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PubMed1999

Integration, acceptance testing, and clinical operation of the Medical Information, Communication and Archive System, phase II.

The Medical Information, Communication and Archive System (MICAS) is a multivendor incremental approach to picture archiving and communications system (PACS). It is a multimodality integrated image management system that is seamlessly integrated with the radiology information system (RIS). Phase II enhancements of MICAS include a permanent archive, automated workflow, study caches, Microsoft (Redmond, WA) Windows NT diagnostic workstations with all components adhering to Digital Information Communications in Medicine (DICOM) standards. MICAS is designed as an enterprise-wide PACS to provide images and reports throughout the Strong Health healthcare network. Phase II includes the addition of a Cemax-Icon (Fremont, CA) archive, PACS broker (Mitra, Waterloo, Canada), an interface (IDX PACSlink, Burlington, VT) to the RIS (IDXrad) plus the conversion of the UNIX-based redundant array of inexpensive disks (RAID) 5 temporary archives in phase I to NT-based RAID 0 DICOM modality-specific study caches (ImageLabs, Bedford, MA). The phase I acquisition engines and workflow management software was uninstalled and the Cemax archive manager (AM) assumed these functions. The existing ImageLabs UNIX-based viewing software was enhanced and converted to an NT-based DICOM viewer. Installation of phase II hardware and software and integration with existing components began in July 1998. Phase II of MICAS demonstrates that a multivendor open-system incremental approach to PACS is feasible, cost-effective, and has significant advantages over a single-vendor implementation.

Compact Disks↗

PubMed2003

The structure of guideline recommendations: a synthesis.

We propose that recommendations in a clinical guideline can be structured either as collections of decisions that are to be applied in specific situations or as processes that specify activities that take place over time. We formalize them as "recommendation sets" consisting of either Activity Graphs that represent guideline-directed processes or Decision Maps that represent atemporal recommendations or recommendations involving decisions made at one time point. We model guideline processes as specializations of workflow processes and provide possible computational models for decision maps. We evaluate the proposed formalism by showing how various guideline-modeling methodologies, including GLIF, EON, PRODIGY3, and Medical Logic Modules can be mapped into the proposed structures. The generality of the formalism makes it a candidate for standardizing the structure of recommendations for computer-interpretable guidelines.

Decision Making, Computer-Assisted↗

PubMed2026

A rapid molecular assay for the detection of hypervirulent Klebsiella pneumoniae in the context of antimicrobial resistance surveillance.

Hypervirulent Klebsiella pneumoniae (hvKP) represents an emerging clinical and public-health concern, particularly as hypervirulence increasingly converges with multidrug resistance. Current diagnostic approaches rely on phenotypic assays, such as the string test, or on whole-genome sequencing (WGS), both of which have limitations in specificity, turnaround time, standardization, and feasibility for routine surveillance. To address this gap, we developed a multiplex real-time PCR assay targeting key hvKP-associated virulence loci, including siderophore systems, hypermucoviscosity regulators, and additional markers linked to invasive potential. The assay was evaluated on 110 K. pneumoniae clinical isolates and 9 positive blood cultures, using WGS and the string test as comparators. The molecular panel demonstrated high concordance with WGS for principal virulence determinants, correctly identifying all high-virulence (score 4) profiles, and most intermediate profiles. Against WGS, the assay yielded a sensitivity of 82% and a specificity of 73%; performance against the string test was 96% and 87%, respectively. Direct testing from blood culture pellets yielded results consistent with both WGS and DNA-based PCR for the limited number of targets detected, supporting the technical feasibility of this approach. However, broader validation is needed to confirm performance in this specimen type. Overall, this multiplex PCR assay provides a targeted molecular screening approach for the rapid identification of hvKP-associated virulence profiles. Its agreement with genomic data supports its potential utility as an accessible complement to WGS for hvKP surveillance, although further workflow optimization will be required before broader routine implementation.IMPORTANCEThe global emergence of hypervirulent and multidrug-resistant K. pneumoniae represents a major public-health threat, as the convergence of virulence and antimicrobial resistance dramatically limits therapeutic options and increases the likelihood of severe, invasive, and potentially untreatable infections. Rapid identification of essential virulence determinants is therefore critical for timely clinical management and for preventing onward transmission. However, current diagnostic approaches are either insufficiently sensitive or require substantial resources, limiting their routine use. By providing a rapid and targeted molecular assay capable of detecting the principal loci associated with hypervirulent K. pneumoniae and by demonstrating the preliminary feasibility of its use directly on blood culture pellets previously identified as Klebsiella spp. by MALDI-TOF MS, this work provides a pragmatic approach for early virulence profiling. Implementation of such assays can significantly enhance epidemiological surveillance, support tailored patient management, and reduce the spread of high-risk K. pneumoniae lineages in both community and healthcare environments.

