SEARCH · PubMed Health

Results for “automated workflows”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources

PubMedDate not supplied

Automating complex guidelines for chronic disease: lessons learned.

There is scant published experience with implementing complex, multistep computerized practice guidelines for the long-term management of chronic diseases. We have implemented a system for creating, maintaining, and navigating computer-based clinical algorithms integrated with our electronic medical record. This article describes our progress and reports on lessons learned that might guide future work in this field. We discuss issues and obstacles related to choosing and adapting a guideline for electronic implementation, representing and executing the guideline as a computerized algorithm, and integrating it into the clinical workflow of outpatient care. Although obstacles were encountered at each of these steps, the most difficult were related to workflow integration.

Algorithms↗

PubMed2006

Creating an IHE ATNA-based audit repository.

Compliance with the Health Insurance Portability and Accountability Act (HIPAA) requires gathering audit information from picture archiving and communications systems (PACS) regarding evidence trails of human interactions. Until recently, most PACS users have had limited access to auditing information. Access required resources to handle manual inspection of audit logs, and access to proprietary databases was not always available. Some vendors now produce eXtensible Markup Language (XML) audit logs based on certain events occurring in PACS. However, it is up to the user to convert this information into an easily mined data repository supporting compliance and quality control. This process can be handled in multiple ways, which could mean different audit mechanisms depending on the PACS (or other hospital system) used. It is apparent that an organized method of dealing with audit information is needed. This help may be provided within the Integrating the Healthcare Environment (IHE) framework. The IHE initiative defines a set of profiles, actors, and transactions that create common scenarios for particular workflow processes. The Integration Profiles depict security as a fundamental requirement of the framework. Specifically, the Audit Trail and Node Authentication (ATNA) profile defines standards based mechanisms for securely transmitting and storing audit records in a central repository. The data structure defined by the profile provides a number of record types that capture different audit events. A general feasibility study for storing currently available PACS audit information following the profile is defined, and steps to an automated solution are discussed.

Feasibility Studies↗

PubMed2004

Computerized physician order entry and online decision support.

Computerized physician order entry (CPOE) and decision support systems (DSS) can reduce certain types of error but often slow clinicians and may increase other types of error. The net effect of these systems on an emergency department (ED) is unknown. The consensus participants combined published evidence with expert opinion to outline recommendations for success. These include seamless integration of CPOE and DSS into systems and workflow; ensuring access to Internet-based and other online support material in the clinical arena; designing systems specifically for the ED and measuring their impact to ensure an overall benefit; ensuring that CPOE systems provide error and interaction checking and facilitate weight- and physiology-based dosing; using interruptive alerts only for the highest-severity events; providing a simple, vendor-independent interface for institutional customization of CPOE alert thresholds; maximizing the use of automated systems and passive data capture; and ensuring the widespread availability of CPOE and DSS using secure wireless and portable technologies where appropriate. Decisions regarding CPOE and DSS in the ED should be guided by the ED chair or designee. Much of what is believed to be true regarding CPOE and DSS has not been adequately studied. Additional CPOE and DSS research is needed quickly, and this research should receive funding priority. DSS and CPOE hold great promise to improve patient care, but not all systems are equal. Evidence must guide these efforts, and the measured outcomes must consider the many factors of quality care.

Decision Support Systems, Clinical↗

PubMed2005

Improving physician communication through an automated, integrated sign-out system.

Communication failures among physicians are a leading cause of medical errors. The resident sign-out sheet is the primary tool used by house staff to facilitate the sign-out process. The resident sign-out sheet is a structured report, with patient-specific information including demographics, such a patient's name, age, sex, room number, and attending physician; problem list; medications; and allergies. Some physicians use handwritten notes to keep track of this information, while others use freestanding word processor or database programs. In a previous study, the authors described serious inaccuracies in a manually updated word-processor based resident sign-out sheet used by pediatric residents at a tertiary-care children's hospital. An automated and integrated sign-out system (AISS) was subsequently developed that retrieves pertinent patient information from a computerized provider order entry (CPOE) system. The AISS generates a resident sign-out sheet, which includes demographic information, weight, current medications, allergies, and diet orders, as well as optional free-text information. The AISS has proven to be enormously popular, increasing physician acceptance of CPOE throughout the organization. This paper discusses lessons learned, including technical, design, and workflow aspects of an integrated resident sign-out sheet. The authors recommend that all future commercial CPOE systems incorporate physician sign-out tools such as the one described in this article.

