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At least 325 records · Page 18Linked to original sources
PubMed1993

Abbott AxSYM random and continuous access immunoassay system for improved workflow in the clinical laboratory.

We describe a new clinical laboratory instrument, the Abbott AxSYM, which provides random- and continuous-access testing for immunoassays, 20 onboard reagents, primary tube sampling, and a throughput of 80 to 120 tests per hour. The AxSYM incorporates three separate analytical technologies for processing immunoassays: microparticle enzyme immunoassay, fluorescence polarization immunoassay, and a novel technology known as ion-capture immunoassay. The system incorporates both common and technology-specific subsystems controlled by a real-time software scheduling processor. Tests can be processed in one- or two-step sandwich or competitive formats, with variable pipetting steps, incubation periods, optical read formats, and wash sequences. Menu capabilities include tests for hepatitis, retrovirus, tumor markers, fertility markers, thyroid functions, and therapeutic drugs. The time to first result is approximately 15-25 min for most routine assays and < or = 15 min for stat assays (i.e., creatine kinase MB isoenzyme, human chorionic gonadotropin beta subunit, and therapeutic drugs). AxSYM assay performance for 23 assays was comparable with that of the Abbott IMx and TDx analyzers; specimen correlation data had correlation coefficients ranging from 0.97 to 0.99 and slopes ranging from 0.99 to 1.10. Within-run imprecision (CV) was 1.5% to 11.4%, with most assays (19 of 23) demonstrating CVs < or = 8.0%.

Autoanalysis↗
PubMed1995

PLACO: a cooperative architecture for managing workflow in CCU.

Computer-Supported Cooperative Work (CSCW) is a multi-disciplinary research theme involving software developers, computer scientists, as well as psychologists and sociologists. CSCW is devoted to the analysis of interactions among humans when performing their work in a collaborative way. The main application fields are work organization, healthcare, education and training. The term of Groupware, as defined by C.A. Ellis, refers to software that assists groups of people in communicating, in collaborating and in coordinating their activities. Our objective is to study software architectures allowing task coordination and conflict management between participants within a distributed environment, in particular medical units. We do not aim to produce a practical system suitable for near-term deployment in the Critical Care Unit (CCU), but rather a "proof of concept", an experimental system that performs and coordinates a range of intelligent planning tasks in CCU activities. The emphasis will be put especially on asynchronous cooperation since the work of physicians and nurses is discontinuous.

Communication↗
PubMed1997

Clinical care management and workflow by episodes.

This paper describes the implementation of clinically defined episodes of care and the introduction of an episode-based summary list of patient problems across Mayo Clinic Rochester in 1996 and 1997. Although Mayo's traditional paper-based system has always relied on a type of 'episode of care' (called the "registration") for patient and history management, a new, more clinically relevant definition of episode of care was put into practice in November 1996. This was done to improve care management and operational processes and to provide a basic construct for the electronic medical record. Also since November 1996, a computer-generated summary list of patient problems, the "Master Sheet Summary Report," organized by episode, has been placed in all patient histories. In the third quarter of 1997, the ability to view the episode-based problem summary online was made available to the 3000+ EMR-capable workstations deployed across the Mayo Rochester campus. In addition, the clinically oriented problem summarization process produces an improved basic "package" of clinical information expected to lead to improved analytic decision support, outcomes analysis and epidemiological research.

Episode of Care↗
PubMedDate not supplied

The case for RIS/PACS integration.

Why integrate PACS with the RIS? To improve workflow, of course, but what workflow? Much of the focus is on improving the flow of images for the radiologist, which is certainly a good thing to do, but what about the rest of the order process? Typical PACS system architecture begins with the HIS since this is where the correct patient demographic information and in many cases the orders originate. Correct patient and order information is sent from the HIS to the RIS using HL7 commands for Admission/Discharge/Transfer (ADT) and Order/Entry. HL7 is the communications protocol used in virtually all information systems. For the first step in communicating with PACS, patient and order information from the RIS is sent to a device called a PACS broker. This is necessary because most PACS systems do not support HL7 directly, and a translation is required. Images from each imaging modality are also sent to the broker using the DICOM standard. If an imaging modality does not support DICOM, then an additional box is used to convert the images to a DICOM file. The broker then sends completed DICOM files to the PACS for storage, distribution and viewing. That approach has worked well for the first stage of PACS utilization. However, experienced PACS users have identified the need to improve workflow, and many feel that closer communication with the RIS will solve many of the current limitations. This approach is sometimes called a "brokerless" solution but is probably better described as incorporating broker functions into the RIS. There are several potential advantages of incorporating the broker functions into the RIS: Access to all RIS information on patients, orders and results is available and can be used in many ways to improve workflow. Supporting all DICOM services directly from the RIS ensures that the latest and most complete information is always used. For example, DICOM Modality Worklists can be provided directly from the RIS, which guarantees that they are updated immediately. The RIS can manage the complete order workflow, not just images. License, implementation and support costs can be reduced by eliminating HL7 interfaces to an external broker. Managing workflow is the key to improved productivity and patient care from PACS. However, coordinated management of order workflow from the RIS and image workflow from the PACS is required to get the full benefit. The RIS has immediate and broad access to patient and order information. As a result, it is the natural place to take the lead in managing this coordinated workflow. While many older RIS and PACS systems are not yet capable of some of the integration features described above, several new systems are moving rapidly in that direction.

