In 2014 the National Science Foundation (NSF) provided support to the National Academies of Sciences, Engineering, and Medicine for a series of Forums on Open Science in response to a government-wide ...directive to support increased public access to the results of research funded by the federal government. However, the breadth of the work resulting from the series precluded a focus on any specific topic or discussion about how to improve public access. Thus, the main goal of the Workshop on Transparency and Reproducibility in Federal Statistics was to develop some understanding of what principles and practices are, or would be, supportive of making federal statistics more understandable and reviewable, both by agency staff and the public. This publication summarizes the presentations and discussions from the workshop.
Purpose
To investigate the repeatability and reproducibility of lung segmentation and their impact on the quantitative outcomes from functional pulmonary MRI. Additionally, to validate an artificial ...neural network (ANN) to accelerate whole‐lung quantification.
Method
Ten healthy children and 25 children with cystic fibrosis underwent matrix pencil decomposition MRI (MP‐MRI). Impaired relative fractional ventilation (RFV) and relative perfusion (RQ) from MP‐MRI were compared using whole‐lung segmentation performed by a physician at two time‐points (At1 and At2), by an MRI technician (B), and by an ANN (C). Repeatability and reproducibility were assess with Dice similarity coefficient (DSC), paired t‐test and Intraclass‐correlation coefficient (ICC).
Results
The repeatability within an observer (At1 vs At2) resulted in a DSC of 0.94 ± 0.01 (mean ± SD) and an unsystematic difference of −0.01% for RFV (P = .92) and +0.1% for RQ (P = .21). The reproducibility between human observers (At1 vs B) resulted in a DSC of 0.88 ± 0.02, and a systematic absolute difference of −0.81% (P < .001) for RFV and −0.38% (P = .037) for RQ. The reproducibility between human and the ANN (At1 vs C) resulted in a DSC of 0.89 ± 0.03 and a systematic absolute difference of −0.36% for RFV (P = .017) and −0.35% for RQ (P = .002). The ICC was >0.98 for all variables and comparisons.
Conclusions
Despite high overall agreement, there were systematic differences in lung segmentation between observers. This needs to be considered for longitudinal studies and could be overcome by using an ANN, which performs as good as human observers and fully automatizes MP‐MRI post‐processing.
IntroductionTo evaluate the aortic valve fibrocalcific volume by computed tomography (CT) angiography in patients with aortic stenosis (AS). In particular, to assess its reproducibility, association ...with disease severity, its ability to predict and track AS progression and to perform histological validation.MethodsIn a post-hoc analysis of 136 patients with AS participating in the SALTIRE 2 trial, fibrocalcific volume was calculated using semi-automated software on CT-angiograms at baseline and after one year. The distributions of CT-attenuation were analysed using Gaussian mixture modelling to derive thresholds for aortic valve tissue types enabling the quantification of calcific, non-calcific and fibrocalcific volumes indexed to annulus area. Scan-rescan reproducibility was assessed. Aortic valves from 41 patients undergoing valve replacement were included in the histological validation cohort.ResultsFibrocalcific volume measurements demonstrated excellent scan-rescan reproducibility (mean difference -1%, limits of agreement -4.5% to 2.8%). Baseline fibrocalcific volumes correlated with baseline mean aortic valve gradients on echocardiography in both men and women (rho=0.64 and 0.69 respectively; p<0.001 for both). The relationship was driven principally by calcific volume in men and fibrotic volume in women. After one year, fibrocalcific volume increased by 17% and correlated with an increase in mean gradient (rho=0.32, p=0.003). Baseline fibrocalcific volume was the strongest predictor of disease progression on multivariable analysis, with a particularly strong association in women (rho=0.75, p<0.001). Histologically, there was a good correlation between fibrocalcific volume and valve weight (r=0.51, p<0.001). Furthermore, non-calcific volumes on CT were higher in patients with a higher fibrosis score on histology and similarly calcific volumes on CT were higher in patients with higher Warren-Yong scores for calcification on histology.ConclusionsThe fibrocalcific volume is a highly reproducible, anatomic, CT-derived assessment of AS. It correlates with AS severity and haemodynamic progression and there is good correlation between fibrocalcific volume and histological parameters.
This thesis comprises a number of studies into controlling the photonic properties of materials by way of controlling their molecular conformation. The absorption and emission behaviours of ...fundamental AIE molecules TPE and HPS were probed in solutions with varying degrees of aggregation. It was found, in contrast to the existing RIR hypothesis, that the monomers were able to emit in good solutions with minimal aggregation, and continued to do so upon low levels of aggregation. The monomer emission of TPE was found to be more prevalent than that of HPS due to the difference in conjugation pathways offered by each molecule. These results suggested that the term AIE is misleading, with the assumption that the molecular emission 'switches on' upon aggregation disregarding the fact that the more efficient fluorescence actually results from a quenching process (excimer formation), with RIR causing the increase in efficiency. A new method for controlling the aggregation in fluorene/fluorenone oligomers was also investigated. Water was found to be highly effective for screening the fluorenone aggregation, with fractions of only 10% sufficient to eliminate the excimer emission. The fluorenone was then successfully reaggregated to varying degrees as the water fraction was increased, due to non-solvent effects. Investigating solutions of thermally oxidised FFF also revealed the method's ability to identify the presence of fluorenone moieties when there was no indication of oxidation in the absorption or PL. Lastly, dip-pen nanolithography was employed to pattern photonic structures in PFO thin films. Beta phase dots with diameter 548nm were achieved, demonstrating the potential of DPN in photonic device fabrication, however there were issues with consistency of feature size and damage to the film. An outline of the development of the microscale PL set-up used to analyse the patterns, and the steps taken to maximise its resolution and spectral contrast is also given. The set-up was found to be well suited to highlight the beta phase of PFO, however there were issues with reproducibility of the PL maps, as well as a trade-off between signal strength and photodegradation of the sample. When compared to patterns imaged on a different set-up, it was clear that the set-up designed here produced too low a signal to accurately compare the new patterns. Further work in sample fabrication, DPN operation and microscale PL optimisation was therefore identified to improve the quality and reproducibility of the patterns.
