SEARCH · PubMed Health

Results for “Clinical workflow”

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 397 records · Page 22Linked to original sources

PubMed2004

An adoption study of a clinical reminder system in ambulatory care using a developmental trajectory approach.

In this study, we assess 41 medical residents' acceptance and adoption of a clinical reminder system for chronic disease and preventive care management in the ambulatory care environment using a novel developmental trajectory approach. This group-based, semi-parametric statistical modeling method identifies distinct groups, following distinct usage trajectories, among those who recorded use of the reminder system within an evaluation period of 10 months. We trace system use within these groups over time using computer-generated logs and user satisfaction surveys. Our preliminary analysis of this small sample of users delineates three categories of users. Feedback from these categories of users is being used to re-engineer the application and adapt it better to their workflow and functionality requirements. Despite the small sample size in this particular study, we conclude that this methodology has considerable promise to provide new insights into system usability and adoption issues that may benefit clinical decision support systems as well as information systems more generally.

Ambulatory Care↗

PubMed2002

PACS implementation in a university hospital in Tuscany.

We describe cost/benefit analysis for the implementation of a picture archiving and communication system in the Department of radiology of University of Siena, Italy. We also highlight technical and functional innovations provided by information of several department units: cost conversion, workflow optimisation and operator development. We analysed: operator costs, paper costs, film costs, chemical costs, costs of optical disks and location rent for hardware and software of RIS/PACS. The results show that advantages provided by PACS implementation derive from a workflow optimization and saving of human resources rather than from a reduction in films and chemicals. Moreover, better management of radiological unit provides improved handling of clinical information, resulting in reduced time to initiate clinical action, with reduction in average length of patient stay and improvements in overall health outcomes.

Cost-Benefit Analysis↗

PubMed2025

LegionProfiler: a computational tool for the identification of virulence factors and classification of Legionella pneumophila serogroup 1 isolates.

SUMMARY: Legionella pneumophila has significantly contributed to multiple cases of pneumonia with a high rate of mortality globally. Its ability to exploit host mechanisms through several expressed virulence factors poses challenges for diagnosis, treatment, and outbreak control. To address this, we developed LegionProfiler, a computational tool that swiftly identifies virulence factor protein domains within genome assemblies of Legionella pneumophila serogroup 1 isolates and classifies them into high- or low-virulence groups. LegionProfiler automates the probing of genome assemblies for virulence-associated protein domains and determines the isolate's potential to cause severe pneumonia infection. The LegionProfiler workflow is made available through a user-friendly interface to enhance technical control of infectious sources and adds important insights to the general epidemiology of clinical isolates. It could also support the development of targeted therapeutic strategies that will improve patient treatment. AVAILABILITY AND IMPLEMENTATION: LegionProfiler is freely accessible as a web service at https://legionprofiler.uni-muenster.de, and can also be run locally in a Docker container. The source code can be found at https://imigitlab.uni-muenster.de/heiderlab/legionprofiler or at Zenodo (DOI: 10.5281/zenodo.15592325).

Legionella pneumophila↗

PubMed2025

ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration.

