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PubMed1999

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

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

Attitude to Computers↗
PubMed2001

Digital radiography and film scanners: automating the transition to filmless radiology.

To facilitate the integration of digital radiography (DR) and legacy film/screen technology, we have devised a methodology for film digitization that optimizes workflow and integrates well with the picture archiving and communication system (PACS). This work was performed at Mercy Medical Center (Cedar Rapids, IA) using a film digitizer with built-in Digital Imaging and Communications in Medicine (DICOM) communication. The radiology department at Mercy has one DR system and three separate film/screen systems. The DR system software suite features DICOM Modality Worklist capability to provide complete radiology information system (RIS) integration functionality. This provides for patient demographic information to be automatically downloaded from the RIS worklist to populate the DICOM image header. Likewise, we have taken advantage of the film scanner's DICOM capability to develop software linking it with the hospital RIS. This capability provides a worklist downloading functionality equivalent to that of the DR. Patient demographics can then be rapidly downloaded as each film is digitized. The worklist capability of the scanner is essential in several respects. First, it guarantees that patient demographic information is completely accurate and, therefore, that the digitized x-ray image will be merged with the correct patient file in the PACS. Additionally, high film scanner throughput is achieved, guaranteeing that all inpatient-digitized films are as readily available on the PACS as their DR image counterparts. The digitized images have proven to be of diagnostic quality on the typical 1K by 1K PACS workstation. Also, as patients are admitted to the hospital, prior films from the radiology archive are digitized to form a readily available patient history for in-house physicians. Over time, we are building archival patient histories of soft-copy images that will enable increased availability of patient x-rays to both in-hospital and outside referring physicians, especially as more internet-viewing software becomes available to the out-of-hospital medical community. Finally, the results of this study show that high-throughput RIS integration of film scanning equipment is a key component to making a graceful transition to the filmless hospital as more DR systems are installed.

Humans↗
PubMed2005

Vocabulary requirements for implementing clinical guidelines in an electronic medical record: a case study.

As part of a larger effort to automate guidelines we determined the number and types of clinical variables required to implement two complex clinical guidelines and the adequacy of the electronic medical record (EMR) to capture them. 178 unique variables were required by both guidelines. Variables were classified as simple (existing observation terms in the EMR), calculated (transformations of simple variables), and complex (requiring multiple simple variables and logical rules for combining them). Many variables are unlikely to be instantiated in an EMR without focused efforts to collect them. In addition, many variables required knowledge that was neither provided in the guideline nor referenced. We conclude that, although the EMR contains the necessary variables to implement these guidelines, successful automated implementation requires unambiguous definition of required terms, incorporation of additional knowledge not provided in the guideline and modification of workflow to collect variables not normally captured in routine clinical care.

Decision Support Systems, Clinical↗
PubMed2026

Accelerate Your Science: Direct-to-Biology Strategies in Medicinal Chemistry.

Direct-to-biology (D2B) is a powerful strategy that accelerates early drug discovery. It enables compounds to be synthesized in miniaturized formats and evaluated directly as crude reaction mixtures. This bypasses the need for purification during the initial design-make-test cycle. Advances in robust synthetic methodologies, automation, reaction miniaturization, and biological screening have transformed D2B from a proof-of-concept approach into a versatile medicinal chemistry platform. This platform is applicable to fragment optimization, covalent ligands, macrocycles, proteolysis-targeting chimeras (PROTACs), molecular glues, and cellular phenotypic screening. This perspective focuses on the synthetic transformations, assay technologies, and platform implementations that drive modern D2B workflows. It emphasizes reaction robustness, assay compatibility, and practical implementation. Analysis of the current literature revealed that D2B is more governed by reaction reliability than synthetic diversity. Amide coupling and click chemistry dominate reported workflows, while more complex transformations remain underexplored. We discuss the complementary strengths and limitations of biochemical, biophysical, and cellular readouts, identify current bottlenecks in reaction scope and data management, and highlight emerging opportunities arising from reaction miniaturization, machine learning, automated experimentation, and advanced synthetic methodologies. Rather than replacing conventional medicinal chemistry, D2B fundamentally shifts experimental effort from purification toward early biological validation and is poised to become an integral component of future medicinal chemistry workflows.

Humans↗
PubMed2026

A scalable HPC framework for bioinformatics in resource-limited settings: design principles, implementation, and sustainability from the UVRI experience.

