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At least 163 records · Page 9Linked to original sources

Pilot study optimizing MEDLINE queries in an automated disease management telemedicine system.

Clinicians encounter many medical questions while providing outpatient medical care. A significant number of these questions can be answered using MEDLINE; however it has proven to be difficult to incorporate MEDLINE into routine clinical workflow and for clinicians to generate well constructed MEDLINE queries. This study however hypothesized that that well-constructed MEDLINE queries could be semi-automatically generated by an application named LitButton which was incorporated into the TeleWatch telemedicine system. The LitButton application was then prospectively evaluated in a pilot study by four nurse case managers (NCM) who monitored sixty-eight outpatients for three weeks. During this period the NCMs used the LitButton application sixteen times, and they subjectively reported in real-time that they obtained an answer in 56% of the cases, but that none of the successful information retrieval events resulted in a change in a patient's clinical management. The small number of LitButton events and lack of clinical impact was likely due to the fact that the LitButton function was designed to search MEDLINE for treatment related information; however the NCMs had limited medical decision making responsibilities. As a result there was a mismatch between the user's information needs and the system capabilities.

Case Management↗

VSQual: a visual system to assist DNA sequencing quality control.

A lack of pliant software tools that support small- to medium-scale DNA sequencing efforts is a major hindrance for recording and using laboratory workflow information to monitor the overall quality of data production. Here we describe VSQual, a set of Perl programs intended to provide simple and powerful tools to check several quality features of the sequencing data generated by automated DNA sequencing machines. The core program of VSQual is a flexible Perl-based pipeline, designed to be accessible and useful for both programmers and non-programmers. This pipeline directs the processing steps and can be easily customized for laboratory needs. Basically, the raw DNA sequencing trace files are processed by Phred and Cross_match, then the outputs are parsed, reformatted into Web-based graphical reports, and added to a Web site structure. The result is a set of real time sequencing reports easily accessible and understood by common laboratory people. These reports facilitate the monitoring of DNA sequencing as well as the management of laboratory workflow, significantly reducing operational costs and ensuring high quality and scientifically reliable results.

Database Management Systems↗

Microwave synthesis solutions from Personal Chemistry.

By fulfilling the specific design criteria required for safe and reproducible microwave synthesis, Personal Chemistry introduced the first microwave system designed for organic chemistry in 2000. The principle of microwave synthesis offers 3 major benefits to chemistry development: speed, reproducibility, and a scalable approach to compound synthesis. Additionally, significant advantages of our technical solution are ease of use, safety, verified synthesis methods to enable new users, and an efficient workflow that fits the drug discovery process. To gain the greatest advantages offered by microwave synthesis, Personal Chemistry has implemented a system called Coherent Synthesis. Incorporating planning systems, automation, distributed system access, searchable databases and reaction optimisation kits, the technology has already proved itself to dramatically improve the quality of output from medicinal chemistry for lead optimisation in all the major pharmaceutical and biotech companies.

Automation↗

A design model for computer-based guideline implementation based on information management services.

Clinical practice guidelines must be implemented effectively if they are to influence the behavior of clinicians. The authors describe a model for computer-based guideline implementation that identifies eight information management services needed to integrate guideline-based decision support with clinical workflow. Recommendation services determine appropriate activities in specific clinical circumstances. Documentation services involve data capture. Registration services integrate demographic and administrative data. Explanation services enhance the credibility of automated recommendations by providing supportive evidence and rating the quality of evidence. Calculation services measure time intervals, suggest medication dosages, and perform other computational tasks. Communication services employ standards for information transfer and provide data security. Effective presentation services facilitate understanding of complex data, clarify trends, and format written materials (including prescriptions) for patients. Aggregation services associate outcomes with specific guideline interventions. The authors provide examples of the eight services that make up the model from five evidence-based practice parameters developed by the American Academy of Pediatrics.

Decision Support Systems, Clinical↗

RESCUE: An end-to-end multi-agent LLM system for proactive rare-disease patient screening in the EHR.

