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At least 1,369 records · Page 76Linked to original sources

PubMed2005

Advanced navigation planning including soft tissue management.

The OrthoPilot TKA Version 4.2 (B. Braun-Aesculap, Tuttlingen, Germany) offers software support for orthopedic surgeons. The system provides nearly normal manual workflow, creates perfect cuts, allows for sophisticated management of soft tissue, and respects individual anatomies. The OrthoPilot TKA Version 4.2 displays information to guide surgical decisions. However, surgeons decide if the information will be used during the resection. The most important advancements in the Version 4.2 software are the calculation of perfect rotation of the femoral component and optimal gap balancing.

Arthroplasty, Replacement, Knee↗

PubMed2005

Webcasting: a new instructional technology in distance graduate nursing education.

Webcasting is a new instructional technology used to deliver audio and video presentations via the Internet, enabling learners to participate in a live class via a personal computer. In this article, we describe the workflow involved in producing a Webcast class and provide a detailed account of the process of adopting Webcasting as a medium to provide distance education at a state university in a rural setting. This article addresses the team members required to seamlessly integrate Webcasting into the curriculum: information technology specialists, faculty, students, and administrators. We also identify problems encountered with implementation of Webcasting and methods used to resolve them.

Adult↗

PubMedDate not supplied

Tissue microarrays: potential in the Indian subcontinent.

Tissue microarrays (TMAs) are a means of combining hundreds of specimens of tissue on to a single slide for analysis simultaneously. The evolution of this technology to validate the results of cDNA microarrays has impacted tremendously in accurately identifying prognostic indicators significant in determining survival demographics for patients. TMAs can be generated from archival paraffin blocks, combined with sophisticated image analysis software for reading TMA immunohistochemistry, and a staggering amount of useful information can be generated in terms of the biomarkers useful in predicting patient outcome. There is a wide range of uses for the TMA technology including profiling of specific proteins in cancerous tissues and non-cancerous tissues. Given the wide variety of tissue resources available in India, investment in a dedicated TMA facility will be of immense use in the research arena in India. This review article discusses the basics of TMA construction, design, the software available for the analysis of this technology and its relevance to Indian scientists. A potential workflow structure for setting up a TMA facility is also included.

Biomarkers, Tumor↗

PubMed1979

Rapid cholesterol measurement: patient classification in heart risk evaluation clinics.

Plasma cholesterol levels of patients attending a heart risk evaluation clinic were measured both in the clinic at the time of attendance, and later in a reference laboratory. The workflow of evaluation clinics may be improved, and patient satisfaction enhanced, by in situ measurement, since more than 60% of patients can be given a complete risk score at the time of attendance.

Cholesterol↗

PubMed2003

General practitioners' perceptions of the pharmaceutical decision-support tools in their prescribing software.

OBJECTIVES: To explore how Australian general practitioners use pharmaceutical decision-support (PDS) systems; to determine GPs' perceptions of the deficiencies and strengths of these systems; and how they believe they can be improved. DESIGN AND SETTING: Qualitative analysis of discussion from three focus groups of GPs (from one rural and two urban Divisions of General Practice) between April and May 2002. PARTICIPANTS: 22 GPs selected to include users of the five most popular prescribing/clinical practice software products available in Australia. MAIN OUTCOME MEASURES: Advantages and disadvantages of using PDS software; ideas for improving PDS systems; attitudes to electronic evidence-based guidelines. RESULTS: GPs believed that important interactions may be missed because of desensitisation resulting from too many alerts (which also intrude on workflow); that interaction alerts need to be severity graded and only significant ones should appear; and that improved computer-user interface design could enhance the usefulness of PDS systems. CONCLUSIONS: Our results will provide useful feedback to government, software vendors and software developers on the needs and expectations of end users and on the development of agreed software standards.

Attitude of Health Personnel↗

PubMed2003

Automation of gross photography using a remote-controlled digital camera system.