MOTIVATION: Building and sustaining High-Performance Computing (HPC) infrastructure for bioinformatics research in resource-limited settings presents significant technical, financial and operational challenges. Institutions in low-and middle-income regions often face constraints such as limited technical expertise, unstable infrastructure and restricted funding which can hinder the deployment of large-scale computational platforms necessary for modern genomics and bioinformatics analyses. RESULTS: We present a scalable and modular HPC framework developed at the Uganda Virus Research Institute (UVRI) to support large-scale genomics and other omics data analyses in resource-limited settings. The framework integrates open-source HPC management tools, infrastructure automation, and reproducible configuration management to enable reliable deployment and maintenance. Optimized storage and networking configurations combined with a phased capacity-building strategy support high-throughput genomic workflows while strengthening local technical expertise. From our implementation experience, we derive ten practical design and operational rules that provide a transferable methodology for establishing and sustaining in-house HPC infrastructure. These rules emphasize strategic investment in human capacity, structured planning, leveraging collaborations, adoption of open-source technologies and service management practices to improve operational resilience and long-term sustainability. AVAILABILITY: The design principles, automation strategies and implementation guidelines described in this work are applicable to institutions seeking to establish sustainable HPC resources for bioinformatics research in resource-constrained environments.

Computational Biology↗
PubMed2006

High-throughput RNAi screening by time-lapse imaging of live human cells.

RNA interference (RNAi) is a powerful tool to study gene function in cultured cells. Transfected cell microarrays in principle allow high-throughput phenotypic analysis after gene knockdown by microscopy. But bottlenecks in imaging and data analysis have limited such high-content screens to endpoint assays in fixed cells and determination of global parameters such as viability. Here we have overcome these limitations and developed an automated platform for high-content RNAi screening by time-lapse fluorescence microscopy of live HeLa cells expressing histone-GFP to report on chromosome segregation and structure. We automated all steps, including printing transfection-ready small interfering RNA (siRNA) microarrays, fluorescence imaging and computational phenotyping of digital images, in a high-throughput workflow. We validated this method in a pilot screen assaying cell division and delivered a sensitive, time-resolved phenoprint for each of the 49 endogenous genes we suppressed. This modular platform is scalable and makes the power of time-lapse microscopy available for genome-wide RNAi screens.

Automation↗
PubMedDate not supplied

Expert clinical rules automate steps in delivering evidence-based care in the electronic health record.

A working framework is presented for interdisciplinary professionals for designing, building, and evaluating clinical decision support rules (expert rules) within the electronic health record. The working framework outlines the key workflow processes for eight health system organizations for selecting, designing, building, activating, and evaluating rules. In preparation, an interdisciplinary team selected expert rules for their organizations. A physician, a nurse, and/or pharmacy informatics specialists led the team for each organization. The team chose from a catalog of expert rules that were supported by regulatory or clinical evidence. The design process ensured that each expert rule followed evidence-based guidelines and was programmed to automate steps in planning and delivering patient care. Expert rules were prioritized when improving the safety and quality of care. Finally, clinical decision support rules were evaluated for abilities to improve the consistency and currency of assessments and follow-through on patient findings from these assessments. The informatics specialists from each of the health system organizations also participated in a health system oversight group to construct the key processes for this beginning framework. The group refined the processes for the selection, design, construction, activation, and evaluation of expert rules over the past 3 years. These steps offered direction to subsequent clinic and hospital organizations in a similar situation. This case study identified four key considerations when implementing and evaluating the clinical decision support expert rules within care delivery. In summary, the processes for decision support expert rules required rigorous development and change control processes to support operation.

Decision Making, Organizational↗
PubMed2005

Comparative evaluation of the Cobas Amplicor HIV-1 Monitor Ultrasensitive Test, the new Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test and the Versant HIV RNA 3.0 assays for quantitation of HIV-1 RNA in plasma samples.

