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Plasma cholesterol levels of patients attending a heart risk evaluation clinic were measured both in the clinic at the time of attendance, and later in a reference laboratory. The workflow of evaluation clinics may be improved, and patient satisfaction enhanced, by in situ measurement, since more than 60% of patients can be given a complete risk score at the time of attendance.
Clinical information systems depend on close integration to workflow for success. We describe a method for user-driven design that guided our development of a computerized rounding and sign-out system. The resulting system supported clinical workflow sufficiently well that it spontaneously attracted new users, required no training, and is currently used by 95% of the house staff at two academic medical centers.
We present here a framework of core components of an ambulatory care computing environment, based on clinical and functional needs and workflow scenarios. We have established this framework through the use of two study devices: a vision of the clinical office of the future, and a survey of possible computer applications, both designed to help clinicians and practice directors communicate their information needs to systems designers. Clinicians prioritize applications based on strategic and practice goals: support for clinical users' workflow, improved quality of care, reduced cost of care, and the ability to measure performance and status. By reorganizing the needed functionality from a clinical viewpoint into a technical viewpoint, we are able to identify core information components for systems design. Based on this analysis, information needs in the ambulatory environment can be divided into five primary functions: patient data retrieval, documentation, communication, knowledge resources, and aggregate reporting. Three other fundamental processes--knowledge-based interventions, information integration, and confidentiality--run through all of these front-line functions. Component applications and data structures built with this framework in mind will afford a maximum combination of functionality and flexibility to handle future changes in the clinical environment.
This paper refers to a project for development and optimization of a clinical pathway for the Lumbar Nerve Root Compression Syndrome. A special focus is taken on computer support for pathway development and implementation. An innovative combination of "rapid prototyping" of a workflow model and a 2 level approach using round robin methods in a large group and individual semi-structured interviews is presented. The method focuses on process optimization instead of process modeling and concentrates on areas of the workflow which may be optimized. Critical parts of the optimized clinical workflow have been implemented inside a commercial electronic patient record system.
Metallo-beta-lactamases (MBLs) have been increasingly recognized from clinical isolates worldwide, but the laboratory detection of these strains is not well defined. We report a study that developed an EDTA disk screen test and a molecular diagnostic assay for the detection of MBL-producing Pseudomonas aeruginosa. Using NCCLS disk methodology, inhibition zone diameters were determined in tests with imipenem (IPM) and meropenem (MEM) disks alone and in combination with 930 microg of EDTA. This test was compared with the MBL Etest. The duplex PCR assay showed 100% sensitivity and specificity for detecting MBL-producing control strains. Of the 241 clinical strains of IPM-nonsusceptible P. aeruginosa from the Calgary Health Region isolated from 2002 to 2004, 110/241 (46%) were MBL positive using phenotypic methods while 107/241 (45%) were PCR positive for MBL genes: 103/241 (43%) for bla(VIM) and 4/241 (2%) for bla(IMP). The EDTA disk screen test using MEM showed 100% sensitivity and 97% specificity for detecting MBLs in control and clinical strains. The EDTA disk screen test is simple to perform and to interpret and can easily be introduced into the workflow of a clinical laboratory. We recommend that all IPM-nonsusceptible P. aeruginosa isolates be routinely screened for MBL production using the EDTA disk screen test and that PCR confirmation be performed at a regional laboratory.
Dual RNA-sequencing (dual RNA-seq) holds significant promise for deciphering bacterial virulence mechanisms during systemic infections. However, its application in sepsis research is hindered by technical challenges, including a low bacterial burden in blood and limited sample volumes and RNA yield from vulnerable populations, such as neonates. We developed an optimized protocol [dual RNA isolation from blood (DRIB)] for simultaneous stabilization, isolation and purification of high-quality host leukocyte and bacterial RNA from low-volume whole blood samples (0.5 ml). This protocol is compatible with clinical sample collection workflows and high-throughput RNA sequencing. The feasibility of DRIB for dual RNA-seq was validated using a pilot cohort of clinical adult sepsis samples, enabling the investigation of host-bacterial gene expression during sepsis. The DRIB protocol yielded 2.10-6.91 µg of total RNA per clinical sample in our pilot cohort. Dual-species ribosomal RNA (rRNA) depletion and RNA-seq generated 16.6-24.8 million filtered reads per sample, with 63±7% of reads uniquely mapped to host or bacterial sequences. Host genes accounted for 51-68% (8.4-10.9 million) reads, while 0.5-6.7% (79,496-789,808 reads) mapped to bacterial genomes. Bioinformatic analysis revealed that both shared and individual transcriptional patterns were identified in host and bacterial responses, including pathways related to immune metabolism and metal-ion binding. Our optimized DRIB protocol and RNA-seq pipeline effectively captured both host and bacterial RNA transcription in clinical sepsis samples. Expanding this approach to larger cohorts and varying disease timepoints will provide crucial new insights into host-bacterial gene co-expression dynamics in sepsis progression and outcomes.
