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PubMed2004

The aging of a clinical information system.

The senescence of a clinical information system is more likely to have administrative than technical bases. Supporting this claim is a case study of one aging oncology information system. The case study is qualitative, as behooves the subject matter. Content analysis of several documents suggests that the change in job description of the data coordinator led to a workflow breakdown. Next, twenty-two individuals were interviewed. Notes from the interviews were coded, and the resulting patterns led to partial support for the workflow breakdown conjecture, refutation of the hypothesis that users disliked the character-based, human-computer interface, support of the conjecture that political rather than technical factors drive the usage patterns of the system, and evidence that 'political' activity will determine the future of the information system. A stakeholder matrix is proposed that addresses administrative concerns. Also, the issue of the uniqueness of any oncology clinical information system is linked to the plans for this legacy system.

Databases, Factual↗

PubMed2026

Detection of antibiotic heteroresistance in clinical microbiology: current and emerging methodologies.

BACKGROUND: Antibiotic heteroresistance (HR) is characterised by the coexistence of susceptible and resistant subpopulations within an apparently isogenic bacterial isolate. Because routine antimicrobial susceptibility testing (AST) primarily assesses the dominant population, HR may escape detection, potentially leading to discrepancies between laboratory susceptibility categorisation and the underlying bacterial population structure. OBJECTIVES: To provide a critical and practice-oriented evaluation of current and emerging methodologies for HR detection and to discuss their strengths, limitations, and potential for clinical implementation. SOURCES: Narrative review based on PubMed searches, complemented by screening of key reference lists and relevant EUCAST and CLSI documents. Peer-reviewed literature was prioritised. CONTENT: Phenotypic approaches, particularly population analysis profiling, remain the reference method for HR definition, but their labour-intensive workflows, long turnaround times, and limited standardisation restrict routine implementation. Alternative strategies, including modified AST assays, metabolic assays, and single-cell platforms, offer gains in speed or throughput but require broader validation. Molecular approaches such as quantitative PCR, droplet digital PCR, targeted deep sequencing, and whole-genome sequencing improve detection of minority resistance determinants. Emerging computational frameworks, including machine learning models integrating phenotypic and genomic data, represent a promising frontier for scalable HR prediction. IMPLICATIONS: Available evidence supports the clinical relevance of HR, although its association with adverse outcomes varies across bacterial species and antibiotic classes. Harmonised methodologies and clinically validated interpretive criteria are needed to support integration of HR assessment into routine diagnostics. Prospective multicentre studies and further standardisation, including engagement with EUCAST and CLSI, will be important to advance clinical implementation.

Antimicrobial resistance↗

PubMed2003

[Digital mammography].

Digital mammography is an irreversible evolution which will gradually replace analog mammography. Detector technology differs among manufacturers. Expected clinical advantages are improved diagnostic performances, improved reproducibility, dose reduction, dedicated applications (CAD), archiving and telemammography. Limiting problems are at cost, reorganization of the breast imaging unit and the medical workflow.

Breast Neoplasms↗

PubMed2026

An open-source clinical bioinformatics pipeline for real-world NGS implementation: translating genomic variants into actionable treatment strategies in oncology.

BACKGROUND: Next-Generation Sequencing (NGS) has become a cornerstone technology in clinical practice, yet its adoption presents significant challenges. Physicians and oncologists must manage vast amounts of genome-scale data and transform it into actionable insights for complex decision-making. While commercial systems exist to synthesize data from NGS experiments into clinical reports, many are hindered by limitations such as closed-source designs that restrict transparency and customization. Additionally, some fail to leverage publicly available genomic databases, missing opportunities to integrate valuable external data. Furthermore, the rigidity of many tools in accommodating diverse NGS panels limits their applicability across varied clinical scenarios. METHODS: To address these limitations, we developed OncoReport, an open-source tool that generates comprehensive reports from NGS analyses. By integrating publicly accessible databases, OncoReport provides a robust, user-friendly environment equipped with essential tools for NGS analysis. This design aims to enhance data interpretation and support informed clinical decision-making. RESULTS: Rigorous testing has demonstrated OncoReport’s effectiveness in producing detailed, actionable reports that are clear and easy to use. By automating key aspects of the workflow, the tool significantly reduces manual effort and expedites the synthesis and interpretation of NGS results, making genomic insights more accessible to clinicians. CONCLUSION: OncoReport offers a transparent, flexible, and efficient framework for clinicians to analyze and apply genomic data in patient care. By streamlining workflows and leveraging open-source principles, it empowers healthcare professionals to make informed, data-driven decisions. OncoReport is freely available at https://oncoreport.atlas.dmi.unict.it, with source code and issue tracking on GitHub: https://github.com/knowmics-lab/oncoreport .