BACKGROUND: There are several commercially available assays for the quantitation of HIV RNA. A new automated specimen preparation system, the Cobas AmpliPrep, was developed to automate this last part of the PCR. OBJECTIVES AND STUDY DESIGN: We compared the results obtained by the Roche Cobas Amplicor HIV-1 Monitor Ultrasensitive Test (MCA, manual sample preparation) with those by the Versant HIV-1 RNA 3.0 assay (bDNA). Secondly we compared the MCA with the new Cobas AmpliPrep/Cobas Amplicor HIV Monitor Ultrasensitive Test (CAP/CA, automated specimen preparation) by investigating clinical patient samples and a panel of HIV-1 non-B subtypes. Furthermore, we assessed the assay throughput and workflow (especially hands-on time) for all three assays. RESULTS: Seventy-two percent of the 140 investigated patient samples gave concordant results in the bDNA and MCA assays. The MCA values were regularly higher than the bDNA values. One sample was detected only by the MCA within the linear range of quantification. In contrast, 38 samples with results <50 copies/ml in the MCA showed in the bDNA results between 51 and 1644 copies/ml (mean value 74 copies/ml); 21 of these specimens were shown to have detectable HIV RNA < 50 copies/ml in the MCA assay. The overall agreement between the MCA and the CAP/CA was 94.3% (551/584). The quantification results showed significant correlation, although the CAP/CA generated values slightly lower than those generated by the manual procedure. We found that the CAP/CA produced comparable results with the MCA test in a panel of HIV-1 non-B subtypes. CONCLUSIONS: All three assays showed comparable results. The bDNA provides a high sample throughput without the need of full automation. The new CAP/CA provides reliable test results with no HIV-subtype specific influence and releases time for other works in the laboratory; thus it is suitable for routine diagnostic PCR.

Automation↗
PubMedDate not supplied

Automated MALDI-TOF-MS sample preparation in combinatorial polymer research.

A new automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) sample spotting technique that allows the integration of MALDI sample preparation in the workflow of combinatorial polymer research is described. The technique is performed utilizing a commercially available synthetic robot and was first evaluated with polymer standards of known composition and later on used for the monitoring of the living cationic ring-opening polymerization of 2-ethyl-2-oxazoline. The spotting was carried out as a multiple layer approach, which offers the ability of complex sample preparation without the requirement of premixing the different components. The described technique reduces the time required for sample preparation and offers the possibility of automated sample spotting during polymerization reactions performed in a synthetic robot. This allows the integration of molecular weight screening and polymer end/group determination utilizing MALDI-TOF-MS as a high-throughput tool in combinatorial polymer research.

Journal Article↗
PubMed2006

A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer.

We describe a novel tissue profiling strategy that improves the cellular specificity and analysis throughput of protein profiles obtained by direct MALDI analysis. The new approach integrates the cellular specificity of histology, the accuracy and reproducibility of robotic liquid dispensing, and the speed and objectivity of automated spectra acquisition. Traditional methodologies for preparing and analyzing tissue samples rely heavily on manual procedures, which for various reasons discussed, restrict cellular specificity and sample throughput. Here, a robotic spotter deposits micron-sized droplets of matrix precisely onto foci of normal mammary epithelium, ductal carcinoma in situ, invasive mammary cancer, and peritumoral stroma selected by a pathologist from high resolution histological images of sectioned human breast cancer samples. The location of each matrix spot was then determined and uploaded into the instrument to facilitate automated profile acquisition by MALDI-TOF. In the example shown, the different lesions were clearly differentiated using mass profiling. Further, the workflow permits a visual projection of any information produced from the profile analyses directly on the histological image for a unique combination of proteomic and histological assessment of sample regions. The higher performance characteristics offered by the new workflow promises to be a significant advancement toward the next generation of tissue profiling studies.

Adult↗
PubMedDate not supplied

Kaiser Permanente Colorado Region Pharmacy Department: innovative leader in pharmacy practice.

OBJECTIVE: To describe innovative programs within the Kaiser Permanente Pharmacy Department in the Colorado Region. SETTING: One of eight regions of the nation's largest nonprofit health maintenance organization. PRACTICE DESCRIPTION: The pharmacy department comprises two services, Clinical Pharmacy Services and Pharmacy Operations/Support Services, which are integrated to provide comprehensive care. PRACTICE INNOVATION: Within Clinical Pharmacy Services, the Primary Care Clinical Pharmacy Services team works alongside physicians to provide integrated patient care. The Centralized Clinical Pharmacy Service teams manage large groups of patients effectively and efficiently. The Clinical Pharmacy Specialty staff and the Disease State Management clinical pharmacy specialists provide focused drug therapy expertise. MAIN OUTCOME MEASURES: Clinical and economic outcomes; recognition by national organizations. RESULTS: Technological innovations are used within Pharmacy Operations/Support Services to increase pharmacists' time for patient care activities. The use of technology by the Pharmacy Automated Refill Center and the implementation of ScriptPro in the medical office pharmacies decrease dispensing demands by processing large volumes of prescriptions. Workflow in the medical office pharmacies has also been reengineered to increase efficiency. Various programs have been developed by the Pharmacy Information Technology Service to support patient care initiatives. Benchmark clinical and economic outcomes have been demonstrated. Positive outcomes have also resulted in quality and safety awards and captured the attention of national pharmacy and medical organizations. CONCLUSION: The Colorado Region Pharmacy Department has been recognized as a leader in pharmacy practice through the development of innovative services that provide exceptional patient care.