Klebsiella pneumoniae↗

PubMed2026

Integrating Next-Generation Sequencing into von Willebrand Disease Diagnostics: Insights from the PCM-EVW-ES Multicenter Project.

Von Willebrand disease (VWD) is the most common inherited bleeding disorder, caused by quantitative or qualitative defects in von Willebrand factor (VWF). Diagnosis is challenging and requires integrating bleeding history, VWF antigen and activity measurements, FVIII assays, and specialized phenotyping. Genetic testing is increasingly recognized as a key component. Here, we review current concepts in VWD diagnostics and highlight the Spanish Clinical and Molecular Profile of von Willebrand Disease (PCM-EVW-ES) project as a model for genomics-enabled precision medicine. PCM-EVW-ES is a multicenter initiative involving 48 hospitals, centralized phenotypic testing, and next-generation sequencing of the VWF coding region, enabling definitive classification in 730 individuals with VWD to date. Harmonized recruitment criteria and standardized workflows improve subtype assignment, uncover complex genotypes, refine genotype-phenotype correlations, and facilitate the identification of asymptomatic carriers. The PCM-EVW-ES variant spectrum highlights recurrent disease-causing variants in Spain and underscores the value of coordinated national registries for variant curation. Building on these data, we propose a diagnostic algorithm in which bleeding assessment and first-line VWF/FVIII assays, combined with, early VWF molecular testing increases diagnostic accuracy and guides targeted second-line investigations to confirm and refine VWD subtype classification. We also outline persisting challenges, including the interpretation of variants of uncertain significance and patients without identifiable pathogenic VWF variants, and future directions integrating third-generation sequencing, expanded gene panels, functional studies, and artificial-intelligence-driven multiomic approaches. Together, these advances illustrate how robust multicenter studies can bridge the gap between complex diagnostics and clinical practice in VWD.

Humans↗

PubMed1997

New tools for laboratory design and management.

The clinical laboratory is changing from a place of activity based on sample analysis to an in vitro diagnostic network. To convince our team, partners, and administrators, we need new comprehensive tools to define a strategy with limited risk of failure or conflicts. Specific quality goals should be established before choosing automated tools for sample handling, analytical systems, laboratory information systems, communication systems, or advanced technologies. A system approach maps and simplifies the process, based more on a functional study than on classical disciplines. A customer-supplier approach establishes the requirements between partners either inside or outside the laboratory. The quality system must be a management tool, linking samples, tasks, information, and documents. Quantitative simulation modeling explores different automation alternatives and their impact on laboratory workflow. Finally, integration of results in interactive semirealistic simulation tools for laboratory design or reengineering can be used as communications tools to involve laboratory professionals in the change of their practice.

Chemistry, Clinical↗

PubMed2005

[KIS-RIS-PACS integration: the Marburg approach].

