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At least 415 records · Page 23Linked to original sources

PubMed2000

Clinical outcomes of point-of-care testing in the interventional radiology and invasive cardiology setting.

BACKGROUND: Point-of-care testing (POCT) can provide rapid test results, but its impact on patient care is not well documented. We investigated the ability of POCT to decrease inpatient and outpatient waiting times for cardiovascular procedures. METHODS: We prospectively studied, over a 7-month period, 216 patients requiring diagnostic laboratory testing for coagulation (prothrombin time/activated partial thromboplastin time) and/or renal function (urea nitrogen, creatinine, sodium, and potassium) before elective invasive cardiac and radiologic procedures. Overall patient management and workflow were examined in the initial phase. In phase 2, we implemented POCT but utilized central laboratory results for patient management. In phase 3, therapeutic decisions were based on POCT results. The final phase, phase 4, sought to optimize workflow around the availability of POCT. Patient wait and timing of phlebotomy, availability of laboratory results, and therapeutic action were monitored. Split sampling allowed comparability of POCT and central laboratory results throughout the study. RESULTS: In phase 1, 44% of central laboratory results were not available before the scheduled time for procedure (n = 135). Mean waiting times (arrival to procedure) were 188 +/- 54 min for patients who needed renal testing (phase 2; n = 14) and 171 +/- 76 min for those needing coagulation testing (n = 24). For patients needing renal testing, POCT decreased patient wait times (phases 3 and 4 combined, 141 +/- 52 min; n = 18; P = 0.02). For patients needing coagulation testing, wait times improved only when systematic changes were made in workflow (phase 4, 109 +/- 41 min; n = 12; P = 0.01). CONCLUSIONS: Although POCT has the potential to provide beneficial patient outcomes, merely moving testing from a central laboratory to the medical unit does not guarantee improved outcomes. Systematic changes in patient management may be required.

Cardiovascular Surgical Procedures↗

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↗

PubMed2004

Integration brings all-round benefits.

Integration of workflow, technology and architecture provides the means to enable hospital staff not only work smarter and more efficiently but also to enjoy their work experience. Patients also benefit from a planned proven outcome in a more ergonomic and pleasant environment--all of which will improve their overall healthcare experience. A process-based approach mirrors the philosophy of a Treatment Centre and we believe that it is a must within an environment of growing complexity that demands faster and improved services--all to be managed with minimal risk. Siemens structures its business according to this approach and is dedicated to helping healthcare providers around the world to improve their performance by enabling truly synchronised workflow throughout the entire healthcare enterprise. We see the massive opportunities for radical efficiency gains in our day-to-day work--all it needs is an early-phase integration of workflow, technology and the physical environment.

Efficiency, Organizational↗

PubMedDate not supplied

HIS/RIS/PACS integration: getting to the gold standard.

The technology for acquiring, storing, retrieving, displaying, and distributing images has advanced dramatically in recent years. The push is toward enterprise-wide image management solutions, where digital images from radiology, cardiology, and other "ologies" are seamlessly linked with information from clinical information systems and other databases, and they are accessed seamlessly from a single point of end-user interaction. The "gold standard" of system integration would provide the platform for improved workflow, patient throughput and patient safety, as well as decreased cost. Unfortunately, the gold standard remains elusive in most healthcare environments, even those with new systems. One of the earliest issues that plagued the progress of hospital information system/radiology information systems/picture archiving and communication systems (HIS/RIS/PACS) integration was a matter of language between Health Level-7 (HL7) and DICOM. This barrier was solved by the broker--a software and hardware device that accepts HL7 messages from the RIS then translates, or maps, the data to produce DICOM messages for transmission to the PACS. Technologist workflow requires patient and exam information from the RIS to flow to the modality. The broker provides support for this by taking advantage of the DICOM Modality Worklist (DMWL). Two primary problems are inherent in most brokered configurations. Workflow is driven by paper, and RIS information flows in 1 direction only, which leads to duplicative databases. Overcoming the limitations of HIS/RIS/PACS connectivity requires industry accepted communication protocols/rules. To facilitate this, the Integrating the Health Care Enterprise (IHE) initiative was developed. The goal of IHE is to provide end-users improved access to critical patient and clinical information across all systems within the healthcare delivery network. While the IHE initiative began to facilitate more efficient, predictable, and functional integration between disparate systems, vendors still had technology hurdles to overcome. System integration continues to be significantly hampered, not by technology limitations, but instead by business and political issues. In response to these challenges, several vendors have begun to offer consolidated RIS/PACS solutions and/or HIS/RIS/PACS solutions. Consequently, the prospect of the gold standard appears to be on the horizon. Single vendor consolidated systems are not, however, feasible for deployment in many healthcare organizations, and they are not necessarily the panacea.