BACKGROUND: In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making integration, cohort selection, and downstream analysis cumbersome. While structured barcoding systems exist in large consortia (e.g., TCGA, GTEx) or domain-specific contexts (e.g., SPREC, GOLD), no unified, extensible framework currently spans both subjects and biosamples in a human- and machine-readable way. METHODS: We developed ClarID, a domain-agnostic specification that supports two identifier formats: (i) a human-readable form (e.g., 'CNAG_Test-HomSap-00001-LIV-TUM-RNA-C22.0-TRT-P1W' that encodes key metadata such as project, species, subject_id, tissue, assay, disease, timepoint and duration (from that event); and (ii) a compact version named 'stub' (e.g., 'CT01001LTR0N401T1W') optimized for filenames, pipelines, and labeling.ClarID is implemented through an open-source command-line tool, ClarID-Tools, which processes tabular metadata files (CSV/TSV) and uses a YAML-based codebook to generate, decode, and validate identifiers, as well as to create and read QR codes. The tool supports bulk and single-sample processing and allows easy integration with institutional workflows. RESULTS: To demonstrate ClarID's utility, we applied it to datasets from the Genomic Data Commons (GDC), generating interpretable identifiers for more than 113,000 clinical records (subjects) and 4,255 biospecimen records. All materials, including pre-processing scripts, input and encoded data, are publicly available and fully reproducible via the accompanying GitHub repository and Google Colab. CONCLUSIONS: ClarID fills a critical gap between opaque accession numbers and rich metadata schemas by embedding key context directly into structured identifiers. It enhances traceability, facilitates downstream analysis, and remains adaptable to project-specific needs through a configurable codebook. The accompanying ClarID-Tools software is freely available, together with full documentation and reproducible pipelines, at https://github.com/CNAG-Biomedical-Informatics/clarid-tools.

Biosample identifiers↗

PubMedDate not supplied

The cost of patient safety.

To ensure patient safety, it costs an organization time, money, and commitment. The clinical laboratory may promote patient safety or may contribute to medical error. Laboratory errors put a patient at risk at any point along the path of workflow. The cost of an initiative in patient safety may be considered from four perspectives: compliance, feasibility, present risk, and financial. Three examples are offered to illustrate the use of these approaches. Most patient-safety strategies in laboratory medicine are not expensive. They are affordable with a structured outlay of existing resources and a willingness to follow defined work practices without exception. More extensive projects, especially those that cross jurisdictional lines within an organization, do require comprehensive project management. Management ofboth kinds of initiatives is addressed by NCCLS' documents on quality practice.

Cost-Benefit Analysis↗

PubMed2004

An ontological framework for the implementation of clinical guidelines in health care organizations.

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems.

Medical Informatics↗

PubMed2005

Multiple sclerosis medical image analysis and information management.

Magnetic resonance imaging (MRI) has become a central tool for patient management, as well as research, in multiple sclerosis (MS). Measurements of disease burden and activity derived from MRI through quantitative image analysis techniques are increasingly being used. There are many complexities and challenges in building computerized processing pipelines to ensure efficiency, reproducibility, and quality control for MRI scans from MS patients. Such paradigms require advanced image processing and analysis technologies, as well as integrated database management systems to ensure the most utility for clinical and research purposes. This article reviews pipelines available for quantitative clinical MRI research in MS, including image segmentation, registration, time-series analysis, performance validation, visualization techniques, and advanced medical imaging software packages. To address the complex demands of the sequential processes, the authors developed a workflow management system that uses a centralized database and distributed computing system for image processing and analysis. The implementation of their system includes a web-form-based Oracle database application for information management and event dispatching, and multiple modules for image processing and analysis. The seamless integration of processing pipelines with the database makes it more efficient for users to navigate complex, multistep analysis protocols, reduces the user's learning curve, reduces the time needed for combining and activating different computing modules, and allows for close monitoring for quality-control purposes. The authors' system can be extended to general applications in clinical trials and to routine processing for image-based clinical research.

Humans↗

PubMed2007

Characteristics of the m2000 automated sample preparation and multiplex real-time PCR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.

Automation↗

PubMed2026

Clinical Variant Interpretation with the Integrative Genomics Viewer (IGV) for Molecular Pathologists.