Efficiency, Organizational↗
PubMed2002

[Change in process management by implementing RIS, PACS and flat-panel detectors].

Implementation of radiological information systems (RIS) and picture archiving and communicating systems (PACS) results in significant changes of workflow in a radiological department. Additional connection with flat-panel detectors leads to a shortening of the work process. RIS and PACS implementation alone reduces the complete workflow by 21-80%. With flatpanel technology the image production process is further shortened by 25-30%. The workflow-steps are changed from original 17-12 with the implementation of RIS and PACS and to 5 with the integrated use of flatpanels. This clearly recognizable advantages in the workflow need an according financial investment. Several studies could show that the capitalisation-factor calculated over eight years is positive, with a gain range between 5-25%. Whether the additional implementation of flatpanel detectors results also in a positive capitalisation over the years, cannot be estimated exactly, at the moment, because the experiences are too short. Particularly critical are the interfaces, which needs a constant quality control. Our flatpanel detector-system is fixed, special images--as we have them in about 3-5% of all cases--need still conventional filmscreen or phosphorplate-systems. Full-spine and long-leg examinations cannot be performed with sufficient exactness. Without any questions implementation of integrated RIS, PACS and flatpanel detector-system needs excellent training of the employees, because of the changes in workflow etc. The main profits of such an integrated implementation are an increase in quality in image and report datas, easier handling--there are almost no more cassettes necessary--and excessive shortening of workflow.

Austria↗
PubMed2005

Proteomic studies of the Singapore grouper iridovirus.

The Singapore grouper iridovirus (SGIV) genome consists of a double-stranded circular DNA of 140,131 base pairs with 162 predicted open reading frames. Our earlier study using peptide mass fingerprints generated from MALDI-TOF MS led to the identification of 26 viral proteins. The present investigation aimed to achieve a more comprehensive and precise identification of the SGIV viral proteome by two workflows: one-dimensional gel electrophoresis (1-DE) separation followed by protein identification by MALDI-TOF/TOF MS/MS (1-DE-MALDI workflow) and shotgun proteomics in which the whole virus was digested by trypsin and the resulting peptides were separated by nano-LC and analyzed by MALDI-TOF/TOF MS/MS (LC-MALDI workflow). In total, 44 viral proteins were identified, 25 of which were reported for the first time. Fourteen proteins were uniquely identified by the 1-DE-MALDI workflow, whereas another 10 proteins were only identified by the LC-MALDI workflow with 20 proteins found by both approaches. Moreover 13 proteins were found to have acetylated N termini. Twenty-three proteins identified contain predicted transmembrane domains, accounting for 52.3% of the total proteins identified. RT-PCR confirmed the transcription products of all the identified viral proteins. A large number of proteins identified by both the 1-DE-MALDI and the LC-MALDI workflows from this study have significantly enhanced the coverage of the SGIV proteome. The SGIV proteome is at present the only iridoviral proteome that has been extensively characterized. Our results should provide further insights into the biology of SGIV and other iridoviruses.

Amino Acid Sequence↗
PubMed2026

CBIcall: a configuration-driven framework for variant calling in large sequencing cohorts.

MOTIVATION: Variant calling for next-generation sequencing (NGS) data relies on a diverse ecosystem of tools and workflows. Large-scale collaborative studies increasingly adopt federated analysis, where each institution processes sensitive data locally using standardized pipelines. Deploying identical pipelines across multiple centers remains challenging because heterogeneous software environments and computing policies can cause workflow divergence and inconsistent results. RESULTS: We developed CBIcall, a workflow backend-flexible, configuration-driven framework that runs standardized variant-calling pipelines from raw FASTQ files to analysis-ready VCFs. Users define each analysis in a single YAML parameters file, which CBIcall resolves against a controlled workflow registry and resource catalog. The execution driver validates parameters and checks compatibility among pipelines, analysis modes, workflow backends, genome builds, tool versions, and resource bundles. CBIcall supports reproducibility auditing by comparing executions using recorded provenance and output fingerprints. CBIcall dispatches validated workflows natively through Bash, Cromwell, Nextflow and Snakemake backends and provides production-ready pipelines for germline WES, WGS (single-sample or cohort joint genotyping following GATK Best Practices), and mitochondrial DNA analysis. We evaluated analytical performance using public benchmark datasets and validated reproducibility across four computing environments. We further deployed CBIcall in the EU HEREDITARY project, where it processed 1102 samples with both WES and mtDNA pipelines on an institutional HPC system, supporting its suitability for reproducible cohort-scale genomic analyses. AVAILABILITY AND IMPLEMENTATION: CBIcall is open source (GPLv3) and distributed with ready-to-run pipelines; full dependency and installation documentation is available at https://github.com/CNAG-Biomedical-Informatics/cbicall.