When describing the development of data processing at the Department of Radiology at the Philipps University of Marburg, three phases can be identified covering the areas of patient care, education, and research as well as administrative and organizational aspects. The first phase (1987-1995) was centered on radiology and characterized by the early implementation of the radiology information system (RIS) and installation of a picture archiving and communication system (PACS). The experiences gained during this phase led to intensive discussion on application-oriented information processing. The second phase (1996-2000) describes the changes in the general framework brought by Internet technology and international standards. The course was set for the future of data processing in the hospital setting. The phase ended with implementation of a clinical workplace system (KAS) as the basis for a comprehensive electronic patient record and the switch in radiology to an integrated RIS solution. The third phase (2001-2006) addressed further implementation and development of clinical data management in which both regular documentation of patient data and information processing not related to patients are optimized by making use of Intranet/Internet technology. It includes the hospital wide implementation of PACS and the forthcoming phase of information processing increasingly shaped by workflow and decision support.

Database Management Systems↗

PubMed2026

Rapid glycomic analysis of serum EVs reveals altered N-glycosylation patterns in ASD.

Objective laboratory diagnostics for autism spectrum disorder (ASD) are lacking, necessitating rapid clinical screening tools. Because serum extracellular vesicle (EV) N-glycosylation captures critical neurodevelopmental signatures, we developed a fast, biologically interpretable diagnostic strategy. EVs from ASD patients with language impairment and neurotypical controls were isolated using a rapid extra-polyethylene glycol precipitation/filtration (EPF) workflow, benchmarked against ultracentrifugation. Following MALDI-TOF/MS profiling, machine learning was re-evaluated using repeated nested cross-validation to reduce optimistic bias and potential information leakage. Among five classifiers, Random Forest (RF) showed the best overall balance across discrimination, calibration, and classification metrics. RF-based SHAP analysis provided transparent interpretation, highlighting key discriminative glycans, including H4N3S1F1, H5N5S1F1, and H3N5F1. To elucidate molecular mechanisms, we integrated public EV transcriptomic data. This revealed significant dysregulation of N-glycosylation machinery genes (e.g., MAN1A1, NEU1, OSTC, RPN2), whose expression directionally aligned with observed glycan shifts in synaptic pathways. Collectively, this rapid serum EV N-glycomic workflow, combined with leakage-controlled RF-based interpretation, provides a promising foundation for non-invasive ASD biomarker discovery and future multicenter validation.

Humans↗

PubMed1999

Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET.

BACKGROUND: Amplified DNA probes provide powerful tools for the detection of infectious diseases, cancer, and genetic diseases. Commercially available amplification systems suffer from low throughput and require decontamination schemes, significant hands-on time, and specially trained laboratory staff. Our objective was to develop a DNA probe system to overcome these limitations. METHODS: We developed a DNA probe system, the BDProbeTecTMET, based on simultaneous strand displacement amplification and real-time fluorescence detection. The system uses sealed microwells to minimize the release of amplicons to the environment. To avoid the need for specially trained labor, the system uses a simple workflow with predispensed reagent devices; a programmable, expandable-spacing pipettor; and the 96-microwell format. Amplification and detection time was 1 h, with potential throughput up to 564 patient results per shift. We tested 122 total patient specimens obtained from a family practice clinic with the BD ProbeTecET and the Abbott LCx(R) amplified system for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae. RESULTS: Based on reportable results, the BDProbeTecET results for both organisms were 100% sensitive and 100% specific relative to the LCx. CONCLUSIONS: The BDProbeTecET is an easy-to-use, high-throughput, closed amplification system for the detection of nucleic acid from C. trachomatis and N. gonorrhoeae and other organisms.

Chlamydia trachomatis↗

PubMed1999

The transition to automated practitioner order entry in a teaching hospital: the VA Puget Sound experience.

We recently installed an automated practitioner order entry system on our busiest inpatient wards and critical care units. The installation followed 20 months preparation in which we created the workstation, network, and host infrastructure, developed requisite policies, recruited personnel to support the system, and installed the software in areas where the pace of order entry was less intense. Since implementing automated order entry, we have experienced problems such as an increase in time required for practitioners to enter orders, workflow changes on inpatient units, difficulties with patient transfers, and others. Our user support system has been heavily used during the transition period. Software tailoring and enhancements designed to address these problems are planned, as is installation of the order entry system in remaining clinical units in our medical centers.

