug reports, requests for new features and comments on the effectiveness of helioviewer.org and JHelioviewer. What would you like to see next from the Helioviewer Project?

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

Directory of Open Access Journals (Sweden)

Jonas S Almeida

2012-01-01

Full Text Available Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results : Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH′s popular ImageJ application. Conclusions : The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

Science.gov (United States)

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

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

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.

Outcome of patients with major depressive disorder after serious suicide attempt.

Science.gov (United States)

Suominen, Kirsi; Haukka, Jari; Valtonen, Hanna M; Lönnqvist, Jouko

2009-10-01

To investigate the outcome of subjects with major depressive disorder after serious suicide attempt and to examine the effect of psychotic symptoms on their outcome. The study population included all individuals aged 16 years or older in Finland who were hospitalized with ICD-10 diagnoses of major depressive disorder and attempted suicide from 1996 to 2003 (N = 1,820). The main outcome measures were completed suicides, overall mortality, and repeated suicide attempts during drug treatment versus no treatment. During the 4-year follow-up period, 13% of patients died, 6% completed suicide, and 31% made a repeat suicide attempt. Subjects with major depression with psychotic features completed suicide more often than subjects without psychotic features during the follow-up (hazard ratio [HR] 3.32; 95% CI, 1.95 - 5.67). Antidepressant treatment reduced all-cause mortality by 24% (HR 0.74; 95% CI, 0.56 - 0.97) but did not reduce suicide mortality (HR 1.06; 95% CI, 0.71 - 1.58). Psychotic symptoms during major depressive episode increase the risk of completed suicide after serious suicide attempt. The quality of treatment for major depression with psychotic features after attempted suicide should be improved to prevent suicide. Copyright 2009 Physicians Postgraduate Press, Inc.

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.

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.

Validation of EURO-CORDEX regional climate models in reproducing the variability of precipitation extremes in Romania

Science.gov (United States)

Dumitrescu, Alexandru; Busuioc, Aristita

2016-04-01

EURO-CORDEX is the European branch of the international CORDEX initiative that aims to provide improved regional climate change projections for Europe. The main objective of this paper is to document the performance of the individual models in reproducing the variability of precipitation extremes in Romania. Here three EURO-CORDEX regional climate models (RCMs) ensemble (scenario RCP4.5) are analysed and inter-compared: DMI-HIRHAM5, KNMI-RACMO2.2 and MPI-REMO. Compared to previous studies, when the RCM validation regarding the Romanian climate has mainly been made on mean state and at station scale, a more quantitative approach of precipitation extremes is proposed. In this respect, to have a more reliable comparison with observation, a high resolution daily precipitation gridded data set was used as observational reference (CLIMHYDEX project). The comparison between the RCM outputs and observed grid point values has been made by calculating three extremes precipitation indices, recommended by the Expert Team on Climate Change Detection Indices (ETCCDI), for the 1976-2005 period: R10MM, annual count of days when precipitation ≥10mm; RX5DAY, annual maximum 5-day precipitation and R95P%, precipitation fraction of annual total precipitation due to daily precipitation > 95th percentile. The RCMs capability to reproduce the mean state for these variables, as well as the main modes of their spatial variability (given by the first three EOF patterns), are analysed. The investigation confirms the ability of RCMs to simulate the main features of the precipitation extreme variability over Romania, but some deficiencies in reproducing of their regional characteristics were found (for example, overestimation of the mea state, especially over the extra Carpathian regions). This work has been realised within the research project "Changes in climate extremes and associated impact in hydrological events in Romania" (CLIMHYDEX), code PN II-ID-2011-2-0073, financed by the Romanian

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

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).

Text feature extraction based on deep learning: a review.

Science.gov (United States)

Liang, Hong; Sun, Xiao; Sun, Yunlei; Gao, Yuan

2017-01-01

Selection of text feature item is a basic and important matter for text mining and information retrieval. Traditional methods of feature extraction require handcrafted features. To hand-design, an effective feature is a lengthy process, but aiming at new applications, deep learning enables to acquire new effective feature representation from training data. As a new feature extraction method, deep learning has made achievements in text mining. The major difference between deep learning and conventional methods is that deep learning automatically learns features from big data, instead of adopting handcrafted features, which mainly depends on priori knowledge of designers and is highly impossible to take the advantage of big data. Deep learning can automatically learn feature representation from big data, including millions of parameters. This thesis outlines the common methods used in text feature extraction first, and then expands frequently used deep learning methods in text feature extraction and its applications, and forecasts the application of deep learning in feature extraction.

Demography-based adaptive network model reproduces the spatial organization of human linguistic groups

Science.gov (United States)

Capitán, José A.; Manrubia, Susanna

2015-12-01

The distribution of human linguistic groups presents a number of interesting and nontrivial patterns. The distributions of the number of speakers per language and the area each group covers follow log-normal distributions, while population and area fulfill an allometric relationship. The topology of networks of spatial contacts between different linguistic groups has been recently characterized, showing atypical properties of the degree distribution and clustering, among others. Human demography, spatial conflicts, and the construction of networks of contacts between linguistic groups are mutually dependent processes. Here we introduce an adaptive network model that takes all of them into account and successfully reproduces, using only four model parameters, not only those features of linguistic groups already described in the literature, but also correlations between demographic and topological properties uncovered in this work. Besides their relevance when modeling and understanding processes related to human biogeography, our adaptive network model admits a number of generalizations that broaden its scope and make it suitable to represent interactions between agents based on population dynamics and competition for space.

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...

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.

Patterns of Dysmorphic Features in Schizophrenia

Science.gov (United States)

Scutt, L.E.; Chow, E.W.C.; Weksberg, R.; Honer, W.G.; Bassett, Anne S.

2011-01-01

Congenital dysmorphic features are prevalent in schizophrenia and may reflect underlying neurodevelopmental abnormalities. A cluster analysis approach delineating patterns of dysmorphic features has been used in genetics to classify individuals into more etiologically homogeneous subgroups. In the present study, this approach was applied to schizophrenia, using a sample with a suspected genetic syndrome as a testable model. Subjects (n = 159) with schizophrenia or schizoaffective disorder were ascertained from chronic patient populations (random, n=123) or referred with possible 22q11 deletion syndrome (referred, n = 36). All subjects were evaluated for presence or absence of 70 reliably assessed dysmorphic features, which were used in a three-step cluster analysis. The analysis produced four major clusters with different patterns of dysmorphic features. Significant between-cluster differences were found for rates of 37 dysmorphic features (P dysmorphic features (P = 0.0001), and validating features not used in the cluster analysis: mild mental retardation (P = 0.001) and congenital heart defects (P = 0.002). Two clusters (1 and 4) appeared to represent more developmental subgroups of schizophrenia with elevated rates of dysmorphic features and validating features. Cluster 1 (n = 27) comprised mostly referred subjects. Cluster 4 (n= 18) had a different pattern of dysmorphic features; one subject had a mosaic Turner syndrome variant. Two other clusters had lower rates and patterns of features consistent with those found in previous studies of schizophrenia. Delineating patterns of dysmorphic features may help identify subgroups that could represent neurodevelopmental forms of schizophrenia with more homogeneous origins. PMID:11803519

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

To optimize data acquisition parameters in cardiac proton MR spectroscopy, and to evaluate the intra- and intersession variability in myocardial triglyceride content. Data acquisition parameters at 3 Tesla (T) were optimized and reproducibility measured using, in total, 49 healthy subjects. The signal-to-noise-ratio (SNR) and the variance in metabolite amplitude between averages were measured for: (i) global versus local power optimization; (ii) static magnetic field (B 0 ) shimming performed during free-breathing or within breathholds; (iii) post R-wave peak measurement times between 50 and 900 ms; (iv) without respiratory compensation, with breathholds and with navigator triggering; and (v) frequency selective excitation, Chemical Shift Selective (CHESS) and Multiply Optimized Insensitive Suppression Train (MOIST) water suppression techniques. Using the optimized parameters intra- and intersession myocardial triglyceride content reproducibility was measured. Two cardiac proton spectra were acquired with the same parameters and compared (intrasession reproducibility) after which the subject was removed from the scanner and placed back in the scanner and a third spectrum was acquired which was compared with the first measurement (intersession reproducibility). Local power optimization increased SNR on average by 22% compared with global power optimization (P = 0.0002). The average linewidth was not significantly different for pencil beam B 0 shimming using free-breathing or breathholds (19.1 Hz versus 17.5 Hz; P = 0.15). The highest signal stability occurred at a cardiac trigger delay around 240 ms. The mean amplitude variation was significantly lower for breathholds versus free-breathing (P = 0.03) and for navigator triggering versus free-breathing (P = 0.03) as well as for navigator triggering versus breathhold (P = 0.02). The mean residual water signal using CHESS (1.1%, P = 0.01) or MOIST (0.7%, P = 0.01) water suppression was significantly lower than using

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.

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

Reconstructed Solar-Induced Fluorescence: A Machine Learning Vegetation Product Based on MODIS Surface Reflectance to Reproduce GOME-2 Solar-Induced Fluorescence

Science.gov (United States)

Gentine, P.; Alemohammad, S. H.

2018-04-01

Solar-induced fluorescence (SIF) observations from space have resulted in major advancements in estimating gross primary productivity (GPP). However, current SIF observations remain spatially coarse, infrequent, and noisy. Here we develop a machine learning approach using surface reflectances from Moderate Resolution Imaging Spectroradiometer (MODIS) channels to reproduce SIF normalized by clear sky surface irradiance from the Global Ozone Monitoring Experiment-2 (GOME-2). The resulting product is a proxy for ecosystem photosynthetically active radiation absorbed by chlorophyll (fAPARCh). Multiplying this new product with a MODIS estimate of photosynthetically active radiation provides a new MODIS-only reconstruction of SIF called Reconstructed SIF (RSIF). RSIF exhibits much higher seasonal and interannual correlation than the original SIF when compared with eddy covariance estimates of GPP and two reference global GPP products, especially in dry and cold regions. RSIF also reproduces intense productivity regions such as the U.S. Corn Belt contrary to typical vegetation indices and similarly to SIF.

The prevalence and illness characteristics of DSM-5-defined "mixed feature specifier" in adults with major depressive disorder and bipolar disorder: Results from the International Mood Disorders Collaborative Project.

Science.gov (United States)

McIntyre, Roger S; Soczynska, Joanna K; Cha, Danielle S; Woldeyohannes, Hanna O; Dale, Roman S; Alsuwaidan, Mohammad T; Gallaugher, Laura Ashley; Mansur, Rodrigo B; Muzina, David J; Carvalho, Andre; Kennedy, Sidney H

2015-02-01

A substantial proportion of individuals with mood disorders present with sub-syndromal hypo/manic features. The objective of this analysis was to evaluate the prevalence and illness characteristics of the Diagnostic and Statistical Manual Version-5 (DSM-5) - defined mixed features specifier (MFS) in adults with major depressive disorder (MDD) and bipolar disorder (BD). Data from participants who met criteria for a current mood episode as part of MDD (n=506) or BD (BD-I: n=216, BD-II: n=130) were included in this post-hoc analysis. All participants were enrolled in the International Mood Disorders Collaborative Project (IMDCP): a collaborative research platform at the Mood Disorders Psychopharmacology Unit, University of Toronto and the Cleveland Clinic, Cleveland, Ohio. Mixed features specifier was operationalized as a score ≥ 1 on 3 or more select items on the Young Mania Rating Scale (YMRS) or ≥ 1 on 3 select items of the Montgomery Åsberg Depression Rating Scale (MADRS) or Hamilton Depression Rating Scale (HAMD-17) during an index major depressive episode (MDE) or hypo/manic episode, respectively. A total of 26.0% (n=149), 34.0% (n=65), and 33.8% (n=49) of individuals met criteria for MFS during an index MDE as part of MDD, BD-I and BD-II, respectively. Mixed features specifier during a hypo/manic episode was identified in 20.4% (n=52) and 5.1% (n=8) in BD-I and BD-II participants, respectively. Individuals with MDE-MFS as part of BD or MDD exhibited a more severe depressive phenotype (p=0.0002 and pdefined MFS is common during an MDE as part of MDD and BD. The presence of MFS identifies a subgroup of individuals with greater illness complexity and possibly a higher rate of cardiovascular comorbidity. The results herein underscore the common occurrence of MFS in adults with either BD or MDD. Moreover, the results of our analysis indicate that adults with mood disorders and MFS have distinct clinical characteristics and comorbidity patterns. Copyright �

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.

