Data consistency
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A method of testing structure-related NMR data prior to structure calculations is presented. The test is applicable to second rank tensor interactions (dipolar coupling, anisotropic chemical shielding, and quadrupolar interaction) observed in partially aligned samples of biomacromolecules. The method utilizes the fact that only limited number of frequencies corresponding to the mentioned interactions can be measured independently in a rigid fragment of the macromolecule. Additional values can be predicted as linear combinations of the set of independent frequencies. Internal consistency of sufficiently large sets of frequencies measured in individual molecular fragments is tested by comparing the experimental data with their predicted values. The method requires only knowledge of local geometry (i.e., definition of the interaction tensors in the local coordinate frames of the fragments). No information about the alignment or shape of the molecule is required. The test is best suited for planar fragments. Application to peptide bonds and nucleic acid bases is demonstrated.
- MeSH
- anizotropie MeSH
- DNA metabolismus MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie * MeSH
- makromolekulární látky * MeSH
- peptidy metabolismus MeSH
- ubikvitin metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA MeSH
- makromolekulární látky * MeSH
- peptidy MeSH
- ubikvitin MeSH
Electronic Health Record (EHR) systems currently in use are not designed for widely interoperable longitudinal health data. Therefore, EHR data cannot be properly shared, managed and analyzed. In this article, we propose two approaches to making EHR data more comprehensive and FAIR (Findable, Accessible, Interoperable, and Reusable) and thus more useful for diagnosis and clinical research. Firstly, the data modeling based on the LinkML framework makes the data interoperability more realistic in diverse environments with various experts involved. We show the first results of how diverse health data can be integrated based on an easy-to-understand data model and without loss of available clinical knowledge. Secondly, decentralizing EHRs contributes to the higher availability of comprehensive and consistent EHR data. We propose a technology stack for decentralized EHRs and the reasons behind this proposal. Moreover, the two proposed approaches empower patients because their EHR data can become more available, understandable, and usable for them, and they can share their data according to their needs and preferences. Finally, we explore how the users of the proposed solution could be involved in the process of its validation and adoption.
- Klíčová slova
- Distributed electronic health records, FAIR principles, HL7 FHIR, bio-data management, ontology,
- MeSH
- data management MeSH
- elektronické zdravotní záznamy * MeSH
- lidé MeSH
- sémantický web * MeSH
- software MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Mitigating rating inconsistency can improve measurement fidelity and detection of treatment response. METHODS: The International Society for CNS Clinical Trials and Methodology convened an expert Working Group that developed logical consistency (LC) checks for ratings of the Young Mania Rating Scale (YMRS), which is widely used in studies of mood and bipolar disorders. LC and statistical outlier-response pattern checks (SC) were applied to 63,228 YMRS administrations from 14 clinical trials evaluating treatments for bipolar disorder. Checks were also applied to Monte Carlo-simulated data as a proxy for their use under conditions of inconsistency. RESULTS: 42 LC flags were developed, and four SC flags were created from the data set (n = 14). Almost 20 % of the rating administrations had at least one LC flag, 6.7 % had two or more, 1.7 % had three or more; 17.3 % percent of the administrations had at least one SC flag and 4.6 % percent had two or more. Overall, 31 % of administrations had at least one flag of any type, 12.1 % had two or more and 5.3 % had three or more. In acute antimanic treatment trials (n = 10) there were more flags of any type compared to relapse prevention trials (n = 4). LIMITATIONS: Flagged ratings may represent less-common presentations assessed correctly. CONCLUSIONS: Using established methods, we illustrate development and application of consistency flags for YMRS ratings. Applying flags and mitigation during trials may improve the value of YMRS data, help focus attention on rater training, and improve reliability and validity of trial data.
- Klíčová slova
- Careless ratings, Consistency of measurement, Inconsistent ratings, YMRS, Young Mania Rating Scale,
- MeSH
- afekt MeSH
- antimanika terapeutické užití MeSH
- bipolární porucha * diagnóza farmakoterapie MeSH
- lidé MeSH
- mánie * farmakoterapie MeSH
- psychiatrické posuzovací škály MeSH
- reprodukovatelnost výsledků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antimanika MeSH
OBJECTIVES: This study aims to describe the data structure and harmonisation process, explore data quality and define characteristics, treatment, and outcomes of patients across six federated antineutrophil cytoplasmic antibody-associated vasculitis (AAV) registries. METHODS: Through creation of the vasculitis-specific Findable, Accessible, Interoperable, Reusable, VASCulitis ontology, we harmonised the registries and enabled semantic interoperability. We assessed data quality across the domains of uniqueness, consistency, completeness and correctness. Aggregated data were retrieved using the semantic query language SPARQL Protocol and Resource Description Framework Query Language (SPARQL) and outcome rates were assessed through random effects meta-analysis. RESULTS: A total of 5282 cases of AAV were identified. Uniqueness and data-type consistency were 100% across all assessed variables. Completeness and correctness varied from 49%-100% to 60%-100%, respectively. There were 2754 (52.1%) cases classified as granulomatosis with polyangiitis (GPA), 1580 (29.9%) as microscopic polyangiitis and 937 (17.7%) as eosinophilic GPA. The pattern of organ involvement included: lung in 3281 (65.1%), ear-nose-throat in 2860 (56.7%) and kidney in 2534 (50.2%). Intravenous cyclophosphamide was used as remission induction therapy in 982 (50.7%), rituximab in 505 (17.7%) and pulsed intravenous glucocorticoid use was highly variable (11%-91%). Overall mortality and incidence rates of end-stage kidney disease were 28.8 (95% CI 19.7 to 42.2) and 24.8 (95% CI 19.7 to 31.1) per 1000 patient-years, respectively. CONCLUSIONS: In the largest reported AAV cohort-study, we federated patient registries using semantic web technologies and highlighted concerns about data quality. The comparison of patient characteristics, treatment and outcomes was hampered by heterogeneous recruitment settings.