Communication↗

PubMed2007

Characteristics of the m2000 automated sample preparation and multiplex real-time PCR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

We evaluated a new real-time PCR-based prototype assay for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae developed by Abbott Molecular Inc. This assay is designed to be performed on an Abbott m2000 real-time instrument system, which consists of an m2000sp instrument for sample preparation and an m2000rt instrument for real-time PCR amplification and detection. The limit of detection of this prototype assay was determined to be 20 copies of target DNA for both C. trachomatis and N. gonorrhoeae, using serially diluted linearized plasmids. No cross-reactivity could be detected when 55 nongonococcal Neisseria isolates and 3 non-C. trachomatis Chlamydia isolates were tested at 1 million genome equivalents per reaction. Concordance with the Roche Amplicor, BDProbeTec ET, and Gen-Probe APTIMA Combo 2 tests was assessed using unlinked/deidentified surplus clinical specimens previously analyzed with these tests. For C. trachomatis, concordance for positive results ranged from 93.7% to 100%, while concordance for negative results ranged from 98.2% to 100%. For N. gonorrhoeae, concordance for positive and negative results ranged from 91.4% to 100% and 99.3% to 100%, respectively. A workflow analysis of the prototype assay was conducted to obtain information on throughput under laboratory conditions. At 48 samples/run, the time to first result for both C. trachomatis and N. gonorrhoeae was 4.5 h. A total of 135 patient specimens could be analyzed in 8.9 h, with 75 min of hands-on time. This study demonstrated the technical and clinical feasibility of the new Abbott real-time PCR C. trachomatis/N. gonorrhoeae assay.

Automation↗

PubMed2004

Child Health Improvement through Computer Automation: the CHICA system.

Clinical guidelines are prevalent but frequently not used. Computer reminder systems can improve adherence to guidelines but have not been widely adopted. We present a computer-based decision support system that combines these elements: 1) pediatric preventive care guidelines encoded in Arden Syntax; 2) a dynamic, scannable paper user interface; and 3) a HL7-compliant interface to existing electronic medical record systems. The result is a system that both delivers "just in time" patient-relevant guidelines to physicians during the clinical encounter and accurately captures structured data from all who interact with the system. The system performs these tasks while remaining sensitive to the workflow constraints of a busy outpatient pediatric practice.

Algorithms↗

PubMed2026

Reimagining research papers as interactive and reliable AI agents.

Here we introduce Paper2Agent, an automated framework that converts research papers into artificial intelligence (AI) agents. Paper2Agent transforms research output from passive artefacts into active systems that accelerate use and discovery. Conventional research papers require readers to understand and adapt the paper's code, data and methods to their work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by converting a paper into an AI agent that functions as a virtual corresponding author, exposing its manuscript, supplementary materials, datasets, code and workflows as active, agent-native knowledge rather than static text. It analyses the paper and codebase using multiple agents to construct a model context protocol (MCP) server, then generates and runs tests to refine and increase robustness of the MCP. These paper MCPs can be connected to a chat agent (such as Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the paper. We demonstrate Paper2Agent's effectiveness through case studies. Paper2Agent created an agent that leveraged AlphaGenome1 to interpret genomic variants and agents based on Scanpy2 and TISSUE (transcript imputation with spatial single-cell uncertainty estimation)3 to conduct single-cell and spatial transcriptomics analyses. We validate that these agents reproduce the results of the original papers and carry out novel user queries. Paper2Agent created multiple agents that collaborate to prioritize a causal gene for psoriasis. By turning static papers into interactive AI agents, Paper2Agent introduces a paradigm for knowledge dissemination and a collaborative ecosystem of AI co-scientists.

Journal Article↗

PubMedDate not supplied

Perspectives on speech recognition technology.