Reproducibility and Validity of a Food Frequency Questionnaire Designed to Assess Diet in Children Aged 4-5 Years.

Science.gov (United States)

Vioque, Jesus; Gimenez-Monzo, Daniel; Navarrete-Muñoz, Eva Maria; Garcia-de-la-Hera, Manuela; Gonzalez-Palacios, Sandra; Rebagliato, Marisa; Ballester, Ferran; Murcia, Mario; Iñiguez, Carmen; Granado, Fernando

2016-01-01

The food frequency questionnaire (FFQ) is the most efficient and cost-effective method to investigate the relationship between usual diet and disease in epidemiologic studies. Although FFQs have been validated in many adult populations worldwide, the number of valid FFQ in preschool children is very scarce. The aim of this study was to evaluate the reproducibility and validity of a semi-quantitative FFQ designed for children aged 4 to 5 years. In this study, we have included 169 children aged 4-5 years from the INMA project in Valencia, a population-based prospective cohort study of mothers and children in Spain. The 105-items FFQ was administered twice to the parents or care-givers of children over a 9-month period. Reproducibility was explored by comparing intake of nutrients by the FFQs, while validity was examined by comparing the nutrient values from the FFQs with the average nutrient values of three 24 hour dietary recall (24hDR) taken in the period, and also, with the concentration in blood specimens for several vitamins (carotenoids, folate, vitamin B12, vitamin C and α-tocopherol). Pearson correlation coefficients and de-attenuated correlation coefficients were calculated and we also evaluated misclassification by quintile distribution. All correlation coefficients for reproducibility for nutrients and major food groups were statistically significant; the average correlation coefficients for daily intake were 0.43 for food groups and 0.41 for nutrients. The average correlation coefficients for validity for daily intakes against 24hDR was r = 0.30, and the average for de-attenuated correlation coefficients was r = 0.44. When evaluating validity against the blood concentration of vitamins, statistically significant correlations were observed for vitamin C (0.35), lycopene (0.31), β-Cryptoxantin (0.40), and vitamin E (0.29); the average of correlation coefficients was r = 0.21. Despite some low to moderate correlations for reproducibility and validity

RESEARCH OF CLASSIFICATION FEATURES OF THE FINANCIAL CONTROL

Directory of Open Access Journals (Sweden)

Knarik K. Arabyan

2013-01-01

Full Text Available One of the major problems is an improvement of classification features in the financial control theory. There is not a consensus concerning the form classification and the methods of financial control. This factor hinders the development of methodology and investigation of other issues of the financial control theory. The author summarizes scientists’ approaches to studying the classification features of financial control in the article.

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

Within-person reproducibility of urinary bisphenol A and phthalate metabolites over a 1 to 3 year period among women in the Nurses’ Health Studies: a prospective cohort study

Science.gov (United States)

2013-01-01

Background Associations of bisphenol A and phthalates with chronic disease health outcomes are increasingly being investigated in epidemiologic studies. The majority of previous studies of within-person variability in urinary bisphenol A and phthalate metabolite concentrations have focused on reproducibility over short time periods. Long-term reproducibility data are needed to assess the potential usefulness of these biomarkers for prospective studies, particularly those examining risk of diseases with long latency periods. Low within-person reproducibility may attenuate relative risk estimates and reduce statistical power to detect associations with disease. Therefore, we assessed within-person reproducibility of bisphenol A, eight phthalate metabolites, and phthalic acid in spot urine samples over 1 to 3 years among women enrolled in two large cohort studies. Methods Women in the Nurses’ Health Study and Nurses’ Health Study II provided two spot urine samples, 1 to 3 years apart (n = 80 women for analyses of bisphenol A; n = 40 women for analyses of phthalate metabolites; n = 34 women for analyses of phthalic acid). To measure within-person reproducibility, we calculated Spearman rank correlation coefficients and intraclass correlation coefficients for creatinine-adjusted concentrations of bisphenol A, phthalate metabolites, and phthalic acid. Results Over 1 to 3 years, within-person variability of bisphenol A was high relative to total variability (intraclass correlation coefficient = 0.14) and rankings of bisphenol A levels between time-points were weakly correlated (Spearman correlation = 0.19). Seven of the eight phthalate metabolites and phthalic acid demonstrated moderate within-person stability over time (Spearman correlation or intraclass correlation coefficient = 0.39-0.55). Restricting analyses to first-morning urine samples did not alter results. Conclusions Single measurements of bisphenol A in spot urine samples were

Within-person reproducibility of urinary bisphenol A and phthalate metabolites over a 1 to 3 year period among women in the Nurses' Health Studies: a prospective cohort study.

Science.gov (United States)

Townsend, Mary K; Franke, Adrian A; Li, Xingnan; Hu, Frank B; Eliassen, A Heather

2013-09-13

Associations of bisphenol A and phthalates with chronic disease health outcomes are increasingly being investigated in epidemiologic studies. The majority of previous studies of within-person variability in urinary bisphenol A and phthalate metabolite concentrations have focused on reproducibility over short time periods. Long-term reproducibility data are needed to assess the potential usefulness of these biomarkers for prospective studies, particularly those examining risk of diseases with long latency periods. Low within-person reproducibility may attenuate relative risk estimates and reduce statistical power to detect associations with disease. Therefore, we assessed within-person reproducibility of bisphenol A, eight phthalate metabolites, and phthalic acid in spot urine samples over 1 to 3 years among women enrolled in two large cohort studies. Women in the Nurses' Health Study and Nurses' Health Study II provided two spot urine samples, 1 to 3 years apart (n = 80 women for analyses of bisphenol A; n = 40 women for analyses of phthalate metabolites; n = 34 women for analyses of phthalic acid). To measure within-person reproducibility, we calculated Spearman rank correlation coefficients and intraclass correlation coefficients for creatinine-adjusted concentrations of bisphenol A, phthalate metabolites, and phthalic acid. Over 1 to 3 years, within-person variability of bisphenol A was high relative to total variability (intraclass correlation coefficient = 0.14) and rankings of bisphenol A levels between time-points were weakly correlated (Spearman correlation = 0.19). Seven of the eight phthalate metabolites and phthalic acid demonstrated moderate within-person stability over time (Spearman correlation or intraclass correlation coefficient = 0.39-0.55). Restricting analyses to first-morning urine samples did not alter results. Single measurements of bisphenol A in spot urine samples were highly variable within women over 1 to 3�

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.

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

Environmental Temperature Effect on the Far-Infrared Absorption Features of Aromatic-Based Titan's Aerosol Analogs

Science.gov (United States)

Gautier, Thomas; Trainer, Melissa G.; Loeffler, Mark J.; Sebree, Joshua A.; Anderson, Carrie M.

2016-01-01

Benzene detection has been reported in Titans atmosphere both in the stratosphere at ppb levels by remote sensing and in the thermosphere at ppm levels by the Cassini's Ion and Neutral Mass Spectrometer. This detection supports the idea that aromatic and heteroaromatic reaction pathways may play an important role in Titans atmospheric chemistry, especially in the formation of aerosols. Indeed, aromatic molecules are easily dissociated by ultraviolet radiation and can therefore contribute significantly to aerosol formation. It has been shown recently that aerosol analogs produced from a gas mixture containing a low concentration of aromatic and/or heteroaromatic molecules (benzene, naphthalene, pyridine, quinoline and isoquinoline) have spectral signatures below 500/cm, a first step towards reproducing the aerosol spectral features observed by Cassini's Composite InfraRed Spectrometer (CIRS) in the far infrared. In this work we investigate the influence of environmental temperature on the absorption spectra of such aerosol samples, simulating the temperature range to which aerosols, once formed, are exposed during their transport through Titans stratosphere. Our results show that environmental temperature does not have any major effect on the spectral shape of these aerosol analogs in the far-infrared, which is consistent with the CIRS observations.

Liquid scintigraphic gastric emptying - is it reproducible?

International Nuclear Information System (INIS)

Cooper, R.G.; Shuter, B.; Leach, M.; Roach, P.J.

1999-01-01

Full text: Radioisotope gastric emptying (GE) studies have been used as a non-invasive technique for motility assessment for many years. In a recent study investigating the correlation of mesenteric vascular changes with GE, six subjects had a repeat study 2-4 months later. Repeat studies were required due to minor technical problems (5 subjects) and a very slow GE (I subject) on the original study. Subjects drank 275 ml of 'Ensure Plus' mixed with 8 MBq 67 Ga-DTPA and were imaged for 2 h while lying supine. GE time-activity curves for each subject were generated and time to half emptying (T l/2 ) calculated. Five of the six subjects had more rapid GE on the second study. Three of the subjects had T l/2 values on their second study which were within ± 15 min of their original T l/2 . The other three subjects had T l/2 values on their second study which were 36 min, 55 min and 280 min (subject K.H.) less than their original T l/2 . Statistical analysis (t-test) was performed on paired T l/2 values. The average T l/2 value was greater in the first study than in the second (149 ± 121 and 86 ± 18 min respectively), although the difference was not statistically significant (P ∼ 0.1). Subjects' anxiety levels were not quantitated during the GE study; however, several major equipment faults occurred during the original study of subject K.H., who became visibly stressed. These results suggest that the reproducibility of GE studies may be influenced by psychological factors

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.

Ceramic coatings: A phenomenological modeling for damping behavior related to microstructural features

International Nuclear Information System (INIS)

Tassini, N.; Patsias, S.; Lambrinou, K.

2006-01-01

Recent research has shown that both stiffness and damping of ceramic coatings exhibit different non-linearities. These properties strongly depend on the microstructure, which is characterized by heterogeneous sets of elastic elements with mesoscopic sizes and shapes, as in non-linear mesoscopic elastic materials. To predict the damping properties of this class of materials, we have implemented a phenomenological model that characterizes their elastic properties. The model is capable of reproducing the basic features of the observed damping behavior for zirconia coatings prepared by air plasma spraying and electron-beam physical-vapor-deposition

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

Psychological features in panic disorder: a comparison with major depression

Directory of Open Access Journals (Sweden)

Almeida Yasmin A.

2002-01-01

Full Text Available OBJECTIVE: We aim to evaluate the psychodymanic model for panic disorder (PD formulated by Shear et al. (1993, comparing PD patients and major depression (MD patients. METHOD: We evaluated these parameters in open interviews in 10 PD patients and 10 patients with MD (DSM-IV. The data were recorded on videotape and were examined by 5 diagnostic blind appraisers. RESULTS: The data allowed a comparative analysis that underscores the existence of a psychological model for PD vs MD: 1 the protracted symbiotic phase of development and the existence of problems with separation in PD patients; 2 patients with MD tended to have a particularly negative impression of relationship with the first objects; furthermore, they had remarkable experiences of loss; and 3 while the PD patients tended to be shy and inhibited in childhood, especially showing a clear difficulty in expressing aggressiveness, the depressed patients tended to disclose an impulsive aggressiveness from infancy to adulthood. CONCLUSION: Exposure to parental behaviours that augment fearfulness may result in disturbances in object relations and persistence of conflicts between dependence and independence may predispose to anxiety symptoms and fears of PD.

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

Grammar-based feature generation for time-series prediction

CERN Document Server

De Silva, Anthony Mihirana

2015-01-01

This book proposes a novel approach for time-series prediction using machine learning techniques with automatic feature generation. Application of machine learning techniques to predict time-series continues to attract considerable attention due to the difficulty of the prediction problems compounded by the non-linear and non-stationary nature of the real world time-series. The performance of machine learning techniques, among other things, depends on suitable engineering of features. This book proposes a systematic way for generating suitable features using context-free grammar. A number of feature selection criteria are investigated and a hybrid feature generation and selection algorithm using grammatical evolution is proposed. The book contains graphical illustrations to explain the feature generation process. The proposed approaches are demonstrated by predicting the closing price of major stock market indices, peak electricity load and net hourly foreign exchange client trade volume. The proposed method ...

