Reproducibility-repeatability of choroidal thickness calculation using optical coherence tomography

Purpose. To evaluate the repeatability and reproducibility of subfoveal choroidal thickness (CT) calculations performed manually using optical coherence tomography (OCT). Methods. The CT was imaged in vivo at each of two visits on 11 healthy volunteers (mean age, 35.72 ± 13.19 years) using the spectral domain OCT. CT was manually measured after applying ImageJ processing filters on 15 radial subfoveal scans. Each radial scan was spaced 12° from each other and contained 2500 A-scans. The coefficient of variability, coefficient of repeatability (CoR), coefficient of reproducibility, and intraclass correlation coefficient determined the reproducibility and repeatability of the calculation. Axial length (AL) and mean spherical equivalent refractive error were measured with the IOLMaster and an open view autorefractor to study their potential relationship with CT. Results. The within-visit and between-visit coefficient of variability, CoR, coefficient of reproducibility, and intraclass correlation coefficient were 0.80, 2.97% 2.44%, and 99%, respectively. The subfoveal CT correlated significantly with AL (R = -0.60, p = 0.05). Conclusions. The subfoveal CT could be measured manually in vivo using OCT and the readings obtained from the healthy subjects evaluated were repeatable and reproducible. It is proposed that OCT could be a useful instrument to perform in vivo assessment and monitoring of CT changes in retinal disease. The preliminary results suggest a negative correlation between subfoveal CT and AL in such a way that it decreases with increasing AL but not with refractive error.

Reproducibility and repeatability of the OcuSense TearLab™ osmometer

BACKGROUND: Some studies report that increased tear osmolarity is a reliable indicator of dry eye syndrome (DES). The OcuSense TearLab™ osmometer requires less than a 100-nl sample of tears and provides an instant quantitative result. Our aim was to clinically evaluate this instrument in terms of its reproducibility and repeatability. METHODS: Twenty-nine participants who ranged in age from 19 to 49 years (mean?±?SD: 23.3?±?5.5 years) were recruited. Osmolarity readings were collected by two operators, in two sessions separated by 1 or 2 weeks in order to assess test reproducibility and repeatability. RESULTS: The coefficient of reproducibility was 39 mOsms/l; the coefficient of repeatability was 33 mOsms/l. CONCLUSIONS: Our mean coefficient of variation over four readings for 29 subjects is 2.9%, which compares well with that reported by the manufacturer. Our results inform practitioners about the level of change over time that can be considered clinically relevant for healthy subjects. This value is 33mOsms/l; any change smaller than this could be attributed to measurement noise.

Retinal vessel analysis:flicker reproducibility, methodological standardisations and practical limitations

The Retinal Vessel Analyser (RVA) is a commercially available ophthalmoscopic instrument capable of acquiring vessel diameter fluctuations in real time and in high temporal resolution. Visual stimulation by means of flickering light is a unique exploration tool of neurovascular coupling in the human retina. Vessel reactivity as mediated by local vascular endothelial vasodilators and vasoconstrictors can be assessed non-invasively, in vivo. In brief, the work in this thesis • deals with interobserver and intraobserver reproducibility of the flicker responses in healthy volunteers • explains the superiority of individually analysed reactivity parameters over vendorgenerated output • links in static retinal measures with dynamic ones • highlights practical limitations in the use of the RVA that may undermine its clinical usefulness • provides recommendations for standardising measurements in terms of vessel location and vessel segment length and • presents three case reports of essential hypertensives in a -year follow-up. Strict standardisation of measurement procedures is a necessity when utilising the RVA system. Agreement between research groups on implemented protocols needs to be met, before it could be considered a clinically useful tool in detecting or predicting microvascular dysfunction.

samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files

MOTIVATION: Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.

RESULTS: We introduce an R package called samExploreR that allows the subsampling (m out of n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth related questions for the experimental design. Overall, this provides a systematic way for exploring the reproducibility and robustness of general RNA-seq studies. We exemplify the usage of samExploreR by studying the influence of the sequencing depth and the annotation on the identification of differentially expressed genes.

AVAILABILITY: Availability: samExploreR is available as an R package from Bioconductor (after acceptance of the paper, download link: http://www.bio-complexity.com/samExploreR_1.0.0.tar.gz).

Multiple training interventions significantly improve reproducibility of PET/CT-based lung cancer radiotherapy target volume delineation using an IAEA study protocol

BACKGROUND AND PURPOSE: To assess the impact of a standardized delineation protocol and training interventions on PET/CT-based target volume delineation (TVD) in NSCLC in a multicenter setting.

MATERIAL AND METHODS: Over a one-year period, 11 pairs, comprised each of a radiation oncologist and nuclear medicine physician with limited experience in PET/CT-based TVD for NSCLC from nine different countries took part in a training program through an International Atomic Energy Agency (IAEA) study (NCT02247713). Teams delineated gross tumor volume of the primary tumor, during and after training interventions, according to a provided delineation protocol. In-house developed software recorded the performed delineations, to allow visual inspection of strategies and to assess delineation accuracy.

