SEARCH · PubMed Health

Results for “Clinical workflow”

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

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

At least 577 records · Page 32Linked to original sources

PubMed2003

[Organisation of studies].

Haemato-oncological studies in private practices for haematology and oncology have been identified as an important instrument for quality assurance in the treatment of haemato-oncological patients. As the organisational structures of private practices for haematology and oncology are usually highly complex the inclusion into studies needs a high motivation and binds resources. Workflow was observed in four private practices for haematology and oncology. With this data, suggestions for a common workflow model for study inclusion in private practices were elaborated and are discussed in this article. A common workflow-model of study inclusion for private practices is illustrated in two flow charts. If patients are to be successfully included in studies, additional structures and resources have to be implemented. Beyond this the necessary steps for study inclusion must be incorporated into the everyday routine of the practices.

Clinical Trials as Topic↗

PubMed2006

The multitasking clinician: decision-making and cognitive demand during and after team handoffs in emergency care.

Several studies have shown that there is information loss during interruptions, and that multitasking creates higher memory load, both of which contribute to medical error. Nowhere is this more critical than in the emergency department (ED), where the emphasis of clinical decision is on the timely evaluation and stabilization of patients. This paper reports on the nature of multitasking and shift change and its implications for patient safety in an adult ED, using the methods of ethnographic observation and interviews. Data were analyzed using grounded theory to study cognition in the context of the work environment. Analysis revealed that interruptions within the ED were prevalent and diverse in nature. On average, there was an interruption every 9 and 14 min for the attending physicians and the residents, respectively. In addition, the workflow analysis showed gaps in information flow due to multitasking and shift changes. Transfer of information began at the point of hand-offs/shift changes and continued through various other activities, such as documentation, consultation, teaching activities and utilization of computer resources. The results show that the nature of the communication process in the ED is complex and cognitively taxing for the clinicians, which can compromise patient safety. The need to tailor existing generic electronic tools to support adaptive processes like multitasking and handoffs in a time-constrained environment is discussed.

Continuity of Patient Care↗

PubMed2026

Herd-level heterogeneity of antimicrobial resistance in commensal Escherichia coli: A nationwide high-throughput survey of Australian pig herds.

Antimicrobial resistance in commensal Escherichia coli provides a useful indicator for overall antimicrobial resistance burden. We applied this approach to assess antimicrobial resistance within and between commercial pig herds across Australia. A high-throughput robotic workflow was used to isolate 2730 E. coli colonies from rectal contents collected in 2022 from healthy slaughter pigs (n = 300) representing 30 herds (∼70% of national production). Up to 94 isolates per herd underwent antimicrobial susceptibility testing using the Robotic Antimicrobial Susceptibility Platform. Isolate- and herd-level antimicrobial resistance indices were calculated, weighting antimicrobials by their human health importance. Resistance to first-line agents was widespread: ampicillin 77% and tetracycline 79%. By contrast, resistance to critically important antimicrobials was rare (ciprofloxacin 0.11%; extended-spectrum cephalosporins 0.04%), and no clinical resistance to carbapenems or colistin was detected. Overall, 56.9% of isolates were multi-class resistant. Herd-level antimicrobial resistance within indices ranged from 1.51 to 5.76, revealing substantial between-herd heterogeneity. Three herds carried critically important antimicrobials-resistant isolates that would likely have been missed using conventional, lower-density sampling approaches. Whole-genome sequencing identified fluoroquinolone-resistant isolates belonging to ST10 and ST69 (both qnrS1), and ST744 (Quinolone Resistance Determining Region mutations plus blaCTX-M-27). By testing approximately tenfold more isolates than conventional surveys, we uncovered considerable antimicrobial resistance with heterogeneity within and between animals and herds, including farm-specific variability. This expanded sampling also enabled detection of critically important antimicrobial resistance at very low prevalence. In conclusion, high-throughput, high-density testing offers a practical early-warning system and herd-level benchmark to inform surveillance and targeted interventions.

Animals↗

PubMed2006

Evidence for electronic health record systems in physical therapy.

With increasing pressures to better manage clinical information, we investigated the role of electronic health record (EHR) systems in physical therapist practice through a critical review of the literature. We reviewed studies that met our predefined criteria after independent review by 3 authors. The investigators in all of the reviewed studies reported benefits, including improved reporting, operational efficiency, interdepartmental communication, data accuracy, and capability for future research. In 7 studies, the investigators reported barriers, including challenges with behavior modification, equipment inadequacy, and training. The investigators in all studies reported key success factors, including end-user participation, adequate training, workflow analysis, and data standardization. This review suggests that EHRs have potential benefits for physical therapists. The authors formed the following recommendations based on the studies' themes: (1) incorporate workflow analysis into system design and implementation; (2) include end users, especially clinicians, in system development; (3) devote significant resources for training; (4) plan and test carefully to ensure adequate software and hardware performance; and (5) commit to data standards.