Attitude to Computers↗

PubMed2005

Proteomics: the next revolution in laboratory medicine?

BACKGROUND: The identification of specific genetic alterations and protein profiles associated with disease offers a unique opportunity to develop proteomics-based assays for early diagnosis. By identifying proteins in serum/plasma, a minimally invasive tool is used to assess the presence of disease and to monitor response to treatment and/or disease progression. The potential clinical applications of this tool are broad-based, including the diagnosis not only of cancer but also cardiovascular and neuromuscular diseases, organ transplantation associated conditions, and infertility. METHODS: A number of competing chromatographic techniques have been proposed for overcoming the complexity and labor-intensive manipulations associated with the traditional technique for proteomic analysis, which is based on two-dimensional gel electrophoretic techniques. However, mass spectrometry has now assumed a central role in most proteomic workflows, and several combinations of ionization sources, analyzers and fragmentations devices have been described and developed. RESULTS: Thanks to proteomic applications in the diagnosis of cancer, several research groups have identified proteomic patterns associated with ovarian, prostatic, colorectal and other cancers. While the sensitivity and specificity of these patterns are highly satisfactory, there are still some open questions concerning the standardization, reproducibility, and inter-laboratory agreement of these data. CONCLUSIONS: Proteomics, and, in particular, serum mass spectroscopic proteomic pattern diagnostics, is a rapid expanding field of research. The plasma proteoma has an important position at the intersection between genes and diseases, and clinical laboratories must adapt to a new era of tests based on proteomics and genomics. In the future, mass spectrometry will become an essential tool in the clinical laboratory.

Biomarkers, Tumor↗

PubMed1990

Strategies of organization and service for the critical-care laboratory.

Critical-care medicine requires rapidity of treatment decisions and clinical management. To meet the objectives of critical-care medicine, the critical-care laboratory must consider four major aspects of laboratory organization in addition to analytical responsibilities: specimen collection and delivery, training of technologists, selection of reliable instrumentation, and efficient data dissemination. One must also consider the advantages and disadvantages of centralization vs decentralization, the influence of such a laboratory on patient care and personnel needs, and the space required for optimal operation. Centralization may lead to workflow interruption and increased turnaround time (TAT); decentralization requires redundancy of instrumentation and staff but may shorten TAT. Minimal TAT is the hallmark of efficient laboratory service. We surveyed 55 laboratories in 33 hospitals and found that virtually all hospitals with 200 or more beds had a critical-care laboratory operating as a satellite of the main laboratory. We present data on actual TAT, although these were available in only eight of the 15 routine laboratories that provided emergency service and in eight of the 40 critical-care laboratories. In meeting the challenges of an increasing workload, a reduced clinical laboratory work force, and the need to reduce TAT, changes in traditional laboratory practice are mandatory. An increased reliance on whole-blood analysis, for example, should eliminate delays associated with sample preparation, reduce the potential hazards associated with centrifugation, and eliminate excess specimen handling.

Centralized Hospital Services↗

PubMed2001

Quality-control issues on high-resolution diagnostic monitors.

