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PubMedDate not supplied

Clinical dashboards: impact on workflow, care quality, and patient safety.

There is a vast array of technical data that is continuously generated within the intensive care unit environment. In addition to physiological monitors, there is information being captured by the ventilator, intravenous infusion pumps, medication dispensing units, and even the patient's bed. The ability to retrieve and synchronize data is essential for both clinical documentation and real-time problem solving for individual patients and the intensive care unit population as a whole. Technical advances that permit the integration of all relevant data into a singular display or "dashboard" may improve staff efficiency, accelerate decisions, streamline workflow processes, and reduce oversights and errors in clinical practice. Critical care nurses must coordinate all aspects of care for one or more patients. Clinical data are constantly being retrieved, documented, analyzed, and communicated to others, all within the daily routine of nursing care. In addition, many bedside monitors and devices have alarms systems that must be evaluated throughout the workday, and actions taken on the basis of the patient's condition and other data. It is obvious that the complexity within such care processes presents many potential opportunities for overlooking important details. The capability to systematically and logically link physiological monitors and other selected data sets into a cohesive dashboard system holds tremendous promise for improving care quality, patient safety, and clinical outcomes in the intensive care unit.

Computer Terminals↗
PubMed2001

Creation of a software application for the clinical radiologist.

PURPOSE: To create a software application that automates a significant portion of a clinical radiologist's work. METHODS: The daily workflow of clinical radiologists in a university-based department was analyzed, specifically looking for manual tasks that could be implemented in software. An application that a practicing radiologist would use in his daily work was created. RESULTS: By using speech recognition, reports could be created, edited, and verified immediately. Online medical reference information could be made instantly accessible. Billing data could be captured accurately and completely at report creation time. A radiologist could be alerted to important upcoming events by use of a reminder system. Reports could be delivered immediately to referring physicians using either the internet or telephone. CONCLUSIONS: It is possible to improve the productivity of busy practicing clinical radiologists by automating a large portion of their workflow and implementing it in an easily mastered software application.

Humans↗
PubMed2000

[Computer support of workflow in the hospital: concepts, technology and application].

For a variety of reasons, hospitals are developing a growing interest in changing their information systems to support patient processes in a more direct way. This means to actively deliver the tasks to be performed to the right persons at the right point in time with the necessary information and the application functions needed for performing these tasks. Process-oriented workflow technology is a very interesting candidate to achieve this goal. It offers components for the computer-based analysis, modeling, animation, coordination and monitoring of (hospital) processes. In this paper we discuss the perspectives offered by workflow-based, clinical information systems. We survey key features of today's business process modeling tools and of workflow management systems, and we show how they can be applied in the clinical domain. To illustrate the huge potential offered by workflow technology, we present results from the project "Using Workflow Management Systems for Clinical Applications". Within this project we thoroughly analyzed and redesigned core processes from the University's Women hospital and we proto-typically implemented a workflow-based application system for the support of processes from the division day clinic. Although our work shows that current workflow technology is still lacking some important features, in the long run, it may strongly influence information processing within hospitals.

Computers↗
PubMed1998

A conceptual representation of clinical and managerial guidelines: the ATREUS workflow model.

In this paper we propose a workflow conceptual model able to represent clinical and managerial activities within healthcare structures, the ATREUS model. This model uses: a) a graphical representation which models the activities and the events that activate them; b) a textual representation of information related to: a set of conditions used for the control of activity execution; the actors who undertake the activity; the resources and tools necessary for its enactment, the clinical and managerial data generated by the activity execution; c) a state diagram which allows the control of the activity execution. The model allows modularity, activity nesting and temporal flexibility using a top-down refinement of processes. This model, unlike others, makes it possible to highlight the different types of decision involved in the performance of an activity.

Hospital Administration↗
PubMedDate not supplied

Integration of a clinical community pharmacist position: emphasis on workflow design.

OBJECTIVE: To design and implement a scope of practice for a clinical pharmacist position and assess the clinical and economic impact of a Diabetes Medication Management Program in a community pharmacy setting. SETTING: Independent community pharmacy in an urban area. PRACTICE DESCRIPTION: Standard dispensing and consultative services and durable medical equipment supplies and services were offered in the pharmacy. Approximately 260 prescriptions were dispensed per 10-hour workday. PRACTICE INNOVATION: Pharmacy workflow was redesigned with workstations in which each position was occupied at all times by pharmacy technicians or pharmacists. Clinical pharmacy interventions were delivered while normal dispensing processes continued. INTERVENTIONS: A Clinical Community Pharmacist provided education and counseling to patients newly diagnosed with diabetes as well as services to patients with other chronic diseases. RESULTS: During the first 6 months of the project, 221 clinical interventions were made; 16 patients with diabetes (who had received 67 of the interventions) were enrolled in a medication management program. CONCLUSION: A Clinical Community Pharmacist in an urban setting can deliver clinical services during the normal dispensing process using an efficient workflow design.