Studying the interactions between nanoengineered materials and biological systems plays a vital role in the development of biological applications of nanotechnology and the improvement of our ...fundamental understanding of the bio-nano interface. A significant barrier to progress in this multidisciplinary area is the variability of published literature with regards to characterizations performed and experimental details reported. Here, we suggest a 'minimum information standard' for experimental literature investigating bio-nano interactions. This standard consists of specific components to be reported, divided into three categories: material characterization, biological characterization and details of experimental protocols. Our intention is for these proposed standards to improve reproducibility, increase quantitative comparisons of bio-nano materials, and facilitate meta analyses and in silico modelling.
Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal ...research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved. Here, we introduce ARRIVE 2.0. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise and divide the items of the guidelines into 2 sets, the “ARRIVE Essential 10,” which constitutes the minimum requirement, and the “Recommended Set,” which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration (E&E) document, which serves (1) to explain the rationale behind each item in the guidelines, (2) to clarify key concepts, and (3) to provide illustrative examples. We aim, through these changes, to help ensure that researchers, reviewers, and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.
While actigraphy is considered objective, the process of setting rest intervals to calculate sleep variables is subjective. We sought to evaluate the reproducibility of actigraphy-derived measures of ...sleep using a standardized algorithm for setting rest intervals.
Observational study.
Community-based.
A random sample of 50 adults aged 18-64 years free of severe sleep apnea participating in the Sueño sleep ancillary study to the Hispanic Community Health Study/Study of Latinos.
N/A.
Participants underwent 7 days of continuous wrist actigraphy and completed daily sleep diaries. Studies were scored twice by each of two scorers. Rest intervals were set using a standardized hierarchical approach based on event marker, diary, light, and activity data. Sleep/wake status was then determined for each 30-sec epoch using a validated algorithm, and this was used to generate 11 variables: mean nightly sleep duration, nap duration, 24-h sleep duration, sleep latency, sleep maintenance efficiency, sleep fragmentation index, sleep onset time, sleep offset time, sleep midpoint time, standard deviation of sleep duration, and standard deviation of sleep midpoint. Intra-scorer intraclass correlation coefficients (ICCs) were high, ranging from 0.911 to 0.995 across all 11 variables. Similarly, inter-scorer ICCs were high, also ranging from 0.911 to 0.995, and mean inter-scorer differences were small. Bland-Altman plots did not reveal any systematic disagreement in scoring.
With use of a standardized algorithm to set rest intervals, scoring of actigraphy for the purpose of generating a wide array of sleep variables is highly reproducible.
Purpose
In this study, we demonstrate the first combination of 3D FID proton MRSI and spatial encoding via concentric‐ring trajectories (CRTs) at 3T. FID‐MRSI has many benefits including high ...detection sensitivity, in particular for J‐coupled metabolites (e.g., glutamate/glutamine). This makes it highly attractive, not only for clinical, but also for, potentially, functional MRSI. However, this requires excellent reliability and temporal stability. We have, therefore, augmented this 3D‐FID‐MRSI sequence with single‐echo, imaging‐based volumetric navigators (se‐vNavs) for real‐time motion/shim‐correction (SHMOCO), which is 2× quicker than the original double‐echo navigators (de‐vNavs), hence allowing more efficient integration also in short‐TR sequences.
Methods
The tracking accuracy (position and B0‐field) of our proposed se‐vNavs was compared to the original de‐vNavs in phantoms (rest and translation) and in vivo (voluntary head rotation). Finally, the intra‐session stability of a 5:40 min 3D‐FID‐MRSI scan was evaluated with SHMOCO and no correction (NOCO) in 5 resting subjects. Intra/inter‐subject coefficients of variation (CV) and intra‐class correlations (ICC) over the whole 3D volume and in selected regions of interest ROI were assessed.
Results
Phantom and in vivo scans showed highly consistent tracking performance for se‐vNavs compared to the original de‐vNavs, but lower frequency drift. Up to ~30% better intra‐subject CVs were obtained for SHMOCO (P < 0.05), with values of 9.3/6.9/6.5/7.8% over the full VOI for Glx/tNAA/tCho/m‐Ins ratios to tCr. ICCs were good‐to‐high (91% for Glx/tCr in motor cortex), whereas the inter‐subject variability was ~11–19%.
Conclusion
Real‐time motion/shim corrected 3D‐FID‐MRSI with time‐efficient CRT‐sampling at 3T allows reliable, high‐resolution metabolic imaging that is fast enough for clinical use and even, potentially, for functional MRSI.
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