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PubMed1999

Workflow analysis and evidence-based medicine: towards integration of knowledge-based functions in hospital information systems.

The large extent and complexity of scientific evidence described in the concept of evidence-based medicine often overwhelms clinicians who want to apply best external evidence. Hospital Information Systems usually do not provide knowledge-based functions to support context-sensitive linking to external information sources. Knowledge-based components need specific data, which must be entered manually and should be well adapted to clinical environment to be accepted by clinicians. This paper describes a workflow-based approach to understand and visualize clinical reality as a preliminary to designing software applications, and possible starting points for further software development.

Artificial Intelligence↗
PubMed2000

Multicentre research and the WISECARE experience. Workflow Information Systems for European Nursing Care.

The benefits of collaborative research are becoming recognized increasingly within the profession of nursing due to the associated increased likelihood of funding, variety of practice settings and increased access to resources that collaboration brings. While such benefits have made collaborative research one of the most desirable strategies for achieving the goals of research, the potential problems of language and communication, culturally sensitive instruments, access to subjects, availability of technology and lack of research resources have complicated collaborative international research initiatives. Review of the literature, although encouraging such initiatives, does little to provide information regarding the processes involved in multinational collaboration or the associated advantages and disadvantages to guide those embarking on such large scale, multinational, cross-cultural studies. The diverse meanings of collaboration within research initiatives further hamper this understanding. Positive definitions focus on aspects such as sharing expertise, making a valuable contribution to the research and ultimately shared ownership of the accomplishments of the research. One such research project led by nurses was the WISECARE project. WISECARE (Workflow Information Systems for European Nursing Care) was funded by the European Commission and aimed to improve cancer nursing practice and ultimately patient outcomes through the integration and utilization of state of the art information technology. Such a project was developed as a result of nursing's apparent invisibility within health care delivery and the problems experienced by nurses in articulating their worth within an increasingly cost-conscious health care system. Oncology care was selected as the domain for the project not only because this speciality of nursing already has an established network of nurses throughout Europe in the European Oncology Nursing Society (EONS) but also because the practice of cancer nursing encompasses all aspects of nursing care. This paper will address the advantages and disadvantages associated with collaboration, using the WISECARE project as an example.

Communication Barriers↗
PubMed2003

Soarian--workflow management applied for health care.

OBJECTIVES: To describe and comment on functionality and architecture of the software product Soarian developed by Siemens, to identify key differentiators to related products, and to comment on predecessor systems and beta versions. This has been done in the framework of a conference on health information systems of the IMIA. METHODS: Analyzing existing literature. Site visit of a predecessor system at Haukeland Sykehus, Bergen. Pilot of a beta version at the Erlangen University Medical Center, elaborating on major characteristics in discussion rounds. RESULTS: Soarian is a functional comprehensive, clinically oriented software product to support health care processes and to be used for health care professional workstations. It is a software product, designed and written completely new. Three major key differentiators were identified in comparison to related software products: Soarian's workflow engine, its embedded analytics, and its 'smart' user interface. The targeted reduced installation time is stated to be 12 months or less. CONCLUSIONS: Soarian has good chances to become one of the major software products for health care professional workstations in the international market to support patient-centered, shared care. Its global design may help to better support and maintain national or language specific versions. The first installations of Soarian will be critical, as they will show how the system will be accepted. To use such software products efficiently, organizational aspects within hospitals as well as between health care institutions have to be considered, e.g. strategic IT planning.

Computer Systems↗
PubMed2003

Workflow and cost analysis on MODULAR ANALYTICS.

Four stand-alone analyzers in a centralized laboratory were replaced by two modular analytical systems processing 45 methods of the general chemistry and specific protein segment. This consolidation led to a reduction of the daily workflow and operational costs. The cost saving with 1.3 million reported results per year was 53,000 Euro, which can be assessed as an important contribution to cost reduction in the health care system.