Community Pharmacy Services↗
PubMed2026

Clinical proteomics in inborn errors of metabolism: from biomarker discovery to implementation.

INTRODUCTION: Inborn errors of metabolism (IEMs) are rare, heterogeneous disorders traditionally diagnosed through genetic testing, enzyme assays, and metabolite measurements. However, these tools often do not fully explain phenotypic variability, organ involvement, disease progression, or treatment response. Clinical proteomics provides a complementary functional layer by capturing changes in protein abundance, proteoforms, post-translational modifications (PTM), and biological pathways, offering insights beyond genotype- and metabolite-based approaches. AREAS COVERED: This review examines the role of high-resolution mass spectrometry and computational proteomics in biomarker discovery and clinical decision-making for IEMs. It focuses on their contribution to diagnosis, variant interpretation, patient stratification, and treatment monitoring. Disease-specific applications are discussed, with the strongest evidence in lysosomal storage disorders, mitochondrial diseases, congenital disorders of glycosylation, and selected neurodegenerative or renal metabolic conditions. The literature search was performed in PubMed, Scopus, Web of Science, and Google Scholar, covering peer-reviewed articles available up to 2026, with emphasis on methodological advances and translational applications in clinical proteomics for IEMs. EXPERT OPINION: Proteomics will not replace established diagnostic tools, but it can help address clinically actionable questions in selected contexts. Translation into clinical practice will require standardized workflows, multicenter validation, clinically anchored endpoints, and integration with other omics approaches.

Humans↗
PubMed2026

PheBee: A Graph-Aware System for Scalable, Traceable, and Semantic Phenotyping.

OBJECTIVES: Phenotype-driven workflows in clinical and translational research require standardized ontology-based representation, ontology-aware cohort discovery, and provenance inspection for each assertion. Existing approaches optimize either for semantic traversal or scalable batch analytics, but not both. We describe PheBee, a hybrid system that links semantic assertions to scalable evidence storage via a deterministic identifier, preserving provenance while supporting ontology-aware discovery at cohort scale. MATERIALS AND METHODS: PheBee represents phenotype assertions in a knowledge graph as ontology-linked nodes with clinical modifier context (e.g., negated, family history), and stores supporting evidence records in a scalable row-oriented evidence table for cohort-scale access. The two layers are connected by a deterministic identifier enabling stable joins across repeated ingestions without duplicating high-volume evidence in the graph. We evaluated PheBee using synthetic datasets designed to exercise end-to-end ingestion and query workflows. RESULTS: Functional evaluation validated hierarchical term expansion, qualifier-aware retrieval, duplicate-free assertion handling under re-ingestion, and privacy-conscious management of subjects shared across multiple research projects. At scale (10,000 subjects producing 12M evidence records) PheBee completed ingestion in ~30 minutes and responded to interactive queries within 6 seconds under concurrent load. DISCUSSION: PheBee exposes a unified API for ontology-aware cohort discovery with hierarchical term expansion, subject-centric retrieval of phenotypes and clinical modifiers, and evidence and provenance queries. Its data model aligns with GA4GH Phenopackets, facilitating interoperability with phenotype exchange standards. CONCLUSION: By combining ontology-aware semantics with scalable, provenance-bearing evidence storage, PheBee provides a practical open-source foundation for phenotype-driven research workflows that demand both semantic precision and cohort-scale traceability.

cohort studies↗
PubMed2026

Longitudinal Clinical, Physiological, and Molecular Profiling of Female Patients With Metastatic Cancer: Protocol and Feasibility of a Multicenter High-Definition Oncology Study.