Repeatability and reproducibility of intracellular molar concentration assessed by synchrotron-based x-ray fluorescence microscopy

Energy Technology Data Exchange (ETDEWEB)

Merolle, L., E-mail: lucia.merolle@elettra.eu; Gianoncelli, A. [Elettra - Sincrotrone Trieste, 34149 Basovizza, Trieste (Italy); Malucelli, E., E-mail: emil.malucelli@unibo.it; Cappadone, C.; Farruggia, G.; Sargenti, A.; Procopio, A. [Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40127 (Italy); Fratini, M. [Museo Storico della Fisica e Centro Studi e Ricerche Enrico Fermi, Piazza del Viminale 1, 00184 Roma Italy (Italy); Department of Science, Roma Tre University, Via della Vasca Navale 84, I-00146 Rome (Italy); Notargiacomo, A. [Institute for Photonics and Nanotechnology, Consiglio Nazionale delle Richerche, 00156 Rome (Italy); Lombardo, M. [Department of Chemistry “G. Ciamician”, University of Bologna, Bologna 40126 (Italy); Lagomarsino, S. [Institute of Chemical-Physical Processes, Sapienza University of Rome, 00185 Rome (Italy); National Institute of Biostructures and Biosystems, 00136 Rome (Italy); Iotti, S. [Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40127 (Italy); National Institute of Biostructures and Biosystems, 00136 Rome (Italy)

2016-01-28

Elemental analysis of biological sample can give information about content and distribution of elements essential for human life or trace elements whose absence is the cause of abnormal biological function or development. However, biological systems contain an ensemble of cells with heterogeneous chemistry and elemental content; therefore, accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. Powerful methods in molecular biology are abundant, among them X-Ray microscopy based on synchrotron light source has gaining increasing attention thanks to its extremely sensitivity. However, reproducibility and repeatability of these measurements is one of the major obstacles in achieving a statistical significance in single cells population analysis. In this study, we compared the elemental content of human colon adenocarcinoma cells obtained by three distinct accesses to synchrotron radiation light.

Reproducibility analysis to validate language processes involving Kanji and Chinese characters under different MRI scanner environments

International Nuclear Information System (INIS)

Chen Shensing Annabel; Matsuo, Kayako; Tseng Wenyih Isaac; Hue Chiwei; Nakai, Toshiharu; Bagarinao, E.; Ho Moonho Ringo; Liou Michelle

2009-01-01

Reading Japanese kanji is similar to reading Chinese characters in that orthography-to-phonology conversion is required. However, a notable difference between kanji and Chinese characters or alphabets is that the majority of kanji are heterophonic-homographic characters, id est (i.e.), one character is mapped to more than one pronunciation. With the goal of developing a standardized functional MRI language task for Japanese and Chinese, we conducted a series of homophone judgment tasks in both populations. Since the Japanese and Chinese data were acquired using MRI scanners with different magnetic field strengths (1.5 T and 3 T, respectively), direct comparison of the activation maps from the two populations using conventional statistical methods was not appropriate. Informal evaluation of the group activations for the homophonic-heterographic condition showed that this homophone judgment task with similar content and standardized design elicited common areas of activation for language in general for the two populations. Further, it is interesting to note that strong activations in the left posterior superior and middle temporal regions were found to be unique to the Taiwanese population. To further investigate this, we applied reproducibility analysis to verify the likelihood that this finding is unique to the Chinese population. The results are presented and the possibility of using reproducibility analysis to evaluate and compare data from different populations and with different scanner strengths is discussed. (author)

18F-Fluorodeoxyglucose positron emission tomography pulmonary imaging in idiopathic pulmonary fibrosis is reproducible: implications for future clinical trials

International Nuclear Information System (INIS)

Win, Thida; Lambrou, Tryphon; Hutton, Brian F.; Kayani, Irfan; Endozo, Raymondo; Shortman, Robert I.; Groves, Ashley M.; Screaton, Nicholas J.; Porter, Joanna C.; Maher, Toby M.; Lukey, Pauline

2012-01-01

Noninvasive markers of disease activity in patients with idiopathic pulmonary fibrosis (IPF) are lacking. We performed this study to investigate the reproducibility of pulmonary 18 F-FDG PET/CT in patients with IPF. The study group comprised 13 patients (11 men, 2 women; mean age 71.1 ± 9.9 years) with IPF recruited for two thoracic 18 F-FDG PET/CT studies performed within 2 weeks of each other. All patients were diagnosed with IPF in consensus at multidisciplinary meetings as a result of typical clinical, high-resolution CT and pulmonary function test features. Three methods for evaluating pulmonary 18 F-FDG uptake were used. The maximal 18 F-FDG pulmonary uptake (SUVmax) in the lungs was determined using manual region-of-interest placement. An 18 F-FDG uptake intensity histogram was automatically constructed from segmented lungs to evaluate the distribution of SUVs. Finally, mean SUV was determined for volumes-of-interest in pulmonary regions with interstitial lung changes identified on CT scans. Processing included correction for tissue fraction effects. Bland-Altman analysis was performed and interclass correlation coefficients (ICC) were determined to assess the reproducibility between the first and second PET scans, as well as the level of intraobserver and interobserver agreement. The mean time between the two scans was 6.3 ± 4.3 days. The interscan ICCs for pulmonary SUVmax analysis and mean SUV corrected for tissue fraction effects were 0.90 and 0.91, respectively. Intensity histograms were different in only 1 of the 13 paired studies. Intraobserver agreement was also excellent (0.80 and 0.85, respectively). Some bias was observed between observers, suggesting that serial studies would benefit from analysis by the same observer. This study demonstrated that there is excellent short-term reproducibility in pulmonary 18 F-FDG uptake in patients with IPF. (orig.)

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

Directory of Open Access Journals (Sweden)

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.

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....

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

Directory of Open Access Journals (Sweden)

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.

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.

Fabrication of narrow surface relief features in a side-chain azobenzene polyester with a scanning near-field microscope

DEFF Research Database (Denmark)

Ramanujam, P.S.; Holme, N. C. R.; Pedersen, M.

2001-01-01

We show that it is possible to fabricate topographic submicron features in a side-chain azobenzene polyester with a scanning near-field optical microscope, Through irradiation at a wavelength of 488 run at intensity levels of 12 W/cm(2), topographic features as narrow as 240 nm and as high as 6 nm...... have been reproducibly recorded in a thin film of the polyester. These observations are consistent with the fact that at low intensities peaks are produced evolving into formation of trenches at high intensities in the case of amorphous side-chain azobenzene polyesters. This may find applications...

Reproducibility analysis of the stability and treatment of vertebral metastatic lesions

Directory of Open Access Journals (Sweden)

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.

Degree of contribution (DoC) feature selection algorithm for structural brain MRI volumetric features in depression detection.

Science.gov (United States)

Kipli, Kuryati; Kouzani, Abbas Z

2015-07-01

Accurate detection of depression at an individual level using structural magnetic resonance imaging (sMRI) remains a challenge. Brain volumetric changes at a structural level appear to have importance in depression biomarkers studies. An automated algorithm is developed to select brain sMRI volumetric features for the detection of depression. A feature selection (FS) algorithm called degree of contribution (DoC) is developed for selection of sMRI volumetric features. This algorithm uses an ensemble approach to determine the degree of contribution in detection of major depressive disorder. The DoC is the score of feature importance used for feature ranking. The algorithm involves four stages: feature ranking, subset generation, subset evaluation, and DoC analysis. The performance of DoC is evaluated on the Duke University Multi-site Imaging Research in the Analysis of Depression sMRI dataset. The dataset consists of 115 brain sMRI scans of 88 healthy controls and 27 depressed subjects. Forty-four sMRI volumetric features are used in the evaluation. The DoC score of forty-four features was determined as the accuracy threshold (Acc_Thresh) was varied. The DoC performance was compared with that of four existing FS algorithms. At all defined Acc_Threshs, DoC outperformed the four examined FS algorithms for the average classification score and the maximum classification score. DoC has a good ability to generate reduced-size subsets of important features that could yield high classification accuracy. Based on the DoC score, the most discriminant volumetric features are those from the left-brain region.

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.

Online feature selection with streaming features.

Science.gov (United States)

Wu, Xindong; Yu, Kui; Ding, Wei; Wang, Hao; Zhu, Xingquan

2013-05-01

We propose a new online feature selection framework for applications with streaming features where the knowledge of the full feature space is unknown in advance. We define streaming features as features that flow in one by one over time whereas the number of training examples remains fixed. This is in contrast with traditional online learning methods that only deal with sequentially added observations, with little attention being paid to streaming features. The critical challenges for Online Streaming Feature Selection (OSFS) include 1) the continuous growth of feature volumes over time, 2) a large feature space, possibly of unknown or infinite size, and 3) the unavailability of the entire feature set before learning starts. In the paper, we present a novel Online Streaming Feature Selection method to select strongly relevant and nonredundant features on the fly. An efficient Fast-OSFS algorithm is proposed to improve feature selection performance. The proposed algorithms are evaluated extensively on high-dimensional datasets and also with a real-world case study on impact crater detection. Experimental results demonstrate that the algorithms achieve better compactness and higher prediction accuracy than existing streaming feature selection algorithms.

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.

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.

Validation of Interobserver Agreement in Lung Cancer Assessment: Hematoxylin-Eosin Diagnostic Reproducibility for Non–Small Cell Lung Cancer

Science.gov (United States)

Grilley-Olson, Juneko E.; Hayes, D. Neil; Moore, Dominic T.; Leslie, Kevin O.; Wilkerson, Matthew D.; Qaqish, Bahjat F.; Hayward, Michele C.; Cabanski, Christopher R.; Yin, Xiaoying; Socinski, Mark A.; Stinchcombe, Thomas E.; Thorne, Leigh B.; Allen, Timothy Craig; Banks, Peter M.; Beasley, Mary B.; Borczuk, Alain C.; Cagle, Philip T.; Christensen, Rebecca; Colby, Thomas V.; Deblois, Georgean G.; Elmberger, Göran; Graziano, Paolo; Hart, Craig F.; Jones, Kirk D.; Maia, Diane M.; Miller, C. Ryan; Nance, Keith V.; Travis, William D.; Funkhouser, William K.

2018-01-01

Context Precise subtype diagnosis of non–small cell lung carcinoma is increasingly relevant, based on the availability of subtype-specific therapies, such as bevacizumab and pemetrexed, and based on the subtype-specific prevalence of activating epidermal growth factor receptor mutations. Objectives To establish a baseline measure of inter-observer reproducibility for non–small cell lung carcinoma diagnoses with hematoxylin-eosin for the current 2004 World Health Organization classification, to estimate interobserver reproducibility for the therapeutically relevant squamous/nonsquamous subsets, and to examine characteristics that improve interobserver reproducibility. Design Primary, resected lung cancer specimens were converted to digital (virtual) slides. Based on a single hematoxylin-eosin virtual slide, pathologists were asked to assign a diagnosis using the 2004 World Health Organization classification. Kappa statistics were calculated for each pathologist-pair for each slide and were summarized by classification scheme, pulmonary pathology expertise, diagnostic confidence, and neoplastic grade. Results The 12 pulmonary pathology experts and the 12 community pathologists each independently diagnosed 48 to 96 single hematoxylin-eosin digital slides derived from 96 cases of non–small cell lung carcinoma resection. Overall agreement improved with simplification from the comprehensive 44 World Health Organization diagnoses (κ = 0.25) to their 10 major header subtypes (κ = 0.48) and improved again with simplification into the therapeutically relevant squamous/nonsquamous dichotomy (κ = 0.55). Multivariate analysis showed that higher diagnostic agreement was associated with better differentiation, better slide quality, higher diagnostic confidence, similar years of pathology experience, and pulmonary pathology expertise. Conclusions These data define the baseline diagnostic agreement for hematoxylin-eosin diagnosis of non–small cell lung carcinoma

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.

Understanding Legacy Features with Featureous

DEFF Research Database (Denmark)

Olszak, Andrzej; Jørgensen, Bo Nørregaard

2011-01-01

Java programs called Featureous that addresses this issue. Featureous allows a programmer to easily establish feature-code traceability links and to analyze their characteristics using a number of visualizations. Featureous is an extension to the NetBeans IDE, and can itself be extended by third...

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

High Reproducibility of ELISPOT Counts from Nine Different Laboratories

DEFF Research Database (Denmark)

Sundararaman, Srividya; Karulin, Alexey Y; Ansari, Tameem

2015-01-01

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...

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

Major depression with psychotic features

Science.gov (United States)

... Updated by: Fred K. Berger, MD, addiction and forensic psychiatrist, Scripps Memorial Hospital, La Jolla, CA. Also ... urac.org). URAC's accreditation program is an independent audit to verify that A.D.A.M. follows ...

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

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.

Finite-rank potential that reproduces the Pade approximant

International Nuclear Information System (INIS)

Tani, S.