Increasingly, health care organizations are considering moving to Computer Based Patient Records (CPR), a trend driven by managed care and capitated payments. Central to the change is recognition of the need for community based and clinically relevant information systems that span the care continuum. Thus, Aurora Health Care chose to start their CPR effort in the ambulatory setting as the focus of health care delivery in the evolving paradigm. This paper describes computerization of the ambulatory record in a 45 physician clinic and associated workflow redesign. Months were spent in the processes of: current state documentation and analysis, future state design, detail system design, and workflow reengineering. There was substantial impact on nursing care delivery with computer system interaction at the point of care in the exam room. Access to clinically relevant longitudinal data was found key to the implementation and evaluation of Care Management strategies.
As the focus of medicine moves from acute episodic care in the hospital to chronic disease management in outpatients, the primary care physician will play an increasingly important role in the coordination of patient care activities. Traditional outpatient informatics systems have largely focused on the workflow during the clinical encounter. Many tasks, including management of test results,coordination of subspecialty referrals and communication between patients and the practice,remain unsupported. When these tasks are not performed well, quality of care, patient safety and satisfaction may suffer. To address these issues ,Partners Healthcare in Boston, MA has recently developed several applications to address these issues. This demonstration will showcase 3 of these new applications: i) Results Manager, ii) Referrals Manager and iii) Patient Gateway. All interoperate with a browser-based electronic medical record already used by over 500 primary care physicians at Partners Healthcare.
The clinical trial has to be rigidly followed because it identifies a uniform clinical behaviour, which has to be adopted by the different physicians carrying out the test. The life cycle of the clinical trial is therefore based on a planning and definition phase, a next experimental phase connected with its diffusion to the involved centres and finally an evaluation phase of the results. An information system, which supports the users in the different phases of the clinical trial life cycle, has to take into account the different characteristics of each phase. The aim of this paper is to illustrate the role of WF technology as a component of an information system which supports the life cycle of a clinical trial also on the basis of the experience of the Italian Group for Haematological Disease of Adults (GIMEMA).
PURPOSE: Prior authorization (PA) for exome or genome sequencing is a time-consuming process that impedes timely rare disease diagnosis. Large language model-based browser agents offer potential for automating these workflows, but their clinical reliability remain uncharacterized. METHODS: We developed a sandbox compromising a simulated ES/GS PA submission payer portal and a synthetic EHR containing 836 patient records spanning compliant profiles and deficient profiles with different types of issues. Gemini 3 Pro, Gemini 3 Flash, and Claude Opus 4.5 were evaluated on task completion rate, form completion accuracy, and appropriate withholding for deficient profiles. RESULTS: Larger models achieved much higher task completion rates (Gemini 3 Pro 95.45%, Claude Opus 4.5 93.67%) compared to Gemini 3 Flash (56.05%), but nearly universally failed to withhold submission for deficient profiles whereas Gemini 3 Flash ironically demonstrated superior withholding performance (17.33%). In a non-agentic setting, Gemini 3 Pro correctly identified 91% of the issues in deficient profiles, indicating that withholding failure is attributable to the browser interaction rather than the model's reasoning limitations. CONCLUSION: Current LLM-based browser agents exhibit a systematic bias towards form submission that poses risks in PA workflows. A modular, multi-agent architecture with human supervision is necessary for a safe clinical deployment.