PURPOSE: A substantial proportion of patients receiving genomically matched therapies do not achieve clinical benefit, underscoring the influence of nongenetic factors on cancer outcomes. High-Definition Oncology (HDO) proposes integrating longitudinal, multimodal patient data-spanning clinical, molecular, physiological, and behavioral domains-to enable truly individualized cancer care. This manuscript describes the HDO study design, framework, and feasibility results in women with metastatic cancer. METHODS: We initiated a prospective, multicenter observational study (HDO study; ClinicalTrials.gov identifier: NCT06590506) enrolling 300 female patients with newly diagnosed metastatic breast, lung, or colorectal cancer. Here, we report the study design, standardized workflows, prespecified feasibility criteria, and early internal pilot results. Eleven data modalities are collected longitudinally, including tumor and germline genomics, germline epigenomics, gut microbiome, blood and stool metabolomics and proteomics, exposome characterization, wearable-derived physiological monitoring, digital footprint assessment, medical imaging, and patient-reported outcomes. Standardized workflows govern clinical procedures, data acquisition, biospecimen processing, and quality control across all participating sites. RESULTS: Feasibility was evaluated in the first 30 participants (10% of planned accrual). Patients completed 100% of scheduled clinical visits, 97.4% of planned plasma collections, 80.7% of stool samples, and all tumor biopsies. Wearable devices captured activity, heart rate, sleep, and blood oxygen saturation data during 95.0%, 84.2%, 90.6%, and 70.7% of total patient-days, respectively. Biospecimens met predefined quality control metrics across all molecular modalities. Engagement with mobile applications for pain and emotion reporting exceeded 80%. CONCLUSION: The HDO study demonstrates the feasibility of comprehensive, longitudinal, multimodal data collection in women with metastatic cancer. This internal pilot establishes an integrated framework for future analyses aimed at characterizing disease trajectories, defining molecular and physiological determinants of outcomes, and developing patient-specific computational models.

Humans↗
PubMed2006

A HIPAA-compliant architecture for securing clinical images.

The Health Insurance Portability and Accountability Act (HIPAA, instituted April 2003) Security Standards mandate health institutions to protect health information against unauthorized use or disclosure. One approach to addressing this mandate is by utilizing user access control and generating audit trails of the various authorized as well as unauthorized user access of health data. Although most current clinical image systems [e.g., picture archiving and communication system (PACS)] have components that generate log files for application debugging purposes, there is a lack of methodology to obtain and synthesize the pertinent data from the large volumes of log data generated by these multiple components within a PACS. We have designed a HIPAA-compliant architecture specifically for tracking and auditing the image workflow of clinical imaging systems such as PACS. As an initial first step, we developed HIPAA-compliant auditing system (H-CAS) based on parts of this HIPAA-compliant architecture. H-CAS was implemented within a test-bed PACS simulator located in the Image Processing and Informatics lab at the University of Southern California. Evaluation scenarios were developed where different user types performed legal and illegal access of PACS image data within each of the different components in the PACS simulator. Results were based on whether the scenarios of unauthorized access were correctly identified and documented as well as on normal operational activity. Integration and implementation pitfalls were also noted and included.

California↗
PubMed2026

Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells.

Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. An updated Clinical Nanopore Cas9-Targeted Sequencing workflow is presented for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the Oxford Nanopore Technologies wf-human-variation Epi2Me workflow, including the Straglr tool to analyze base-called reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 and introduces new gene panels for ataxia, myopathy, neurodegeneration, and amyotrophic lateral sclerosis/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. In this work, the use of multiplexing, Flongle flow cells, and single-gene targeting were explored as alternatives to panel-based approaches in the Clinical Nanopore Cas9-Targeted Sequencing workflow, finding that only single-gene targeting provides compatibility and reliable performance.

Journal Article↗
PubMed2026

Digital and computational morphology in hematology: current platforms, clinical evidence, and future requirements.

INTRODUCTION: Morphologic examination of peripheral blood and bone marrow remains central to the diagnosis and classification of hematologic disorders. Conventional optical microscopy, however, is labor-intensive, dependent on operator expertise, and affected by interobserver variability. Digital morphology has developed from automated image acquisition and cell pre-classification into a broader field that includes whole-slide imaging, remote review, quantitative morphometry, and artificial intelligence-based analysis. CONTENT: This review examines current applications of digital morphology in peripheral blood, bone marrow aspirates, malaria detection, and body-fluid analysis. Commercial platforms are evaluated with particular attention to the distinction between raw automated pre-classification, expert digital post-classification, and comparison with independent optical microscopy. Digital systems generally perform well for common mature leukocyte populations but remain less reliable for rare or diagnostically critical cells, including blasts, abnormal lymphoid cells, plasma cells, and intermediate maturation stages. Research systems increasingly extend analysis from individual-cell classification to whole-slide, specimen-level, and patient-level assessment. SUMMARY: Digital morphology can improve standardization, image traceability, remote consultation, education, proficiency testing, quality assurance, and selected aspects of laboratory workflow. Its clinical value depends on appropriate validation, transparent reporting of reference methods, recognition of algorithm-specific failure modes, and clearly defined criteria for expert review and conventional microscopy. Human expertise remains essential not only for validating results but also for adapting cell taxonomies and interpretive rules to evolving classifications of hematologic diseases. OUTLOOK: Future progress will require representative multicenter datasets, harmonized morphologic terminology, external validation, interoperability with laboratory information systems, and continuous monitoring after software or hardware updates. Integration of morphology with quantitative hematology, flow cytometry, cytogenetics, genomics, and clinical data may support more comprehensive computational diagnosis. Digital platforms may also broaden access to specialist expertise, training, and quality programs in resource-limited institutions and regions, provided that infrastructure, governance, and professional competency are adequately supported.