RESULTS: Following the first training, overall concordance indices for 3 repetitive cases increased from 0.57±0.07 to 0.66±0.07. The overall mean surface distance between observer and expert contours decreased from -0.40±0.03 cm to -0.01±0.33 cm. After further training overall concordance indices for another 3 repetitive cases further increased from 0.64±0.06 to 0.80±0.05 (p=0.01). Mean surface distances decreased from -0.34±0.16 cm to -0.05±0.20 cm (p=0.01).

CONCLUSION: Multiple training interventions improve PET/CT-based TVD delineation accuracy in NSCLC and reduces interobserver variation.

Myocardial blood flow quantification by Rb-82 cardiac PET/CT: A detailed reproducibility study between two semi-automatic analysis programs.

BACKGROUND: Several analysis software packages for myocardial blood flow (MBF) quantification from cardiac PET studies exist, but they have not been compared using concordance analysis, which can characterize precision and bias separately. Reproducible measurements are needed for quantification to fully develop its clinical potential. METHODS: Fifty-one patients underwent dynamic Rb-82 PET at rest and during adenosine stress. Data were processed with PMOD and FlowQuant (Lortie model). MBF and myocardial flow reserve (MFR) polar maps were quantified and analyzed using a 17-segment model. Comparisons used Pearson's correlation ρ (measuring precision), Bland and Altman limit-of-agreement and Lin's concordance correlation ρc = ρ·C b (C b measuring systematic bias). RESULTS: Lin's concordance and Pearson's correlation values were very similar, suggesting no systematic bias between software packages with an excellent precision ρ for MBF (ρ = 0.97, ρc = 0.96, C b = 0.99) and good precision for MFR (ρ = 0.83, ρc = 0.76, C b = 0.92). On a per-segment basis, no mean bias was observed on Bland-Altman plots, although PMOD provided slightly higher values than FlowQuant at higher MBF and MFR values (P < .0001). CONCLUSIONS: Concordance between software packages was excellent for MBF and MFR, despite higher values by PMOD at higher MBF values. Both software packages can be used interchangeably for quantification in daily practice of Rb-82 cardiac PET.

DEVELOPMENT AND REPRODUCIBILITY OF THE INSTRUMENTO DE AVALIAÇÃO DA PROMOÇÃO DA SAÚDE NA UNIVERSIDADE - IAPSU (ASSESSMENT TOOL FOR HEALTH PROMOTION AT THE UNIVERSITY)

Objective: To present the Instrumento de Avaliação da Promoção da Saúde na Universidade – IAPSU (Assessment Tool for Health Promotion at the University) and its reproducibility assessment process. Methods: Cross-sectional study conducted between May and July 2014 with 50 students from a university of Fortaleza, Ceará, which developed the IAPSU through the analysis of government documents and a systematic review of the literature on a potentially healthy university. The tool has 41 questions divided into five domains: physical activity, diet, environmental factors, psychosocial factors and alcohol and drug use, integrative and complementary practices. To assess the inter-examiner reproducibility, the students answered the IAPSU twice, applied by two different examiners; to assess the intraexaminer reproducibility, another application of the instrument was performed after seven days. Results: The study comprised 40 Nursing students and 10 Physical Therapy students, with a mean age of 25 ± 5.4 years; 88% were women and white individuals were predominant. In the reproducibility assessment, strong intraclass, intra- and inter-examiner correlation coefficients - above 0.8 - were observed in all the domains. Conclusion: The IAPSU is a reproducible and reliable instrument for assessing health promotion at the university.

Classifying And Predicting Software Security Vulnerabilities based on Reproducibility

Security defects are common in large software systems because of their size and complexity. Although efficient development processes, testing, and maintenance policies are applied to software systems, there are still a large number of vulnerabilities that can remain, despite these measures. Some vulnerabilities stay in a system from one release to the next one because they cannot be easily reproduced through testing. These vulnerabilities endanger the security of the systems. We propose vulnerability classification and prediction frameworks based on vulnerability reproducibility. The frameworks are effective to identify the types and locations of vulnerabilities in the earlier stage, and improve the security of software in the next versions (referred to as releases). We expand an existing concept of software bug classification to vulnerability classification (easily reproducible and hard to reproduce) to develop a classification framework for differentiating between these vulnerabilities based on code fixes and textual reports. We then investigate the potential correlations between the vulnerability categories and the classical software metrics and some other runtime environmental factors of reproducibility to develop a vulnerability prediction framework. The classification and prediction frameworks help developers adopt corresponding mitigation or elimination actions and develop appropriate test cases. Also, the vulnerability prediction framework is of great help for security experts focus their effort on the top-ranked vulnerability-prone files. As a result, the frameworks decrease the number of attacks that exploit security vulnerabilities in the next versions of the software. To build the classification and prediction frameworks, different machine learning techniques (C4.5 Decision Tree, Random Forest, Logistic Regression, and Naive Bayes) are employed. The effectiveness of the proposed frameworks is assessed based on collected software security defects of Mozilla Firefox.