CONTEXT: Conventional gross photography requires a series of tedious and time-consuming steps, including taking, developing, labeling, sorting, filing, and tracking numerous photographs. OBJECTIVE: To describe how to automate the gross photographic process by way of controlling a digital camera remotely. DESIGN: After defining the requirements of automation regarding gross photography, a remote control board, foot switch, barcode system, and image retrieval system were devised. SETTING: The surgical pathology laboratory of a university medical center with a commercially available megapixel digital camera. RESULTS: The digital camera zoom and shutter were controlled remotely by a foot switch. A large portion of the gross photographic process, including specimen number labeling, image downloading, labeling, sorting, filing, and tracking, were automated. In addition, the elimination of several manual specimen-processing steps, along with not having to wait for the developing and mounting of conventional 35-mm film, reduced the entire time span required in conventional gross photography from 2 to 5 days, to a few minutes. It was also possible to review the gross images at the time of microscopic sign-out. CONCLUSIONS: The automation of gross photography using a remote-controlled digital camera changes the conventional gross workflow markedly. We found use of a remote-controlled gross photography system to be practical, convenient, and efficient.

Cost-Benefit Analysis↗

PubMed2004

Physician survey of a laboratory medicine interpretive service and evaluation of the influence of interpretations on laboratory test ordering.

CONTEXT: Complex coagulation test panels ordered by clinicians are typically reported to clinicians without a patient-specific interpretive paragraph. OBJECTIVES: To survey clinicians regarding pathologist-generated interpretations of complex laboratory testing panels and to assess the ability of the interpretations to educate test orderers. DESIGN: Surveys were conducted of physicians ordering complex coagulation laboratory testing that included narrative interpretation. Evaluation of order requisitions was performed to assess the interpretation's influence on ordering practices. SETTING: Physicians ordering coagulation testing at a large academic medical center hospital in Boston, Mass, and physicians from outside hospitals using the academic medical center as a reference laboratory for coagulation testing. OUTCOME MEASURES: Physician surveys and evaluation of laboratory requisition slips. RESULTS: In nearly 80% of responses, the ordering clinicians perceived that the interpretive comments saved them time and improved the diagnostic process. Moreover, the interpretations were perceived by ordering clinicians to help prevent a misdiagnosis or otherwise impact the differential diagnosis in approximately 70% of responses. In addition, interpretations appeared to be able to train the ordering clinicians as to the standard ordering practices. CONCLUSIONS: The results demonstrate physician satisfaction with an innovative information delivery approach that provides laboratory diagnostic interpretation and test-ordering education to clinicians in the context of their daily workflow.

Academic Medical Centers↗

PubMed2005

Error and error reduction in pathology.

CONTEXT: Since publication of the Institute of Medicine's report on medical error in late 1999, there has been widespread interest in improving patient safety and in error reduction in all disciplines of medicine. In fields other than medicine, considerable knowledge has been obtained concerning error and error reduction. This body of knowledge can be successfully applied to pathology in order to make the specialty safer and less error prone. OBJECTIVES: To review the fundamental conclusions of the Institute of Medicine's report on medical error, to provide a taxonomy of error that can be adapted to pathology, to provide a framework for studying and analyzing error in pathology, to contrast different approaches to error, and to explain the concept of a culture of safety. DESIGN: Review of pertinent literature, analysis of concepts of error reduction and safety used in other disciplines, analysis of pathology workflow, and adaptation of safety practices to the practice of pathology. RESULTS: A taxonomy for error is described and adapted to pathology, a framework for error in the specialty is described, and characteristics of a culture of safety for pathology are proposed. CONCLUSIONS: Fundamental concepts of error reduction and safety improvement exist in other disciplines and can successfully be adapted to pathology.

Diagnostic Errors↗

PubMed2026

Long-Read Haplotype Phasing Resolves Allelic Configuration as a Missing Layer of Precision Oncology.

Conventional short-read sequencing cannot determine whether co-occurring variants within a cancer gene reside on the same allele (cis) or on opposing alleles (trans), a distinction with direct biological and therapeutic consequences. Trans configurations confirm biallelic tumor suppressor inactivation and inform therapy selection, while cis configurations generate compound oncogenic alleles with enhanced activity. We analyzed 768 patients with prostate, breast, or ovarian cancers in the PROBLEM cohort, using mutational signatures to nominate cryptic genomic instability cases where the causative biallelic event was not apparent from short-read sequencing. Long-read nanopore sequencing resolved 32 of 46 cryptic cases (69.6%), leveraging its unique advantages in direct methylation detection, long insertion resolution, and complex structural variant characterization, confirming trans biallelic inactivation in all resolved tumor suppressor cases. Systematic analysis of 4,496 MiOncoSeq samples identified 17,519 multi-hit gene pairs, of which 78.7% exceeded the 500 bp short-read phasing limit. Long-read phasing further revealed recurrent compound cis oncogenic alleles in NOTCH1, PIK3CA, PDGFRB, and KIT with functionally synergistic activity. Haplotype phasing resolves a systematically overlooked gap in cancer variant interpretation and warrants broader integration into precision oncology workflows.