Clinical Laboratory Techniques↗
PubMed1994

Towards effective implementation of a pediatric asthma guideline: integration of decision support and clinical workflow support.

Successful local implementation of national guideline recommendations requires attention to factors that promote clinician compliance. Design of a computerized system is described that will implement recommendations from a recently published guideline for outpatient management of childhood asthma exacerbations. Logical analysis of the guideline shows that it is incomplete and contains several ambiguities that must be addressed before the guideline can be operationalized. Once the user-audience is defined guideline decision points are examined and a structured data entry system is devised. Support of clinicians' workflow is provided by an integrated capability for encounter documentation, dosage calculation, and prescription-writing. A pen-based, graphical interface represents an appropriate platform for implementation of the system because of its ease of use and portability.

Asthma↗
PubMed1995

Enhancement of clinician workflow with computer order entry.

Physician-operated order entry systems can bring great benefits to an institution. Such systems can improve the consistency, accuracy, safety, and cost-effectiveness of orders. When building or selecting order entry for an institution, consideration must be given to the many different scenarios in which orders are written and communicated. Transfer, post-op, pre-admission and discharge orders have different communication requirements from standard inpatient orders. In certain services, orders from a very limited set (such as warfarin orders) must be written frequently for a large number of patients. Intensive-care patients, chemotherapy patients, and others have particular requirements for ordering. A computerized order entry system should respond to these requirements in order to promote correct and efficient ordering. We present a number of these issues, their specific requirements, and the approach we have taken to ensure that the system both supports and enhances workflow.

Clinical Pharmacy Information Systems↗
PubMed1995

Workflow: a new modeling concept in critical care units.

The term Groupware concerns computer-based systems that support groups of people engaged in a common task (goal) and that provide an interface to a shared environment [1]. The absence of a common tool for exchanges between physicians and nurses causes a multiplication of paper supports for the recording of information. Our objective is to study software architectures in particular medical units that allow task coordination and managing conflicts between participants within a distributed environment. The final goal of this research is to propose a computer solution that could answer the user requirements in Critical Care Units (CCUs). This paper describes the Workflow management approach [5] for supporting group work in health care field. The emphasis is especially on asynchronous cooperation. This approach was applied to CCUs through the analysis and the proposal of a new architecture [6]. We shall limit ourselves to explaining control board and analyzing the message management we support.

Critical Care↗
PubMed2024

metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis.

Analysis of large-scale data-independent acquisition mass spectrometry metaproteomics data remains a computational challenge. Here, we present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS, protein identification and quantification using data-independent acquisition mass spectrometry, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap and timsTOF MS instruments. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples indicated that metaExpertPro quantified an average of 45,000 peptides in a 60-min diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual false discovery rate of approximately 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67-0.90) in genus diversity and showed a high correlation (rSpearman = 0.73-0.82) between the measured and true genus relative abundance in benchmark tests. Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.

Proteomics↗
PubMed2024

Proteome-Scale Tissue Mapping Using Mass Spectrometry Based on Label-Free and Multiplexed Workflows.

Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ∼3500 proteins at a spatial resolution of 50 μm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provides robust protein quantifications in identifying differentially abundant proteins and spatially covariable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial coexpression analysis.

Proteome↗
PubMed2026

Targeted Modulation of Abundant Proteins Enhances Proteomic Profiling of Ovarian Cancer Ascites: A Pilot Technical Workflow Comparison.

