Long-term repeatability and interlaboratory reproducibility of high-precision ID-TIMS U-Pb geochronology.
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ABSTRACT:
SUBMITTER: Schaltegger U
PROVIDER: S-EPMC8262554 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:To identify robust and reproducible methods of cerebellar morphometry that can be used in future large-scale structural MRI studies, we investigated the replicability, repeatability, and long-term reproducibility of three fully automated software tools: FreeSurfer, CEREbellum Segmentation (CERES), and automatic cerebellum anatomical parcellation using U-Net with locally constrained optimization (ACAPULCO). Replicability was defined as computational replicability, determined by comparing two analyses of the same high-resolution MRI data set performed with identical analysis software and computer hardware. Repeatability was determined by comparing the analyses of two MRI scans of the same participant taken during two independent MRI sessions on the same day for the Kirby-21 study. Long-term reproducibility was assessed by analyzing two MRI scans of the same participant in the longitudinal OASIS-2 study. We determined percent difference, the image intraclass correlation coefficient, the coefficient of variation, and the intraclass correlation coefficient between two analyses. Our results show that CERES and ACAPULCO use stochastic algorithms that result in surprisingly high differences between identical analyses for ACAPULCO and small differences for CERES. Changes between two consecutive scans from the Kirby-21 study were less than ± 5% in most cases for FreeSurfer and CERES (i.e., demonstrating high repeatability). As expected, long-term reproducibility was lower than repeatability for all software tools. In summary, CERES is an accurate, as demonstrated before, and reproducible tool for fully automated segmentation and parcellation of the cerebellum. We conclude with recommendations for the assessment of replicability, repeatability, and long-term reproducibility in future studies on cerebellar structure.
| S-EPMC8213608 | biostudies-literature
Project description:PurposeTo evaluate the repeatability and reproducibility of corneal power measurements obtained by Topcon KR-1W and iTrace, and assess the agreement with measurements obtained by Allegro Topolyzer and IOLMaster.MethodsThe right eyes of 100 normal subjects were prospectively scanned 3 times using all the 4 devices. Another observer performed additional 3 consecutive scans using the Topcon KR-1W and iTrace in the same session. About one week later, the first observer repeated the measurements using the Topcon KR-1W and iTrace. The steep keratometry (Ks), flat keratometry (Kf), mean keratometry (Km), J0 and J45 were analyzed. Repeatability and reproducibility of measurements were evaluated by the within-subject standard deviation (Sw), coefficient of variation (CoV), test-retest repeatability (2.77Sw), and intraclass correlation coefficient (ICC). Agreements between devices were assessed using Bland-Altman analysis and 95% limits of agreement (LoA).ResultsIntraobserver repeatability and interobserver and intersession reproducibility of the Ks, Kf and Km showed a CoV of no more than 0.5%, a 2.77Sw of 0.70 D or less, and an ICC of no less than 0.99. However, J0 and J45 showed poor intraobserver repeatability and interobserver and intersession reproducibility (all ICCs not greater than 0.446). Statistically significant differences existed between Topcon KR-1W and IOLMaster, Topcon KR-1W and iTrace, Topcon KR-1W and Topolyzer, iTrace and Topolyzer, iTrace and IOLMaster for Ks, Kf and Km measurements (all P < 0.05). The mean differences between Topcon KR-1W, iTrace, and the other 2 devices were small. The 95% LoA were approximately 1.0 D to 1.5 D for all measurements.ConclusionsThe Ks, Kf and Km obtained by Topcon KR-1W and iTrace showed excellent intraobserver repeatability and interobserver and intersession reproducibility in normal eyes. The agreement between Topcon KR-1W and Topolyzer, Topcon KR-1W and IOLMaster, iTrace and Topolyzer, iTrace and IOLMaster, Topcon KR-1W and iTrace were not so good, they should not be interchangeable in clinical application. Given that the intraobserver repeatability and interobserver and intersession reproducibility of corneal astigmatism measurements obtained by Topcon KR-1W and iTrace were poor, it should be cautious that Topcon KR-1W and iTrace were applied for the preparation of toric lens implantation.
| S-EPMC4709181 | biostudies-literature
Project description:Here, we document a detailed characterisation of two zircon gemstones, GZ7 and GZ8. Both stones had the same mass at 19.2 carats (3.84 g) each; both came from placer deposits in the Ratnapura district, Sri Lanka. The U-Pb data are in both cases concordant within the uncertainties of decay constants and yield weighted mean 206Pb/238U ages (95% confidence uncertainty) of 530.26 Ma ± 0.05 Ma (GZ7) and 543.92 Ma ± 0.06 Ma (GZ8). Neither GZ7 nor GZ8 have been subjected to any gem enhancement by heating. Structure-related parameters correspond well with the calculated alpha doses of 1.48 × 1018 g-1 (GZ7) and 2.53 × 1018 g-1 (GZ8), respectively, and the (U-Th)/He ages of 438 Ma ± 3 Ma (2s) for GZ7 and 426 Ma ± 9 Ma (2s) for GZ8 are typical of unheated zircon from Sri Lanka. The mean U mass fractions are 680 μg g-1 (GZ7) and 1305 μg g-1 (GZ8). The two zircon samples are proposed as reference materials for SIMS (secondary ion mass spectrometry) U-Pb geochronology. In addition, GZ7 (Ti mass fractions 25.08 μg g-1 ± 0.18 μg g-1; 95% confidence uncertainty) may prove useful as reference material for Ti-in-zircon temperature estimates.
