PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Interoperability”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2026

Associations between smart infusion pump-electronic health record interoperability and healthcare outcomes: A systematic review.

OBJECTIVE: This study synthesized available evidence on the associations between smart infusion pump-electronic health record (EHR) interoperability and healthcare outcomes. METHODS: A systematic review of PubMed, CINAHL, Embase, and Scopus databases identified 901 records, which were imported into Rayyan® for duplicate removal, independent screening by three reviewers, and resolution of discrepancies. Eligible studies were peer-reviewed, data-driven, and reported associations between smart infusion pump-EHR interoperability and healthcare outcomes. Studies focused solely on technical validation or interoperability prototypes were excluded. A backward citation search identified additional studies. Two reviewers independently extracted and cross-validated study characteristics using standardized templates. Methodological quality was assessed with the Joanna Briggs Institute Critical Appraisal Tools. RESULTS: Twenty records of 14 full-text studies and 6 conference proceedings were included. Most records reported positive associations between smart infusion pump-EHR interoperability and outcomes related to safety (e.g., medication administration errors, safety-reported events, pump alerts, and compliance with interoperability and drug library), operational efficiency (e.g., programming and documentation time and technical issues), financial performance (e.g., charges captured, and cost avoided), and user experience domains. Most studies used observational designs, reflecting real-world interoperability implementations, where controlling confounding factors is challenging. Limited reporting of baseline characteristics, pump type, and sample sizes limited comparability across studies. CONCLUSIONS: Smart infusion pump-EHR interoperability was associated with improvements in patient safety, efficiency, charge capture, and user experience, with variable findings across studies. Future research should use rigorous methodologies and standardized measures, examine relationships across outcome domains, assess limitations of pump-EHR interoperability, and evaluate underexplored outcomes, including team communication, cognitive workload, and AI-enabled pumps. IMPLICATIONS FOR CLINICAL PRACTICE: Interoperability should be viewed as a component of a broader sociotechnical system, in which technology, user, workflow, clinical content, and organizational practices collectively determine overall effectiveness.

Humans↗
PubMed1992

DeoR repression at-a-distance only weakly responds to changes in interoperator separation and DNA topology.

The interoperator distance between a synthetic operator Os and the deoP2O2-galK fusion was varied between 46 and 176 bp. The repression of the deoP2 directed galK expression as a function of the interoperator distance (center-to-center) was measured in vivo in a single-copy system. The results show that the DeoR repressor efficiently can repress transcription at all the interoperator distances tested. The degree of repression depends very little on the spacing between the operators, however, a weak periodic dependency of 8-11 bp may exist.

Bacterial Proteins↗
PubMed2025

PMkbase (version 1.0): an interactive web-based tool for tracking bacterial metabolic traits using phenotype microarrays made interoperable with sequence information and visualizing/processing PM data.

Bacteria showcase remarkable metabolic diversity and traits, even among strains of the same species. In recent years, a large number of bacterial genomes have been sequenced, leading to the elucidation and documentation of genomic differences and commonalities across and within species. Genome-scale metabolic reconstructions, which are often defined and curated using data from phenotype microarrays, elucidate the differences in metabolic traits resulting from genomic diversity. These microarrays measure cellular respiration on a variety of carbon, nitrogen, phosphorus, and sulfur sources and various stressors and inhibitors over a period of time to determine the metabolic activity of a given strain. Despite their popularity in measuring bacterial metabolic activity and traits, no public databases that allow researchers to warehouse, access, and analyze this information currently exist. Additionally, there are no publicly available tools that allow researchers to view the variance of these metabolic traits across bacterial strains. To address this need, we present Phenotype Microarray Knowledgebase (PMkbase [version 1.0], https://pmkbase.com/), an interactive database that acts as a repository of phenotype microarray (PM) data with integrated sequence information. Binarized activity calls, along with associated kinetic parameters, are made for all metabolic substrates and inhibitors. Users can upload their own data for analysis and visualization and to perform quality checks on their experiments. PMkbase will address an unmet need to track and view bacterial metabolic traits and provide researchers with valuable information to develop metabolic models, enrich pangenomic analyses, and design new experiments.IMPORTANCEBacterial species can be differentiated by their metabolic profiles or the type of nutrients they consume. Interestingly, strains within the same species also display differences in nutrient consumption. Phenotype microarrays are a high-throughput, widely used technology to measure which substrates can be metabolized by various microbial strains and the extent to which inhibitors can affect it. Despite their widespread use, public databases to parse and access this data type at scale do not exist. PMkbase, which contains 9,024 data points for nitrogen substrate utilization, 41,664 data points for carbon substrate utilization, 8,448 data points for phosphorus/sulfur substrate utilization, and 27,264 data points on various antibiotics across three species (Escherichia coli, Pseudomonas putida, and Staphylococcus aureus), has been developed to allow researchers to freely access PM data, along with enriching the data with sequence information.