Anticoagulants↗
PubMed2004

Application of receiver operating characteristics curve (ROC) analysis when definitive and suspect morphologic flags appear in the new Coulter LH 750 analyzer.

Workflow efficiency is important in every laboratory. Manual assessment of white blood cell counts and differentials that have been rejected by an automated analyzer is one of the most time-consuming tasks in the routine hematology laboratory. In this study, receiver operating characteristics (ROC) curve analysis was used for the first time when anomalous distribution and suspect flag alarms appeared in hemograms carried out with the new Beckman Coulter LH 750 analyzer. This article is our second about the LH 750 analyzer published in this journal; we increased the number of cases and describe the novel application of statistical analysis of ROC curves. In processing of specimens from patients with 3% to 6% immature granulocytes (myelocytes + metamyelocytes + bands ), the suspect flag Imm Ne 1 (immature granulocytes) showed 77% diagnostic efficiency with a maximum area under curve (AUC) of 0.71 and a 95% confidence interval (CI) of 0.597 to 0.831 without significant differences between the 3 available levels of alarms in the analyzer (L1, L2, L2). In processing of specimens from patients with >6% immature granulocytes, the Imm Ne 1 flag showed superior diagnostic efficiency of 98% with a maximum AUC of 0.80 and a CI of 0.713 to 0.879. The suspect flag Imm Ne 2 in processing of specimens from patients with >6% of immature granulocytes showed diagnostic efficiency of 92% with a maximum AUC of 0.77 and a CI of 0.665 to 0.871, finding a significant positive difference in level L3 regarding sensitivity in comparison with the other 2 levels of the analyzer (L1, L2). For specimens from patients with >2% blasts, the suspect Blasts alarm showed a diagnostic efficiency of 94%, an AUC of 0.91, and a CI of 0.775 to 1.043; positive differences were observed between the levels L2/L3 and L1. In processing of specimens with variant lymphocytes (large, granular, prolymphocytes, cleaved, chronic lymphocytic leukemia type, and so forth) >10% (x = 14%), the suspect alarm Var Lym (variant lymphocytes) showed a low diagnostic sensitivity of 20% with a maximum AUC of 0.59 and a CI of 0.300 to 0.870 without significant differences between the 3 available levels (L1, L2, L3). However, in processing of specimens presenting values >10% reactive or activated lymphocytes (x = 23%), typical for patients with infectious mononucleosis, the Var Lym flag showed a superior sensitivity of 75% with a diagnostic efficiency of 92% and an AUC of 0.84 with a CI of 0.587 to 1.089. Finally, the laboratory can easily program definitive abnormal morphological flags of distribution (granulocytosis, eosinophilia, monocytosis, and so forth) on the basis of its patient population. In this study we were able to carry out comparisons of AUC and to choose the values for the automated counts in percentage, absolute value, or both. Therefore we were able to define the reliability and impact on the alarm routine to optimize the performance of the user-adjustable definitive alarms for anomalous distribution.

Adult↗
PubMed2026

Applications of artificial intelligence in robot-assisted surgery: a systematic review.

To characterize applications of artificial intelligence (AI) in robot-assisted surgery, summarize technical and clinical performance, and assess the quality of the available evidence. PubMed, Web of Science Core Collection, and Scopus were searched for English-language journal articles published from 1 January 2020 through 31 October 2025. Randomized, observational, model-development, validation, and feasibility studies evaluating AI in robot-assisted surgery or closely related image-guided minimally invasive workflows were eligible. Two reviewers independently performed study selection, data extraction, and risk-of-bias assessment. Owing to heterogeneity in surgical procedures, AI tasks, analytical units, validation strategies, and outcomes, findings were synthesized descriptively without statistical pooling. The review was registered in the International Prospective Register of Systematic Reviews (CRD420251175699). Seventeen studies were included: seven clinical prediction or decision-support studies, eight intraoperative recognition, segmentation, or image-guided studies, and two training or workflow studies. Five prediction studies reported area-under-the-curve values of 0.74-0.95. Technical studies reported F1 or Dice scores of 0.525-0.995 and task-specific accuracies of 0.840-0.998. Two randomized studies suggested benefits for personalized suturing feedback and automated camera control, but neither established improved patient outcomes. Only one study had low overall risk of bias; the remaining studies were at high or unclear risk or raised some concerns. AI applications in robot-assisted surgery show promise for prediction, intraoperative perception, training, and workflow support. Evidence primarily demonstrates technical feasibility rather than established clinical effectiveness. Independent multicenter validation and prospective evaluation of patient, educational, and workflow outcomes are required before widespread implementation.