BACKGROUND: Rare diseases affect a significant portion of the global population, yet patients often endure a lengthy diagnostic odyssey, frequently missing the opportunity for timely diagnoses with exome or genome sequencing (ES/GS). Existing informatics tools often rely on pre-identified patients or rigid, institution-specific rule sets, failing to address the broader operational question of clinical utility and feasibility. METHODS: We introduce RESCUE (Rare Disease Detection and Escalation Support via a Learning Health System), an end-to-end, multi-agent LLM-powered workflow designed for proactive rare-disease diagnosis across the entire electronic health record (EHR). RESCUE utilizes a team of specialized agents including Ontology, Modeling, Screening, and Review, to automate the screening process to identify candidates for diagnostic testing based on their clinical features. The Ontology Agent classifies clinical data into a four-tier genetic-evidence taxonomy; the Modeling Agent builds a positive-unlabeled (PU) XGBoost classifier to identify potential cases; the Screening Agent applies these models across the EHR population; and the Review Agent evaluates candidates by sampling clinical notes to ensure medical necessity and operational feasibility for genomic testing. RESULTS: Using electronic medical record data from a pediatric hospital, our retrospective evaluation on a holdout set (n=12,591) demonstrates strong discrimination between patients who received diagnostic genomic testing and those who did not (AUC 0.808). Of nearly 500,000 patients in the institutional base, 175,842 met inclusion criteria for screening; among these, RESCUE-flagged candidates were 7.4-fold more likely to receive subsequent genomic assessments compared to controls. Blinded manual chart reviews confirmed that RESCUE identifies previously missed, medically appropriate patients for ES/GS with 80% precision, while simultaneously accounting for prior testing history. CONCLUSIONS: By decoupling expert roles into modular agents, RESCUE offers a flexible, scalable, and adaptable framework for screening patients for rare-disease diagnostic genomic testing. This approach overcomes the limitations of traditional rule-based methods and provides a reproducible, agentic pathway to reduce diagnostic delays and improve patient care at an institutional scale.

Journal Article↗

Automated Classification of Lymphoma Subtypes From Histopathological Images Using a U-Net Deep Learning Model: Comparative Evaluation Study.

BACKGROUND: Accurate classification and grading of lymphoma subtypes are essential for treatment planning. Traditional diagnostic methods face challenges of subjectivity and inefficiency, highlighting the need for automated solutions based on deep learning techniques. OBJECTIVE: This study aimed to investigate the application of deep learning technology, specifically the U-Net model, in classifying and grading lymphoma subtypes to enhance diagnostic precision and efficiency. METHODS: In this study, the U-Net model was used as the primary tool for image segmentation integrated with attention mechanisms and residual networks for feature extraction and classification. A total of 620 high-quality histopathological images representing 3 major lymphoma subtypes were collected from The Cancer Genome Atlas and the Cancer Imaging Archive. All images underwent standardized preprocessing, including Gaussian filtering for noise reduction, histogram equalization, and normalization. Data augmentation techniques such as rotation, flipping, and scaling were applied to improve the model's generalization capability. The dataset was divided into training (70%), validation (15%), and test (15%) subsets. Five-fold cross-validation was used to assess model robustness. Performance was benchmarked against mainstream convolutional neural network architectures, including fully convolutional network, SegNet, and DeepLabv3+. RESULTS: The U-Net model achieved high segmentation accuracy, effectively delineating lesion regions and improving the quality of input for classification and grading. The incorporation of attention mechanisms further improved the model's ability to extract key features, whereas the residual structure of the residual network enhanced classification accuracy for complex images. In the test set (N=1250), the proposed fusion model achieved an accuracy of 92% (1150/1250), a sensitivity of 91.04% (1138/1250), a specificity of 89.04% (1113/1250), and an F1-score of 90% (1125/1250) for the classification of the 3 lymphoma subtypes, with an area under the receiver operating characteristic curve of 0.95 (95% CI 0.93-0.97). The high sensitivity and specificity of the model indicate strong clinical applicability, particularly as an assistive diagnostic tool. CONCLUSIONS: Deep learning techniques based on the U-Net architecture offer considerable advantages in the automated classification and grading of lymphoma subtypes. The proposed model significantly improved diagnostic accuracy and accelerated pathological evaluation, providing efficient and precise support for clinical decision-making. Future work may focus on enhancing model robustness through integration with advanced algorithms and validating performance across multicenter clinical datasets. The model also holds promise for deployment in digital pathology platforms and artificial intelligence-assisted diagnostic workflows, improving screening efficiency and promoting consistency in pathological classification.