Humans↗

PubMed2005

Datamining methodology for LC-MALDI-MS based peptide profiling.

This report will provide a brief overview of the application of data mining in proteomic peptide profiling used for medical biomarker research. Mass spectrometry based profiling of peptides and proteins is frequently used to distinguish disease from non-disease groups and to monitor and predict drug effects. It has the promising potential to enter clinical laboratories as a general purpose diagnostic tool. Data mining methodologies support biomedical science to manage the vast data sets obtained from these instrumentations. Here we will review the typical workflow of peptide profiling, together with typical data mining methodology. Mass spectrometric experiments in peptidomics raise numerous questions in the fields of signal processing, statistics, experimental design and discriminant analysis.

Animals↗

PubMed2001

Use of handheld computers as bedside information providers.

Access to clinical reference information at the point-of-care is a goal that is difficult to achieve by lack of really portable reference material. Handheld computers have matured to the point where they are powerful enough to be used as clients of a distributed knowledge system serving reference information and decision-aid applications in a highly portable form factor. We describe a pilot project launched at the Geneva University Hospital studying the use of handhelds and associated clinical applications in two internal medicine clinics. Results garnered by this study will help answer the many questions raised by the use of handhelds in medical practice, in term of cost, benefits, risk and change in workflow.

Hospitals, University↗

PubMedDate not supplied

The nursing shortage: can information technology help?

There is no doubt that the nursing shortage is a real and valid concern for the medical community. American Hospital Association President Dick Davidson reports: "America needs up to 126,000 nurses now, as well as more pharmacists, lab technicians, support staff and others. We need immediate action to help alleviate this situation" (American Hospital Association, 2001). Clinical information systems can be one of those immediate actions that can help nurses feel more confident about the care they are delivering. In addition to preventing medical errors, streamlining workflow and communications, and reducing redundant data entry, these systems can have a lasting and positive effect on overall job satisfaction, providing a significant influence on retaining our invaluable nursing resources.

Hospital Information Systems↗

PubMed2001

The socio-organizational age of artificial intelligence in medicine.

The increasing pressure on Health Care Organizations (HCOs) to ensure efficiency and cost-effectiveness, balancing quality of care and cost containment, will drive them towards a more effective management of medical knowledge derived from research findings. The relation between science and health services has until recently been too casual. The primary job of medical research has been to understand the mechanisms of disease and produce new treatments, not to worry about the effectiveness of the new treatments or their implementation. As a result many new treatments have taken years to become part of routine practice, ineffective treatments have been widely used, and medicine has been opinion rather than evidence based. This results in suboptimal care for patients. Knowledge management technology may provide effective approaches in speeding up the diffusion of innovative medical procedures whose clinical effectiveness have been proved: the most interesting one is represented by computer-based utilization of evidence-based clinical guidelines. As researchers in Artificial Intelligence in Medicine (AIM), we are committed to foster the strategic transition from opinion to evidence-based decision making. Reviews of the effectiveness of various methods of guideline dissemination show that the most predictable impact is achieved when the guideline is made accessible through computer-based and patient specific reminders that are integrated into the clinician's workflow. However, the traditional single doctor-patient relationship is being replaced by one in which the patient is managed by a team of health care professionals, each specializing in one aspect of care. Such shared care depends critically on the ability to share patient-specific information and medical knowledge easily among them. Strategically there is a need to take a more clinical process view of health care delivery and to identify the appropriate organizational and information infrastructures to support this process. Thus, the great challenge for AIM researchers is to exploit the astonishing capabilities of new technologies to disseminate their tools to benefit HCOs by assuring the conditions of knowledge management and organizational learning at the fullest extent possible. To achieve such a strategic goal, a guideline can be viewed as a model of the care process. It must be combined with an organization model of the specific HCO to build patient careflow management systems. Artificial intelligence can be extensively used to design innovative tools to support all the development stages of those systems. However, exploiting the knowledge represented in a guideline to build them requires to extend today's workflow technology by solving some challenging problems.