Bacteria↗
PubMed1991

Interoperator variability in quantitative electroencephalography.

The purpose of the study was to determine whether quantitative or discriminant analysis of the electroencephalograph (EEG) would vary significantly when the same EEG was analysed by 3 different operators. EEGs on 10 healthy volunteers were recorded on the Cadwell Spectrum AT 386, using the Electrocap (10-20 system). The EEGs were analysed independently, with each operator selecting the first 48 artifact-free epochs. The results were analysed using the non-parametric Friedman two-way analysis of variance (ANOVA) for the discrimination analysis and a one-way ANOVA for the monopolar and bipolar Absolute Power raw measures. Statistical analysis of the discriminant data showed no significant differences between operators, with 7 of 10 studies yielding the same results. The remaining 3 studies were classified either as borderline or normal when analysed by different operators. Although a series of "t" tests comparing 2 operators showed most variability occurring in Absolute Power as compared with Relative Power, Power Asymmetry and Coherence, ANOVA of the raw mono- and bipolar Absolute Power measures showed no significant differences between the operators at the P = 0.05 level. Thus the differences between the operators were non-significant when comparing quantitative EEG analyses with respect to both the raw measures and the discriminant analyses.

Analysis of Variance↗
PubMed2025

Privacy-preserving framework for genomic computations via multi-key homomorphic encryption.

MOTIVATION: The affordability of genome sequencing and the widespread availability of genomic data have opened up new medical possibilities. Nevertheless, they also raise significant concerns regarding privacy due to the sensitive information they encompass. These privacy implications act as barriers to medical research and data availability. Researchers have proposed privacy-preserving techniques to address this, with cryptography-based methods showing the most promise. However, existing cryptography-based designs lack (i) interoperability, (ii) scalability, (iii) a high degree of privacy (i.e. compromise one to have the other), or (iv) multiparty analyses support (as most existing schemes process genomic information of each party individually). Overcoming these limitations is essential to unlocking the full potential of genomic data while ensuring privacy and data utility. Further research and development are needed to advance privacy-preserving techniques in genomics, focusing on achieving interoperability and scalability, preserving data utility, and enabling secure multiparty computation. RESULTS: This study aims to overcome the limitations of current cryptography-based techniques by employing a multi-key homomorphic encryption scheme. By utilizing this scheme, we have developed a comprehensive protocol capable of conducting diverse genomic analyses. Our protocol facilitates interoperability among individual genome processing and enables multiparty tests, analyses of genomic databases, and operations involving multiple databases. Consequently, our approach represents an innovative advancement in secure genomic data processing, offering enhanced protection and privacy measures. AVAILABILITY AND IMPLEMENTATION: All associated code and documentation are available at https://github.com/farahpoor/smkhe.

Computer Security↗
PubMed2026

The European Health Data Space and the Secondary Use of Sensitive Health Data.

INTRODUCTION: The European Health Data Space (EHDS) is one of the European Union's most ambitious data-governance projects. It aims to create a common framework through which electronic health data can be accessed and reused across Member States for care, research, innovation, policy, and public-interest purposes. Its practical viability depends not only on digital infrastructure, but also on legal, ethical, and organisational harmonisation, particularly for genetic and genomic data. METHODS: This paper examines the EHDS with emphasis on the secondary use of health data. It reviews the EHDS institutional architecture, discusses Finland's Findata as a national model for structured access, and analyses challenges for data holders and data donors, including interoperability, governance burdens, privacy protection, residual re-identification risk, and genomic-data sensitivity. RESULTS: A cross-border cancer-genomics case study shows that the EHDS can streamline data discovery and the routing of access requests, but does not by itself eliminate legal fragmentation, heterogeneous ethics review, and consent-related barriers. DISCUSSION: Effective implementation will require harmonisation beyond infrastructure, including clearer consent standards, more consistent ethics procedures, interoperable metadata, and proportionate safeguards for genomic data.