Humans↗

Automation and high through-put for a DNA database laboratory: development of a laboratory information management system.

Automation and high through-put production of DNA profiles has become a necessity in every DNA database unit. In our laboratory we developed a Laboratory Information Management System (LIMS) controlled workflow architecture, which comprises a robotic DNA extraction- and pipetting-system and a capillary electrophoresis unit. This allows a through-put of 4,000 samples per person per year. Improved sample handling and data management, full sample- and batch-histories, and software-aided supervision of result data, with a consequent average turn-around time of 8 days, are the main features of our new system.

Austria↗

Automated protein function prediction--the genomic challenge.

Overwhelmed with genomic data, biologists are facing the first big post-genomic question--what do all genes do? First, not only is the volume of pure sequence and structure data growing, but its diversity is growing as well, leading to a disproportionate growth in the number of uncharacterized gene products. Consequently, established methods of gene and protein annotation, such as homology-based transfer, are annotating less data and in many cases are amplifying existing erroneous annotation. Second, there is a need for a functional annotation which is standardized and machine readable so that function prediction programs could be incorporated into larger workflows. This is problematic due to the subjective and contextual definition of protein function. Third, there is a need to assess the quality of function predictors. Again, the subjectivity of the term 'function' and the various aspects of biological function make this a challenging effort. This article briefly outlines the history of automated protein function prediction and surveys the latest innovations in all three topics.

Algorithms↗

Enabling virtual emergency healthcare enterprises using Web services.

Emergency healthcare delivery involves a variety of activities performed from the time of a call to the ambulance service till the time of patient's disposal from the emergency department of a hospital. As these activities are performed in at least two organizations (i.e. ambulance service and hospital) and they are interrelated to form inter-organizational healthcare processes, collaboration and coordination become a vital issue for patients and for emergency healthcare service performance. Web-based workflow systems in conjunction with web services present a new way for service-oriented integration (SOI) of disparate systems and for developing distributed applications within and between organizations. Thus, through process automation and the use of web services ambulance service and hospital emergency departments can automate their operations by making information available where and when needed and by providing an infrastructure for the integration of pre-hospital and in-hospital emergency healthcare. A prototype implementation of this approach is presented in this paper.

Computer Systems↗

Integration of radiologist peer review into clinical review workstation.

Professional peer review of random prior radiologist's interpretations is mandated by the Joint Commission on Accreditation of Healthcare Organizations (JCAHO). The JCAHO expects documentation of 5% rate of random peer-review cases. Countless hours are spent in departments fulfilling these requirements. The integration of the peer-review process into the radiologist's interpretation workflow was expected to increase the percentage of documented peer review, yet decrease the time and effort for this documentation. radStation clinical review workstations are deployed at every reading station. When a requisition is bar-coded, radStation retrieves the patient's clinical information and automatically displays the prior comparison report. If the radiologist agrees with the prior report, a single click on a "quality assurance' agree box documents the agreement. In the case of a discordance, an additional dialog box automatically appears and the radiologist enters the reason for disagreement and then submits the case as a discrepancy. The system holds the discordance for 3 to 5 working days, then notifies the original radiologist via E-mail that a prior interpretation has been submitted for peer review, lists the submitted discrepancy reason, and provides a link to display the discordant report. The peer-review database is separate from the existing radiology information system (RIS). At the end of every month, summary reports of all peer-review activity are generated automatically. Initial benchmarks of our deployed system anticipate documentation of long-term random peer-review rate at greater than 50% of interpreted cases. The system enhances the peer-review process by integrating it with the normal interpretation workflow. The time to complete peer review using radStation is less than 1 second per normal case and less than 60 seconds for a discordant case. The E-mail notification system is fully automated, eliminating the need for secretarial involvement in the data collection. This system has completely replaced a manual paper-based system. The integration of peer review directly into the radiologist's interpretation workstation greatly enhances the capability to easily exceed JCAHO standards. The overall increase in peer-review documentation should continue to improve the ability to document a consistent high quality of patient care.