The integrative genomics viewer (IGV) is a pivotal tool in clinical genomics, enabling the visualization and interpretation of complex sequencing data. Bringing clinical knowledge to bear with visual evaluation of sequencing results is the primary means by which molecular pathologists and other professionals assess and finalize cases. A variety of software tools can assist, but their relationship to the underlying data must be understood and applied systematically. This study includes essential background on next-generation sequencing (NGS) data file types (e.g., FASTQ, BAM, VCF) with a discussion of their format and purpose. We then describe features of IGV that derive nuances from these files. We utilize a series of curated practical cases based on clinical vignettes through which the reader will interact with clinical NGS sequencing data using the IGV software to review various types of clinically relevant variants relative to the human reference genome. These clinical vignettes have been curated to describe examples of some of the complexities of interpretation of genomic data, and how utilizing IGV as part of a routine workflow can provide additional interpretive information for variants beyond routine bioinformatic software algorithm variant calls. The visual inspection of genomic variants utilizing the tools within IGV can unmask subtle contextual cues (i.e., variant allele frequency, strand bias, tissue-specific context) that can influence the interpretation of genomic variants. Although this study focuses on using IGV for the detection and interpretation of somatic variants, the provided applications can be extrapolated for use in the germline setting, including analysis of complex variants and detection of mosaicism.

Humans↗

PubMed2003

Mass spectrometry-based proteomics: current status and potential use in clinical chemistry.

For some years now, scientists have been spending a lot of effort in developing methods to analyse and compare complex protein samples. One of the goals of such global analyses of what is known as proteomes is to discover specific protein markers--or fingerprints of protein markers--from various types of affected biological samples. Considering the battery of technologies currently available, mass spectrometry (MS) constitutes an essential tool in proteomics. We describe here the type of MS instrumentation that is currently dedicated to proteomics research. We also describe the major experimental workflows that are typically used in proteomics today, with a focus on those incorporating MS as a major analysis tool.

Chemistry, Clinical↗

PubMed2004

"I wish I had seen this test result earlier!": Dissatisfaction with test result management systems in primary care.

BACKGROUND: Failure to review and follow up on outpatient test results in a timely manner represents a patient safety and malpractice concern. Therefore, we sought to identify problems in current test result management systems and possible ways to improve these systems. METHODS: We surveyed 262 physicians working in 15 internal medicine practices affiliated with 2 large urban teaching hospitals (response rate, 64%). We asked physicians about systems they used and the amount of time they spent managing test results. We asked them to report delays in reviewing test results and their overall satisfaction with their management of test results. We also asked physicians to rate features they would find useful in a new test result management system. RESULTS: Overall, 83% of respondents reported at least 1 delay in reviewing test results during the previous 2 months. Despite reporting that they spent on average 74 minutes per clinical day managing test results, only 41% of physicians reported being satisfied with how they managed test results. Satisfaction was associated with fewer self-reported delays in reviewing test results. Physicians who actively tracked their test orders to completion were also more likely to be satisfied. The most highly desired features of a test result management system were tools to help physicians generate result letters to patients, prioritize their workflow, and track test orders to completion. CONCLUSIONS: Delays in test result review are common, and many physicians are not satisfied with how they manage test results. Tools to improve test result management in office practices need to improve workflow efficiency and track test orders to completion.

Adult↗

PubMed2000

PACS databases and enrichment of the folder manager concept.

Current challenges facing picture archiving and communication systems (PACS) center around database design and functionality. Workflow issues and folder manager concepts such as autorouting, prefetching, hanging protocols, and hierarchical storage management are driven by a properly designed database that ultimately directly impacts the clinical utility of a PACS. The key issues in PACS database design that enable radiologist-friendly, cost-effective, and data-secure systems will be discussed, including database difficulties of the DICOM standard, HIS/RIS/PACS (hospital information system/radiology information system) connectivity, and database issues in data acquisition, data dissemination, and data display.

Databases as Topic↗

PubMed2003

Medical decision support systems: old dilemmas and new paradigms?