artificial intelligence↗
PubMed2026

Whole-Exome Sequencing in a Consanguinity-Enriched South Indian Retinitis Pigmentosa Cohort: Diagnostic Yield and Molecular Spectrum.

PURPOSE: To determine the molecular diagnostic yield, variant spectrum, inheritance architecture, and influence of consanguinity on whole-exome sequencing outcomes in a South Indian retinitis pigmentosa (RP) cohort. DESIGN: Prospective, registry-based cohort study. SUBJECTS: A total of 113 affected participants were enrolled through the Aravind Registry for Inherited Diseases of the Eye, including 109 unrelated probands and 4 affected relatives from already represented families. Primary analyses were restricted to the 109 unrelated probands. METHODS: Whole-exome sequencing was performed using a clinical exome workflow. Variants were interpreted using American College of Medical Genetics and Genomics/Association for Molecular Pathology criteria and cases were categorized as solved, possibly solved, inconclusive, or unsolved using prespecified inheritance-aware rules. MAIN OUTCOME MEASURES: Molecular diagnostic yield, distribution of implicated genes and variant classes, inheritance architecture, and diagnostic yield stratified by consanguinity status. RESULTS: Among the 109 unrelated probands, mean age at testing was 39.3 ± 14.1 years and 58.7% were male. Whole-exome sequencing identified 186 distinct rare variants across 92 inherited retinal disease genes, including 26 pathogenic and 33 likely pathogenic variants. A molecular diagnosis was established in 50 of 109 probands (45.9%), including 42 solved and 8 possibly solved cases; 45 (41.3%) were inconclusive and 14 (12.8%) remained unsolved, including 4 (3.7%) in whom no candidate variant was identified. EYS, USH2A, and ADGRV1 were the most frequently implicated genes. Autosomal recessive (AR) disease predominated (44/50, 88.0%). Consanguineous AR cases were exclusively homozygous (17/17); notably, 68.0% of nonconsanguineous AR cases were also homozygous (P = 0.013). Diagnostic yield was higher in consanguineous probands (51.4% vs. 41.7%), without reaching significance. Recurrent alleles included an established South Asian founder variant (MFSD8 c.1361T>C) and candidate founder alleles in EYS (c.4321C>T) and ADGRV1 (c.14329C>T). CONCLUSIONS: Whole-exome sequencing established a molecular diagnosis in nearly half of this South Indian RP cohort and revealed a predominantly recessive, homozygosity-enriched architecture shaped by consanguinity. These findings define a region-specific variant landscape to support clinical interpretation, genetic counseling, and future trial enrollment in this underrepresented population. FINANCIAL DISCLOSURES: The authors have no proprietary or commercial interest in any materials discussed in this article.

Consanguinity↗
PubMed2005

Bedside, classroom and bench: collaborative strategies to generate evidence-based knowledge for nursing practice.

The rise of evidence-base practice (EBP) as a standard for care delivery is rapidly emerging as a global phenomenon that is transcending political, economic and geographic boundaries. Evidence-based nursing (EBN) addresses the growing body of nursing knowledge supported by different levels of evidence for best practices in nursing care. Across all health care, including nursing, we face the challenge of how to most effectively close the gap between what is known and what is practiced. There is extensive literature on the barriers and difficulties of translating research findings into practical application. While the literature refers to this challenge as the "Bench to Bedside" lag, this paper presents three collaborative strategies that aim to minimize this gap. The Bedside strategy proposes to use the data generated from care delivery and captured in the massive data repositories of electronic health record (EHR) systems as empirical evidence that can be analysed to discover and then inform best practice. In the Classroom strategy, we present a description for how evidence-based nursing knowledge is taught in a baccalaureate nursing program. And finally, the Bench strategy describes applied informatics in converting paper-based EBN protocols into the workflow of clinical information systems. Protocols are translated into reference and executable knowledge with the goal of placing the latest scientific knowledge at the fingertips of front line clinicians. In all three strategies, information technology (IT) is presented as the underlying tool that makes this rapid translation of nursing knowledge into practice and education feasible.