Artificial Intelligence↗

PubMed2002

The strategy to be "paperless" via a cost-effective filmless plan.

The group of folks assigned to the project were identified, and on April 23, 2001, an Request For Information (RFI) was released to 11 preidentified Picture Archiving Communication System (PACS) vendors. Our project was unique in 2 respects. First, there was an aggressive timeline. Second there was specific outpatient environment requirements. There was a need to move images and other patient-related data between several sites while depending heavily on the Wide Area Network (WAN) design rather than the typical Local Area Network (LAN) configuration. We learned quickly that there was not one live site, at which we could visit to observe our vision in action, nor had any solution been built to accomplish our specific objectives. The months of May, June, and July consisted of vendor meetings, RFI response reviews and, clinical and corporate visits ending on August 9, 2001 when our prime vendor of choice was selected. During this process, we identified deal breakers outlining specific needs for "go live," which is targeted for Q2 (2nd Quarter) 2002. The biggest workflow opportunity is to be paperless as well as filmless. By this we not only mean traditional RIS information but also patient documents (insurance information, physician script) as well as modality-patient-specific information. All of this information needs to be available electronically to accomplish) any patient record, any place, any time! The month of August was filled with WAN and LAN solution investigations. The solution of choice will be both cost effective and challenged to achieve 99.9% reliability. A cost-benefit analysis was performed and reviewed to better understand our return on investment. The months of September and October have been dedicated to Computerized Radiography (CR) technology. The TEAM reviewed 3 solutions, which consisted of both sit-down sessions as well as clinical site assessments. Again, "deal breaker" criteria were summarized and a solution chosen. Contract negotiations will soon conclude, and an aggressive implementation will begin!

Ambulatory Care Facilities↗

PubMed2005

Clinical research subject recruitment: the Volunteer for Vanderbilt Research Program www.volunteer.mc.vanderbilt.edu.

This article provides information concerning a novel research subject recruitment registry developed at Vanderbilt University. Project goals were (1) to provide a mechanism for lay individuals to self-enter information conveying interest in volunteering for clinical research and (2) provide tools for researchers to select and contact potential volunteers based on study-specific inclusion criteria. The registry was built and offered as an institutional resource to all university scientists conducting institutional review board-approved research. The authors present (1) a model for redesigning workflow associated with subject registration, volunteer retrieval, and subject contact; (2) details of a Web-based software application used as a focal point in designing workflow for our system; (3) descriptive statistics for volunteer and researcher use of the system during the first 32 months of operation; (4) cost estimates for the project; and (5) a set of recommendations for other medical centers wishing to adopt similar methodology.

Biomedical Research↗

PubMed2002

[Improving productivity by implementing RIS and PACS throughout the clinic: a case study].