Database Management Systems↗

PubMed2004

The impact of automation on organizational changes in a community hospital clinical microbiology laboratory.

The diagnosis of infectious diseases and the role of the microbiology laboratory are currently undergoing a process of change. The need for overall efficiency in providing results is now given the same importance as accuracy. This means that laboratories must be able to produce quality results in less time with the capacity to interpret the results clinically. To improve the clinical impact of microbiology results, the new challenge facing the microbiologist has become one of process management instead of pure analysis. A proper project management process designed to improve workflow, reduce analytical time, and provide the same high quality results without losing valuable time treating the patient, has become essential. Our objective was to study the impact of introducing automation and computerization into the microbiology laboratory, and the reorganization of the laboratory workflow, i.e. scheduling personnel to work shifts covering both the entire day and the entire week. In our laboratory, the introduction of automation and computerization, as well as the reorganization of personnel, thus the workflow itself, has resulted in an improvement in response time and greater efficiency in diagnostic procedures.

Automation↗

PubMed2002

Implementation of a publication-subscription environment within a multi-agents paradigm.

Information management are workflow are one of the most important challenges to be met in hospitals. This challenge is even more important when having to deal with getting the right information at the right place, including such tools as alerts and notification. Open distributed intelligent agents constitute one of the most promising ways to explore, providing both ability to work in heterogeneous environment, and dealing with highly structured semantic knowledge. The paradigm proposed in this work is to consider a publication/subscription system as collaborative procedures network organized in workflows modelled by Petri nets. Each stage of workflow is carried out by a set of agent units having placed their competences in a workspace with a semantic description. Finally, robustness and tolerance are implicit properties of such agents; two mandatory characteristics of healthcare information systems.

Efficiency, Organizational↗

PubMedDate not supplied

Improving medical imaging report turnaround times: the role of technolgy.

At Southern Ohio Medical Center (SOMC), the medical imaging department and the radiologists expressed a strong desire to improve workflow. The improved workflow was a major motivating factor toward implementing a new RIS and speech recognition technology. The need to monitor workflow in a real-time fashion and to evaluate productivity and resources necessitated that a new solution be found. A decision was made to roll out both the new RIS product and speech recognition to maximize the resources to interface and implement the new solution. Prior to implementation of the new RIS, the medical imaging department operated in a conventional electronic-order-entry to paper request manner. The paper request followed the study through exam completion to the radiologist. SOMC entered into a contract with its PACS vendor to participate in beta testing and clinical trials for a new RIS product for the US market. Backup plans were created in the event the product failed to function as planned--either during the beta testing period or during clinical trails. The last piece of the technology puzzle to improve report turnaround time was voice recognition technology. Speech recognition enhanced the RIS technology as soon as it was implemented. The results show that the project has been a success. The new RIS, combined with speech recognition and the PACS, makes for a very effective solution to patient, exam, and results management in the medical imaging department.

Contract Services↗

PubMed2005

Purchasing a PACS: from planning to procurement.

Picture archiving and communication systems (PACS) are highly versatile data storage and retrieval systems that facilitate the transfer of digital images and patient data throughout a healthcare enterprise. They process images from diagnostic modalities and are interfaced to radiology information systems and hospital information systems to improve workflow. Ensuring that you select a PACS that is optimal for your facility requires planning and judgment. It also requires that you define your needs based on optimal workflow, clearly convey those needs to prospective suppliers, and organize responses for easy comparison. In this article, we outline the steps needed to prepare for a PACS purchase: (1) defining the scope of your PACS, (2) analyzing your workflow requirements so that you can plan workstation deployment, (3) ensuring adequate integration, (4) planning for your image-storage needs, (5) ensuring security, and (6) putting together an effective request for proposal.

Humans↗

PubMed2006

Benefiting from ambulatory EHR implementation: solidarity, six sigma, and willingness to strive.