BACKGROUND: The Architect ci8200 is an integrated serum analyzer for photometric, electrochemical and immunological assays. Several assays of each category and the workflow performance of the system were compared with established laboratory procedures in two laboratories. METHODS: Measurements were compared with the ELECSYS 2010 (Roche Diagnostics) for CEA, PSA, FPSA, AFP, folate, vitamin B12, with the CENTAUR (Bayer) for TSH, T4, FT4, FSH and Estradiol, with the LIAISON (DiaSorin) for TSH, FT4 and FT3, with the Behring Nephelometer BN II (Dade-Behring) for ferritin, and with the INTEGRA 800 (Roche Diagnostics), and the AU640 (Olympus) for clinical chemistry assays. Workflow studies were performed to compare times of analysis required for defined analytical workloads. RESULTS: The coefficients of variation (CVs) for within-run imprecision were between 3% and 6% for CEA, PSA, FPSA, AFP and ferritin, and between 3% and 11% for TSH, FT4, FT3, folate and vitamin B12. The CVs for day-to-day imprecision for immunoassays were between 3% and 10%, except for vitamin B12 (CVs 11-13%) and FT4 (CV 10% -13%). For clinical chemistry tests corresponding CVs for within-run imprecision were < 1%, except for HDL, triglyceride, creatinine, ALT, LD and lipase (CVs<2%) and bicarbonate (CV 3%-6%) and magnesium (CV < 3%). The CVs for day-to-day imprecision for clinical chemistry tests were < 1%, except for sodium, CO(2), magnesium, phosphorus, glucose, uric acid, HDL, triglyceride, ALT, AST CK, lipase with CVs < 6% and for CO(2)<11%. Dilutional linearity testing of seven immunoassays and five clinical chemistry analytes resulted in recovery rates of 90-110%. Correlation studies with 15 immunoassays and 25 clinical chemistry tests showed acceptable agreements with established methods. Work flow analyses demonstrated a net gain in time of analysis up to 109 min depending on the size of the sample batch analyzed with the Architect ci8200 as the main analyzer as compared to the currently installed routine laboratory equipment. Median turn-around times were 7 and 30 min for chemistry assays and immunoassays, respectively, when ordered as STAT analyses, and 18 min when chemistry assays were ordered as routine determinations. CONCLUSIONS: Assays on the Architect ci8200 performed well, fulfilling quality control requirements as defined for instance by German quality control guidelines (RiliBAK). Method comparisons showed acceptable agreements with established assays. Workflow studies using the Architect ci8200 documented shorter times of analyses as compared with the conventionally established laboratory routine demonstrating the potential of integrated chemistry/immunoassay analyzers to provide faster and more efficient performance.
Electronic data capture helps improving the quality of clinical research; mainly yielding a more reliable data collection process, but also introducing new resources for controlling the execution of clinical trials and facilitating the monitoring tasks. The protocol can be implemented rather than followed, and tools are at hand to help minimising the human error. The principal difficulty in the use of the electronic data capture lays in a more complex set up. This forces the adaptation of the people involved in the execution of clinical trials to a different workflow. In the future, most of the clinical research will use electronic data capture systems, and the paper shall be left for a few particular cases.
This project provides educational support for students enrolled in a family practice clerkship by supplying PDA-based clinical references and tools to collect information about the patients they see and the seminars they attend. Each student is supplied with a Handspring Visor Deluxe to use during the clerkship. Supplied software includes a clinical reference (Five Minute Clinical Consult) and Lexidrugs drug reference and a medical calculator. The data collection software consists of a patient log for recording simple demographic and diagnostic information about each patient seen during the clerkship, a seminar evaluation module for recording student feedback about each didactic presentation during the course, and an evaluation form where they students supply their reactions to the use of the Visor. Despite encountering a number of problems, the devices appear to be beneficial tools. The applications provide useful references for students who do not have access to the resources of the University in their family medicine clerkship. They also provide an improved, though not perfect, means to capture data regarding patient encounters and course evaluations. However, the challenge remains to better integrate the PDA with the student s workflow in the clinic.
During the last decade, studies have shown the benefits of using clinical guidelines in the practice of medicine. Although the importance of these guidelines is widely recognized, health care organizations typically pay more attention to guideline development than to guideline implementation for routine use in daily care. However, studies have shown that clinicians are often not familiar with written guidelines and do not apply them appropriately during the actual care process. Implementing guidelines in computer-based decision support systems promises to improve the acceptance and application of guidelines in daily practice because the actions and observations of health care workers are monitored and advice is generated whenever a guideline is not followed. Such implementations are increasingly applied in diverse areas such as policy development, utilization management, education, clinical trials, and workflow facilitation. Many parties are developing computer-based guidelines as well as decision support systems that incorporate these guidelines. This paper reviews generic approaches for developing and implementing computer-based guidelines that facilitate decision support. It addresses guideline representation, acquisition, verification and execution aspects. The paper describes five approaches (the Arden Syntax, GuideLine Interchange Format (GLIF), PROforma, Asbru and EON), after the approaches are compared and discussed.