Speech recognition technology is used in all sorts of applications. However, for radiology, the issues are more complex than merely being able to dial a contact from an address book. In addition, radiologists have been hesitant to embrace the technology, with some preferring the status quo. Speech recognition technology has dramatically improved over the past several years, and they generally have been broadly commercialized. However, the use of speech recognition for composition of text reports or email has had only limited acceptance. The overriding reasons appear to be that most computer users prefer not to talk to their computers. They have learned to compose text documents via a "type-and-organize" methodology rather than composing the document "in their heads" and dictating. Radiologists are still required to dictate their reports, whether it is digitally, into an analog tape recording device or via a speech recognition system. The benefits extend to the radiologist's patients, and to the radiologist's employers--the hospitals or imaging centers--but it could be said that there is little direct benefit for the radiologist There is a belief that systems should focus more on improving radiologist efficiency rather than emphasizing cost savings and turnaround time. Integration with existing systems is critical. But any technology, in order for it to be well accepted by the primary user, needs to benefit that user. Before selecting any speech recognition technology a radiology administrator should do some research and find answers to several questions that address the basics of speech recognition technology and the companies that provide this technology. In addition, the radiology administrator must ensure that the facility is prepared to implement the technology and address any workflow- or culture-related issues that may arise. There are a number of opportunities for improvement in speech recognition radiology applications. These include the ongoing need for improvement recognition rates, the need to streamline integration with picture archiving and communication system (PACS) and radiology information system (RIS) technologies, and the general need to improve the user interface. In addition to these improvements, one can expect an increased adoption of structured reporting technologies within radiology. These techniques allow easier automated extraction of content and more flexible communication and organization of data (such as communication to electronic medical record systems).

Diffusion of Innovation↗

PubMed2000

Standardized comparison of processing capacity and efficiency of five new-generation immunoassay analyzers.

BACKGROUND: With the trend toward laboratory and workstation consolidation, more studies are necessary to evaluate instrumentation, solutions for coping with workflow and test diversity, and opportunities for increasing the overall efficiency of laboratory testing. We assessed the processing capacity and efficiency of new-generation immunoassay analyzers by determining productivity parameters of five commercially available systems. METHODS: A workload protocol was developed and used to assess processing capacity and efficiency parameters of five immunoassay analyzers under standardized conditions in a real-life routine situation. We studied the ACS:Centaur((R)) (analyzer A), Architect(TM) i2000 (analyzer B), Elecsys((R)) 2010 tandem (analyzer C), Immulite((R)) 2000 (analyzer D), and Vitros ECi (analyzer E) on the basis of a standardized workload protocol that reflected a routine laboratory situation. This workload encompassed reflex and STAT testing, dilutions, and in-run calibration of a new reagent lot number. The analyzers were compared for hands-on labor time, unattended time (UT), throughput, and differentiated relative productivity indexes [RPI((UT)); number of reportable results/(processing time - sum of unattended time)]. The RPI data for analyzers linked to an automated (aut) sample-handling system [RPI((aut))] were also calculated. RESULTS: The evaluation produced a set of parameters for the productivity of the instruments. An overview of the most important parameters revealed the following: the throughput was 193, 123, 97, 109, and 46 tests/hour for instruments A, B, C, D and E, respectively; the RPI((10)) was 425, 238, 161, 445, and 151 tests/operator-hour; the RPI((30)) was 229, 136, 118, 264, and 86 tests/operator-hour; the RPI((10,aut)) was 1701, 637, 235, 964, and 223 tests/operator-hour; and the RPI((30, aut)) was 298, 150, 174, 400, and 114 tests/operator-hour. CONCLUSIONS: The combination of a standardized workload protocol and determination of parameters for productivity and labor efficiency, especially the differentiated RPIs, made it possible to make an objective comparison of the organizational consequences of the use of these instruments. The described parameters allow for a scientifically based choice, given a certain workflow and a particular laboratory organization.

Humans↗

PubMed2005

Designing better radiology workstations: impact of two user interfaces on interpretation errors and user satisfaction.

This paper presents our solution for supporting radiologists' interpretation of digital images by automating image presentation during sequential interpretation steps. We extended current hanging protocols with support for "stages" which reflect the presentation of digital information required to complete a single step within a complex task. We demonstrated the benefits of staging in a user experiment with 20 lay subjects involved in a comparative visual search for targets, similar to a radiology task of identifying anatomical abnormalities. We designed a task and a set of stimuli that allowed us to simulate the interpretation workflow from a typical radiology scenario-reading a chest radiography exam when a prior study is also available. The simulation was enabled by abstracting both the radiologist's task and the basic workstation navigation functionality. The staged interface was significantly faster than the traditional user interface, provided a 37% reduction in the interpretation errors, and improved user satisfaction.

Analysis of Variance↗

PubMed2004

arrayMagic: two-colour cDNA microarray quality control and preprocessing.

UNLABELLED: arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica merging, quality diagnostics and data export. The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured and preprocessed microarray data to high-level follow-up analysis. AVAILABILITY: The R package arrayMagic is available with BSD license at http://www.bioconductor.org CONTACT: a.buness@dkfz.de SUPPLEMENTARY INFORMATION: The package contains documentation in the form of manual pages and a vignette with a guided tour of a typical workflow.