Robotic Surgical Procedures↗
PubMed2026

Managing workflow executions with WESkit.

SUMMARY: In biomedical research, managing computational workflows across numerous projects-with varying parameters, tools, and environments-creates major challenges in scalability, reproducibility, and collaboration. Here, we present WESkit, an implementation of the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) interface, designed to streamline the execution, monitoring, and documentation of data processing workflows. It addresses the complexities involved in managing numerous executions with varying parameters across diverse research projects. Supporting both Snakemake and Nextflow, the system enables consistent automation and centralized monitoring, which benefits research groups aiming for long-term reproducibility and scalable collaboration. Its suitability for larger teams and service units is further enhanced by seamless integration into cloud environments, contributing to the GA4GH cloud framework. AVAILABILITY AND IMPLEMENTATION: The software WESkit is available under MIT license at the GitLab repository (https://gitlab.com/one-touch-pipeline/weskit). The WESkit main repository is archived at Software Heritage (https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://gitlab.com/one-touch-pipeline/weskit/api.git) and can be found using "one-touch-pipeline/weskit" term in the search section.

Workflow↗
PubMed2006

Driving out errors through tight integration between software and automation.

A clear case has been made for using clinical IT to improve medication safety, particularly bar-code point-of-care medication administration and computerized practitioner order entry (CPOE) with clinical decision support. The equally important role of automation has been overlooked. When the two are tightly integrated, with pharmacy information serving as a hub, the distinctions between software and automation become blurred. A true end-to-end medication management system drives out errors from the dockside to the bedside. Presbyterian Healthcare Services in Albuquerque has been building such a system since 1999, beginning by automating pharmacy operations to support bar-coded medication administration. Encouraged by those results, it then began layering on software to further support clinician workflow and improve communication, culminating with the deployment of CPOE and clinical decision support. This combination, plus a hard-wired culture of safety, has resulted in a dramatically lower mortality and harm rate that could not have been achieved with a partial solution.

Humans↗
PubMed2025

LegionProfiler: a computational tool for the identification of virulence factors and classification of Legionella pneumophila serogroup 1 isolates.

SUMMARY: Legionella pneumophila has significantly contributed to multiple cases of pneumonia with a high rate of mortality globally. Its ability to exploit host mechanisms through several expressed virulence factors poses challenges for diagnosis, treatment, and outbreak control. To address this, we developed LegionProfiler, a computational tool that swiftly identifies virulence factor protein domains within genome assemblies of Legionella pneumophila serogroup 1 isolates and classifies them into high- or low-virulence groups. LegionProfiler automates the probing of genome assemblies for virulence-associated protein domains and determines the isolate's potential to cause severe pneumonia infection. The LegionProfiler workflow is made available through a user-friendly interface to enhance technical control of infectious sources and adds important insights to the general epidemiology of clinical isolates. It could also support the development of targeted therapeutic strategies that will improve patient treatment. AVAILABILITY AND IMPLEMENTATION: LegionProfiler is freely accessible as a web service at https://legionprofiler.uni-muenster.de, and can also be run locally in a Docker container. The source code can be found at https://imigitlab.uni-muenster.de/heiderlab/legionprofiler or at Zenodo (DOI: 10.5281/zenodo.15592325).

Legionella pneumophila↗
PubMed2002

End of visit: design considerations for an ambulatory order entry module.

Current paper-based processes for performing billing documentation and test ordering at the end of a clinic visit are fraught with problems, resulting in numerous workflow inefficiencies and significant revenue losses for a healthcare organization. Paper forms are often filled out inaccurately or incompletely, or can be misrouted or lost. Computerizing these processes can alleviate many of these problems. We are building a new module for our ambulatory electronic medical record system to automate these "end of visit" (EOV) activities, which includes completing encounter forms, ordering lab and diagnostic tests, and printing patient visit summaries. An EOV module must be carefully designed to incorporate the needs of clinicians, front office staff, ancillary labs, medical records, and finance departments. An optimally designed EOV system should be customizable to fit into the clinician's workflow, and should help reduce financial losses, improve clinical documentation, and reduce workflow inefficiencies.

Ambulatory Care Information Systems↗