1979-01-01

If a scattering potential is of a finite rank, say N, the exact solution of the problem can be obtained from the Born series, if the potential strength is within the radius of convergence; the exact solution can be obtained from the analytical continuation of the formal Born series outside the radius of convergence. Beyond the first 2N terms of the Born series, an individual term of the Born series depends on the first 2N terms, and the [N/N] Pade approximant and the exact solution agree with each other. The above-mentioned features of a finite-rank problem are relevant to scattering theory in general, because most scattering problems may be handled as an extension of the rank-N problem, in which the rank N tends to infinity. The foregoing aspects of scattering theory will be studied in depth in the present paper, and in so doing we proceed in the opposite direction. Namely, given a potential, we calculate the first 2N terms of the Born series for the K matrix and the first N terms of the Born series for the wave function. Using these data, a special rank-N potential is constructed in such a way that it reproduces the [N/N] Pade approximant of the K matrix of the original scattering problem. One great advantage of obtaining such a rank-N potential is that the wave function of the system may be approximated in the same spirit as done for the K matrix; hence, we can introduce a new approximation method for dealing with an off-shell T matrix. A part of the mathematical work is incomplete, but the physical aspects are thoroughly discussed

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.

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

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...

Quantum features of natural cellular automata

International Nuclear Information System (INIS)

Elze, Hans-Thomas

2016-01-01

Cellular automata can show well known features of quantum mechanics, such as a linear rule according to which they evolve and which resembles a discretized version of the Schrödinger equation. This includes corresponding conservation laws. The class of “natural” Hamiltonian cellular automata is based exclusively on integer-valued variables and couplings and their dynamics derives from an Action Principle. They can be mapped reversibly to continuum models by applying Sampling Theory. Thus, “deformed” quantum mechanical models with a finite discreteness scale l are obtained, which for l → 0 reproduce familiar continuum results. We have recently demonstrated that such automata can form “multipartite” systems consistently with the tensor product structures of nonrelativistic many-body quantum mechanics, while interacting and maintaining the linear evolution. Consequently, the Superposition Principle fully applies for such primitive discrete deterministic automata and their composites and can produce the essential quantum effects of interference and entanglement. (paper)

Discrimination Of The Land Features In Al Hasa Oasi, Saudi Arabia, Using Color Ratio Technique On Land Sat Tm Data

International Nuclear Information System (INIS)

Al Saud, M.B.M.

2003-01-01

Landsat Thematic Mapper (TM) data for Al Rasa Oasis area was processed for delineating characteristic land features represented mainly by sand dunes, sabkhas, cultivated land and urban areas using procedures that take advantage of distinctive spectral reflectance of these land features. The method employs a color ratio technique based on comprising different ratios 2/3, 2/4, 3/4, 3/5, 4/5, 5/6, and 5/7. A number of ratio triplets were processed using a three colored composite ratio. The ratio images (3/4,3/5,5/6,and 5/7) succeeded to distinguish the main land features in the studied arid region and generate detailed maps over wide area by using quantitative reproducible mapping criteria and helping in identifying the characteristics of the different land features

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.

When Quality Beats Quantity: Decision Theory, Drug Discovery, and the Reproducibility Crisis.

Directory of Open Access Journals (Sweden)

Jack W Scannell

Full Text Available A striking contrast runs through the last 60 years of biopharmaceutical discovery, research, and development. Huge scientific and technological gains should have increased the quality of academic science and raised industrial R&D efficiency. However, academia faces a "reproducibility crisis"; inflation-adjusted industrial R&D costs per novel drug increased nearly 100 fold between 1950 and 2010; and drugs are more likely to fail in clinical development today than in the 1970s. The contrast is explicable only if powerful headwinds reversed the gains and/or if many "gains" have proved illusory. However, discussions of reproducibility and R&D productivity rarely address this point explicitly. The main objectives of the primary research in this paper are: (a to provide quantitatively and historically plausible explanations of the contrast; and (b identify factors to which R&D efficiency is sensitive. We present a quantitative decision-theoretic model of the R&D process. The model represents therapeutic candidates (e.g., putative drug targets, molecules in a screening library, etc. within a "measurement space", with candidates' positions determined by their performance on a variety of assays (e.g., binding affinity, toxicity, in vivo efficacy, etc. whose results correlate to a greater or lesser degree. We apply decision rules to segment the space, and assess the probability of correct R&D decisions. We find that when searching for rare positives (e.g., candidates that will successfully complete clinical development, changes in the predictive validity of screening and disease models that many people working in drug discovery would regard as small and/or unknowable (i.e., an 0.1 absolute change in correlation coefficient between model output and clinical outcomes in man can offset large (e.g., 10 fold, even 100 fold changes in models' brute-force efficiency. We also show how validity and reproducibility correlate across a population of simulated

Highly Efficient Reproducible Perovskite Solar Cells Prepared by Low-Temperature Processing

Directory of Open Access Journals (Sweden)

Hao Hu

2016-04-01

Full Text Available In this work, we describe the role of the different layers in perovskite solar cells to achieve reproducible, ~16% efficient perovskite solar cells. We used a planar device architecture with PEDOT:PSS on the bottom, followed by the perovskite layer and an evaporated C60 layer before deposition of the top electrode. No high temperature annealing step is needed, which also allows processing on flexible plastic substrates. Only the optimization of all of these layers leads to highly efficient and reproducible results. In this work, we describe the effects of different processing conditions, especially the influence of the C60 top layer on the device performance.

BRAF Mutation Is Associated With a Specific Cell Type With Features Suggestive of Senescence in Ovarian Serous Borderline (Atypical Proliferative) Tumors

DEFF Research Database (Denmark)

Zeppernick, Felix; Ardighieri, Laura; Hannibal, Charlotte G

2014-01-01

features could be reproduced in cultured epithelial cells by ectopic expression of BRAF(V600E). Senescence was further established by markers such as SA-β-gal staining, expression of p16 and p21, and reduction in DNA synthesis. In conclusion, this study sheds light on the pathogenesis of this unique group...

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.

Performance profiles of major energy producers 1996

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-01-01

This publication examines developments in the operations of the major US e energy-producing companies on a corporate level, by major line of business, by major function within each line of business, and by geographic area. In 1996, 24 companies filed Form EIA-28. The analysis and data presented in this report represents the operations of the Financial Reporting System companies in the context of their worldwide operations and in the context of the major energy markets which they serve. Both energy and nonenergy developments of these companies are analyzed. Although the focus is on developments in 1996, important trends prior to that time are also featured. Sections address energy markets in 1996; key financial developments; oil and gas exploration, development, and production; downstream petroleum in 1996; coal and alternative energy; and foreign direct investment in US energy. 30 figs., 104 tabs.

Performance profiles of major energy producers 1996

International Nuclear Information System (INIS)

1998-01-01

This publication examines developments in the operations of the major US e energy-producing companies on a corporate level, by major line of business, by major function within each line of business, and by geographic area. In 1996, 24 companies filed Form EIA-28. The analysis and data presented in this report represents the operations of the Financial Reporting System companies in the context of their worldwide operations and in the context of the major energy markets which they serve. Both energy and nonenergy developments of these companies are analyzed. Although the focus is on developments in 1996, important trends prior to that time are also featured. Sections address energy markets in 1996; key financial developments; oil and gas exploration, development, and production; downstream petroleum in 1996; coal and alternative energy; and foreign direct investment in US energy. 30 figs., 104 tabs

SHOCKING TAILS IN THE MAJOR MERGER ABELL 2744

Energy Technology Data Exchange (ETDEWEB)

Owers, Matt S.; Couch, Warrick J. [Center for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, VIC 3122 (Australia); Nulsen, Paul E. J.; Randall, Scott W., E-mail: mowers@aao.gov.au [Harvard Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States)

2012-05-01

We identify four rare 'jellyfish' galaxies in Hubble Space Telescope imagery of the major merger cluster Abell 2744. These galaxies harbor trails of star-forming knots and filaments which have formed in situ in gas tails stripped from the parent galaxies, indicating they are in the process of being transformed by the environment. Further evidence for rapid transformation in these galaxies comes from their optical spectra, which reveal starburst, poststarburst, and active galactic nucleus features. Most intriguingly, three of the jellyfish galaxies lie near intracluster medium features associated with a merging 'Bullet-like' subcluster and its shock front detected in Chandra X-ray images. We suggest that the high-pressure merger environment may be responsible for the star formation in the gaseous tails. This provides observational evidence for the rapid transformation of galaxies during the violent core passage phase of a major cluster merger.

Short- and long-term quantitation reproducibility of brain metabolites in the medial wall using proton echo planar spectroscopic imaging.

Science.gov (United States)

Tsai, Shang-Yueh; Lin, Yi-Ru; Wang, Woan-Chyi; Niddam, David M

2012-11-15

Proton echo planar spectroscopic imaging (PEPSI) is a fast magnetic resonance spectroscopic imaging (MRSI) technique that allows mapping spatial metabolite distributions in the brain. Although the medial wall of the cortex is involved in a wide range of pathological conditions, previous MRSI studies have not focused on this region. To decide the magnitude of metabolic changes to be considered significant in this region, the reproducibility of the method needs to be established. The study aims were to establish the short- and long-term reproducibility of metabolites in the right medial wall and to compare regional differences using a constant short-echo time (TE30) and TE averaging (TEavg) optimized to yield glutamatergic information. 2D sagittal PEPSI was implemented at 3T using a 32 channel head coil. Acquisitions were repeated immediately and after approximately 2 weeks to assess the coefficients of variation (COV). COVs were obtained from eight regions-of-interest (ROIs) of varying size and location. TE30 resulted in better spectral quality and similar or lower quantitation uncertainty for all metabolites except glutamate (Glu). When Glu and glutamine (Gln) were quantified together (Glx) reduced quantitation uncertainty and increased reproducibility was observed for TE30. TEavg resulted in lowered quantitation uncertainty for Glu but in less reliable quantification of several other metabolites. TEavg did not result in a systematically improved short- or long-term reproducibility for Glu. The ROI volume was a major factor influencing reproducibility. For both short- and long-term repetitions, the Glu COVs obtained with TEavg were 5-8% for the large ROIs, 12-17% for the medium sized ROIs and 16-26% for the smaller cingulate ROIs. COVs obtained with TE30 for the less specific Glx were 3-5%, 8-10% and 10-15%. COVs for N-acetyl aspartate, creatine and choline using TE30 with long-term repetition were between 2-10%. Our results show that the cost of more specific

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

The impact of image reconstruction settings on 18F-FDG PET radiomic features. Multi-scanner phantom and patient studies

International Nuclear Information System (INIS)

Shiri, Isaac; Abdollahi, Hamid; Rahmim, Arman; Ghaffarian, Pardis; Geramifar, Parham; Bitarafan-Rajabi, Ahmad

2017-01-01

The purpose of this study was to investigate the robustness of different PET/CT image radiomic features over a wide range of different reconstruction settings. Phantom and patient studies were conducted, including two PET/CT scanners. Different reconstruction algorithms and parameters including number of sub-iterations, number of subsets, full width at half maximum (FWHM) of Gaussian filter, scan time per bed position and matrix size were studied. Lesions were delineated and one hundred radiomic features were extracted. All radiomics features were categorized based on coefficient of variation (COV). Forty seven percent features showed COV ≤ 5% and 10% of which showed COV > 20%. All geometry based, 44% and 41% of intensity based and texture based features were found as robust respectively. In regard to matrix size, 56% and 6% of all features were found non-robust (COV > 20%) and robust (COV ≤ 5%) respectively. Variability and robustness of PET/CT image radiomics in advanced reconstruction settings is feature-dependent, and different settings have different effects on different features. Radiomic features with low COV can be considered as good candidates for reproducible tumour quantification in multi-center studies. (orig.)