- Klíčová slova
- epidemiology, granulomatosis with polyangiitis, quality indicators, health care, systemic vasculitis,
- MeSH
- ANCA-asociované vaskulitidy * farmakoterapie epidemiologie komplikace MeSH
- granulomatóza s polyangiitidou * farmakoterapie epidemiologie komplikace MeSH
- lidé MeSH
- mikroskopická polyangiitida * farmakoterapie epidemiologie MeSH
- protilátky proti cytoplazmě neutrofilů MeSH
- registrace MeSH
- správnost dat MeSH
- ukládání a vyhledávání informací MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- metaanalýza MeSH
- Názvy látek
- protilátky proti cytoplazmě neutrofilů MeSH
BACKGROUND: Mitigating rating inconsistency can improve measurement fidelity and detection of treatment response. METHODS: The International Society for CNS Clinical Trials and Methodology convened an expert Working Group that developed consistency checks for ratings of the Hamilton Anxiety Rating Scale (HAM-A) and Clinical Global Impression of Severity of anxiety (CGIS) that are widely used in studies of mood and anxiety disorders. Flags were applied to 40,349 HAM-A administrations from 15 clinical trials and to Monte Carlo-simulated data as a proxy for applying flags under conditions of inconsistency. RESULTS: Thirty-three flags were derived these included logical consistency checks and statistical outlier-response pattern checks. Twenty-percent of the HAM-A administrations had at least one logical scoring inconsistency flag, 4 % had two or more. Twenty-six percent of the administrations had at least one statistical outlier flag and 11 % had two or more. Overall, 35 % of administrations had at least one flag of any type, 19 % had one and 16 % had 2 or more. Most of administrations in the Monte Carlo- simulated data raised multiple flags. LIMITATIONS: Flagged ratings may represent less-common presentations of administrations done correctly. Conclusions-Application of flags to clinical ratings may aid in detecting imprecise measurement. Flags can be used for monitoring of raters during an ongoing trial and as part of post-trial evaluation. Appling flags may improve reliability and validity of trial data.
- Klíčová slova
- Careless ratings, Consistency of measurement, HAM-A, Hamilton Anxiety Rating Scale, Inconsistent ratings,
- MeSH
- lidé MeSH
- psychiatrické posuzovací škály MeSH
- psychometrie MeSH
- reprodukovatelnost výsledků MeSH
- úzkost * MeSH
- úzkostné poruchy * diagnóza farmakoterapie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Symptom manifestations in mood disorders can be subtle. Cumulatively, small imprecisions in measurement can limit our ability to measure treatment response accurately. Logical and statistical consistency checks between item responses (i.e., cross-sectionally) and across administrations (i.e., longitudinally) can contribute to improving measurement fidelity. METHODS: The International Society for CNS Clinical Trials and Methodology convened an expert Working Group that assembled flags indicating consistency/inconsistency ratings for the Hamilton Rating Scale for Depression (HAM-D17), a widely-used rating scale in studies of depression. Proposed flags were applied to assessments derived from the NEWMEDS data repository of 95,468 HAM-D administrations from 32 registration trials of antidepressant medications and to Monte Carlo-simulated data as a proxy for applying flags under conditions of known inconsistency. RESULTS: Two types of flags were derived: logical consistency checks and statistical outlier-response pattern checks. Almost thirty percent of the HAMD administrations had at least one logical scoring inconsistency flag. Seven percent had flags judged to suggest that a thorough review of rating is warranted. Almost 22% of the administrations had at least one statistical outlier flag and 7.9% had more than one. Most of the administrations in the Monte Carlo- simulated data raised multiple flags. LIMITATIONS: Flagged ratings may represent less-common presentations of administrations done correctly. CONCLUSIONS: Application of flags to clinical ratings may aid in detecting imprecise measurement. Reviewing and addressing these flags may improve reliability and validity of clinical trial data.