OBJECTIVES: The purpose of this paper is to examine past and present medical decision support systems and the environment in which they operate and to propose specific research tracks that improve integration and adoption of these systems in today's health care systems. METHODS: In preamble, we examine the objectives, decision models, and performances of past decision support systems. RESULTS: Medical decision support tools were essentially formulated from a technical capability perspective and this view has met limited adoption and slowed down new development as well as integration of these important systems into patient management work flows and clinical information systems. The science base of these systems needs to include evidence-based medicine and clinical practice guidelines and the paradigms need to be extended to include a collaborative provider model, the users and the organization perspectives. The availability of patient record and medical terminology standards is essential to the dissemination of decision support systems and so is their integration into the care process. CONCLUSION: To build new decision support systems based on practice guidelines and taking into account users preferences, we do not so much advocate new technological solutions but rather suggest that technology is not enough to ensure successful adoption by the users, the integration into practice workflow, and consequently, the realisation of improved health care outcomes.

Cooperative Behavior↗

PubMed2025

Triage and workflow optimization with artificial intelligence in pediatric imaging.

Artificial intelligence (AI) is being increasingly utilized in various aspects by the radiology department. With an ever-increasing burden on the healthcare system, particularly in emergency units, the need to incorporate AI in patient triage and workflow optimization cannot be overstated. Machine learning (ML)-based algorithms form the core of AI-based software, aiding healthcare professionals at nearly every step in delivering appropriate patient care. Regarding the radiology section of the hospital, AI-based algorithms have proven exceptionally useful in assisting radiologists and technicians with image acquisition. From accurate clinical referrals to scheduling computed tomography/magnetic resonance imaging scan appointments, from ensuring the lowest radiation exposure to offering timely follow-up reminders, ML-based software has indeed revolutionized the concept of modern image acquisition, especially in the pediatric radiology section. Although the implementation of these algorithms is swift, several technical challenges and the limited availability of pediatric datasets preclude their widespread use. The utility of multimodal pediatric datasets, which combine imaging, genomics, and clinical data, for comprehensive AI triage models can help AI systems evolve toward greater adaptability and integration, resulting in enhanced efficiency, reduced turnaround times, and improved patient outcomes in pediatric radiology departments in the future. In this article, we highlight and review the utility of AI and machine learning-based algorithms in efficiently aiding triage and streamlining the workflow in the pediatric radiology section, thereby ensuring an overall improvement in the departmental workflow.

Triage↗

PubMed2005

Analytical evaluation of HgbA1c, microalbumin, CRP, and RF on Architect ci8200 integrated system and workflow performance evaluation using computer simulation.

BACKGROUND: Recently, hemoglobin A1c (HgbA1c), microalbumin (MA), C-reactive protein (CRP) and rheumatoid factor (RF) have been introduced on high throughput general chemistry system. We evaluated analytical performance of these assays on an integrated clinical chemistry and immunoassay analyzer and studied the impact of testing these assays on these systems on the overall efficiency of the analyzer, via computer simulation. METHODS: The analytical performance was measured by determining precision, linearity and correlation of patient sample results with in-house testing methodology. MedModel simulation software is used to develop simulation model and process efficiency is determined by measuring turnaround times and resource utilization. RESULTS: Between-days CVs ranged from 8.59% for MA to 3.22% for HgbA1c level 1 controls. Less than 2% carryover for all 4 methods was observed on the integrated analyzer. For HgbA1c on HPLC analyzer, the minimum and maximum TAT for a batch of 50 samples was 3.78 and 160 min, respectively, while for the integrated system it was 28.2 and 35.1 min, respectively. Labor utilization for the 2 processes ranged from 3.21% to 3.75%. CONCLUSION: Chemistry module on an integrated system can be used to determine the HgbA1c and other serum proteins.

Albuminuria↗

PubMed1994

Automated Speech-recognition Anatomic Pathology (ASAP) reporting.

Artificial intelligence speech-recognizers integrated with Laboratory information and Telefaxcommunication Systems have allowed for totally automated surgical pathology reporting. Automated Speech-Recognition Anatomic Pathology (ASAP) reporting improves the speed, text accuracy, comprehensiveness, and workflow management of diagnostic reports while eliminating support personnel. Healthcare reform goals of increased productivity and economy are furthered. Reports are rendered "as soon as possible" (ASAP) expediting appropriate clinical management and decreased length of stay and hospital costs.