The impact of image reconstruction settings on 18F-FDG PET radiomic features. Multi-scanner phantom and patient studies

Energy Technology Data Exchange (ETDEWEB)

Shiri, Isaac; Abdollahi, Hamid [Iran University of Medical Sciences, Department of Medical Physics, School of Medicine, Tehran (Iran, Islamic Republic of); Rahmim, Arman [Johns Hopkins University, Department of Radiology, Baltimore, MD (United States); Johns Hopkins University, Department of Electrical and Computer Engineering, Baltimore, MD (United States); Ghaffarian, Pardis [Shahid Beheshti University of Medical Sciences, Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Tehran (Iran, Islamic Republic of); Shahid Beheshti University of Medical Sciences, PET/CT and Cyclotron Center, Masih Daneshvari Hospital, Tehran (Iran, Islamic Republic of); Geramifar, Parham [Tehran University of Medical Sciences, Research Center for Nuclear Medicine, Shariati Hospital, Tehran (Iran, Islamic Republic of); Bitarafan-Rajabi, Ahmad [Iran University of Medical Sciences, Department of Medical Physics, School of Medicine, Tehran (Iran, Islamic Republic of); Iran University of Medical Sciences, Department of Nuclear Medicine, Rajaei Cardiovascular, Medical and Research Center, Tehran (Iran, Islamic Republic of)

2017-11-15

The purpose of this study was to investigate the robustness of different PET/CT image radiomic features over a wide range of different reconstruction settings. Phantom and patient studies were conducted, including two PET/CT scanners. Different reconstruction algorithms and parameters including number of sub-iterations, number of subsets, full width at half maximum (FWHM) of Gaussian filter, scan time per bed position and matrix size were studied. Lesions were delineated and one hundred radiomic features were extracted. All radiomics features were categorized based on coefficient of variation (COV). Forty seven percent features showed COV ≤ 5% and 10% of which showed COV > 20%. All geometry based, 44% and 41% of intensity based and texture based features were found as robust respectively. In regard to matrix size, 56% and 6% of all features were found non-robust (COV > 20%) and robust (COV ≤ 5%) respectively. Variability and robustness of PET/CT image radiomics in advanced reconstruction settings is feature-dependent, and different settings have different effects on different features. Radiomic features with low COV can be considered as good candidates for reproducible tumour quantification in multi-center studies. (orig.)

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.

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

Unlike twins: an NMR comparison of two α-synuclein polymorphs featuring different toxicity.

Directory of Open Access Journals (Sweden)

Julia Gath

Full Text Available We structurally compare, using solid-state NMR, two different polymorphs of α-synuclein which, as established recently, display contrasting biochemical properties, toxicity, and tropism for cells. We show that both forms, which can each be produced as a pure polymorph, are greatly different in secondary structure. While β-sheets are the dominating secondary structure elements for both polymorphs, they are markedly divergent in terms of number of elements, as well as their distribution. We demonstrate that all identified β-sheets feature an in-register parallel stacking for both polymorphs. The two forms show a different molecular arrangement in the unit cell and distinct dynamic features, while sharing a highly flexible C-terminal domain. The use of reproducible, well-identified conditions for sample preparation and the recording of identical NMR experiments allows for a direct comparison of the results.

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

Community-based Approaches to Improving Accuracy, Precision, and Reproducibility in U-Pb and U-Th Geochronology

Science.gov (United States)

McLean, N. M.; Condon, D. J.; Bowring, S. A.; Schoene, B.; Dutton, A.; Rubin, K. H.

2015-12-01

The last two decades have seen a grassroots effort by the international geochronology community to "calibrate Earth history through teamwork and cooperation," both as part of the EARTHTIME initiative and though several daughter projects with similar goals. Its mission originally challenged laboratories "to produce temporal constraints with uncertainties approaching 0.1% of the radioisotopic ages," but EARTHTIME has since exceeded its charge in many ways. Both the U-Pb and Ar-Ar chronometers first considered for high-precision timescale calibration now regularly produce dates at the sub-per mil level thanks to instrumentation, laboratory, and software advances. At the same time new isotope systems, including U-Th dating of carbonates, have developed comparable precision. But the larger, inter-related scientific challenges envisioned at EARTHTIME's inception remain - for instance, precisely calibrating the global geologic timescale, estimating rates of change around major climatic perturbations, and understanding evolutionary rates through time - and increasingly require that data from multiple geochronometers be combined. To solve these problems, the next two decades of uranium-daughter geochronology will require further advances in accuracy, precision, and reproducibility. The U-Th system has much in common with U-Pb, in that both parent and daughter isotopes are solids that can easily be weighed and dissolved in acid, and have well-characterized reference materials certified for isotopic composition and/or purity. For U-Pb, improving lab-to-lab reproducibility has entailed dissolving precisely weighed U and Pb metals of known purity and isotopic composition together to make gravimetric solutions, then using these to calibrate widely distributed tracers composed of artificial U and Pb isotopes. To mimic laboratory measurements, naturally occurring U and Pb isotopes were also mixed in proportions to mimic samples of three different ages, to be run as internal

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.

{sup 18}F-Fluorodeoxyglucose positron emission tomography pulmonary imaging in idiopathic pulmonary fibrosis is reproducible: implications for future clinical trials

Energy Technology Data Exchange (ETDEWEB)

Win, Thida [Lister Hospital, Respiratory Medicine, Stevenage (United Kingdom); Lambrou, Tryphon; Hutton, Brian F.; Kayani, Irfan; Endozo, Raymondo; Shortman, Robert I.; Groves, Ashley M. [UCL/UCH, Institute of Nuclear Medicine, London (United Kingdom); Screaton, Nicholas J. [Papworth Hospital, Radiology Department, Cambridge (United Kingdom); Porter, Joanna C. [UCL/UCH, Centre for Respiratory Diseases, London (United Kingdom); Maher, Toby M. [Royal Brompton Hospital, Interstitial Lung Disease Unit, London (United Kingdom); Lukey, Pauline [GSK, Fibrosis DPU, Research and Development, Stevenage (United Kingdom)

2012-03-15

Noninvasive markers of disease activity in patients with idiopathic pulmonary fibrosis (IPF) are lacking. We performed this study to investigate the reproducibility of pulmonary {sup 18}F-FDG PET/CT in patients with IPF. The study group comprised 13 patients (11 men, 2 women; mean age 71.1 {+-} 9.9 years) with IPF recruited for two thoracic {sup 18}F-FDG PET/CT studies performed within 2 weeks of each other. All patients were diagnosed with IPF in consensus at multidisciplinary meetings as a result of typical clinical, high-resolution CT and pulmonary function test features. Three methods for evaluating pulmonary {sup 18}F-FDG uptake were used. The maximal {sup 18}F-FDG pulmonary uptake (SUVmax) in the lungs was determined using manual region-of-interest placement. An {sup 18}F-FDG uptake intensity histogram was automatically constructed from segmented lungs to evaluate the distribution of SUVs. Finally, mean SUV was determined for volumes-of-interest in pulmonary regions with interstitial lung changes identified on CT scans. Processing included correction for tissue fraction effects. Bland-Altman analysis was performed and interclass correlation coefficients (ICC) were determined to assess the reproducibility between the first and second PET scans, as well as the level of intraobserver and interobserver agreement. The mean time between the two scans was 6.3 {+-} 4.3 days. The interscan ICCs for pulmonary SUVmax analysis and mean SUV corrected for tissue fraction effects were 0.90 and 0.91, respectively. Intensity histograms were different in only 1 of the 13 paired studies. Intraobserver agreement was also excellent (0.80 and 0.85, respectively). Some bias was observed between observers, suggesting that serial studies would benefit from analysis by the same observer. This study demonstrated that there is excellent short-term reproducibility in pulmonary {sup 18}F-FDG uptake in patients with IPF. (orig.)

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 ...

Binary palmprint representation for feature template protection

NARCIS (Netherlands)

Mu, Meiru; Ruan, Qiuqi; Shao, X.; Spreeuwers, Lieuwe Jan; Veldhuis, Raymond N.J.

2012-01-01

The major challenge of biometric template protection comes from the intraclass variations of biometric data. The helper data scheme aims to solve this problem by employing the Error Correction Codes (ECC). However, many reported biometric binary features from the same user reach bit error rate (BER)

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.

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 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.

Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype

Directory of Open Access Journals (Sweden)

K. Brennan

2017-03-01

Further distinguishing features of this ‘CIMP-Atypical’ subtype include an antiviral gene expression profile associated with pro-inflammatory M1 macrophages and CD8+ T cell infiltration, CASP8 mutations, and a well-differentiated state corresponding to normal SOX2 copy number and SOX2OT hypermethylation. We developed a gene expression classifier for the CIMP-Atypical subtype that could classify atypical disease features in two independent patient cohorts, demonstrating the reproducibility of this subtype. Taken together, these findings provide unprecedented evidence that atypical HNSCC is molecularly distinct, and postulates the CIMP-Atypical subtype as a distinct clinical entity that may be caused by chronic inflammation.

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.

Improved initial guess with semi-subpixel level accuracy in digital image correlation by feature-based method

Science.gov (United States)

Zhang, Yunlu; Yan, Lei; Liou, Frank

2018-05-01

The quality initial guess of deformation parameters in digital image correlation (DIC) has a serious impact on convergence, robustness, and efficiency of the following subpixel level searching stage. In this work, an improved feature-based initial guess (FB-IG) scheme is presented to provide initial guess for points of interest (POIs) inside a large region. Oriented FAST and Rotated BRIEF (ORB) features are semi-uniformly extracted from the region of interest (ROI) and matched to provide initial deformation information. False matched pairs are eliminated by the novel feature guided Gaussian mixture model (FG-GMM) point set registration algorithm, and nonuniform deformation parameters of the versatile reproducing kernel Hilbert space (RKHS) function are calculated simultaneously. Validations on simulated images and real-world mini tensile test verify that this scheme can robustly and accurately compute initial guesses with semi-subpixel level accuracy in cases with small or large translation, deformation, or rotation.

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 ...

Control-group feature normalization for multivariate pattern analysis of structural MRI data using the support vector machine.

Science.gov (United States)

Linn, Kristin A; Gaonkar, Bilwaj; Satterthwaite, Theodore D; Doshi, Jimit; Davatzikos, Christos; Shinohara, Russell T

2016-05-15

Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization, it utilizes the total variability of these features. This total variation is inevitably dependent on the amount of marginal separation between groups. Thus, such a normalization may attenuate the separability of the data in high dimensional space. In this work we propose an alternate approach that uses an estimate of the control-group standard deviation to normalize features before training. We study our proposed approach in the context of group classification using structural MRI data. We show that control-based normalization leads to better reproducibility of estimated multivariate disease patterns and improves the classifier performance in many cases. Copyright © 2016 Elsevier Inc. All rights reserved.

Au coated PS nanopillars as a highly ordered and reproducible SERS substrate

Science.gov (United States)

Kim, Yong-Tae; Schilling, Joerg; Schweizer, Stefan L.; Sauer, Guido; Wehrspohn, Ralf B.

2017-07-01

Noble metal nanostructures with nanometer gap size provide strong surface-enhanced Raman scattering (SERS) which can be used to detect trace amounts of chemical and biological molecules. Although several approaches were reported to obtain active SERS substrates, it still remains a challenge to fabricate SERS substrates with high sensitivity and reproducibility using low-cost techniques. In this article, we report on the fabrication of Au sputtered PS nanopillars based on a template synthetic method as highly ordered and reproducible SERS substrates. The SERS substrates are fabricated by anodic aluminum oxide (AAO) template-assisted infiltration of polystyrene (PS) resulting in hemispherical structures, and a following Au sputtering process. The optimum gap size between adjacent PS nanopillars and thickness of the Au layers for high SERS sensitivity are investigated. Using the Au sputtered PS nanopillars as an active SERS substrate, the Raman signal of 4-methylbenzenethiol (4-MBT) with a concentration down to 10-9 M is identified with good signal reproducibility, showing great potential as promising tool for SERS-based detection.

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.

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.

Decision time horizon for music genre classification using short time features

DEFF Research Database (Denmark)

Ahrendt, Peter; Meng, Anders; Larsen, Jan

2004-01-01

In this paper music genre classification has been explored with special emphasis on the decision time horizon and ranking of tapped-delay-line short-time features. Late information fusion as e.g. majority voting is compared with techniques of early information fusion such as dynamic PCA (DPCA......). The most frequently suggested features in the literature were employed including mel-frequency cepstral coefficients (MFCC), linear prediction coefficients (LPC), zero-crossing rate (ZCR), and MPEG-7 features. To rank the importance of the short time features consensus sensitivity analysis is applied...

Prediction of cervical cancer recurrence using textural features extracted from 18F-FDG PET images acquired with different scanners.