Journal Article↗
PubMed2004

A web services choreography scenario for interoperating bioinformatics applications.

BACKGROUND: Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow. RESULTS: To demonstrate the benefit of using web services over traditional web interfaces, we compare the two implementations of HAPI, a gene expression analysis utility developed by the University of California San Diego (UCSD) that allows visual characterization of groups or clusters of genes based on the biomedical literature. This utility takes a set of microarray spot IDs as input and outputs a hierarchy of MeSH Keywords that correlates to the input and is grouped by Medical Subject Heading (MeSH) category. While the HTML output is easy for humans to visualize, it is difficult for computer applications to interpret semantically. To facilitate the capability of machine processing, we have created a workflow of three web services that replicates the HAPI functionality. These web services use document-style messages, which means that messages are encoded in an XML-based format. We compared three approaches to the implementation of an XML-based workflow: a hard coded Java application, Collaxa BPEL Server and Taverna Workbench. The Java program functions as a web services engine and interoperates with these web services using a web services choreography language (BPEL4WS). CONCLUSION: While it is relatively straightforward to implement and publish web services, the use of web services choreography engines is still in its infancy. However, industry-wide support and push for web services standards is quickly increasing the chance of success in using web services to unify heterogeneous bioinformatics applications. Due to the immaturity of currently available web services engines, it is still most practical to implement a simple, ad-hoc XML-based workflow by hard coding the workflow as a Java application. For advanced web service users the Collaxa BPEL engine facilitates a configuration and management environment that can fully handle XML-based workflow.

Computational Biology↗
PubMed2006

Managing the life cycle of electronic clinical documents.

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

Documentation↗
PubMed2005

Towards an intelligent hospital environment: OR of the future.

Patients, providers, payers, and government demand more effective and efficient healthcare services, and the healthcare industry needs innovative ways to re-invent core processes. Business process reengineering (BPR) showed adopting new hospital information systems can leverage this transformation and workflow management technologies can automate process management. Our research indicates workflow technologies in healthcare require real time patient monitoring, detection of adverse events, and adaptive responses to breakdown in normal processes. Adaptive workflow systems are rarely implemented making current workflow implementations inappropriate for healthcare. The advent of evidence based medicine, guideline based practice, and better understanding of cognitive workflow combined with novel technologies including Radio Frequency Identification (RFID), mobile/wireless technologies, internet workflow, intelligent agents, and Service Oriented Architectures (SOA) opens up new and exciting ways of automating business processes. Total situational awareness of events, timing, and location of healthcare activities can generate self-organizing change in behaviors of humans and machines. A test bed of a novel approach towards continuous process management was designed for the new Weinburg Surgery Building at the University of Maryland Medical. Early results based on clinical process mapping and analysis of patient flow bottlenecks demonstrated 100% improvement in delivery of supplies and instruments at surgery start time. This work has been directly applied to the design of the DARPA Trauma Pod research program where robotic surgery will be performed on wounded soldiers on the battlefield.

Appointments and Schedules↗
PubMed2004

Result-driven strategies for protein identification and quantitation--a way to optimize experimental design and derive reliable results.

Uni- or multidimensional microcapillary liquid chromatography (microLC) matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS/MS) approaches have gained significant attention for quantifying and identifying proteins in complex biological samples. The off-line coupling of microLC with MS quantitation and MS/MS identification methods makes new result-dependent workflows possible. A relational database is used to store the results from multiple high performance liquid chromatography runs, including information about MALDI plate positions, and both peptide and protein quantitations, and identifications. Unlike electrospray methodology, where all the decisions about which peptide to fragment, must be made during peptide fractionations, in the MALDI experiments the samples are effectively "frozen in time". Therefore, additional MS and MS/MS spectra can be acquired, to promote more accurate quantitation or additional identifications until reliable results are derived that meet experimental design criteria. In the case of what can be designated the expression-dependent workflow, quantitation can be detached from identification and only peak pairs with biological relevant expression changes can be selected for further MS/MS analyses. Alternatively, additional MS/MS data can be acquired to confirm tentative peptide mass fingerprint hits in what is designated a search result-dependent workflow. In the MS data-dependent workflow, the goal is to collect as many meaningful spectra as possible by judiciously adjusting the acquisition parameters based on characteristics of the parent masses. This level of sophistication requires the development of innovative algorithms for these three result-dependent workflows that make MS and MS/MS analysis more efficient and also add confidence to experimental results.

Chromatography, High Pressure Liquid↗