The stimulation of healing within a rat calvarial defect by mPCL–TCP/collagen scaffolds loaded with rhBMP-2

Bone morphogenetic proteins (BMPs) have been widely investigated for their clinical use in bone repair and it is known that a suitable carrier matrix to deliver them is essential for optimal bone regeneration within a specific defect site. Fused deposited modeling (FDM) allows for the fabrication of medical grade poly 3-caprolactone/tricalcium phosphate (mPCL–TCP) scaffolds with high reproducibility and tailor designed dimensions. Here we loaded FDM fabricated mPCL–TCP/collagen scaffolds with 5 mg recombinant human (rh)BMP-2 and evaluated bone healing within a rat calvarial critical-sized defect. Using a comprehensive approach, this study assessed the newly regenerated bone employing microcomputed tomography (mCT), histology/histomorphometry, and mechanical assessments. By 15 weeks, mPCL–TCP/collagen/rhBMP-2 defects exhibited complete healing of the calvarium whereas the non- BMP-2-loaded scaffolds showed significant less bone ingrowth, as confirmed by mCT. Histomorphometry revealed significantly increased bone healing amongst the rhBMP-2 groups compared to non-treated scaffolds at 4 and 15 weeks, although the % BV/TV did not indicate complete mineralisation of the entire defect site. Hence, our study confirms that it is important to combine microCt and histomorphometry to be able to study bone regeneration comprehensively in 3D. A significant up-regulation of the osteogenic proteins, type I collagen and osteocalcin, was evident at both time points in rhBMP-2 groups. Although mineral apposition rates at 15 weeks were statistically equivalent amongst treatment groups, microcompression and push-out strengths indicated superior bone quality at 15 weeks for defects treated with mPCL–TCP/collagen/rhBMP-2. Consistently over all modalities, the progression of healing was from empty defect < mPCL–TCP/collagen < mPCL–TCP/collagen/rhBMP-2, providing substantiating data to support the hypothesis that the release of rhBMP-2 from FDM-created mPCL–TCP/collagen scaffolds is a clinically relevant approach to repair and regenerate critically-sized craniofacial bone defects. Crown Copyright 2008 Published by Elsevier Ltd. All rights reserved.

Calculation of habitable dwelling surfaces : an empirical analysis for the agglomerations of Munich and Sydney

In many countries the calculation of habitable dwelling surface is characterised by a chaotic variety of calculation variants hardly comprehensible for the end user - sometimes not even reproducible for the expert. Therefore dossiers were analysed on the basis of a random choice in order to determine the method according to which the habitable dwelling surface was measured and to find out wether customers can scrutinize the calculations. The paper compares Sydney and Munich, where in both cases property prices are situated at the high end of the market

Somatic embryogenesis, organogenesis and plant regeneration in taro (Colocasia esculenta var. esculenta)

Callus was initiated in three different ‘‘esculenta’’ taro cultivars by culturing corm slices in the dark on half-strength MS medium supplemented with 2.0 mg/l 2,4- dichlorophenoxyacetic acid (2,4-D) for 20 days followed by subculture of all corm slices to half-strength MS medium containing 1.0 mg/l thidiazuron (TDZ). Depending on the cultivar, 20–30% of corm slices produced compact, yellow, nodular callus on media containing TDZ. Histological studies revealed the presence of typical embryogenic cells which were small, isodiametric with dense cytoplasms. Somatic embryos formed when callus was transferred to hormone-free medium and *72% of the embryos germinated into plantlets on this medium. Simultaneous formation of roots and shoots during germination, and the presence of shoot and root poles revealed by histology, confirmed that these structures were true somatic embryos. Plants derived from somatic embryos appeared phenotypically normal following 2 months growth in a glasshouse. This method is a significant advance on those previously reported for the esculenta cultivars of taro due to its efficiency and reproducibility.

Treadmill adaptation and verification of self-selected walking speed : a protocol for children

The term self-selected (i.e., individual or comfortable walking pace or speed) is commonly used in the literature (Frost, Dowling, Bar-Or, & Dyson, 1997; Jeng, Liao, Lai, & Hou, 1997; Wergel-Kolmert & Wohlfart, 1999; Maltais, Bar-Or, Pienynowski, & Galea, 2003; Browning & Kram, 2005; Browning, Baker, Herron, & Kram, 2006; Hills, Byrne, Wearing, & Armstrong, 2006) and is identified as the most efficient walking speed, with increased efficiency defined by lower oxygen uptake (VO^sub 2^) per unit mechanical work (Hoyt & Taylor, 1981; Taylor, Heglund, & Maloiy, 1982; Hreljac, 1993). [...] assessing individual and group differences in metabolic energy expenditure using oxygen uptake requires individuals to be comfortable with, and able to accommodate to, the equipment.