Journal Article↗

PubMed2026

Functional screening of ZIP8 naturally occurring variants identifies pathogenic mutations and trafficking defects.

The rapid expansion of human genomic data has revealed a large number of naturally occurring variants, creating a major challenge for functional annotation. The human metal transporter SLC39A8 (ZIP8) is a clinically important, promiscuous divalent metal transporter, yet most of its documented variants remain uncharacterized. Here, we developed a workflow to functionally evaluate ZIP8 variants by integrating laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) with scaled-up cell-based transport assays. Using this method, we systematically analyzed 33 naturally occurring missense variants located in the extracellular domain (ECD) of ZIP8. The assay enables direct quantification of intracellular metal accumulation with substantially improved throughput (~150 samples per hour). Functional screening identified 14 potential pathogenic variants with significantly reduced transport activity. Comparison with computational predictions revealed a moderate correlation between activity and AlphaMissense pathogenicity scores (R2 = 0.423), while an error rate of ~20% underscores the need for experimental validation. Flow cytometry analysis showed that most loss-of-function variants exhibit impaired trafficking of the protein to the cell surface possibly due to mutation-caused protein misfolding or instability. Structural mapping of activity-compromised variants, together with functional assessment of the ZIP8-ECD, highlights the importance of this domain in ZIP8 expression and intracellular trafficking. Together, this work establishes a scalable approach for functional screening of metal transporter variants and provides new insights into the structure-function relationships of ZIP8.

Journal Article↗

PubMed2026

High-Dimensional Sensitivity Analysis for Genomic Studies: An Adversarial Framework for Learning Worst-Case Latent Confounders.

High-dimensional genomics studies are frequently confounded by unmeasured biological processes that obscure disease-specific signals. While existing workflows can estimate these latent confounders, they fail to quantify how robust a discovery is to varying levels of hypothetical confounding. We introduce sensGAN, a deep-learning adversarial framework that systematically explores the confounding spectrum by learning "worst-case" latent variables that nullify the most gene associations under novel predictive-gain constraints. By identifying the minimum confounding strength required to explain away an observed effect, our method shifts the paradigm toward a formal, quantitative sensitivity analysis. In diverse simulations, sensGAN accurately recovers latent structures and outperforms existing methods in identifying confounder-sensitive genes. Applied to human Alzheimer's disease microglia, our framework prioritizes robust disease pathways while successfully isolating signals driven by unmeasured co-occurring neurodegenerative pathologies. Our method is publicly available, deposited at the GitHub repository yifanlinz/ADsensitivityICML.

Journal Article↗

PubMed2026

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↗

PubMed2026

MKMC enables reference-free transcriptomic analysis using k-mer representations.

Traditional RNA-seq analysis depends heavily on genome alignment and gene annotation, limiting its utility in non-model organisms and introducing biases that can obscure regulatory complexity. We present MKMC (Multi-sample Kmer Counter), a scalable, reference-free toolkit for RNA-seq analysis that leverages k-mer-based statistics to detect biological variation without requiring alignment. MKMC integrates fast k-mer counting, abundance matrix generation, normalization, dimensionality reduction, and differential analysis into a unified workflow. Across diverse datasets, MKMC recapitulates key biological signals-including sex differences in killifish liver-and matches alignment-based pipelines in differential expression analysis and transcriptomic age prediction. Notably, MKMC detects isoform-specific events missed by traditional methods, one of which we validated using in situ hybridization. These results reveal previously hidden isoform-level regulatory events that contribute to sex- and age-associated transcriptional programs. MKMC offers a robust, extensible alternative to alignment-based approaches, enabling transcriptomic discovery across both model and non-model systems. While we focus here on RNA-seq as a primary application, MKMC is broadly applicable to any k-mer-based analysis of next-generation sequencing data.

MKMC↗

PubMed2026

DNA-FISH Metaphase Spreads to Distinguish Extrachromosomal DNA from Homogeneously Staining Regions in Human Cancer Cell Lines.