Ambulatory electronic health record systems have the potential to improve healthcare quality. Optimizing the value of EHR implementation requires that providers and staff become effective and efficient EHR users so paper charts are no longer required or desired. Transitioning from paper charts to EHR systems requires new learning, significant effort, and workflow changes associated with an initial adverse effect on provider efficiency. This case study describes how timely EHR implementation and regular use in a large academic internal medicine clinic was encouraged, achieved, and demonstrated. Critical success factors included readiness to change, solidarity in EHR use, a commitment to striving, and process improvement strategies that used the EHR system to repair suboptimal clinic workflows. Observed benefits include improvements in patient access, workflow efficiency, communication, decision support use, and financial performance. These success factors and implementation strategies may help others seeking to encourage greater adoption and use of EHRs.

Cost-Benefit Analysis↗

PubMed2006

Developing a lean culture in the laboratory.

The Director of Pathology at Jackson Memorial Hospital was interested in improving the operational efficiencies of the department in order to enhance the department's level of service in conjunction with the expansion of the overall health system. The decision was made to implement proven Lean practices in the laboratory under the direction of a major consulting firm. This article details the scope of the initial project as well as the operating principles of Lean manufacturing practices as applied to the clinical laboratory. The goals of the project were to improve turnaround times of laboratory results, reduce inventory and supply costs, improve staff productivity, maximize workflow, and eliminate waste. Extensive data gathering and analysis guided the work process by highlighting the areas of highest opportunity. This systematic approach resulted in recommendations for the workflow and physical layout of the laboratory. It also included the introduction of "standard workflow" and "visual controls" as critical items that streamlined operational efficiencies. The authors provide actual photographs and schematics of the reorganization and improvements to the physical layout of the laboratory. In conclusion, this project resulted in decreased turnaround times and increased productivity, as well as significant savings in the overall laboratory operations.

Clinical Laboratory Techniques↗

PubMed2006

Integrating anatomical pathology to the healthcare enterprise.

For medical decisions, healthcare professionals need that all required information is both correct and easily available. We address the issue of integrating anatomical pathology department to the healthcare enterprise. The pathology workflow from order to report, including specimen process and image acquisition was modeled. Corresponding integration profiles were addressed by expansion of the IHE (Integrating the Healthcare Enterprise) initiative. Implementation using respectively DICOM Structured Report (SR) and DICOM Slide-Coordinate Microscopy (SM) was tested. The two main integration profiles--pathology general workflow and pathology image workflow--rely on 13 transactions based on HL7 or DICOM standard. We propose a model of the case in anatomical pathology and of other information entities (orders, image folders and reports) and real-world objects (specimen, tissue samples, slides, etc). Cases representation in XML schemas, based on DICOM specification, allows producing DICOM image files and reports to be stored into a PACS (Picture Archiving and Communication System.

Diagnostic Imaging↗

PubMed2006

Clinical pathways development and computer support in the EPR: lessons learned.

This paper refers to a project for development and optimization of a clinical pathway for the Lumbar Nerve Root Compression Syndrome. A special focus is taken on computer support for pathway development and implementation. An innovative combination of "rapid prototyping" of a workflow model and a 2 level approach using round robin methods in a large group and individual semi-structured interviews is presented. The method focuses on process optimization instead of process modeling and concentrates on areas of the workflow which may be optimized. Critical parts of the optimized clinical workflow have been implemented inside a commercial electronic patient record system.

Critical Pathways↗

PubMed1995

A case study: business process re-engineering (BPR) of the order-/delivery process at the pediatric clinic at the University Hospital of Lund.

The traditional order and delivery activities have been characterized by manual routines and a paper-based workflow management. Problems such as the time consuming processes in which a laboratory service order is created or that of getting the laboratory service report with results from the requested investigations from the laboratories and the entry of the same information by different persons at different points in the workflow with the possibilities of transfer errors are well known. The development of modern information technology, along with the developing of standards for communication protocols and the message structure for the electronic interchange of information (EDI) gives us the tools to change the way we work and manage workflow. An important input to the business process reengineering process is a thorough knowledge of the context within which the order-/delivery activities exist. One has to take into account that the activities are: 1) heavily integrated in the whole treatment and care process, 2) together with routines and the taking of samples and related requests many times are a part of the daily work of a ward, and 3) many decisions about the treatment of a patient are based on the results in the laboratory service report from the laboratories.

Hospital Information Systems↗

PubMed2025

Backtracking Cell Phylogenies in the Human Brain with Somatic Mosaic Variants.

Somatic mosaic variants, and especially somatic single nucleotide variants (sSNVs), occur in progenitor cells in the developing human brain frequently enough to provide permanent, unique, and cumulative markers of cell divisions and clones. Here, we describe an experimental workflow to perform lineage studies in the human brain using somatic variants. The workflow consists in two major steps: (1) sSNV calling through whole-genome sequencing (WGS) of bulk (non-single-cell) DNA extracted from human fresh-frozen tissue biopsies, and (2) sSNV validation and cell phylogeny deciphering through single nuclei whole-genome amplification (WGA) followed by targeted sequencing of sSNV loci.