| S-EPMC6334521 | biostudies-literature
Project description:The magmatic history of the Oldest Toba Tuff (OTT), the second largest in volume after the Youngest Toba Tuff (YTT), northern Sumatra, Indonesia, was investigated using U-Pb zircon dating by LA-ICP-MS. Zircon dates obtained from surface and interior sections yielded ages of 0.84 ± 0.03 Ma and 0.97 ± 0.03 Ma, respectively. The youngest OTT zircon ages were in accordance with the 40Ar/39Ar eruption age of ~ 0.8 Ma, whereas the oldest zircon dates were ~ 1.20 Ma. Therefore, the distribution of zircon U-Pb ages is interpreted to reflect protracted zircon crystallization, suggesting that the estimated 800-2,300 km3 of OTT magma accumulated and evolved for at least 400,000 years prior to eruption. This result is comparable to the volume and timescales of YTT magmatism. The similarities of both magmatic duration and geochemistry between OTT and YTT may indicate that they are similar in size and that the caldera collapse that generated OTT might be much larger previously interpreted.
| S-EPMC7566466 | biostudies-literature
Project description:The "mid-Cretaceous" (~125-80 Ma) was punctuated by major plate-tectonic upheavals resulting in widespread volcanism, mountain-building, eustatic sea-level changes, and climatic shifts that together had a profound impact on terrestrial biotic assemblages. Paleontological evidence suggests terrestrial ecosystems underwent a major restructuring during this interval, yet the pace and pattern are poorly constrained. Current impediments to piecing together the geologic and biological history of the "mid-Cretaceous" include a relative paucity of terrestrial outcrop stemming from this time interval, coupled with a historical understudy of fragmentary strata. In the Western Interior of North America, sedimentary strata of the Turonian-Santonian stages are emerging as key sources of data for refining the timing of ecosystem transformation during the transition from the late-Early to early-Late Cretaceous. In particular, the Moreno Hill Formation (Zuni Basin, New Mexico) is especially important for detailing the timing of the rise of iconic Late Cretaceous vertebrate faunas. This study presents the first systematic geochronological framework for key strata within the Moreno Hill Formation. Based on the double-dating of (U-Pb) detrital zircons, via CA-TIMS and LA-ICP-MS, we interpret two distinct depositional phases of the Moreno Hill Formation (initial deposition after 90.9 Ma (middle Turonian) and subsequent deposition after 88.6 Ma (early Coniacian)), younger than previously postulated based on correlations with marine biostratigraphy. Sediment and the co-occurring youthful subset of zircons are sourced from the southwestern Cordilleran Arc and Mogollon Highlands, which fed into the landward portion of the Gallup Delta (the Moreno Hill Formation) via northeasterly flowing channel complexes. This work greatly strengthens linkages to other early Late Cretaceous strata across the Western Interior.
| S-EPMC7953880 | biostudies-literature
Project description: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, toxicogenomics predominately remains a tool for investigative research rather than for regulatory risk assessment. In this study, we aimed to determine 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 sites 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 B[a]P and the human hepatocyte 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 still observed between the test sites, a common subset of B[a]P responsive genes was identified across all test sites which included both genes previously reported in the literature as B[a]P responsive in addition to the same most highly up and down regulated genes. Pending further analysis, these preliminary 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 reproducibly generated in independent laboratories. Future work will need to determine whether in vitro model(s) can be not only reproducible but also predictive for a range of toxic chemicals with different mechanisms of action. Such an approach may potentially be part of future in vitro testing regimes for regulatory risk assessment.
2011-12-31 | GSE25936 | GEO
Project description:To assess the precision (repeatability and reproducibility) of ocular parameters measured by the Tomey OA-2000 biometer, and to compare them with those measured by the IOLMaster.In this prospective study, the right eyes of 108 healthy subjects were included. Three consecutive scans were obtained by 2 observers using the Tomey OA-2000, and in the same session one observer used the IOLMaster (version 5.4.4.0006) for the measurements. About 1 week later, 3 scans were obtained by one observer using the Tomey OA-2000. The axial length (AL), central corneal thickness (CCT), anterior chamber depth (ACD), lens thickness (LT), keratometer readings, pupil diameter (PD) and corneal diameter (CD) values measured by the Tomey OA-2000 and IOLMaster were analyzed. The coefficient of variation (CoV), intraclass correlation coefficient (ICC), within subject standard deviation (Sw) and 2.77Sw were calculated to assess the repeatability and reproducibility. The paired t test and Bland-Altman plots were used to analyze the differences and agreements of parameters measured by the two devices, respectively.Intraobserver repeatability, and interobserver and intersession reproducibility of the AL, CCT, ACD, LT, Kf, Ks, Km, PD and CD values measured by the Tomey OA-2000 biometer showed a CoV of less than 1% except that for PD, and an ICC of more than 0.97 except that for PD and CD. The AL, Kf, Ks, Km and CD values measured by the Tomey OA-2000 were 0.058 ± 0.094 mm, 0.088± 0.150 diopters (D), 0.163 ± 0.170 D, 0.127 ± 0.117 D and 0.171 ± 0.217 mm lower than those measured by the IOLMaster, respectively (all Ps < 0.05). However, the ACD values from the two devices were comparable (P = 0.169). The 95% linite of agreement (LoA) of the AL, ACD, CD and all keratometer readings were no more than 0.24 mm, 0.14 mm 0.60 mm and 0.5 D, respectively.Except for the PD and CD, the ocular parameters measured by the Tomey OA-2000 were highly repeatable and reproducible. Except for the CD value, there was good agreement of ocular parameters measured by the Tomey OA-2000 and the IOLMaster in healthy eyes.