Cooperative Behavior↗
PubMed2026

Identification of a G-quadruplex-forming cell-free DNA fragment as a biomarker for the precise diagnosis of hepatocellular carcinoma.

Early detection of hepatocellular carcinoma (HCC) remains challenging, as the currently recommended surveillance strategy based on ultrasound combined with alpha-fetoprotein (AFP) is limited by suboptimal sensitivity and accessibility. Cell-free DNA (cfDNA) provides a minimally invasive avenue for cancer detection. However, most existing cfDNA-based approaches either perform unreliably in low-input samples or require analytically complex workflows. Here, we systematically profiled serum cfDNA from individuals with HCC and without HCC and identified a high-abundance tumor-associated single cfDNA fragment at the FAM230F genomic region. Integrative analysis of liver assay for transposase-accessible chromatin with sequencing (ATAC-seq) data revealed consistent tumor-specific chromatin accessibility at this locus, suggesting a tumor-derived origin. Structural characterization further demonstrated enrichment of G-quadruplex (G4) features within the target sequence, which may increase resistance to serum nuclease degradation and promote its preferential retention in circulation. Based on these properties, we established a qPCR-based detection workflow with clinical accessibility. In a validation cohort independent of the discovery cohort, a ΔC t cutoff of 2 was selected by maximizing the Youden index within the same cohort. The assay showed a sensitivity of 94.5% and a specificity of 90.5% for distinguishing HCC from non-HCC. Collectively, our study identifies FAM230F as a structurally stable tumor-associated cfDNA fragment and establishes a simple and scalable qPCR-based assay for HCC detection, providing a practical framework for translating cfDNA fragment analysis into clinical biomarkers.

Journal Article↗
PubMed2006

Thorough planning and full participation by pharmacists is key to MOE/MAR success.

The successful implementation of the Medication Order Entry/Medication Administration Record project was dependent on the Pharmacy department working collaboratively with many other stakeholders in the organization. To do this, the Pharmacy department faced numerous technical, staffing, workflow and clinical practice challenges during the design and implementation of MOE/ MAR.

Diffusion of Innovation↗
PubMed2006

Managing the life cycle of electronic clinical documents.

OBJECTIVE: To develop a model of the life cycle of clinical documents from inception to use in a person's medical record, including workflow requirements from clinical practice, local policy, and regulation. DESIGN: We propose a model for the life cycle of clinical documents as a framework for research on documentation within electronic medical record (EMR) systems. Our proposed model includes three axes: the stages of the document, the roles of those involved with the document, and the actions those involved may take on the document at each stage. The model includes the rules to describe who (in what role) can perform what actions on the document, and at what stages they can perform them. Rules are derived from needs of clinicians, and requirements of hospital bylaws and regulators. RESULTS: Our model encompasses current practices for paper medical records and workflow in some EMR systems. Commercial EMR systems include methods for implementing document workflow rules. Workflow rules that are part of this model mirror functionality in the Department of Veterans Affairs (VA) EMR system where the Authorization/ Subscription Utility permits document life cycle rules to be written in English-like fashion. CONCLUSIONS: Creating a model of the life cycle of clinical documents serves as a framework for discussion of document workflow, how rules governing workflow can be implemented in EMR systems, and future research of electronic documentation.

Documentation↗
PubMedDate not supplied

Why we don't come: patient perceptions on no-shows.

PURPOSE: Patients who schedule clinic appointments and fail to keep them have a negative impact on the workflow of a clinic in many ways. This study was conducted to identify the reasons patients in an urban family practice setting give for not keeping scheduled appointments. METHODS: Semistructured interviews were conducted with 34 adult patients coming to the clinic for outpatient care. Interviews were audiotaped and transcribed verbatim. A multidisciplinary team used an immersion-crystallization organizing style to analyze the content of the qualitative interviews individually and in team meetings. RESULTS: Participants identified 3 types of issues related to missing appointments without notifying the clinic staff: emotions, perceived disrespect, and not understanding the scheduling system. Although they discussed logistical issues of appointment keeping, participants did not identify these issues as key reasons for nonattendance. Appointment making among these participants was driven by immediate symptoms and a desire for self-care. At the same time, many of these participants experienced anticipatory fear and anxiety about both procedures and bad news. Participants did not feel obligated to keep a scheduled appointment in part because they felt disrespected by the health care system. The effect of this feeling was compounded by participants' lack of understanding of the scheduling system. CONCLUSIONS: The results of this study suggest that reducing no-show rates among patients who sometimes attend might be addressed by reviewing waiting times and participants' perspectives of personal respect.

Adult↗