Data Collection↗

PubMed2006

Safety portal: the safest goes through the air--ubiquitous high-risk reminders bridging out the patient safety in emergency department.

UNLABELLED: Under the safety net of hospital-based patient safety informatics (PSI) system, RFID is build to adapt emergency department safety needs and the process improvement activities. We implemented the RFID framework as the electronic patient identifier into the process improvement of ED workflow; it defined as the safety portal to introduce PSI safety features on the real-time basis. METHODS: Since 2004, we were applying RFID technology into a 200 daily visits emergency department of the regional medical center in Taipei, Taiwan. We then developed wireless web-based RFID safety portal to implement the real-time safety reminders such as the laboratory and radiology reports to the physician who can make decision promptly to the patients in the ED. RESULTS: Under the ED safety portal, the diagnosis time for physicians to make clinical decision is largely reduced nearly 40 percent due to the safety enhancement RFID system. ED physician who could actively receive patient's updated clinical data to make clinical decision via web-based informatics system reasonably decreases. CONCLUSIONS: The effectiveness of RFID system not only enhance patient identification during ED process but combine ED safety net which providing needed data for ED physician and staff who visit ED patients with valuable real-time data on time. Patient safety on ED can be clearly improved from the embracing modern technology and build up a patient centered ED environment.

Emergency Service, Hospital↗

PubMed2003

Beyond the genome--SMi Conference 27-28 January 2003, London, UK.

Over a decade of astonishing developments, genomics and proteomics have promised a fundamentally new approach to drug discovery. Although there has been an undeniable increase in the range of potential targets available, this has not led to an increased output of the drug discovery pipeline into the clinic. With tighter markets and increasing competition, the major pharmaceutical companies are under intense pressure to achieve rapid, concrete delivery of those early promises, but there remain acute problems in the genes-to-drugs pipeline. This meeting showcased a range of novel approaches from proteomics and bioinformatics to address these problems. A common theme in the range of proteomics offerings was the prioritization of potential novel targets on the basis of their accessibility to drugs and their functional link to disease phenotypes. Informatics and in silico offerings also concentrated on fast, accurate, drug-focused workflows built on large integrative databases and novel data-mined algorithms.

Animals↗

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↗

PubMedDate not supplied

Surveying improvement activities in health care on a national level--the Swedish internal collaborative strategy and its challenges.

In order to map improvement activities in Swedish health care, we surveyed the managers of all primary health care centers (n = 958) and clinical hospital departments (n = 1355), with a response rate of 46%. The majority reports that their staff view improvement work positively. The most common driver of improvement is work environment problems, whereas external drivers have less influence. Among 35 methods, the most commonly used are educational initiatives, stress management, guidelines, and leadership development, whereas accreditation is used the least. Respondents who report extensive improvement efforts indicate the greatest benefit from educational interventions, analysis of patient incidents, guidelines, and rapid cycle tests. Respondents claim that improvement initiatives yield positive results, in particular regarding the working environment, administrative routines, workflow, and communication, although only 15%-30% of respondents report having data to support their claims. Our findings indicate an introverted focus of most improvement efforts, starting with staff and administration needs. Further research is needed to understand how and why some centers and departments have managed to achieve strategic, measurable, patient-focused, systems improvements, whereas most have not.

Administrative Personnel↗

PubMedDate not supplied

From telepathology to virtual pathology institution: the new world of digital pathology.