Algorithms↗

PubMed2006

Correction of patient positioning errors based on in-line cone beam CTs: clinical implementation and first experiences.

BACKGROUND: The purpose of the study was the clinical implementation of a kV cone beam CT (CBCT) for setup correction in radiotherapy. PATIENTS AND METHODS: For evaluation of the setup correction workflow, six tumor patients (lung cancer, sacral chordoma, head-and-neck and paraspinal tumor, and two prostate cancer patients) were selected. All patients were treated with fractionated stereotactic radiotherapy, five of them with intensity modulated radiotherapy (IMRT). For patient fixation, a scotch cast body frame or a vacuum pillow, each in combination with a scotch cast head mask, were used. The imaging equipment, consisting of an x-ray tube and a flat panel imager (FPI), was attached to a Siemens linear accelerator according to the in-line approach, i.e. with the imaging beam mounted opposite to the treatment beam sharing the same isocenter. For dose delivery, the treatment beam has to traverse the FPI which is mounted in the accessory tray below the multi-leaf collimator. For each patient, a predefined number of imaging projections over a range of at least 200 degrees were acquired. The fast reconstruction of the 3D-CBCT dataset was done with an implementation of the Feldkamp-David-Kress (FDK) algorithm. For the registration of the treatment planning CT with the acquired CBCT, an automatic mutual information matcher and manual matching was used. RESULTS AND DISCUSSION: Bony landmarks were easily detected and the table shifts for correction of setup deviations could be automatically calculated in all cases. The image quality was sufficient for a visual comparison of the desired target point with the isocenter visible on the CBCT. Soft tissue contrast was problematic for the prostate of an obese patient, but good in the lung tumor case. The detected maximum setup deviation was 3 mm for patients fixated with the body frame, and 6 mm for patients positioned in the vacuum pillow. Using an action level of 2 mm translational error, a target point correction was carried out in 4 cases. The additional workload of the described workflow compared to a normal treatment fraction led to an extra time of about 10-12 minutes, which can be further reduced by streamlining the different steps. CONCLUSION: The cone beam CT attached to a LINAC allows the acquisition of a CT scan of the patient in treatment position directly before treatment. Its image quality is sufficient for determining target point correction vectors. With the presented workflow, a target point correction within a clinically reasonable time frame is possible. This increases the treatment precision, and potentially the complex patient fixation techniques will become dispensable.

Automation↗

PubMed2006

Robust online orientation correction for radiographs in PACS environments.

In picture archiving and communications systems (PACS), images need to be displayed in standardized ways for radiologists' interpretations. However, for most radiographs acquired via computed radiography (CR), digital radiography (DR), or digitized films, the image orientation is undetermined because of the variations in examination conditions and patients' situations. To address this problem, an automatic orientation correction method is developed. It first detects the most indicative region in a radiograph for image orientation, and then extracts a set of low-level visual features from the region. Based on these features, a well-trained classifier, using support vector machines, is employed to recognize the correct orientation of the radiograph and reorient it to the desired position. A large-scale experiment was conducted on more than 12 000 radiographs, which covered a wide variety of exam types, to validate the method. The overall success rate of orientation correction was 96.1%. A workflow study on the method also demonstrated a significant improvement in efficiency for image display. To our knowledge, this work represents the first robust system designed to handle all radiographic exam types using a unified framework instead of using dedicated strategies for different exam types.

Algorithms↗

PubMed2006

Gbrowse Moby: a Web-based browser for BioMoby Services.

BACKGROUND: The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client--Gbrowse Moby--that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface. RESULTS: Gbrowse Moby is a low-throughput, exploratory tool specifically aimed at non-informaticians. It provides a straightforward, minimal interface that enables a researcher to query the BioMoby Central web service registry for data retrieval or analytical tools of interest, and then select and execute their chosen tool with a single mouse-click. The data is preserved at each step, thus allowing the researcher to manually "click" the data from one service to the next, with the Gbrowse Moby application managing all data formatting and interface interpretation on their behalf. The path of manual exploration is preserved and can be downloaded for import into automated, high-throughput tools such as Taverna. Gbrowse Moby also includes a robust data rendering system to ensure that all new data-types that appear in the BioMoby registry can be properly displayed in the Web interface. CONCLUSION: Gbrowse Moby is a robust, yet facile entry point for both newcomers to the BioMoby interoperability project who wish to manually explore what is known about their data of interest, as well as experienced users who wish to observe the functionality of their analytical workflows prior to running them in a high-throughput environment.