| S-EPMC5828443 | biostudies-literature
Project description:Plutons are formed by protracted crystallization of magma bodies several kilometers deep within the crust. The temporal frequency (i.e. episodicity or 'tempo') of pluton formation is often poorly constrained as timescales of pluton formation are largely variable and may be difficult to resolve by traditional dating methods. The Hida Mountain Range of central Japan hosts the youngest exposed plutons on Earth and provides a unique opportunity to assess the temporal and spatial characteristics of pluton emplacement at high temporal resolution. Here we apply U-Pb geochronology to zircon from the Quaternary Kurobegawa Granite and Takidani Granodiorite in the Hida Mountain Range, and from modern river sediments whose fluvial catchments include these plutons in order to reconstruct their formation. The U-Pb data demonstrate that the Kurobegawa pluton experienced two magmatic pulses at ~2.3?Ma and ~0.9?Ma; whereas, to the south, the Takidani pluton experienced only one magmatic pulse at ~1.6?Ma. These data imply that each of these magmatic systems were both spatially and temporally distinct. The apparent ~0.7?Myr age gap between each of the three magmatic pulses potentially constrains the recharge duration of a single pluton within a larger arc plutonic complex.
| S-EPMC5622053 | biostudies-literature
Project description:Reduced pancreas volume, as measured by non-contrast magnetic resonance imaging (MRI), is observed in individuals with newly-diagnosed type 1 diabetes (T1D) and declines over the first year after diagnosis. In this study, we determined the repeatability and inter-reader reproducibility of pancreas volume measurements by MRI. Test-retest scans in individuals with or without T1D (n?=?16) had an intraclass correlation coefficient (ICC) of 0.985 (95% CI 0.961 to 0.995) for pancreas volume. Independent pancreas outlines by two board-certified radiologists (n?=?30) yielded an ICC of 0.945 (95% CI 0.889 to 0.973). The mean Dice coefficient, a measurement of the degree of overlap between pancreas regions of interest between the two readers, was 0.77. Prandial state did not influence pancreatic measurements, as stomach volume did not correlate with pancreas volume. These data demonstrate that MRI measurements of pancreas volume between two readers are repeatable and reproducible with ICCs that correspond to excellent clinical significance (ICC?>?0.9), are not related to changes in stomach volume, and could be a useful tool for clinical investigation of diabetes and other pancreas pathologies.
| S-EPMC7076034 | biostudies-literature
Project description:PurposeAn ever-growing number of predictive models used to inform clinical decision making have included quantitative, computer-extracted imaging biomarkers, or "radiomic features." Broadly generalizable validity of radiomics-assisted models may be impeded by concerns about reproducibility. We offer a qualitative synthesis of 41 studies that specifically investigated the repeatability and reproducibility of radiomic features, derived from a systematic review of published peer-reviewed literature.Methods and materialsThe PubMed electronic database was searched using combinations of the broad Haynes and Ingui filters along with a set of text words specific to cancer, radiomics (including texture analyses), reproducibility, and repeatability. This review has been reported in compliance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. From each full-text article, information was extracted regarding cancer type, class of radiomic feature examined, reporting quality of key processing steps, and statistical metric used to segregate stable features.ResultsAmong 624 unique records, 41 full-text articles were subjected to review. The studies primarily addressed non-small cell lung cancer and oropharyngeal cancer. Only 7 studies addressed in detail every methodologic aspect related to image acquisition, preprocessing, and feature extraction. The repeatability and reproducibility of radiomic features are sensitive at various degrees to processing details such as image acquisition settings, image reconstruction algorithm, digital image preprocessing, and software used to extract radiomic features. First-order features were overall more reproducible than shape metrics and textural features. Entropy was consistently reported as one of the most stable first-order features. There was no emergent consensus regarding either shape metrics or textural features; however, coarseness and contrast appeared among the least reproducible.ConclusionsInvestigations of feature repeatability and reproducibility are currently limited to a small number of cancer types. Reporting quality could be improved regarding details of feature extraction software, digital image manipulation (preprocessing), and the cutoff value used to distinguish stable features.
| S-EPMC6690209 | biostudies-literature