PROBLEM: How are improvements in productivity in connection with RIS/PACS to be defined? What do they cost? To limit the problem to the relevant topics, we first describe the objectives of a radiology department and the identified bottlenecks in the workflow. How to define and assess the improvements is discussed. METHODS: The case in question for this study is the RIS/PACS project at the "Klinikum der Universität München, Campus Grosshadern". The goals of the project and its present status are reviewed. The project is not yet completed, so this is a "midterm" report. RESULTS AND DISCUSSION: We describe the status of the achieved and not yet achieved goals and of the eliminated bottlenecks. On the plus side, for example, nearly 100% of all digitally generated images (except mammogramms) are digitally archived. They are accessible to the same percentage in radiology via PACS and in the hospital via the webbased intranet image distribution system when needed. In some radiology areas, such as multislice CT, already the reporting can no longer be performed without softcopy image interpretation. However, the full elimination of hardcopy images is still not reality, since the distribution to DICOM viewers for selected requesters with demands for almost reporting quality, high cost image displays is still in the testphase. To reduce film costs, images are being printed on a high resolution paper printer in addition to the intranet distribution during this transition period. On the negative side, due to a lack of job positions in the transcription rooms, about 40% of the reports are still being handwritten by radiologists. Furthermore, the dictated and transcribed reports are usually still not available early enough in the RIS and thereby in the intranet report distribution of the hospital. Here only a speech recognition system can remedy the situation. As soon as this problem is solved and the image distribution to the DICOM viewers works routinely, the reports and the images will be accessible within minutes to maximally within some hours after the examination. CONCLUSION: The goals reached so far suffered delays due to unforeseen problems and pitfalls. Altogether, a quieter operation and workflow in radiology has already been achieved, due to less inquiries from the requestors for unfinished examinations, images and/or image copies.

Computer Systems↗

PubMed2025

The development and usability of 'The Genetics Navigator': a digital solution for adult and paediatric clinical genetics services.

Clinical genetic services address diverse genetic testing needs, but there is no comprehensive digital solution to meet this variety. We aimed to develop and test the usability of the Genetics Navigator (GN), a platform designed to enhance genetic services for paediatric and adult patients. The GN prototype was created with input from a patient and clinician advisory board, informed by prior research. Usability testing involved genetics patients (N = 14), parents of paediatric patients (N = 4), and the general public (N = 10). Participants provided feedback using the 'think aloud' method when using the platform. We used the System Usability Scale (SUS) for quantitative evaluation. Qualitative data were coded by platform section, item, and identified key areas for improvement. Building on the Genetics Adviser platform, we added video and written content for various genetic conditions and patient groups, including pre-test education, counselling, decision support, history collection, post-test result disclosure, and management. Key feedback during rounds of usability testing emphasized the need for a supportive design, seamless workflow, and engaging experience of the tool. The tool was modified to reflect the feedback, and the GN achieved an average SUS score of 87.7 ± 10.9 (N = 28), indicating above-average usability. Future research will evaluate its clinical and cost-effectiveness in a randomized trial.

Humans↗

PubMed2005

A review and a framework of handheld computer adoption in healthcare.

Wide adoption of mobile computing technology can potentially improve information access, enhance workflow, and promote evidence-based practice to make informed and effective decisions at the point of care. Handheld computers or personal digital assistants (PDAs) offer portable and unobtrusive access to clinical data and relevant information at the point of care. This article reviews the literature on issues related to adoption of PDAs in health care and barriers to PDA adoption. Studies showed that PDAs were used widely in health care providers' practice, and the level of use is expected to rise rapidly. Most care providers found PDAs to be functional and useful in areas of documentation, medical reference, and access to patient data. Major barriers to adoption were identified as usability, security concerns, and lack of technical and organizational support. PDAs offer health care practitioners advantages to enhance their clinical practice. However, better designed PDA hardware and software applications, more institutional support, seamless integration of PDA technology with hospital information systems, and satisfactory security measures are necessary to increase acceptance and wide use of PDAs in healthcare.

Access to Information↗

PubMed2026

Failure modes and effects analysis for clinical implementation of online adaptive radiotherapy: A systematic review.