Science.gov (United States)

Reuzé, Sylvain; Orlhac, Fanny; Chargari, Cyrus; Nioche, Christophe; Limkin, Elaine; Riet, François; Escande, Alexandre; Haie-Meder, Christine; Dercle, Laurent; Gouy, Sébastien; Buvat, Irène; Deutsch, Eric; Robert, Charlotte

2017-06-27

To identify an imaging signature predicting local recurrence for locally advanced cervical cancer (LACC) treated by chemoradiation and brachytherapy from baseline 18F-FDG PET images, and to evaluate the possibility of gathering images from two different PET scanners in a radiomic study. 118 patients were included retrospectively. Two groups (G1, G2) were defined according to the PET scanner used for image acquisition. Eleven radiomic features were extracted from delineated cervical tumors to evaluate: (i) the predictive value of features for local recurrence of LACC, (ii) their reproducibility as a function of the scanner within a hepatic reference volume, (iii) the impact of voxel size on feature values. Eight features were statistically significant predictors of local recurrence in G1 (p features were significantly different between G1 and G2 in the liver. Spatial resampling was not sufficient to explain the stratification effect. This study showed that radiomic features could predict local recurrence of LACC better than SUVmax. Further investigation is needed before applying a model designed using data from one PET scanner to another.

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

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.

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 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

Polygons of global undersea features for geographic searches

Science.gov (United States)

Hartwell, Stephen R.; Wingfield, Dana K.; Allwardt, Alan O.; Lightsom, Frances L.; Wong, Florence L.

2018-01-01

A shapefile of 311 undersea features from all major oceans and seas has been created as an aid for retrieving georeferenced information resources. Geospatial information systems with the capability to search user-defined, polygonal geographic areas will be able to utilize this shapefile or secondary products derived from it, such as linked data based on well-known text representations of the individual polygons within the shapefile. Version 1.1 of this report also includes a linked data representation of 299 of these features and their spatial extents.

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

Clinical features of patients with dysthymia in a large cohort of Han Chinese women with recurrent major depression.

Science.gov (United States)

Wu, Wenqing; Wang, Zhoubing; Wei, Yan; Zhang, Guanghua; Shi, Shenxun; Gao, Jingfang; Li, Youhui; Tao, Ming; Zhang, Kerang; Wang, Xumei; Gao, Chengge; Yang, Lijun; Li, Kan; Shi, Jianguo; Wang, Gang; Liu, Lanfen; Zhang, Jinbei; Du, Bo; Jiang, Guoqing; Shen, Jianhua; Liu, Ying; Liang, Wei; Sun, Jing; Hu, Jian; Liu, Tiebang; Wang, Xueyi; Miao, Guodong; Meng, Huaqing; Li, Yi; Hu, Chunmei; Li, Yi; Huang, Guoping; Li, Gongying; Ha, Baowei; Deng, Hong; Mei, Qiyi; Zhong, Hui; Gao, Shugui; Sang, Hong; Zhang, Yutang; Fang, Xiang; Yu, Fengyu; Yang, Donglin; Liu, Tieqiao; Chen, Yunchun; Hong, Xiaohong; Wu, Wenyuan; Chen, Guibing; Cai, Min; Song, Yan; Pan, Jiyang; Dong, Jicheng; Pan, Runde; Zhang, Wei; Shen, Zhenming; Liu, Zhengrong; Gu, Danhua; Wang, Xiaoping; Liu, Xiaojuan; Zhang, Qiwen; Li, Yihan; Chen, Yiping; Kendler, Kenneth S; Flint, Jonathan; Zhang, Zhen

2013-01-01

Dysthymia is a form of chronic mild depression that has a complex relationship with major depressive disorder (MDD). Here we investigate the role of environmental risk factors, including stressful life events and parenting style, in patients with both MDD and dysthymia. We ask whether these risk factors act in the same way in MDD with and without dysthymia. We examined the clinical features in 5,950 Han Chinese women with MDD between 30-60 years of age across China. We confirmed earlier results by replicating prior analyses in 3,950 new MDD cases. There were no significant differences between the two data sets. We identified sixteen stressful life events that significantly increase the risk of dysthymia, given the presence of MDD. Low parental warmth, from either mother or father, increases the risk of dysthymia. Highly threatening but short-lived threats (such as rape) are more specific for MDD than dysthymia. While for MDD more severe life events show the largest odds ratio versus controls, this was not seen for cases of MDD with or without dysthymia. There are increased rates of stressful life events in MDD with dysthymia, but the impact of life events on susceptibility to dysthymia with MDD differs from that seen for MDD alone. The pattern does not fit a simple dose-response relationship, suggesting that there are moderating factors involved in the relationship between environmental precipitants and the onset of dysthymia. It is possible that severe life events in childhood events index a general susceptibility to chronic depression, rather than acting specifically as risk factors for dysthymia.

Camouflaging in a complex environment--octopuses use specific features of their surroundings for background matching.

Directory of Open Access Journals (Sweden)

Noam Josef

Full Text Available Living under intense predation pressure, octopuses evolved an effective and impressive camouflaging ability that exploits features of their surroundings to enable them to "blend in." To achieve such background matching, an animal may use general resemblance and reproduce characteristics of its entire surroundings, or it may imitate a specific object in its immediate environment. Using image analysis algorithms, we examined correlations between octopuses and their backgrounds. Field experiments show that when camouflaging, Octopus cyanea and O. vulgaris base their body patterns on selected features of nearby objects rather than attempting to match a large field of view. Such an approach enables the octopus to camouflage in partly occluded environments and to solve the problem of differences in appearance as a function of the viewing inclination of the observer.

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

Repeat: a framework to assess empirical reproducibility in biomedical research

Directory of Open Access Journals (Sweden)

Leslie D. McIntosh

2017-09-01

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

On the reproducibility of expert-operated and robotic ultrasound acquisitions.

Science.gov (United States)

Kojcev, Risto; Khakzar, Ashkan; Fuerst, Bernhard; Zettinig, Oliver; Fahkry, Carole; DeJong, Robert; Richmon, Jeremy; Taylor, Russell; Sinibaldi, Edoardo; Navab, Nassir

2017-06-01

We present the evaluation of the reproducibility of measurements performed using robotic ultrasound imaging in comparison with expert-operated sonography. Robotic imaging for interventional procedures may be a valuable contribution, but requires reproducibility for its acceptance in clinical routine. We study this by comparing repeated measurements based on robotic and expert-operated ultrasound imaging. Robotic ultrasound acquisition is performed in three steps under user guidance: First, the patient is observed using a 3D camera on the robot end effector, and the user selects the region of interest. This allows for automatic planning of the robot trajectory. Next, the robot executes a sweeping motion following the planned trajectory, during which the ultrasound images and tracking data are recorded. As the robot is compliant, deviations from the path are possible, for instance due to patient motion. Finally, the ultrasound slices are compounded to create a volume. Repeated acquisitions can be performed automatically by comparing the previous and current patient surface. After repeated image acquisitions, the measurements based on acquisitions performed by the robotic system and expert are compared. Within our case series, the expert measured the anterior-posterior, longitudinal, transversal lengths of both of the left and right thyroid lobes on each of the 4 healthy volunteers 3 times, providing 72 measurements. Subsequently, the same procedure was performed using the robotic system resulting in a cumulative total of 144 clinically relevant measurements. Our results clearly indicated that robotic ultrasound enables more repeatable measurements. A robotic ultrasound platform leads to more reproducible data, which is of crucial importance for planning and executing interventions.

On general features of warm dark matter with reduced relativistic gas

Science.gov (United States)

Hipólito-Ricaldi, W. S.; vom Marttens, R. F.; Fabris, J. C.; Shapiro, I. L.; Casarini, L.

2018-05-01

Reduced relativistic gas (RRG) is a useful approach to describe the warm dark matter (WDM) or the warmness of baryonic matter in the approximation when the interaction between the particles is irrelevant. The use of Maxwell distribution leads to the complicated equation of state of the Jüttner model of relativistic ideal gas. The RRG enables one to reproduce the same physical situation but in a much simpler form. For this reason RRG can be a useful tool for the theories with some sort of a "new Physics". On the other hand, even without the qualitatively new physical implementations, the RRG can be useful to describe the general features of WDM in a model-independent way. In this sense one can see, in particular, to which extent the cosmological manifestations of WDM may be dependent on its Particle Physics background. In the present work RRG is used as a complementary approach to derive the main observational features for the WDM in a model-independent way. The only assumption concerns a non-negligible velocity v for dark matter particles which is parameterized by the warmness parameter b. The relatively high values of b ( b^2˜ 10^{-6}) erase the radiation (photons and neutrinos) dominated epoch and cause an early warm matter domination after inflation. Furthermore, RRG approach enables one to quantify the lack of power in linear matter spectrum at small scales and in particular, reproduces the relative transfer function commonly used in context of WDM with accuracy of ≲ 1%. A warmness with b^2≲ 10^{-6} (equivalent to v≲ 300 km/s) does not alter significantly the CMB power spectrum and is in agreement with the background observational tests.

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

Analysis of reproducibility of respiration-triggered gated radiotherapy for lung tumors

International Nuclear Information System (INIS)

Spoelstra, Femke O.B.; Soernsen de Koste, John R. van; Cuijpers, Johan P.; Lagerwaard, Frank J.; Slotman, Ben J.; Senan, Suresh

2008-01-01

Purpose: Respiration-gated radiotherapy (RGRT) can decrease the toxicity of chemo-radiotherapy (CT-RT) by allowing use of smaller treatment fields. RGRT requires a predictable relationship between tumor position and external surrogate, which must be verified during treatment. Time-integrated electronic portal imaging (TI-EPI) identifies mean intra-fractional positions of moving structures, and was used to study reproducibility of anatomy during RGRT for lung tumors. Materials and methods: TI-EPIs were acquired using an amorphous silicon-based electronic portal imaging system (EPID, aS500) in continuous image acquisition mode in 11 patients treated with audio-coached RGRT at end-inspiration. The Varian Real-time Position Management (RPM) system was used for 4DCT imaging and RGRT delivery. All TI-EPI portals were co-registered to corresponding digitally reconstructed radiographs (DRR) of the planning 4DCT using the spinal column. Displacements in tumor position or that of an adjacent bronchus during RGRT was measured relative to the reference structure on the DRR. Results: Vertebra-matched portals revealed systematic (Σ) and random (σ) errors of 1.8 and 1.3 mm in medial-lateral direction and 1.7 and 1.7 mm in cranial-caudal direction, indicating a reproducible tumor/bronchus position during the RPM-triggered gates. Conclusions: RGRT delivery at end-inspiration can achieve reproducible internal anatomy in 'gated' fields delivered with audio-coaching

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.

Implementation of an experimental pilot reproducing the fouling of the exhaust gas recirculation system in diesel engines

Directory of Open Access Journals (Sweden)

Crepeau Gérald

2012-04-01

Full Text Available The European emission standards EURO 5 and EURO 6 define more stringent acceptable limits for exhaust emissions of new vehicles. The Exhaust Gas Recirculation (EGR system is a partial but essential solution for lowering the emission of nitrogen oxides and soot particulates. Yet, due to a more intensive use than in the past, the fouling of the EGR system is increased. Ensuring the reliability of the EGR system becomes a main challenge. In partnership with PSA Peugeot Citroën, we designed an experimental setup that mimics an operating EGR system. Its distinctive features are (1 its ability to reproduce precisely the operating conditions and (2 its ability to measure the temperature field on the heat exchanger surface with an Infra Red camera for detecting in real time the evolution of the fooling deposit based on its thermal resistance. Numerical codes are used in conjunction with this experimental setup to determine the evolution of the fouling thickness from its thermal resistance.

Music genre classification using temporal domain features

Science.gov (United States)

Shiu, Yu; Kuo, C.-C. Jay

2004-10-01

Music genre provides an efficient way to index songs in the music database, and can be used as an effective means to retrieval music of a similar type, i.e. content-based music retrieval. In addition to other features, the temporal domain features of a music signal are exploited so as to increase the classification rate in this research. Three temporal techniques are examined in depth. First, the hidden Markov model (HMM) is used to emulate the time-varying properties of music signals. Second, to further increase the classification rate, we propose another feature set that focuses on the residual part of music signals. Third, the overall classification rate is enhanced by classifying smaller segments from a test material individually and making decision via majority voting. Experimental results are given to demonstrate the performance of the proposed techniques.

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

Detrended fluctuation analysis for major depressive disorder.