Recently, studies have shown the benefits of using clinical guidelines in the practice of medicine. Computer-based clinical guidelines are increasingly applied in diverse areas such as policy development, utilization management, education, conduct of clinical trials, and workflow facilitation. This paper discusses some of the representations suggested in literature, discusses their weak and strong points, and demonstrates and discusses a new approach that extends earlier developed formalisms by combining primitives, ontologies and the use of problem-solving methods (PSMs). The approach is supported by a framework that facilitates the entire guideline authoring process. The paper demonstrates this framework and presents examples of guidelines, PSMs and systems that were developed by means of this approach. The overall goal of this approach is to improve the acceptance of shareable guidelines and decision support systems in daily care by facilitating the guideline acquisition and execution phases.
PURPOSE: Reanalysis of exome sequencing (ES) data increases diagnostic utility; however, there is no consensus on when and under what circumstances reanalysis should occur. Requesting and performing ES reanalysis burdens both clinical and laboratory workflows. Maximizing the potential for reclassification is essential. Here, we describe the impact of a laboratory-driven proactive reanalysis process that triggers reanalysis when new evidence is identified. METHODS: We reviewed reanalysis outcomes of an ES cohort. Reanalysis events were categorized based on initiating factors (laboratory-driven proactive, family studies, and clinician-initiated). Laboratory-driven proactive reclassifications are prompted by systematic review of new scientific data. Outcomes were evaluated by initiating factors, reclassification types, evidence used, and time since original report. RESULTS: Overall, 23% of cases underwent at least 1 reanalysis, with 35% of reanalyses resulting in reclassification. There was a 4% increase in diagnostic yield, including 5% of initially unsolved ES receiving diagnostic reports. Diagnostic reclassifications rates were significantly higher for laboratory-driven proactive reanalyses (54%; P < .0001) than family studies (18%) and clinician-initiated reanalyses (4%). New gene-disease relationships were the most efficacious evidence source. Laboratory-driven proactive reclassifications occurred steadily over time. CONCLUSION: Laboratory-driven proactive reanalysis effectively provides more diagnostic reclassifications compared with clinician-initiated reanalysis. Laboratories should curate and integrate emerging evidence into ES reanalysis.
SUMMARY: DNAvi is a Python-based tool for rapid grouped analysis and visualization of cell-free DNA fragment size profiles directly from electrophoresis data, overcoming the need for sequencing in basic fragmentomic screenings. It enables normalization, statistical comparison, and publication-ready plotting of multiple samples, supporting quality control and exploratory fragmentomics in clinical and research workflows. AVAILABILITY AND IMPLEMENTATION: DNAvi is implemented in Python and freely available on GitHub at https://github.com/anjahess/DNAvi under a GNU General Public License v3.0, along with source code, documentation, and examples. An archived version is available under https://doi.org/10.5281/zenodo.18401705.
BACKGROUND: Inherited variants in the LDL (low-density lipoprotein) receptor (LDLR) gene are the most common cause of familial hypercholesterolemia, significantly increasing coronary artery disease risk. Early identification of pathogenic LDLR variants enables prompt lipid-lowering therapy and cascade testing of at-risk relatives; however, most LDLR variants observed in the population have uncertain or absent clinical classifications, leaving many patients without actionable information. METHODS: We developed the first activity-normalized prime editing screening pipeline to measure the impact of 5184 LDLR coding variants on LDL-cholesterol (LDL-C) uptake. Each prime editing guide RNA is paired with a genotypic outcome reporter to correct for variable editing efficiency, overcoming a key limitation of previous pooled genome editing screens. A statistical framework further improves variant effect estimates by jointly analyzing all missense variants at each amino acid position. RESULTS: We show that prime editing of the reporter construct correlates with endogenous variant installation frequency, validating the activity normalization approach. The resulting scores capture a continuous spectrum of functional effects, robustly separate pathogenic versus benign ClinVar variants, and show concordance with LDL-C levels in UK Biobank participants. We calibrate functional evidence strengths to the ACMG/AMP variant interpretation framework, enabling integration into a clinical variant classification workflow. By combining functional, computational, population, and contextual evidence, 322 of 434 LDLR variants currently classified as variants of uncertain significance, conflicting, or absent from ClinVar appear to meet evidence thresholds for reclassification and can be prioritized for expert review, substantially expanding the pool of actionable variant classifications. The screen also reveals a cluster of gain-of-function variants in LDLR class A repeat 5, at least some of which enhance LDL-C uptake through increased apolipoprotein B interaction, with implications for therapeutic genome editing. Last, prime editing uniquely detects splice-altering coding variants missed by cDNA-based screens and pathogenicity predictors, revealing an advantage of endogenous variant installation. CONCLUSIONS: Altogether, activity-normalized prime editing provides a scalable framework for LDLR variant classification that substantially expands the proportion of variants with evidence for genetic diagnosis and reveals novel biology with therapeutic relevance.