Artificial Intelligence↗

PubMed2005

Lack of effect of shorter turnaround time of microbiological procedures on clinical outcomes: a randomised controlled trial among hospitalised patients in the Netherlands.

Shortening the turnaround time of microbiological procedures was associated with an improved clinical outcome in two studies performed in the USA. To study the clinical impact of a shortened turnaround time in a northwest European setting in which an automated system was used for bacterial identification and susceptibility testing, a single-blind, prospective, randomised controlled trial was conducted in a hospital in the Netherlands. All hospitalised patients with a bacterial infection confirmed by culture were randomly assigned to a control (conventional) group or an intervention (rapid) group. Overnight methods were used for identification and susceptibility testing in the control group, while the Vitek 2 system (bioMerieux, Marcy l'Etoile, France) was used in the rapid group. In each of three consecutive study periods, accelerating factors were added progressively to the laboratory workflow of the rapid group to increase same-day reporting, whereas methods remained identical in the conventional group. The turnaround time of the microbiological cycle using the Vitek 2 system as compared to conventional methods was studied and the clinical impact of a shortened turnaround time assessed in terms of mortality, morbidity, and cost. For the rapid groups, the turnaround time was significantly shorter for oral reporting of final susceptibility results in all three study periods and for reporting on paper in the third study period. There was no significant difference between groups in any of the clinical impact variables. Vitek 2 results were available for reporting significantly earlier as compared to conventional testing. For the overall patient group in our hospital setting, however, this had no clinical impact.

Aged↗

PubMed2025

Novel antibodies for identification, selection, and manipulation of T cells expressing Whitlow linker-containing CARs.

BACKGROUND: The translational study of chimeric antigen receptor (CAR) T-cell function, persistence, immunophenotype, and spatial localization after infusion is crucial for understanding factors that influence clinical outcomes. However, research has been limited by a lack of optimized tools to reliably detect CAR-engineered cells. To address this, we developed a novel platform to generate monoclonal antibodies (mAbs) targeting a linker peptide incorporated in single-chain variable fragments (scFvs) of most CAR constructs. METHODS: Using recombinant proteins and scFv linker peptides as immunogens, we generated murine mAbs against the Whitlow linker peptide, capable of binding cells expressing Whitlow linker-containing CARs in both fresh and formalin-fixed paraffin-embedded (FFPE) tissues. We evaluated these antibodies in multiple in vitro translational applications relevant to CAR T-cell research and manufacturing. RESULTS: We identified five unique mAbs reactive against the Whitlow linker and characterized their binding properties and three-dimensional structural conformation. One clone was evaluated in depth, demonstrating comparable capacity to identify CAR T cells in peripheral blood relative to other methods using anti-idiotype antibodies or recombinant CAR-target proteins. In contrast to these reagents, the anti-Whitlow mAb detects cells expressing Whitlow linker-containing CARs with different antigen specificities, including those harboring the widely employed anti-CD19 FMC63-derived scFv as well as other scFvs, such as those targeting B-cell maturation antigen (BCMA) or CD33. Importantly, the anti-Whitlow mAb identified CAR T cells in situ in archival FFPE tissues, and a DNA-barcoded format enabled their spatial characterization and immunophenotyping in highly multiplexed immunohistochemistry. We also assessed the functional consequences of antibody binding on CAR T cells in vitro and demonstrated the feasibility of anti-Whitlow mAb-mediated selective enrichment of CAR-expressing T cells for potential utility in manufacturing workflows. CONCLUSIONS: Anti-Whitlow mAb clones exhibited distinct structural and functional properties that can be leveraged for multiple applications, providing versatile tools for detection, selection and manipulation of a broad range of clinical and preclinical CAR T-cell products.

Humans↗