Computer Communication Networks↗

Use of hybridization probes in a real-time PCR assay on the LightCycler for the detection of methicillin-resistant Staphylococcus aureus.

The rapid and accurate identification of methicillin-resistant Staphylococcus aureus (MRSA) is of great importance for the affected patient, the involved ward, and the microbiological laboratory. Resistance to methicillin is encoded by the mecA gene in S. aureus. Because routine laboratory diagnostics may be time consuming and because species differentiation encounters a variety of difficulties, molecular techniques detecting both the mecA and a S. aureus-specific gene are used for rapid and accurate detection and identification of MRSA. Various protocols, including the manual extraction of DNA have been established. In this chapter, the identification of MRSA based on simultaneous detection of the mecA gene and the S. aureus-specific Sa442 DNA fragment using automated DNA extraction and real-time polymerase chain reaction is described. This method is an attractive alternative to labor-intensive manual protocols and can easily be incorporated into the diagnostic microbiology laboratory workflow, with the ability to obtain results within 4 h.

Bacterial Proteins↗

A task-targeted automation system: a case study.

Kaiser Permanente's Northern California Regional Laboratory recently achieved an important milestone in its continuous quality improvement project by automating time-consuming and labor-intensive tasks involved in preanalytical and postanalytical sample processing. The new task-targeted automation system, the most sophisticated of its kind in the world, consists of three key components: the Roche Diagnostics PSD 1 primary sample decapper/sorter/archiver, the Roche Diagnostics VS 250 aliquoter, and a data manager/process controller developed by Data Innovations. The system was placed into service in April 1998, culminating more than a year of planning and implementation. Within months after the system went into operation, the laboratory observed significant improvements in workflow and efficiency, as well as a reduction in work-related injuries. The purpose of this article is to provide management teams in other laboratories with a description of the planning and implementation process and offer suggestions for those contemplating a similar program.

Automation↗

[Aspects of electronic patient records in radiology].

PURPOSE: The computerized patient record must provide patient- and problem-oriented access to all relevant patient data for health care professionals. The aspects of such systems will be analyzed in the light of the radiologist's needs. METHODS: Integration of the computerized patient record in a hospital communication network allows automated data exchange with the ancillary systems. Accessibility of electronic textbooks supports case-based learning during routine work. RESULTS: The computerized patient record not only supports routine clinical tasks but also training, education and research. The workflow in a hospital can be supported by the computerized patient record. Studying the tasks of a radiology department shows that both clinicians and radiologists will benefit from such a system. DISCUSSION: Current implementations of clinical computerized workstations offer only a fraction of these features. Advances in technology and increasing demands at the point of care will promote the development of new information systems of this kind.

Computer Systems↗

Lectin capture strategies combined with mass spectrometry for the discovery of serum glycoprotein biomarkers.

The application of mass spectrometry to identify disease biomarkers in clinical fluids like serum using high throughput protein expression profiling continues to evolve as technology development, clinical study design, and bioinformatics improve. Previous protein expression profiling studies have offered needed insight into issues of technical reproducibility, instrument calibration, sample preparation, study design, and supervised bioinformatic data analysis. In this overview, new strategies to increase the utility of protein expression profiling for clinical biomarker assay development are discussed with an emphasis on utilizing differential lectin-based glycoprotein capture and targeted immunoassays. The carbohydrate binding specificities of different lectins offer a biological affinity approach that complements existing mass spectrometer capabilities and retains automated throughput options. Specific examples using serum samples from prostate cancer and hepatocellular carcinoma subjects are provided along with suggested experimental strategies for integration of lectin-based methods into clinical fluid expression profiling strategies. Our example workflow incorporates the necessity of early validation in biomarker discovery using an immunoaffinity-based targeted analytical approach that integrates well with upstream discovery technologies.