UNLABELLED: Whole-genome sequencing identifies focal DNA amplifications with base-pair resolution but cannot determine whether amplified sequences reside on extrachromosomal DNA (ecDNA, also known as double minutes) or within chromosomally integrated homogeneously staining regions (HSRs). DNA fluorescence in situ hybridization (DNA-FISH) metaphase spreads remain the gold standard for distinguishing these amplification states at single-cell resolution. Here, we present a detailed protocol for DNA-FISH metaphase spreads using human cancer cell lines, encompassing cell culture, metaphase arrest, hypotonic treatment, fixation, chromosome spreading, fluorescent probe hybridization, and fluorescence imaging. The protocol incorporates intermediate quality-control steps to verify successful chromosome dispersion and optimize metaphase spread quality, making the workflow accessible to laboratories without specialized cytogenetics expertise. Results demonstrate clear visualization of ecDNA and HSR amplification states using locus-specific probes and illustrate common technical artifacts that can affect interpretation. This protocol provides a robust and reproducible approach for studying the structural organization of oncogene amplification in cancer cells. SUMMARY: We report a DNA-FISH metaphase spread protocol that visually detects locus copy number and location within the genome. This approach enables single-cell resolution of amplification states, specifically in cancer cell lines containing extrachromosomal DNA and homogeneously staining regions.

Journal Article↗

PubMed2026

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses.

Electronic health record (EHR)-linked biobanks generate unprecedented genomic and phenotypic datasets, but their scientific utility is constrained by data fragmentation across institutional silos and incompatible computing infrastructures, forcing researchers to rewrite ad-hoc scripts for each new environment. We present the PMBB Geno-Pheno Toolkit, a suite of modular Nextflow pipelines for biobank-scale association analyses. This note focuses on the toolkit's SAIGE family of pipelines - supporting genome-wide (GWAS), exome-wide (ExWAS), and phenome-wide (PheWAS) association testing - together with the companion GWAMA and ExWAS meta-analysis pipelines that enable cross-biobank replication. All components are containerized (Docker/Apptainer) and orchestrated with Nextflow, allowing the same workflows to run unmodified on local HPC clusters, cloud platforms, and the All of Us Research Workbench. Complementary toolkit pipelines for PLINK-based GWAS, polygenic scoring, LD-based clumping, and phenotype harmonization are also available and briefly noted.

Journal Article↗

PubMed2006

Current challenges in adherence to clinical guidelines for antibiotic prophylaxis in surgery.

UNLABELLED: To study the impact of guidelines on surgical antibiotic prophylaxis in clinical practice, barriers involved in adherence to guidelines and how to overcome the same. METHODS: Literature pertaining to prophylactic antibiotic usage was searched. Medscape, Medline, Cochrane, Surgical Infection Prevention (SIP) project databases were reviewed. Recent articles from relevant journals, texts, and standard guidelines were also studied. RESULTS: Local guidelines seem more likely to be accepted and followed than those developed nationally. Major barriers involved in adherence to guidelines include lack of awareness about the guidelines, general perception of guideline as a bureaucratic rather than educational tool. Some practitioners perceive guidelines as "cookbook medicine" that does not permit them to make their own medical decisions. Other barriers are complex, multi-step systems that create confusion, decrease accountability. Methods for guideline adherence include surveillance and data analysis, new systems to facilitate documentation and improving workflow, education regarding current evidence-based guidelines and promoting the development of local guidelines or protocol, development and implementation of reminders to facilitate adherence to the local guidelines. CONCLUSION: A multidisciplinary steering team of surgeons, infectious disease specialists, pharmacists, anesthesiologists, microbiologists and nurses should develop local guidelines suitable to their institution and methods for adherence to prevent the surgical site infections. The gap between evidence-based guidelines and practice must be addressed in order to achieve optimal practice in this domain.

Antibiotic Prophylaxis↗

PubMed1991

CQI (continuous quality improvement) system puts process into improving hospital.

Hospital departments in the 1990s will be increasingly called on to run efficiently if institutions are to improve their bottom lines. But, how do administrators address problems that interfere with workflow and completing jobs? In the following article, the author introduces a quality process to identify and deal with those issues.

California↗

PubMed1992

Washer-sterilizers vs. indexed washer-decontaminators: a cost comparison.

Washer-sterilizers are the most common type of automated decontamination equipment in hospitals today, but from a cost standpoint, installing an indexed washer-decontaminator makes more sense for hospitals with active decontamination areas. An indexed washer-decontaminator is a highly productive and efficient machine that results in streamlined workflow in decontamination. Even in hospitals that own washer-sterilizers, the economics can be so compelling that they might want to consider replacing them with indexed washer-decontaminators.

Costs and Cost Analysis↗