Telepathology has left its childhood. Its technical development is mature, and its use for primary (frozen section) and secondary (expert consultation) diagnosis has been expanded to a great amount. This is in contrast to a virtual pathology laboratory, which is still under technical constraints. Similar to telepathology, which can also be used for e-learning and e-training in pathology, as exemplarily is demonstrated on Digital Lung Pathology (Klaus.Kayser@charite.de) at least two kinds of virtual pathology laboratories will be implemented in the near future: a) those with distributed pathologists and distributed (> or = 1) laboratories associated to individual biopsy stations/surgical theatres, and b) distributed pathologists (usually situated in one institution) and a centralized laboratory, which digitizes complete histological slides. Both scenarios are under intensive technical investigations. The features of virtual pathology comprise a virtual pathology institution (mode a) that accepts a complete case with the patient's history, clinical findings, and (pre-selected) images for first diagnosis. The diagnostic responsibility is that of a conventional institution. The Internet serves as platform for information transfer, and an open server such as the iPATH (http://telepath.patho.unibas.ch) for coordination and performance of the diagnostic procedure. The size and number of transferred images have to be limited, and usual different magnifications have to be used. The sender needs to possess experiences in image sampling techniques, which present with the most significant information. A group of pathologists is "on duty", or selects one member for a predefined duty period. The diagnostic statement of the pathologist(s) on duty is retransmitted to the sender with full responsibility. The first experiences of a virtual pathology institution group working with the iPATH server working with a small hospital of the Salomon islands are promising. A centralized virtual pathology institution (mode b) depends upon the digitalization of a complete slide, and the transfer of large sized images to different pathologists working in one institution. The technical performance of complete slide digitalization is still under development. Virtual pathology can be combined with e-learning and e-training, that will serve for a powerful daily-work-integrated pathology system. At present, e-learning systems are "stand-alone" solutions distributed on CD or via Internet. A characteristic example is the Digital Lung Pathology CD, which includes about 60 different rare and common lung diseases with some features of electronic communication. These features include access to scientific library systems (PubMed), distant measurement servers (EuroQuant), automated immunohisto-chemistry measurements, or electronic journals (Elec J Pathol Histol, www.pathology-online.org). It combines e-learning and e-training with some acoustic support. A new and complete database based upon this CD will combine e-learning and e-teaching with the actual workflow in a virtual pathology institution (mode a). The technological problems are solved and do not depend upon technical constraints such as slide scanning systems. At present, telepathology serves as promoter for a complete new landscape in diagnostic pathology, the so-called virtual pathology institution. Industrial and scientific efforts will probably allow an implementation of this technique within the next two years with exciting diagnostic and scientific perspectives.

Computer Communication Networks↗

PubMed2026

Towards a Robust cell-free DNA Isolation Protocol for NGS Applications in a Clinical Molecular Diagnostics Setting.

Cell-free DNA (cfDNA), released from apoptotic and necrotic cells into body fluids, is a non-invasive source of genetic information for disease prediction, diagnosis, and monitoring. However, its low abundance makes cfDNA highly susceptible to various pre-analytical influences, potentially increasing high molecular weight (HMW) or genomic DNA (gDNA) compromising downstream cfDNA analyses. This study evaluated the impact of different cfDNA-stabilizing blood collection tubes (BCT; Cell-Free DNA BCT, Streck; S-Monovette cfDNA Exact, Sarstedt) stored at room temperature for 1, 5, or 10 days, prior to plasma isolation using different isolation methods (magnetic bead-based or silica column-based) on cfDNA stability and yield. DNA quantity and quality were assessed by fluorometric quantification, automated fragment analysis, and gene-specific quantitative PCR. Streck-based workflows maintained stable cfDNA yields and characteristic mononucleosomal fragmentation profiles across all storage times. In contrast, Sarstedt tubes showed reduced cfDNA concentrations after 5 days and a pronounced increase at 10 Days, accompanied by high-molecular weight DNA patterns consistent with white-blood cells (WBC) lysis. These trends were largely independent of the extraction method. Overall, the results demonstrate that blood collection tube chemistry critically influences cfDNA integrity during delayed processing. Streck tubes, particularly when combined with silica column-based isolation method, provided the most robust and reproducible workflow for routine molecular diagnostics, whereas Sarstedt tubes produced physiologically implausible results after extended storage.

blood collection tubes↗

PubMed2004

Information management for entomology screening.

The successful introduction of genetically modified (GM) crops has created a revolutionary transformation of the agricultural industry with GM crops currently planted on some 130 million acres. Historically, agricultural companies were involved in the discovery of conventional insecticide chemistries in processes that were very similar to those in the pharmaceutical industry. With the introduction of GM technologies, the process has radically changed. The new process is best described as the pharmaceutical equivalent of a very large-scale limited clinical trial conducted at the discovery stage. For example, unlike pharmaceutical screens, GM crop discovery screens frequently involve live insects challenged with complex protein containing soups. Furthermore, the nature of the potential avenues for discovery mandates that assay models also support protein engineering, proteomics, and genomics efforts. The range in sample demand ranges from ultra-low to high throughput. Finally, regulatory and good business stewardship demands that data integrity and tractability is in place, from discovery through varietal introduction, to manage the information generated in support of a commercialized GM plant variety. The authors describe their discovery workflow and detail how they have customized a commercially available database software package to achieve an optimum configuration for entomology screening.

Animals↗

PubMed2007

'Wet Reads' in the age of PACS: technical and workflow considerations for a preliminary report system.