Ascites from ovarian cancer patients are increasingly recognized as a valuable biofluid for cancer research, as its protein composition reflects the disease state and may reveal biomarkers of treatment sensitivity and response. However, the detection of low-abundance proteins is hindered by the presence of highly abundant proteins such as albumin. In this study, we evaluated five protein preparation methods for their effectiveness in depleting high-abundance or enriching low-abundance proteins in ovarian cancer ascites. The Norgen (Nor), Minutes (Min), and Perchloric acid (PerCA) methods were based on abundant protein depletion, while the Urine (Uri) and Nanomics (Nano) kits focused on low-abundance protein enrichment. Processed samples were analyzed using label-free quantitative bottom-up proteomics by LC-MS/MS, followed by a bioinformatics assessment. Compared with undepleted ascites (UnD), Min, Nor, Nano, and PerCA increased protein identifications, whereas Uri produced profiles similar to those of UnD. Notably, PerCA and Nano enabled the identification of distinct protein subsets associated with cancer-related pathways, including immune responses and autophagy. PerCA enriched transmembrane and secreted immunomodulatory glycoproteins, whereas Nano enrichment primarily captured secreted, nuclear, and cytoplasmic soluble proteins. Overall, our results show that both high-abundance protein depletion and low-abundance enrichment improve ascites proteome coverage, each offering distinct advantages in identifying biologically relevant low-abundance proteins.

Female↗
PubMed2026

ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome.

SUMMARY: The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation plays a key role in gene regulation, genome stability, and disease. Recent advances in long-read sequencing now enable large-scale, haplotype-resolved, and DNA methylation-informative analysis of the human genome, including on previously inaccessible complex and repetitive regions. However, the comprehensive, simultaneous characterisation of the "human repeatome" remains challenging, largely due to the lack of comprehensive tools integrated in a single pipeline that can capture the full spectrum of variation across diverse types of DNA repeats. Here, we present ECHO, a user-friendly, Snakemake-based pipeline for the "(Epi)genomic Characterisation of Human Repetitive Elements using Oxford Nanopore Sequencing." ECHO provides a reproducible and scalable framework for end-to-end analysis of whole-genome nanopore sequencing data, enabling integrative but also tailored (epi)genetic analyses of the human repeatome. AVAILABILITY AND IMPLEMENTATION: ECHO is freely available at Github: https://github.com/leenput/ECHO-pipeline, with the archived version at Zenodo: https://zenodo.org/records/19068468.

Humans↗
PubMed1997

Processes involved in reading imaging studies: workflow analysis and implications for workstation development.

Software development for imaging workstations has lagged behind hardware availability. To guide development and to analyze work flow involved in interpretation of cross-sectional imaging studies, we assessed the cognitive and physical processes. We observed the performance and interpretation of body computed tomography (CT) scans and recorded the events that occurred during this process. We studied work flow using a bottleneck analysis. Twenty-four of a total of 54 cases (44%) involved comparing the images with those of prior scans. Forty-seven of 54 scans (87%) were viewed using windows other than soft tissue, or compared with precontrast scans. In 46 cases (85%), the interpretation stopped to return to a previous level for review. Measurement of lesions was performed in 24 of 54 (44%) cases, and in 15 (63%) of these cases, measurements were taken of lesions on old studies for comparison. Interpretation was interrupted in 14 of 54 cases (26%) by referring clinicians desiring consultation. The work flow analysis showed film folder retrieval by the film room to be the bottleneck for interpretation by film. For picture archiving and communication system (PACS) reading, the CT examination itself proved to be the bottleneck. We conclude that workstations for CT interpretation should facilitate movement within scans, comparison with prior examinations, and measuring lesions on these scans. Workstation design should consider means of optimizing time currently not used between interpretation sessions, minimizing interruptions and providing more automated functions currently requiring physician interaction.

Cross-Sectional Studies↗
PubMed2001

Support of clinician image-related workflow by a user-edited, web-based patient list manager.

Clinician efficiency can be enhanced by worklists that compile useful data for rapid access at the time of need. The authors report development of a web-based, user-edited "Patient List Manager" for the Clinical Image Management System (CIMS). The CIMS List Manager interfaces with the CIMS Archive to provide the user with available studies. It has tools that let the user build personal lists from the available studies. Listed studies are moved from the archive to the cache for rapid access at the time of need. Users can build/edit the list through a browser (without viewing pictures) or from within the image viewer. In this way, the List Manager distributes list building into knowledgeable hands. This is particularly valuable at the current time when health system patient registries are not mature enough to reliably support building build anticipatory patient lists.