Journal Article↗

PubMed2006

High performance GRID based implementation for genomics and protein analysis.

Starting from the genomic and proteomic sequence data, a complex computational infrastructure as been established with the objective to develop a GRID based system to to automate the analysis, prediction and annotation processes of genomic DNA. To support of this type of analysis, several algorithms as been used to recognize biological signals involved in the identification of genes and proteins. The system implemented can be use to analyse the content of the large number of genomic sequences. For this reason, the system realized is capable of using a computational architecture specifically designed for intensive computing based on GRID technologies developed throughout the BIOINFOGRID European project. We developed a GRID based workflow to correlate different kind of Bioinformatics data, going from the Genomics Nucleotide to the Protein Sequence. The first step in the workflow consists of submitting a nucleotide sequence that is elaborated by a specific software for gene prediction. In particular this tool performs a search in the nucleotide sequence to find out the key components of gene. The predicted gene is then translated in the corresponding protein sequence. Based on protein sequence is then possible to identify the domains that characterize the protein functionality using specific tools of domain prediction. Protein domains classification are very important in the analysis of the macromolecular functionality. To analyze a whole protein family from large genome of various organism means to elaborate a large amount of data that requires huge computational resources. To analyze all this data we suggest the use of a high performance platform based on grid technology. We have implemented our applications on a wide area grid platform for scientific applications [http://www.grid.it and http://grid-it.cnaf.infn.it] composed of about 1000 CPU's. The grid infrastructure consists in a collection of computing elements and storage elements that jointly concur to define a platform for high performance elaboration. In this study a grid based application is presented to compute the protein domain analysis in a distributed way. This approach has high performance because the protein domains are checked with different software in parallel in different grid sites.

Computational Biology↗

PubMed1999

Comparison of two automated systems for the isolation of mycobacteria from clinical specimens.

The Bactec MGIT 960 (Becton-Dickinson, UK) automated mycobacterial liquid culture system was compared with the Bactec 9000 MB (Becton-Dickinson) in order to assess ease of use, diagnostic reliability and safety features. One thousand twenty-nine clinical specimens were cultured in parallel, yielding a total of 125 (12.1%) mycobacterial isolates, including 71 Mycobacterium tuberculosis and 18 Mycobacterium avium. The Bactec MGIT 960 demonstrated a mycobacterial recovery rate and speed of detection equivalent to that of the Bactec 9000 MB for clinically important isolates. The Bactec MGIT 960 integrates smoothly into laboratory workflow, does not require needle inoculation and has a much larger capacity than the Bactec 9000 MB.

Bacteriological Techniques↗

PubMed2000

Distributed information system architecture for Primary Health Care.

We present a distributed architectural framework for Primary Health Care (PHC) Centres. Distribution is handled through the introduction of the Roaming Electronic Health Care Record (R-EHCR) and the use of local caching and incremental update of a global index. The proposed architecture is designed to accommodate a specific PHC workflow model. Finally, we discuss a pilot implementation in progress, which is based on CORBA and web-based user interfaces. However, the conceptual architecture is generic and open to other middleware approaches like the DHE or HL7.

Computer Communication Networks↗

PubMed1996

Documenting data delivery: design, deployment, and decision.

Developing and deploying informatics solutions which are useful and acceptable to busy physicians are challenging tasks. We describe the design, deployment, and evaluation process by which the delivery of routine clinical laboratory reports is automated using electronic mail. Data from TMR, an operational computer-based patient record (CPR), are presented to providers using an individualized, modern interface. This system is compared to the existing, paper-based system for delivery of data from the same CPR. Differences between the two systems of data delivery are analyzed, with emphases on 1) electronic documentation of data delivery and receipt, 2) electronic and/or paper documentation of clinical action taken as a result of laboratory reports, 3) timeliness of report availability, 4) costs, 5) workflow compatibility, and 6) physician satisfaction. The new delivery system employs inexpensive, commercially available software applications and entails only trivial changes to the proprietary CPR. Built into the new system are features which allow quantitative measurements of its performance for analysis along with survey-based user satisfaction data. The open systems design is deliberately non-proprietary, inexpensive, and generalizable. Accordingly, it offers practical possibilities for settings in which clinical information systems are just being planned, as well as for those in which such systems are already established.

Clinical Laboratory Information Systems↗