Communication between clinicians, technologists, and radiologists has become more complex, with Picture Archiving and Communication Systems (PACS) now allowing the radiologist to be removed from the physical location of the patients and the site of imaging. With these changes, effective communication becomes an ongoing challenge. Efficient communication of study interpretations has also become a priority for radiologists as they struggle to maintain relevance and provide added value to patient care when clinicians have ready access to radiology images. The purpose of this paper is to share our experience in developing and implementing the Collaborative Notification System (CNS), a communication tool used to inform referring clinicians of urgent findings-a.k.a. "wet reads." The system utilizes a system of web pages integrated into PACS for the sending and receiving of succinct messages to provide clinical information at the point of need. A second system of pager alerts provides notification of the need for such communication through a relatively unintrusive, one-way, acknowledged alert system. The CNS provides asynchronous, integrated communication for the reporting of urgent and emergent radiology findings in a complex, geographically distributed medical environment.

Efficiency, Organizational↗

PubMed2026

Standardizing stem cell enumeration: A methodological comparison of single and dual flow cytometry platforms.

Two flow cytometry methods are used for stem cell (CD34+) enumeration; single platform (SP) and dual platform (DP). While several studies reported comparable results, others suggested superiority of the SP method. This study evaluated variations between both methods using a modified workflow. A total of 54 fresh and thawed specimens, including mobilized peripheral blood, apheresis products, and umbilical cord blood, were analyzed using both methods. High concordance between SP and DP methods was observed for absolute viable CD34+ counts in fresh and thawed specimens (p = 0.088 and 0.427, respectively), as well as for CD34+ viability (p = 0.085 and 0.801). Absolute viable WBC counts were comparable between methods in thawed specimens (p = 0.124), whereas a modest statistical variation was observed in fresh specimen group (p = 0.039), largely influenced by umbilical cord blood samples. Variation in absolute viable CD34+ counts remained within clinically acceptable limits, with median variations of 2.4 for fresh and 1.4 for thawed samples. SP and DP methods demonstrated high concordance for absolute viable CD34+ enumeration and CD34+ viability in fresh and thawed specimens. Although a modest variation in viable WBC counts was observed in fresh samples, this did not affect CD34+ enumeration and remained clinically acceptable. While SP provides a standardized approach, the DP method offered greater gating flexibility, with fewer technical resources required, and was approximately 70% more cost-effective, supporting its use as a practical alternative in appropriate laboratory settings.

Humans↗

PubMed2005

[Multimedia preoperative patient information].

Due to heavy workloads and shortage of staff, doctors often find it difficult to explain operations to their patients with the legally required detail and timing (in Germany, 24 h preop). This is however mandatory for obtaining informed consent. We developed a computer program that generates films explaining 24 common orthopedic operations and blood transfusion. They explain the operation, early postoperative phase, and benefits and risks to the patient. At our clinic, this program is used in daily routine and precedes the actual doctor-patient conversation for informed consent. We asked 300 patients about their satisfaction with the newly developed program. The multimedia presentation gives the patient more time, enough detail and clarity, and the chance to repeat parts of the film. For the doctor, it saves time. The time gap required in Germany between explanation and operation is thus easily adhered to. In case of legal problems, the film can be used for evidence. The use of this multimedia presentation to help in getting informed consent is improving workflow considerably.

Computer-Assisted Instruction↗

PubMed2026

TaxTriage: an open-source metagenomic sequencing data analysis pipeline enabling putative pathogen detection.

MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.

Software↗

PubMed2026

A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.

BACKGROUND: Accurate species-level identification of bacteria in complex environmental samples is essential for applications in biotechnology, ecological monitoring, and clinical diagnostics. Short-read platforms such as Illumina frequently truncate the 16S rRNA gene, limiting taxonomic resolution. In this work, we applied Oxford Nanopore Technology (ONT) long-read sequencing to full-length 16S rRNA amplicon in samples from natural soil amended with lignocellulosic biomass and a simplified microbial community derived from cultures grown on selective and differential carboxymethyl cellulose (CMC)-based substrates, with the aim to evaluate the difference in performance between a real, complex community and a less complex system. To reduce consumable costs, we substituted the standard ONT Barcoding kits with an in-house hybrid barcoding workflow. Specifically, PacBio PCR-based barcoding protocol was used for sample indexing, followed by library preparation using the ONT Ligation Sequencing Kit. This simplified approach retained compatibility with MinION and Flongle flow cells and supported accurate downstream demultiplexing while lowering barcode costs substantially. Additionally, a new bioinformatic workflow tailored to ONT data was implemented. RESULTS: Overall, the hybrid protocol significantly reduced per-sample barcoding costs while preserving high sequencing quality and throughput. The sequencing run yielded over 5 Gb of quality-filtered data (Q-score ≥ 10). Furthermore, the new bioinformatic workflow allowed taxonomic assignment at the species level for 49.38% of annotated taxa, compared to just 4.59% using Illumina NovaSeq sequencing of the V3-V4 region. ONT also recovered 2.3 times more genera and 1.3 times more families. Although 16S rRNA gene sequencing often cannot distinguish between closely related species, particularly within taxonomically complex groups, in this work, full-length reads substantially improved both taxonomic resolution and database matching. CONCLUSIONS: These results show that full-length 16S rRNA sequencing with ONT, paired with a low-cost barcoding strategy, enhanced taxonomic resolution compared to short-read workflows. This approach also offers a scalable and cost-effective option for high-resolution microbiome profiling in research and applied settings.