Previous literature indicates a need for more data collection in the area of quality control of high-resolution diagnostic monitors. Throughout acceptance testing, which began in June 2000, stability of monitor calibration was analyzed. Although image quality on all monitors was found to be acceptable upon initial acceptance testing using VeriLUM software by Image Smiths, Inc (Germantown, MD), it was determined to be unacceptable during the clinical phase of acceptance testing. High-resolution monitors were evaluated for quality assurance on a weekly basis from installation through acceptance testing and beyond. During clinical utilization determination (CUD), monitor calibration was identified as a problem and the manufacturer returned and recalibrated all workstations. From that time through final acceptance testing, high-resolution monitor calibration and monitor failure rate remained a problem. The monitor vendor then returned to the site to address these areas. Monitor defocus was still noticeable and calibration checks were increased to three times per week. White and black level drift on medium-resolution monitors had been attributed to raster size settings. Measurements of white and black level at several different size settings were taken to determine the effect of size on white and black level settings. Black level remained steady with size change. White level appeared to increase by 2.0 cd/m2 for every 0.1 inches decrease in horizontal raster size. This was determined not to be the cause of the observed brightness drift. Frequency of calibration/testing is an issue in a clinical environment. The increased frequency required at our site cannot be sustained. The medical physics division cannot provide dedicated personnel to conduct the quality-assurance testing on all monitors at this interval due to other physics commitments throughout the hospital. Monitor access is also an issue due to radiologists' need to read images. Some workstations are in use 7 AM to 11 PM daily. An appropriate monitor calibration frequency must be established during acceptance testing to ensure unacceptable drift is not masked by excessive calibration frequency. Standards for acceptable black level and white level drift also need to be determined. The monitor vendor and hospital staff agree that currently, very small printed text is an acceptable method of determining monitor blur, however, a better method of determining monitor blur is being pursued. Although monitors may show acceptable quality during initial acceptance testing, they need to show sustained quality during the clinical acceptance-testing phase. Defocus, black level, and white level are image quality concerns, which need to be evaluated during the clinical phase of acceptance testing. Image quality deficiencies can have a negative impact on patient care and raise serious medical-legal concerns. The attention to quality control required of the hospital staff needs to be realistic and not have a significant impact on radiology workflow.

Calibration↗

PubMed2026

A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics.

Adopting a safety-centric approach, this article explores how generative artificial intelligence (AI), and more specifically, foundation models for biological sequences, can exacerbate data quality issues, technical biases, and dual-use potential, particularly in critical applications such as clinical genetics, precision medicine, and pathogen engineering. This work centres on how misuse risks emerge throughout the innovation pipeline and how these intersect with the growing accessibility of generative genomic models. Particular attention is given to dual-use governance and infrastructure hardening in sequence analysis workflows. The work aims to provide scientists, regulators, and policymakers with a toolkit to discuss beneficial innovation in genomic AI while maintaining robust safeguards against harm and misuse.

Genomics↗

PubMed2026

Syndromic cholera diagnosis masks diverse causes of diarrhoeal disease in Burundi revealed by portable metagenomics.

BACKGROUND: Cholera outbreaks remain a major public-health challenge in sub-Saharan Africa, where diagnostic capacity is limited and clinical case definitions are non-specific and re ly heavily on syndromic diagnosis. Rapid identification of Vibrio cholerae is critical, yet cholera-suspected diarrhoea can have multiple infectious causes not captured by targeted diagnostics. METHODS: We evaluated a mobile, culture-independent metagenomic sequencing workflow for on-site detection of gastrointestinal pathogens directly from faecal samples in Burundi. The offline workflow combined long-read Oxford Nanopore Technologies (ONT) sequencing with rapid, laptop-based taxonomic and antimicrobial resistance (AMR) screening and was deployed across a health centre, a district hospital, and a refugee transit camp. The frontline and real-time results were verified using both conventional culturing and in-depth bioinformatic analyses. RESULTS: V. cholerae signals were only detected in a subset of suspected cholera cases, while many samples were dominated by alternative bacterial taxa, most frequently Escherichia coli. V. cholerae abundance correlated strongly with detection of the C holera T oxin P hage CTXφ, supporting differentiation between toxigenic signal and background exposure. AMR genes were detected across samples, providing early situational insight into resistance determinants among gastrointestinal bacteria. CONCLUSIONS: Mobile, offline metagenomic sequencing enables rapid frontline characterization of gastrointestinal disease, especially cholera-suspected, in resource-limited settings and complements existing diagnostics by improving etiological resolution and outbreak response.

Humans↗

PubMedDate not supplied

Lean Management and Six-Sigma yield big gains in hospital's immediate response laboratory. Quality improvement techniques save more than $400,000.