Electronic Health Records↗
PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS: To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS: Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗
PubMed2026

Programmatic access to ICTV virus taxonomy through a public ontology API.

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗
PubMed1986

Reproducibility of optic disc measurements with computerized analysis of stereoscopic video images.

Computerized digital image analysis of the optic nerve head was performed using a simultaneous stereoscopic video camera system to provide rapid, quantitative measurements of optic nerve head topography. Determination of the variability of the measurements is required to estimate the magnitude of optic nerve change over time that can be reliably detected. Total variability, operator variability, and interoperator variability were studied. Total variability was assessed by analyzing ten sets of video recordings made in each of seven eyes of seven normal subjects, and in seven eyes of seven patients with glaucoma. The median coefficients of variation for measurements of total variability in glaucoma patients were as follows: vertical disc measurement, 1.4%; horizontal disc measurement, 2.1%; disc area, 1.9%; vertical cup/disc, 3.9%; horizontal cup/disc, 3.3%; disc rim area, 7.5%; and volume, 7.6%. Operator and interoperator variabilities were considerably smaller in magnitude.

Data Display↗
PubMed2027

Global Genomic Surveillance.

Global genomic surveillance has emerged as a foundational pillar of public health in the twenty-first century, enabling real-time tracking of pathogen evolution and informing outbreak response. This chapter examines the strategic architecture of global genomic surveillance, focusing on its application to arboviruses such as chikungunya virus (CHIKV). It explores the integration of genomic data with epidemiological, clinical, and environmental information within a One Health framework, while addressing critical challenges in governance, equity, and interoperability. The discussion covers the entire genomic surveillance workflow, from sample collection and sequencing to bioinformatic analysis and phylogenetic inference, and highlights the transformative role of artificial intelligence (AI) in predictive surveillance. By analyzing global initiatives, operational barriers, and emerging technologies, this chapter underscores the necessity of sustainable, equitable, and interoperable genomic systems to proactively address current and future infectious disease threats.

Humans↗
PubMed2026

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗
PubMed1988

Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process.

Plasmid constructs containing a wild-type (O+) lac operator upstream of an operator-constitutive (Oc) lac control element exhibit a length-dependent, oscillatory pattern of repression of expression of the regulated gene as interoperator spacing is varied from 115 to 177 base pairs (bp). Both the length dependence and the periodicity of repression are consistent with a thermodynamic model involving a stable looped complex in which bidentate lac repressor interacts simultaneously with both O+ and Oc operators. The oscillatory pattern of repression with distance occurs with a period approximating the helical repeat of DNA and presumably reflects the necessity for proper alignment of interacting operators along the helical face of the DNA. In the length regime examined, the presence of the upstream operator enhances repression between 6-fold and 50-fold depending upon phasing. This reflects a torsional rigidity of DNA in vivo that is consistent with in vitro measurements. The oscillatory pattern of repression is best fit with a period of either 9.0 or 11.7 bp/cycle but not 10.5 bp/cycle. This periodicity is interpreted as reflecting the average helical repeat of the 40-bp interoperator region of plasmid DNA in vivo, suggesting that the local helical repeat of DNA in vivo may differ significantly from 10.5 bp/turn. The apparent persistence length needed to fit the data (aapp) is only one-fifth the standard in vitro value. This low value of aapp may be due in part to DNA bending induced by catabolite activator protein (CAP) bound to its site between the interacting operators.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA, Bacterial↗
PubMed2026

The need for standardization and improved open (meta)data practices in metaproteomics.

Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder reproducibility and comparability, limiting integration with other omics data. We here present a community-developed reporting checklist tailored to the specific needs of metaproteomics. We also outline current efforts to enable structured and interoperable metadata capture, drawing on standards from proteomics and microbiome research wherever possible. By promoting transparent reporting and advancing metadata practices, our recommendations aim to align metaproteomics more closely with FAIR principles and support reproducible and interoperable research practices. Video Abstract.

Proteomics↗
PubMed1992

Blinded evaluation of planar technetium-99m-sestamibi myocardial perfusion studies.