RNA, Ribosomal, 16S↗

PubMed2026

The diagnostic potential of combined quantitative polymerase chain reaction and next-generation sequencing using the same primers for periprosthetic joint infection.

Next-generation sequencing (NGS) enables the detection of specific pathogens unidentifiable by conventional cultures, but its application in orthopedics remains inconsistent due to background contamination and irreproducible findings. This study evaluated the diagnostic performance of a novel workflow combining broad-range 16S rRNA gene quantitative PCR (qPCR) screening with downstream NGS, focusing on bacterial biomass thresholds. The qPCR assay demonstrated excellent intrarater reliability, with an intraclass correlation coefficient (ICC) of 0.961 (95% confidence interval, 0.881 to 0.997). Based on serially diluted positive controls, a quantitative threshold of 10⁵ CFU/mL was established as the minimum concentration required for the consistent detection of fastidious taxa, such as Escherichia coli. When evaluated against conventional cultures using 95 sonicate fluid and 276 pre/intraoperative tissue samples, the qPCR assay achieved a sensitivity of 80% and a specificity of 72%. Subsequent NGS sequencing of 26 clinical samples and 9 controls showed concordance in 4 of 6 culture-positive infected cases with NGS taxonomy, whereas the remaining discrepancies were likely attributable to culture-based phenotypic misidentification. Notably, among the qPCR-positive cases, three were culture-negative, including two hip prosthesis loosening cases exhibiting polymicrobial profiles, and one post-traumatic osteoarthritis case harboring low-level Staphylococcus. Crucially, this post-traumatic patient developed delayed periprosthetic joint infection (PJI) 2 years post-surgery, with cultures identifying Staphylococcus previously detected by the initial NGS analysis. Integrating qPCR screening with targeted NGS effectively refines pathogen identification, filters environmental artifacts, and overcomes the diagnostic limitations of culture-negative infections in orthopedic practice.IMPORTANCENext-generation sequencing (NGS) enables the detection of specific pathogens in clinical samples that are not identifiable by conventional methods. However, NGS applications in orthopedics have not been quantitatively evaluated, and findings have been inconsistent owing to contaminants and the presence of non-credible causative organisms. These factors primarily stem from the failure to evaluate low-biomass samples and the absence of proper controls, such as negative controls or mock community DNA samples. This study demonstrates that interpreting results from low-biomass samples requires careful consideration because NGS relies on relative bacterial abundances; distinguishing likely pathogens from contaminants is particularly challenging when bacterial loads are low. We demonstrated that combining NGS with quantitative PCR (qPCR) and applying a Cq cutoff can reduce false positives.

Humans↗

PubMedDate not supplied

Medical archiving: solutions for medical image management.

Within the field of radiology, innovations in digital imaging have led to the development of the picture archival and communication system (PACS), which is now a part of the fundamental technological infrastructure supporting radiology practice in the digital age. Healthcare providers like hospitals, outpatient centers, and clinics are facing an explosion of medical imaging content as the industry continues the transfer from film to digital format. As a result, providers need to rethink their storage architecture strategies to better address the varied applications of the modern healthcare organization. Digital medical images are typically very large and technological advances are constantly increasing the rate at which such data is being recorded, image volume can present a storage capacity challenge. In addition, the images must be safely stored for a long time and easy to access. Regardless of strategy, the continued deployment of PACS as the primary vehicle to streamline medical imaging workflow, manage image access and increase user productivity is important. Grid computing, typically associated with the capture of idle computational cycles on heterogeneous servers, employs computing techniques that can offer providers unique solutions to their storage problems.

Efficiency, Organizational↗