- Klíčová slova
- Careless ratings, Consistency of measurement, HAM-D17, Hamilton Rating Scale for Depression, Inconsistent ratings, NEWMEDS,
- MeSH
- antidepresiva * terapeutické užití MeSH
- deprese * diagnóza MeSH
- lidé MeSH
- poruchy nálady farmakoterapie MeSH
- psychiatrické posuzovací škály MeSH
- reprodukovatelnost výsledků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- antidepresiva * MeSH
BACKGROUND: Preoperative knowledge of tumor consistency and the likelihood of gross total resection (GTR) would greatly benefit planning of pituitary adenoma surgery, however, no reliable methods currently exist. OBJECTIVES: To evaluate the utility of radiomic analysis of MRI for predicting tumor consistency and GTR. To explore the interpretability of contributing radiomic features. METHODS: Patients undergoing first endoscopic surgery for pituitary macroadenomas were included. Tumor consistency was assessed intraoperatively, GTR was assessed based on postoperative MRI. Radiomic features were extracted from axial T2-weighted MRI. Low-variability and highly intercorrelated features were removed. Random Forest Classifiers were optimized using 70 % of patient data and evaluated on the remaining 30 %. Relative feature importance was assessed using the Gini-Simpson index. RESULTS: 542 patients were included. GTR was achieved in 325 (60.0 %) cases, firm tumors were encountered in 122 (22.5 %) cases. There was a significant correlation between GTR and tumor consistency (67.1 % vs. 35.2 %, p < 0.001). 1688 radiomic variables were extracted, 442 were removed due to low variance and 699 due to high intercorrelation. The consistency prediction model achieved an accuracy of 81.6 % and utilized 32 features, GTR prediction model achieved 79.1 % accuracy using 73 features. CONCLUSIONS: Radiomic analysis demonstrated significant potential for preoperative evaluation of pituitary adenomas. Texture and intensity-based features were the primary contributors to consistency prediction. However, the explanation of these features was insufficient. GTR prediction was predominantly driven by shape-related features. Our findings highlight the challenges of linking radiomic features to underlying tissue properties and emphasize the need for cautious interpretation.
- Klíčová slova
- Gross total resection, Magnetic resonance imaging, Pituitary adenoma, Radiomics, Tumor consistency,
- Publikační typ
- časopisecké články MeSH
The scoping review is one of the alternatives of producing a literature review. However, this approach still lacks a clearly accepted definition, and the scoping terminology is also somewhat fuzzy. Although the methodology of scoping review processing is relatively uniform, terminological chaos appears in the titles of studies with scoping review methodology. This paper presents an analysis of selected published studies with a focus on the content of their titles. A total of 13 thematic dimensions were identified covering the content of titles that show a degree of inconsistency and frequent terminological and methodological "chaos." This study includes a broad scope of themes and areas for which scoping reviews were produced. We would like to recommend to authors (especially scoping review beginners) to - if not necessary or desirable - avoid introducing new concepts and specifications of titles of produced and published scoping review studies. In the case of literature reviews and knowledge synthesis it is necessary to search according to specific keywords and search phrases - more fragmented scoping review terminology makes literature search more difficult or even impossible.
- Klíčová slova
- nursing research, scoping review, terminology, title analysis,
- MeSH
- lidé MeSH
- scoping review jako téma MeSH
- výzkumný projekt normy trendy MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
OBJECTIVE: Health data standardized to a common data model (CDM) simplifies and facilitates research. This study examines the factors that make standardizing observational health data to the Observational Medical Outcomes Partnership (OMOP) CDM successful. MATERIALS AND METHODS: Twenty-five data partners (DPs) from 11 countries received funding from the European Health Data Evidence Network (EHDEN) to standardize their data. Three surveys, DataQualityDashboard results, and statistics from the conversion process were analyzed qualitatively and quantitatively. Our measures of success were the total number of days to transform source data into the OMOP CDM and participation in network research. RESULTS: The health data converted to CDM represented more than 133 million patients. 100%, 88%, and 84% of DPs took Surveys 1, 2, and 3. The median duration of the 6 key extract, transform, and load (ETL) processes ranged from 4 to 115 days. Of the 25 DPs, 21 DPs were considered applicable for analysis of which 52% standardized their data on time, and 48% participated in an international collaborative study. DISCUSSION: This study shows that the consistent workflow used by EHDEN proves appropriate to support the successful standardization of observational data across Europe. Over the 25 successful transformations, we confirmed that getting the right people for the ETL is critical and vocabulary mapping requires specific expertise and support of tools. Additionally, we learned that teams that proactively prepared for data governance issues were able to avoid considerable delays improving their ability to finish on time. CONCLUSION: This study provides guidance for future DPs to standardize to the OMOP CDM and participate in distributed networks. We demonstrate that the Observational Health Data Sciences and Informatics community must continue to evaluate and provide guidance and support for what ultimately develops the backbone of how community members generate evidence.
- Klíčová slova
- OMOP common data model, data standardization, observational data,
- MeSH
- celosvětové zdraví * MeSH
- databáze faktografické MeSH
- elektronické zdravotní záznamy MeSH
- lékařství * MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- pozorovací studie MeSH
- Geografické názvy
- Evropa MeSH
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