BACKGROUND: The accuracy of radiotherapy is limited by anatomical variations occurring over time scales ranging from sub-seconds to days. Online Adaptive Radiotherapy (OART) addresses this by enabling daily plan adaptation based on real-time imaging. While OART offers improved dose conformity, its dynamic, time-constrained workflow introduces novel failure modes that challenge traditional quality assurance protocols. PURPOSE: This study aims to synthesize the existing literature on Failure Modes and Effects Analysis (FMEA) for OART to systematically catalog risks and identify mitigation strategies. METHODS: A systematic literature search was conducted to identify studies applying FMEA to OART workflows. Eleven studies were included, covering MR-guided (ViewRay MRIdian, Elekta Unity), CBCT-guided (Varian Ethos), and MR-enhanced C-arm linac systems. To address heterogeneity in risk scoring methodologies (e.g., TG-100 10-point scales vs. 5-point rankings), extracted failure modes were harmonized into a standardized three-tier risk classification system (Class I: Low, Class II: Intermediate, Class III: High). RESULTS: A total of 300 unique failure modes were identified, with 49.6 percent classified as high-risk (Class III). Analysis revealed that the majority of high-risk failures were concentrated in the online treatment delivery phase, specifically within human-computer interactions and anatomical contouring steps. CONCLUSIONS: This study supports the development of tailored, robust QA frameworks that prioritize human factors and process consistency to guide safe implementation in diverse clinical settings.

Humans↗

PubMed1998

The LabFlow system for workflow management in large scale biology research laboratories.

LabFlow is a workflow management system designed for large scale biology research laboratories. It provides a workflow model in which objects flow from task to task under programmatic control. The model supports parallelism, meaning that an object can flow down several paths simultaneously, and sub-workflows which can be invoked subroutine-style from a task. The system allocates tasks to Unix processes to achieve requisite levels of multiprocessing. The system uses the LabBase data management system to store workflow-state and laboratory results. LabFlow provides a Per15 object-oriented framework for defining workflows, and an engine for executing these. The software is freely available.

Artificial Intelligence↗

PubMed2002

A randomized, controlled trial of clinical information shared from another institution.

STUDY OBJECTIVE: Emergency physicians often must deliver medical care with minimal access to historical clinical information. We demonstrate the feasibility and potential value of increased access to patients' clinical information from another hospital while they are receiving care in the emergency department. METHODS: We conducted a pilot randomized, controlled trial of providing information from a large, longitudinal, computer-based patient record system of clinical data from an urban hospital to emergency physicians at either of 2 urban EDs. We randomized patients seen at either ED to have the information from the computer-based patient record system provided to their physician or to not have the information provided. We delivered information to the emergency physician both as a printed abstract and by means of online access to the computer-based patient record. We assessed charges, hospital admissions, repeat visits to EDs, and the emergency physicians' satisfaction with the information. RESULTS: Under certain assumptions, the intervention was estimated to decrease charges for ED care by approximately $26 per encounter (P =.03) at 1 hospital, but there was no effect on charges at the other hospital. This result was likely because of marked differences in the workflows and information access at these 2 EDs. We demonstrated no differences in admission rates or repeat visits to the ED. Emergency physicians identified that remembering their passwords and the time required to search for the information were significant barriers to accessing clinical information online. CONCLUSION: Our pilot study is the first to demonstrate the feasibility of sharing clinical information between different health care systems. We observed a trend toward cost savings at 1 of 2 hospitals and no differences in the quality measures we studied. Our experience underscores the difficulties inherent in studying the effects of community-wide health care interventions on cost and quality of ED care.

Adult↗

PubMed2000

[Internet technology for clinical applications in a digital radiography department].

PROBLEM: To provide an overview and to assess the clinical feasibility of Internet technology-based systems for hospital-wide image and report distribution as well as for video conferencing. METHODS: The paper describes the theoretical concept behind, the various technical approaches and the experience gained from different systems. RESULTS: Image and report distribution: Advantages include the universal availability of images and reports inside and outside hospitals; ease of use; security features; image and report integration; cost savings by reducing support and training efforts and by optimising available hardware. The main critical issues are performance and workflow integration with RIS and PACS. Video conferencing: main advantages are the standardised, software-based approach and the low investments for hard- and software. Depending on the desired usage the communication performance can be seen as inappropriate. CONCLUSION: Today, Internet technology-based systems appear to satisfy the main clinical needs in radiology. The mentioned drawbacks could be eliminated by means of modified software implementation and focused standardisation efforts. Considering the numerous advantages of these systems a further distribution can be expected for the future.

Communication↗

PubMed2025

Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.

BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs). METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation. FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae. INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies. FUNDING: None.

Humans↗