Dataset Information

Statistical quality indicators for electron-density maps.

ABSTRACT: The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a ?(2) significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

SUBMITTER: Tickle IJ

PROVIDER: S-EPMC3322605 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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Statistical quality indicators for electron-density maps.

Tickle Ian J IJ

Acta crystallographica. Section D, Biological crystallography 20120316 Pt 4

The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the ...[more]

PMID: 22505266

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Project description:Good quality indicators should have face validity, relevance to patients, and be able to be measured reliably. Beyond these general requirements, good quality indicators should also have certain statistical properties, including sufficient variability to identify poor performers, relative insensitivity to severity adjustment, and the ability to capture what providers do rather than patients' characteristics. We assessed the performance of candidate indicators of ICU quality on these criteria. Indicators included ICU readmission, mortality, several length of stay outcomes, and the processes of venous-thromboembolism and stress ulcer prophylaxis provision.Retrospective cohort study.One hundred thirty-eight U.S. ICUs from 2001-2008 in the Project IMPACT database.Two hundred sixty-eight thousand eight hundred twenty-four patients discharged from U.S. ICUs.None.We assessed indicators' (1) variability across ICU-years; (2) degree of influence by patient vs. ICU and hospital characteristics using the Omega statistic; (3) sensitivity to severity adjustment by comparing the area under the receiver operating characteristic curve (AUC) between models including vs. excluding patient variables, and (4) correlation between risk adjusted quality indicators using a Spearman correlation. Large ranges of among-ICU variability were noted for all quality indicators, particularly for prolonged length of stay (4.7-71.3%) and the proportion of patients discharged home (30.6-82.0%), and ICU and hospital characteristics outweighed patient characteristics for stress ulcer prophylaxis (?, 0.43; 95% CI, 0.34-0.54), venous thromboembolism prophylaxis (?, 0.57; 95% CI, 0.53-0.61), and ICU readmissions (?, 0.69; 95% CI, 0.52-0.90). Mortality measures were the most sensitive to severity adjustment (area under the receiver operating characteristic curve % difference, 29.6%); process measures were the least sensitive (area under the receiver operating characteristic curve % differences: venous thromboembolism prophylaxis, 3.4%; stress ulcer prophylaxis, 2.1%). None of the 10 indicators was clearly and consistently correlated with a majority of the other nine indicators.No indicator performed optimally across assessments. Future research should seek to define and operationalize quality in a way that is relevant to both patients and providers.

Dataset Information

Statistical quality indicators for electron-density maps.

Publications

Statistical quality indicators for electron-density maps.

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