Sestamibi planar myocardial perfusion studies were performed at Hotel-Dieu de Montreal on 28 patients with documented coronary artery disease and 16 normal subjects. Stress and rest studies were performed on separate days. These studies were sent to Virginia for interpretation while blinded as to age, sex, and other clinical information. Studies were quantitated independently by two operators (using a computer program modified for Sestamibi), and interpreted independently by two experienced interpreters. Computer quantitation of 2816 segments gave an average interoperator deviation of 2.2%. Pure quantitative criteria were applied for computer interpretation. By varying the detection threshold, we produced the entire ROC curve relating sensitivity and specificity as a function of detection threshold. Using only computer criteria for normal or abnormal, interoperator agreement by patient was 98% and 93% by view. The computer could achieve equal positive and negative predictive accuracy of 87%. Interpreters, allowed both quantitative and subjective judgment, agreed on 91% of 44 patients, 90% of 132 views, and 92% of 660 segments. Interpreters averaged 94% positive and 86% negative predictive accuracy.

Adult↗
PubMed1979

Cine-densitometric measurement of coronary arterial stenoses.

Computer-aided operator-interactive densitometry has been developed and applied to determine the percent stenosis for obstructive lesions in the coronary arterial tree. Phantom experiments performed to assess system linearity, accuracy of densitometric measurements, nonuniformity in image amplified response, and the interference of structure noise in measuring precision have been described. Three observers assessed the reproducibility of the method by repeating analyses on 20 stenoses in man recorded on 35-mm cine angiograms. Calculation of the intra- and interobserver errors found that their values significantly decrease with increasing percent stenosis. The reproducibility of the technique was also tested on stenoses that were exposed at multiple angles. The results agreed with those found for the intra- and interoperator errors. Limitations of the densitometric approach and desirability of further automation of the measurements are also discussed.

Cineangiography↗
PubMed1992

Determination of bone mineral density by dual x-ray absorptiometry in patients with uncemented total hip arthroplasty.

Bone remodeling is an expected sequela with total hip arthroplasty (THA). Although there are several methods of estimating bone response in THA patients from radiographs, there are no accurate and generally accepted methods for quantitative determinations in vivo. In this study, we describe an application of dual x-ray absorptiometry (DXA) for measuring bone mineral content and bone mineral density in the proximal femur following THA. DXA is a noninvasive technique with minimal radiation exposure (< 5 mrem). Various aspects of measurement error (accuracy and reliability) of this application of DXA were determined in a series of studies reported here. Accuracy error (how similar are the measured and actual values) was < 1% determined in bone phantoms of four densities. Precision error (how reproducible are the measurements) was also < 1% at all four densities in the phantoms and was only slightly elevated (0.9-1.5%) in repeated measurements of implanted cadaver femora. Precision error in vivo, determined both from multiple replicates on five patients and from duplicate scans on 30 patients, was further elevated but remained < 5%. Contributions to precision error, rotation of the leg, and interoperator variability were assessed; none was found to elevate precision error appreciably. We suggest that DXA is a feasible method for quantifying bone response following THA, and will allow discrimination of small changes (> 5%) not previously measurable.

Absorptiometry, Photon↗
PubMed1992

Reproducibility of lateral spine scans using dual energy X-ray absorptiometry.

Reproducibility of lateral spine dual energy X-ray absorptiometry (LAT DEXA) scans using a Lunar DPX-L scanner was assessed in a cadaveric phantom and in patients. One hundred phantom measurements over 7 months demonstrated a longitudinal stability of 1.7% (coefficient of variation, CV). Additional scans were performed with the phantom rotated by up to 20 degrees in each of the three orthogonal planes to assess the effects of variable patient positioning. Horizontal and vertical rotation of the spine had little effect on the estimated bone mineral density (BMD), however, axial rotation of greater than 8 degrees led to errors in the BMD measurement. One hundred consecutive patients had two lateral scans performed within 1 month. BMD (range 0.10-1.6 g/cm2) was determined for each scan by one operator. Significant overlap from ribs and pelvis was often seen with L2 and L4 vertebrae but one vertebra (L3) could be measured in every case. Intraoperator and interoperator variability was assessed by three experienced operators, each analyzing 10 patients' scans on five separate occasions, and was found to be less than 1.1% for a single vertebra. BMD estimation of vertebral bodies and midslices by lateral DEXA scans (CV% of 3.8% and 4.6%) have a 95% confidence interval of 0.074 g/cm2 and 0.096 g/cm2, respectively for two vertebrae. This variability is due mainly to axial rotation, with operator variability, horizontal rotation, and vertical rotation having little effect on BMD estimation.

Absorptiometry, Photon↗