DSI Laboratories has used Lean and Six-Sigma methodologies to systematically eliminate waste and reduce variation in its hospital clinical laboratory. The net result was a savings of more than $400,000 in the first year. After mapping its process, the laboratory found that phlebotomists were submitting samples in large batches, which created an early-morning flood of specimens. Switching to single-piece workflow and distributing the workload more evenly allowed DSI to cover the same number of patients with two to three phlebotomists instead of 12. By establishing a more efficient workflow process within the laboratory, a single technologist could quickly move between stations and perform those tests that made up 80% of the work volume. New inventory management techniques reduced both excess inventory and the risk of shortages. Cost savings for the first year were: Reduced overtime spending by 60% ($78,000), Reassigned six phlebotomists for an annual savings of $160,000, 4.5 fewer technologist positions for a savings of $250,000.

Cost Savings↗

PubMed1998

Building patient workflow management systems by integrating medical and organizational knowledge.

Patient management is a distributed activity involving general practitioners, clinicians, analysts, nurses, etc. Thus an integrated Patient Workflow Management System (WfMS), based on a detailed model of both the organizational and medical knowledge, could heavily improve Health Care System's performance in terms of collaborative work and resource utilization. A set of tools was developed to improve 1) acquisition of medical knowledge represented through clinical practice Guideline, and 2) acquisition of organizational knowledge describing the work process.

Computer Simulation↗

PubMed2004

Multicentre performance evaluation of the E170 module for modular analytics.

The E170 module was evaluated at 13 sites in an international multicentre study. The objective of the study was to assess the analytical performance of 49 analytes, and to collect feedback on the system's reliability and practicability. The typical, within-run coefficients of variation (CVs) for most of the quantitative assays ranged between 1 and 2% while a range of 2-4% was achieved with the infectious disease methods. Total precision CVs were found to be within the manufacturer's expected performance ranges, demonstrating good concordance of the system's measuring channels and a high reproducibility during the 2-4-week trial period. The functional sensitivity of 11 selected assays met the clinical requirements (e.g., thyreotroponin (TSH) 0.008 mU/l, troponin T 0.02 microg/l, total prostate-specific antigen (PSA) 0.03 microg/l). The E170 showed no drift during an 8-hour period and no relevant reagent carryover. Accuracy was confirmed by ring trial experiments and method comparisons vs. Elecsys 2010. The reliability and practicability of the system's hardware and software met with, or even exceeded, the evaluator's requirements. Workflow studies showed that E170 can cover the combined workload of various routine analysers in a variety of laboratory environment. Throughput and sample processing time requirements were achieved while personnel 'hands-on-time' could be reduced.

Calibration↗

PubMed2003

Cerner Millennium: the Innsbruck experience.

OBJECTIVES: A Clinical Information System, serving more than 2,000 users was to be implemented at three hospitals of TILAK (Tiroler Landeskrankenanstalten GmbH), including the University Hospital of Innsbruck. The system was intended to integrate data from radiology, laboratory, and pathology subsystems with patient data. METHODS: Using Cerner Millennium software and Health Level 7 standards, the first stage of an Electronic Patient Record (EPR) was built. Direct data entry was facilitated using either a Microsoft Word text processor (with subsequent authentication workflow) or structured forms. An enterprise-wide scheduling module allows coordination and storage of patient appointments directly in the EPR. As required by security policy, the Cerner software regulates the varying degrees of information exchange among organizations and departments within the enterprise. RESULTS: First experiences indicate satisfactory acceptance of system functionalities. The introduction of Cerner Millennium at TILAK has achieved essential goals defined at the beginning of the project. Basic functionalities--free text documentation, standardized documentation, scheduling, and some parts of order entry--are offered in a user friendly manner. Integration with existing systems to complete the EPR has been successful using standard interfaces (HL7). CONCLUSION: TILAK concluded that it was possible to successfully implement a Clinical Information System (CIS) developed mainly for the American market in a European healthcare environment. Some adaptations and functional extensions were necessary (e.g., the discharge summary "Arztbrief"). The system had enough flexibility to meet the requirements and specifications of European healthcare processes. A key factor of success was the establishment of a basic level of understanding and communication between the software vendor and the TILAK user community.

Austria↗