Amino Acid Sequence↗

Bridging the gap: linking a legacy hospital information system with a filmless radiology picture archiving and communications system within a nonhomogeneous environment.

A health level 7 (HL7)-conformant data link to exchange information between the mainframe hospital information system (HIS) of our hospital and our home-grown picture archiving and communications system (PACS) is a result of a collaborative effort between the HIS department and the PACS development team. Based of the ability to link examination requisitions and image studies, applications have been generated to optimise workflow and to improve the reliability and distribution of radiology information. Now, images can be routed to individual radiologists and clinicians; worklists facilitate radiology reporting; applications exist to create, edit, and view reports and images via the internet; and automated quality control now limits the incidence of "lost" cases and errors in image routing. By following the HL7 standard to develop the gateway to the legacy system, the development of a radiology information system for booking, reading, reporting, and billing remains universal and does not preclude the option to integrate off-the-shelf commercial products.

Computer Communication Networks↗

AI In Leukemia Diagnostics: Complementing the Pathologist's Role.

Artificial intelligence (AI) is reshaping every stage of leukemia diagnostics, from digital morphology and multiparameter flow cytometry to next-generation sequencing, multi-omics analysis, and emerging computational frontiers such as quantum-inspired feature selection. This review outlines how contemporary AI tools can automate labor-intensive quantitation, flag diagnostically salient patterns, and standardize interpretation, while the pathologist or hematologist retains authority over validation, context-specific integration, and clinical decision-making. We present an illustrative "human-in-the-loop" workflow that embeds AI modules within current laboratory information systems, emphasizing points where expert oversight mitigates algorithmic bias and resolves discordant findings. We further map the validator-integrator role across morphology, flow cytometry, and genomic/multi-omic interpretation and provide practical training competencies and use cases for AI-assisted hematopathology. Beyond technical deployment, the article addresses the educational transformation required for sustainable adoption. Drawing on international competency frameworks, including the Digital Health Competencies in Medical Education Framework and recently proposed AI-specific Entrustable Professional Activities, we map core skills that future hematopathologists must master: data-science literacy, critical appraisal of AI outputs, and ethical governance. We highlight evaluated training models such as the Pathology Informatics Essentials for Residents curriculum, Stanford Artificial Intelligence in Machine and Imaging workshops, and College of American Pathologists bootcamps and propose integration strategies adaptable across resource settings. By pairing rigorous validation with targeted education, AI can elevate rather than eclipse the diagnostic role of the leukemia specialist, enabling more timely, reproducible, and personalized patient care.

Humans↗

AI-driven CRISPR screening: optimizing gene editing through automation and intelligent decision support.

BACKGROUND: CRISPR-based genetic screening has become a central methodology in functional genomics, enabling systematic interrogation of gene function, genetic interactions and context-dependent vulnerabilities at scale. However, the rapid expansion of screening modalities-including multi-condition designs, combinatorial perturbations, in vivo applications and single-cell readouts-has exposed fundamental limitations of heuristic-driven experimental design and post hoc statistical analysis. MAIN BODY: This Review synthesizes how artificial intelligence is reshaping CRISPR screening by introducing predictive, adaptive and system-level intelligence across the experimental lifecycle. We organize recent advances into two tightly coupled modules. First, machine learning and deep learning (ML/DL) methods optimize experimental design by learning context-dependent perturbation behavior, anticipating confounding effects and enabling iterative, information-efficient screening strategies. Second, large language model-agent (LLM-agent) systems complement these advances by externalizing scientific reasoning, integrating biological knowledge at scale and coordinating analysis and decision-making in human-in-the-loop workflows. CONCLUSIONS: Together, ML/DL and LLM-agent approaches reframe CRISPR screening from a static analytical pipeline into an intelligent experimental system, with important implications for robustness, scalability and biological discovery.

Artificial Intelligence↗