Humans↗

PubMed2026

CoMR: an integrative scoring pipeline for comprehensive mitochondrial proteome reconstruction across eukaryotes.

Mitochondrial proteome reconstruction from eukaryotic sequence data typically relies on prediction of mitochondrial targeting signals (MTSs). However, MTS predictors are primarily trained on model organisms and may perform poorly in phylogenetically divergent lineages or in organisms with atypical or reduced targeting sequences. Accurate reconstruction therefore requires integration of complementary sources of evidence beyond targeting prediction alone. We developed Comprehensive Mitochondrial Reconstructor (CoMR), an integrative workflow that combines targeting prediction, curated homology searches, large-scale similarity searches, and automated phylogenetic analysis within a unified scoring framework. Benchmarking on the model yeast Saccharomyces cerevisiae yielded strong discriminatory performance [receiver operating characteristic (ROC)-area under the curve (AUC) = 0.92], exceeding standalone prediction with TargetP2, a predictor of N-terminal targeting peptides (ROC-AUC = 0.72). In the divergent anaerobic protist Paratrimastix pyriformis, CoMR maintained robust performance (ROC-AUC = 0.86) validated with an experimental proteome despite extreme class imbalance, achieving a precision-recall AUC of 0.183 (~78-fold enrichment over random expectation and ~10-fold improvement over TargetP2). Ablation analyses demonstrate that predictive performance is robust to individual evidence-layer removal, while overlap analyses showed that homology-based searches recovered candidates missed by targeting predictors, particularly in P. pyriformis. Overall, CoMR improves mitochondrial proteome reconstruction over targeting prediction alone and provides a reproducible workflow for predicting mitochondrial and mitochondrion-related organelle protein repertoires across eukaryotes to aid investigations of organelle evolution and proteome reduction.

Proteome↗

PubMed2025

ShortCake: an integrated platform for efficient and reproducible single-cell analysis.

SUMMARY: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For the research community, minimizing the time spent on environment setup and installation issues is essential. We present ShortCake, a containerized platform that integrates a suite of single-cell analysis tools written in R and Python. ShortCake isolates competing Python tools into separate virtual environments that can be easily accessed within a Jupyter notebook. This enables users to effortlessly transition between various environments, including R, even within a single notebook. Additionally, ShortCake offers multiple "flavors," enabling users to select container images tailored to their specific needs. ShortCake provides a unified environment with fixed versions of various tools, thus streamlining workflows, reducing setup time, and improving reproducibility. AVAILABILITY AND IMPLEMENTATION: The ShortCake image is available on DockerHub (https://hub.docker.com/r/rnakato/shortcake) and Zenodo (DOIs: 10.5281/zenodo.17116765 and 10.5281/zenodo.17118158). The source code is available on GitHub (https://github.com/rnakato/ShortCake).

Single-Cell Analysis↗

PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗

PubMed2004

"I wish I had seen this test result earlier!": Dissatisfaction with test result management systems in primary care.

BACKGROUND: Failure to review and follow up on outpatient test results in a timely manner represents a patient safety and malpractice concern. Therefore, we sought to identify problems in current test result management systems and possible ways to improve these systems. METHODS: We surveyed 262 physicians working in 15 internal medicine practices affiliated with 2 large urban teaching hospitals (response rate, 64%). We asked physicians about systems they used and the amount of time they spent managing test results. We asked them to report delays in reviewing test results and their overall satisfaction with their management of test results. We also asked physicians to rate features they would find useful in a new test result management system. RESULTS: Overall, 83% of respondents reported at least 1 delay in reviewing test results during the previous 2 months. Despite reporting that they spent on average 74 minutes per clinical day managing test results, only 41% of physicians reported being satisfied with how they managed test results. Satisfaction was associated with fewer self-reported delays in reviewing test results. Physicians who actively tracked their test orders to completion were also more likely to be satisfied. The most highly desired features of a test result management system were tools to help physicians generate result letters to patients, prioritize their workflow, and track test orders to completion. CONCLUSIONS: Delays in test result review are common, and many physicians are not satisfied with how they manage test results. Tools to improve test result management in office practices need to improve workflow efficiency and track test orders to completion.

Adult↗