Science.gov (United States)

Mumtaz, Wajid; Malik, Aamir Saeed; Ali, Syed Saad Azhar; Yasin, Mohd Azhar Mohd; Amin, Hafeezullah

2015-01-01

Clinical utility of Electroencephalography (EEG) based diagnostic studies is less clear for major depressive disorder (MDD). In this paper, a novel machine learning (ML) scheme was presented to discriminate the MDD patients and healthy controls. The proposed method inherently involved feature extraction, selection, classification and validation. The EEG data acquisition involved eyes closed (EC) and eyes open (EO) conditions. At feature extraction stage, the de-trended fluctuation analysis (DFA) was performed, based on the EEG data, to achieve scaling exponents. The DFA was performed to analyzes the presence or absence of long-range temporal correlations (LRTC) in the recorded EEG data. The scaling exponents were used as input features to our proposed system. At feature selection stage, 3 different techniques were used for comparison purposes. Logistic regression (LR) classifier was employed. The method was validated by a 10-fold cross-validation. As results, we have observed that the effect of 3 different reference montages on the computed features. The proposed method employed 3 different types of feature selection techniques for comparison purposes as well. The results show that the DFA analysis performed better in LE data compared with the IR and AR data. In addition, during Wilcoxon ranking, the AR performed better than LE and IR. Based on the results, it was concluded that the DFA provided useful information to discriminate the MDD patients and with further validation can be employed in clinics for diagnosis of MDD.

Scientific Reproducibility in Biomedical Research: Provenance Metadata Ontology for Semantic Annotation of Study Description.

Science.gov (United States)

Sahoo, Satya S; Valdez, Joshua; Rueschman, Michael

2016-01-01

Scientific reproducibility is key to scientific progress as it allows the research community to build on validated results, protect patients from potentially harmful trial drugs derived from incorrect results, and reduce wastage of valuable resources. The National Institutes of Health (NIH) recently published a systematic guideline titled "Rigor and Reproducibility " for supporting reproducible research studies, which has also been accepted by several scientific journals. These journals will require published articles to conform to these new guidelines. Provenance metadata describes the history or origin of data and it has been long used in computer science to capture metadata information for ensuring data quality and supporting scientific reproducibility. In this paper, we describe the development of Provenance for Clinical and healthcare Research (ProvCaRe) framework together with a provenance ontology to support scientific reproducibility by formally modeling a core set of data elements representing details of research study. We extend the PROV Ontology (PROV-O), which has been recommended as the provenance representation model by World Wide Web Consortium (W3C), to represent both: (a) data provenance, and (b) process provenance. We use 124 study variables from 6 clinical research studies from the National Sleep Research Resource (NSRR) to evaluate the coverage of the provenance ontology. NSRR is the largest repository of NIH-funded sleep datasets with 50,000 studies from 36,000 participants. The provenance ontology reuses ontology concepts from existing biomedical ontologies, for example the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), to model the provenance information of research studies. The ProvCaRe framework is being developed as part of the Big Data to Knowledge (BD2K) data provenance project.

Longitudinal in vivo reproducibility of cartilage volume and surface in osteoarthritis of the knee

Energy Technology Data Exchange (ETDEWEB)

Brem, M.H. [Harvard Medical School, Brigham and Women' s Hospital, Musculoskeletal Division, Department of Radiology, ASB-1, L-1, Room 003E, Boston, MA (United States); University of Erlangen-Nuremberg, Division of Trauma Surgery and Orthopaedic Surgery, Department of Surgery, Erlangen (Germany); Pauser, J.; Yoshioka, H.; Stratmann, J.; Kikinis, R.; Duryea, J.; Lang, P. [Harvard Medical School, Brigham and Women' s Hospital, Musculoskeletal Division, Department of Radiology, ASB-1, L-1, Room 003E, Boston, MA (United States); Brenning, A. [University of Erlangen-Nuremberg, Department of Medical Informatics, Biometry and Epidemiology, Erlangen (Germany); Hennig, F.F. [University of Erlangen-Nuremberg, Division of Trauma Surgery and Orthopaedic Surgery, Department of Surgery, Erlangen (Germany); Winalski, C.S. [Harvard Medical School, Brigham and Women' s Hospital, Musculoskeletal Division, Department of Radiology, ASB-1, L-1, Room 003E, Boston, MA (United States); Cleveland Clinic Foundation, Division of Radiology, Cleveland, OH (United States)

2007-04-15

The aim of this study was to evaluate the longitudinal reproducibility of cartilage volume and surface area measurements in moderate osteoarthritis (OA) of the knee. We analysed 5 MRI (GE 1.5T, sagittal 3D SPGR) data sets of patients with osteoarthritis (OA) of the knee (Kellgren Lawrence grade I-II). Two scans were performed: one baseline scan and one follow-up scan 3 months later (96 {+-} 10 days). For segmentation, 3D Slicer 2.5 software was used. Two segmentations were performed by two readers independently who were blinded to the scan dates. Tibial and femoral cartilage volume and surface were determined. Longitudinal and cross-sectional precision errors were calculated using the standard deviation (SD) and coefficient of variation (CV%=100 x [SD/mean]) from the repeated measurements in each patient. The in vivo reproducibility was then calculated as the root mean square of these individual reproducibility errors. The cross-sectional root mean squared coefficient of variation (RMSE-CV) was 1.2, 2.2 and 2.4% for surface area measurements (femur, medial and lateral tibia respectively) and 1.4, 1.8 and 1.3% for the corresponding cartilage volumes. Longitudinal RMSE-CV was 3.3, 3.1 and 3.7% for the surface area measurements (femur, medial and lateral tibia respectively) and 2.3, 3.3 and 2.4% for femur, medial and lateral tibia cartilage volumes. The longitudinal in vivo reproducibility of cartilage surface and volume measurements in the knee using this segmentation method is excellent. To the best of our knowledge we measured, for the first time, the longitudinal reproducibility of cartilage volume and surface area in participants with mild to moderate OA. (orig.)

Highly Efficient and Reproducible Nonfullerene Solar Cells from Hydrocarbon Solvents

KAUST Repository

Wadsworth, Andrew; Ashraf, Raja; Abdelsamie, Maged; Pont, Sebastian; Little, Mark; Moser, Maximilian; Hamid, Zeinab; Neophytou, Marios; Zhang, Weimin; Amassian, Aram; Durrant, James R.; Baran, Derya; McCulloch, Iain

2017-01-01

With chlorinated solvents unlikely to be permitted for use in solution-processed organic solar cells in industry, there must be a focus on developing nonchlorinated solvent systems. Here we report high-efficiency devices utilizing a low-bandgap donor polymer (PffBT4T-2DT) and a nonfullerene acceptor (EH-IDTBR) from hydrocarbon solvents and without using additives. When mesitylene was used as the solvent, rather than chlorobenzene, an improved power conversion efficiency (11.1%) was achieved without the need for pre- or post-treatments. Despite altering the processing conditions to environmentally friendly solvents and room-temperature coating, grazing incident X-ray measurements confirmed that active layers processed from hydrocarbon solvents retained the robust nanomorphology obtained with hot-processed chlorinated solvents. The main advantages of hydrocarbon solvent-processed devices, besides the improved efficiencies, were the reproducibility and storage lifetime of devices. Mesitylene devices showed better reproducibility and shelf life up to 4000 h with PCE dropping by only 8% of its initial value.

Highly Efficient and Reproducible Nonfullerene Solar Cells from Hydrocarbon Solvents

KAUST Repository

Wadsworth, Andrew

2017-06-01

With chlorinated solvents unlikely to be permitted for use in solution-processed organic solar cells in industry, there must be a focus on developing nonchlorinated solvent systems. Here we report high-efficiency devices utilizing a low-bandgap donor polymer (PffBT4T-2DT) and a nonfullerene acceptor (EH-IDTBR) from hydrocarbon solvents and without using additives. When mesitylene was used as the solvent, rather than chlorobenzene, an improved power conversion efficiency (11.1%) was achieved without the need for pre- or post-treatments. Despite altering the processing conditions to environmentally friendly solvents and room-temperature coating, grazing incident X-ray measurements confirmed that active layers processed from hydrocarbon solvents retained the robust nanomorphology obtained with hot-processed chlorinated solvents. The main advantages of hydrocarbon solvent-processed devices, besides the improved efficiencies, were the reproducibility and storage lifetime of devices. Mesitylene devices showed better reproducibility and shelf life up to 4000 h with PCE dropping by only 8% of its initial value.

Reproducibility of P-31 spectroscopic imaging of normal human myocardium

International Nuclear Information System (INIS)

Tavares, N.J.; Chew, W.; Auffermann, W.; Higgins, C.B.

1988-01-01

To assess reproducibility of P-31 MR spectroscopy of human myocardium, ten normal male volunteers were studied on two separate occasions. Spectra were acquired on a clinical 1.5-T MR imaging unit (Signa, General Electric) using a one-dimensional gated spectroscopic imaging sequence (matrix size, 32 X 256) over 20 minutes. Peaks in the adenosine triphosphate (ATP) region, phosphocreatine (PCR), phosphodiesters (PD), and peaks attributable to 2,3 diphosphoglycerate from blood were observed. Interindividual and intraindividual variability expressed as standard errors of the mean (mean +- SEM) were 1.54 +- 0.04 (variability among subjects) and 0.04 (variability between first and second studies) for PCR/β ATP; 0.97 +- 0.18 and 0.06 for PD/β ATP; and 0.62 +- 0.10 and 0.05 for PD/PCR, respectively. In conclusion, P-31 MR spectroscopy yields consistent and reproducible myocardial spectra that might be useful in the future for the evaluation and monitoring of cardiac disease

Towards reproducibility of research by reuse of IT best practices

CERN Multimedia

CERN. Geneva

2013-01-01

Reproducibility of any research gives much higher credibility both to research results and to the researchers. This is true for any kind of research including computer science, where a lot of tools and approaches have been developed to ensure reproducibility. In this talk I will focus on basic and seemingly simple principles, which sometimes look too obvious to follow, but help researchers build beautiful and reliable systems that produce consistent, measurable results. My talk will cover, among other things, the problem of embedding machine learning techniques into analysis strategy. I will also speak about the most common pitfalls in this process and how to avoid them. In addition, I will demonstrate the research environment based on the principles that I will have outlined. About the speaker Andrey Ustyuzhanin (36) is Head of CERN partnership program at Yandex. He is involved in the development of event indexing and event filtering services which Yandex has been providing for the LHCb experiment sinc...

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

Reproducibility of retinal circulation measurements obtained using laser speckle flowgraphy-NAVI in patients with glaucoma

Directory of Open Access Journals (Sweden)

Nakamura M

2011-08-01

Full Text Available Naoko Aizawa, Yu Yokoyama, Naoki Chiba, Kazuko Omodaka, Masayuki Yasuda, Takaaki Otomo, Masahiko Nakamura, Nobuo Fuse, Toru NakazawaDepartment of Ophthalmology, Tohoku University Graduate School of Medicine Sendai, Miyagi, JapanBackground: Laser speckle flowgraphy (LSFG enables noninvasive quantification of the retinal circulation in glaucoma patients. In this study, we tested the intrasession reproducibility of LSFG-NAVI, a modified LSFG technique.Methods: Sixty-five eyes from 33 subjects (male (M:female (F = 17:16 with a mean age of 49.4 ± 11.2 years were examined in this study. Two parameters indicating reproducibility – the coefficient of variation (COV and the intraclass correlation coefficient (ICC – were analyzed three times on the same day that mean blur rate (MBR was measured using LSFG-NAVI. The sites analyzed were the retinal artery and vein, the optic disk, and the choroid. Following classification according to the Glaucoma Hemifield Test (GHT; SITA-Standard 30-2 program, the COV and ICC were examined in patients with (GHT+; 38 eyes, M:F = 20:18, average age 48.9 ± 12.8 years and without (GHT-; 27 eyes, M:F = 13:14, average age 50.1 ± 8.7 years abnormal glaucomatous visual fields.Results: For all subjects, the intrasession reproducibility of MBR in the optic disk (COV: 3.4 ± 2.0; ICC: 0.95 and choroid (COV: 4.7 ± 3.4; ICC: 0.98 was excellent. The reproducibility for the retinal vein (COV: 8.4 ± 5.6, ICC: 0.90 and retinal artery (COV: 10.9 ± 9.9, ICC: 0.9 was moderate. MBRs in the optic disk had good reproducibility in both the GHT+ group (COV: 3.8 ± 2.0; ICC: 0.97 and the GHT− group (COV: 2.9 ± 2.1; ICC: 0.95. Local assessment of the optic disk in normal or glaucoma patients showed that the COVs of the quadrant optic disk areas were best in the temporal area of MBR (3.4%, 4.2%, respectively.Conclusion: LSFG-NAVI showed favorable reproducibility in evaluation of retinal circulation of glaucoma patients, particularly in

Reproducing butterflies do not increase intake of antioxidants when they could benefit from them.