Humans↗
PubMed2001

The Digital Imaging and Communications in Medicine (DICOM) archive is a dynamic component of a clinician image-related workflow solution.

The authors investigated clinician transactions against the Digital Imaging and Communications in Medicine (DICOM) archive within a clinical image management system (CIMS) in support of patient care. A Neurosurgical Oncology practice was audited for image utilization. There were 400 requests for 233 image studies during 297 sessions. Fifty percent were for current studies, and 50% were for historical studies. Current studies alone were requested in 37% of the sessions, current plus historical in 31%, and historical alone in 32% of the sessions. Seventy percent of studies were within 8 weeks old and were rapidly available from the CIMS disk cache without an archive image transaction. Conversely, 30% were older than 8 weeks, requiring a clinician transaction against the archive for image retrieval. Approximately 25% of studies were older than 3 months and 10% older than 6 months. Clinician image needs are complex and any CIMS solution must include a DICOM archive that can support clinician-based transactions.

Database Management Systems↗
PubMed2001

Impact of a diagnostic workstation on workflow in the emergency department at a level I trauma center.

PURPOSE: When a computed tomography (CT) scan on a patient from the emergency department is completed at University of Medicine and Dentistry of New Jersey (UMDNJ)-University Hospital, a non-picture archiving and communication system (PACS) environment, formal diagnostic review cannot begin until the images are printed and transported to the on-call radiology resident. The time to reach a final diagnosis has been significantly reduced by the introduction of a single workstation in the on-call reading room. MATERIALS AND METHODS: Five radiology residents were studied. Each read 10 CT studies on film and 10 on a workstation. After a training period to familiarize the residents with the workstation, measurements were taken of the time required to read the examination and the time required for printing and transporting or networking the images. RESULTS: The average time required to transmit the images was reduced from approximately 40 minutes to 16 minutes. Interpretation times between the workstation and film were comparable. CONCLUSION: The addition of a single workstation significantly reduces the time required to reach a final diagnosis by obviating the need to print and transport the images to the on-call radiology resident. Such time savings can have a significant impact on the care of trauma patients.

Emergency Service, Hospital↗
PubMed2002

[Modern operations management in workflow operation. Spectrum of responsibilities and challenges for the future].

The operating unit is one of the cost-intensive facilities in a surgical clinic with a pacemaking function for most of the internal procedures. The power of performance of the operating unit is based on the co-operation of all disciplines and professions involved. The key to management of the operating unit is not only to co-ordinate the daily procedures, but also to interact with support personnel. To ensure successful OR management, the internal structure of the OR must fit the clinical tasks and the available quantity of personnel in each profession must be co-ordinated. Sufficient utilization of resources and equipment must be guaranteed without cost-intensive over-capacities and patient flow must be orientated to OR capacities. The development of such a business structure requires the management to clearly define the goal, to know the actual on-site data in detail with regard to the idiosyncratic workings of each speciality and to clearly assign the competence of each member of the team working in the OR. Co-ordination of the operating unit is the main task of OR management, which must ensure the following: transparent and co-ordinated schedule management in the various operative specialities, goal-directed changes of the schedule with incorporation of emergencies, as well as effective organization of staff. In order to realize these tasks, it is reasonable to implement interdisciplinary rules of procedures. In addition, the assignment of a neutral decision-making body within the OR and the creation of an information center for all OR personnel. The challenge of OR organization in the future is to implement more effective documentation systems and active controlling within the OR. One can ensure adequate utilization of resources in the OR with prospectively oriented planning. Better transparence of operations in the OR contributes to increased efficiency. Implementation of quality management is the foundation for a successfully operating surgical hospital. Not only the productivity of individual members of the staff, but also the precise documentation of the quality of results will become important parameters in a successful surgical hospital, whose nucleus is the OR.

Efficiency, Organizational↗