Science.gov (United States)

Beaulieu, Michaël; Bischofberger, Ines; Lorenz, Isabel; Scheelen, Lucie; Fischer, Klaus

2016-02-01

The significance of dietary antioxidants may be limited by the ability of animals to exploit them. However, past studies have focused on the effects of dietary antioxidants after 'antioxidant forced-feeding', and have overlooked spontaneous antioxidant intake. Here, we found that reproducing female Bicyclus anynana butterflies had higher antioxidant defences and enhanced fecundity when forced to consume antioxidants (polyphenols). Interestingly, these positive effects were not constant across the oviposition period. When given the choice between food resources with and without antioxidants, reproducing butterflies did not target antioxidants when they could have benefited the most from them. Moreover, they did not consume more antioxidants than non-reproducing butterflies. These results emphasize that, despite potential positive effects of dietary antioxidants, the ability of animals to exploit them is likely to restrict their ecological significance. © 2016 The Author(s).

3-D FEATURE-BASED MATCHING BY RSTG APPROACH

Directory of Open Access Journals (Sweden)

J.-J. Jaw

2012-07-01

Full Text Available 3-D feature matching is the essential kernel in a fully automated feature-based LiDAR point cloud registration. After feasible procedures of feature acquisition, connecting corresponding features in different data frames is imperative to be solved. The objective addressed in this paper is developing an approach coined RSTG to retrieve corresponding counterparts of unsorted multiple 3-D features extracted from sets of LiDAR point clouds. RSTG stands for the four major processes, "Rotation alignment"; "Scale estimation"; "Translation alignment" and "Geometric check," strategically formulated towards finding out matching solution with high efficiency and leading to accomplishing the 3-D similarity transformation among all sets. The workable types of features to RSTG comprise points, lines, planes and clustered point groups. Each type of features can be employed exclusively or combined with others, if sufficiently supplied, throughout the matching scheme. The paper gives a detailed description of the matching methodology and discusses on the matching effects based on the statistical assessment which revealed that the RSTG approach reached an average matching rate of success up to 93% with around 6.6% of statistical type 1 error. Notably, statistical type 2 error, the critical indicator of matching reliability, was kept 0% throughout all the experiments.

How well can DFT reproduce key interactions in Ziegler-Natta systems?

KAUST Repository

Correa, Andrea; Bahri-Laleh, Naeimeh; Cavallo, Luigi

2013-01-01

The performance of density functional theory in reproducing some of the main interactions occurring in MgCl2-supported Ziegler-Natta catalytic systems is assessed. Eight model systems, representatives of key interactions occurring in Ziegler

Integral fast reactor concept inherent safety features

International Nuclear Information System (INIS)

Marchaterre, J.F.; Sevy, R.H.; Cahalan, J.E.

1987-01-01

The Integral Fast Reactor (IFR) is an innovative liquid-metal-cooled reactor concept being developed at Argonne National Laboratory. The two major goals of the IFT development effort are improved economics and enhanced safety. The design features that together fulfill these goals are: 1) a liquid metal (sodium) coolant, 2) a pool-type reactor primary system configuration, 3) an advanced ternary alloy metallic fuel, and 4) an integral fuel cycle. This paper reviews the design features that contribute to the safety margins inherent to the IFR concept. Special emphasis is placed on the ability of the IFR design to accommodate anticipated transients without scram (ATWS)

Integral Fast Reactor concept inherent safety features

International Nuclear Information System (INIS)

Marchaterre, J.F.; Sevy, R.H.; Cahalan, J.E.

1986-01-01

The Integral Fast Reactor (IFR) is an innovative liquid-metal-cooled reactor concept being developed at Argonne National Laboratory. The two major goals of the IFR development effort are improved economics and enhanced safety. The design features that together fulfill these goals are: (1) a liquid metal (sodium) coolant, (2) a pool-type reactor primary system configuration, (3) an advanced ternary alloy metallic fuel, and (4) an integral fuel cycle. This paper reviews the design features that contribute to the safety margins inherent to the IFR concept. Special emphasis is placed on the ability of the IFR design to accommodate anticipated transients without scram (ATWS)

CT features of olivopontocerebellar atrophy in children

International Nuclear Information System (INIS)

Kumar, S.D.; Gururaj, A.K.; Jeans, W.D.

1995-01-01

Between 1990 and 1992, 14 children were seen in whom a clinical diagnosis of olivopontocerebellar atrophy (OPCA) had been made. The majority of patients presented with cerebellar ataxia and hypotonia. Five children had a family history of a similar illness in first-degree relatives. All cases had undergone clinical and neurologic examinations, routine laboratory tests and cranial CT. CT features were graded to quantitative the degree of atrophy in each cerebellar hemisphere, vermis and brain stem. All patients had varying degrees of atrophic changes of cerebellum, brain stem and cerebrum. These CT features appear to be distinctive enough to enable the diagnosis of OPCA to be made. (orig.)

Everware toolkit. Supporting reproducible science and challenge-driven education.

Science.gov (United States)

Ustyuzhanin, A.; Head, T.; Babuschkin, I.; Tiunov, A.

2017-10-01

Modern science clearly demands for a higher level of reproducibility and collaboration. To make research fully reproducible one has to take care of several aspects: research protocol description, data access, environment preservation, workflow pipeline, and analysis script preservation. Version control systems like git help with the workflow and analysis scripts part. Virtualization techniques like Docker or Vagrant can help deal with environments. Jupyter notebooks are a powerful platform for conducting research in a collaborative manner. We present project Everware that seamlessly integrates git repository management systems such as Github or Gitlab, Docker and Jupyter helping with a) sharing results of real research and b) boosts education activities. With the help of Everware one can not only share the final artifacts of research but all the depth of the research process. This been shown to be extremely helpful during organization of several data analysis hackathons and machine learning schools. Using Everware participants could start from an existing solution instead of starting from scratch. They could start contributing immediately. Everware allows its users to make use of their own computational resources to run the workflows they are interested in, which leads to higher scalability of the toolkit.

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.

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.

Annotating with Propp's Morphology of the Folktale: Reproducibility and Trainability

NARCIS (Netherlands)

Fisseni, B.; Kurji, A.; Löwe, B.

2014-01-01

We continue the study of the reproducibility of Propp’s annotations from Bod et al. (2012). We present four experiments in which test subjects were taught Propp’s annotation system; we conclude that Propp’s system needs a significant amount of training, but that with sufficient time investment, it

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...

REPRODUCIBILITY OF MASKED HYPERTENSION AMONG ADULTS 30 YEARS AND OLDER

Science.gov (United States)

Viera, Anthony J.; Lin, Feng-Chang; Tuttle, Laura A.; Olsson, Emily; Stankevitz, Kristin; Girdler, Susan S.; Klein, J. Larry; Hinderliter, Alan L.

2015-01-01

Objective Masked hypertension (MH) refers to non-elevated office blood pressure (BP) with elevated out-of-office BP, but its reproducibility has not been conclusively established. We examined one-week reproducibility of MH by home BP monitoring (HBPM) and ambulatory BP monitoring (ABPM). Methods We recruited 420 adults not on BP-lowering medication with recent clinic BP between 120/80 and 149/95 mm Hg. For main comparisons, participants with office average ABPM average was ≥135/85 mm Hg; they were considered to have MH by HBPM if the average was ≥135/85 mm Hg. Percent agreements were quantified using kappa. We also examined prevalence of MH defined as office average ABPM average ≥130/80 mm Hg. We conducted sensitivity analyses using different threshold BP levels for ABPM-office pairings and HBPM-office pairings for defining MH. Results Prevalence rates of MH based on office-awake ABPM pairings were 44% and 43%, with agreement of 71% (kappa=0.40; 95% CI 0.31–0.49). MH was less prevalent (15% and 17%) using HBPM-office pairings, with agreement of 82% (kappa=0.30; 95% CI 0.16–0.44), and more prevalent when considering 24-hour average (50% and 48%). MH was also less prevalent when more stringent diagnostic criteria were applied. Office-HBPM pairings and office-awake ABPM pairings had fair agreement on MH classification on both occasions, with kappas of 0.36 and 0.30. Conclusions MH has fair short-term reproducibility, providing further evidence that for some people, out-of-office BP is systematically higher than when measured in the office setting. PMID:24842491

Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters.

Science.gov (United States)

Galavis, Paulina E; Hollensen, Christian; Jallow, Ngoneh; Paliwal, Bhudatt; Jeraj, Robert

2010-10-01

Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45-60 minutes post-injection of 10 mCi of [(18)F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range ≤ 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% ≤ range ≤ 25%) were entropy-GLCM, sum entropy, high gray level run emphsis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be considered as a good candidates for tumor

Variability of textural features in FDG PET images due to different acquisition modes and reconstruction parameters

International Nuclear Information System (INIS)

Galavis, Paulina E.; Jallow, Ngoneh; Paliwal, Bhudatt; Jeraj, Robert; Hollensen, Christian

2010-01-01

Background. Characterization of textural features (spatial distributions of image intensity levels) has been considered as a tool for automatic tumor segmentation. The purpose of this work is to study the variability of the textural features in PET images due to different acquisition modes and reconstruction parameters. Material and methods. Twenty patients with solid tumors underwent PET/CT scans on a GE Discovery VCT scanner, 45-60 minutes post-injection of 10 mCi of [ 18 F]FDG. Scans were acquired in both 2D and 3D modes. For each acquisition the raw PET data was reconstructed using five different reconstruction parameters. Lesions were segmented on a default image using the threshold of 40% of maximum SUV. Fifty different texture features were calculated inside the tumors. The range of variations of the features were calculated with respect to the average value. Results. Fifty textural features were classified based on the range of variation in three categories: small, intermediate and large variability. Features with small variability (range = 5%) were entropy-first order, energy, maximal correlation coefficient (second order feature) and low-gray level run emphasis (high-order feature). The features with intermediate variability (10% = range = 25%) were entropy-GLCM, sum entropy, high gray level run emphasis, gray level non-uniformity, small number emphasis, and entropy-NGL. Forty remaining features presented large variations (range > 30%). Conclusion. Textural features such as entropy-first order, energy, maximal correlation coefficient, and low-gray level run emphasis exhibited small variations due to different acquisition modes and reconstruction parameters. Features with low level of variations are better candidates for reproducible tumor segmentation. Even though features such as contrast-NGTD, coarseness, homogeneity, and busyness have been previously used, our data indicated that these features presented large variations, therefore they could not be

Reproducibility of biomarkers in induced sputum and in serum from chronic smokers.

Science.gov (United States)

Zuiker, Rob G J A; Kamerling, Ingrid M C; Morelli, Nicoletta; Calderon, Cesar; Boot, J Diderik; de Kam, Marieke; Diamant, Zuzana; Burggraaf, Jacobus; Cohen, Adam F

2015-08-01

Soluble inflammatory markers obtained from non-invasive airway sampling such as induced sputum may be useful biomarkers for targeted pharmaceutical interventions. However, before these soluble markers can be used as potential targets, their variability and reproducibility need to be established in distinct study populations. This study aimed to assess the reproducibility of biomarkers obtained from induced sputum and serum in chronic smokers and non-smokers. Sputum and serum samples were obtained from 16 healthy non-smokers and 16 asymptomatic chronic smokers (for both groups: 8M/8F, 30-52 years, FEV1 ≥80% pred.; ≥10 pack years for the smokers) on 2 separate visits 4-10 days apart. Soluble markers in serum and sputum were analysed by ELISA. The differences between smokers vs non-smokers were analysed with a t-test and variability was assessed on log-transformed data by a mixed model ANOVA. Analysable sputum samples could be obtained from all 32 subjects. In both study populations neutrophils and macrophages were the predominant cell types. Serum Pulmonary Surfactant Associated Protein D had favourable reproducibility criteria for reliability ratio (0.99), intra-subject coefficient of variation (11.2%) and the Bland Altman limits of agreement. Furthermore, chronic smokers, compared to non-smokers, had significantly higher sputum concentrations of IL-8 (1094.6 pg/mL vs 460.8 pg/mL, p = 0.006)), and higher serum concentrations of Pulmonary Surfactant Associated Protein D (110.9 pg/mL vs 64.7 pg/mL, p = 0.019), and lower concentrations of Serum Amyloid A (1352.4 pg/mL vs 2297.5 pg/mL, p = 0.022). Serum Pulmonary Surfactant Associated Protein D proved to be a biomarker that fulfilled the criteria for reproducibility in both study groups. Copyright © 2015 Elsevier Ltd. All rights reserved.