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PubMedDate not supplied

Applying e-health to case management.

The healthcare industry is only beginning to understand e-health. E-health can be defined as the use of technology to directly improve healthcare delivery-affording patients the opportunity to participate in their own healthcare management, provider, and institution. The market is changing rapidly, and innovations, partnerships, and mergers are taking place daily. For healthcare institutions, setting a long-term, yet adaptable e-health strategy is of vital importance for the continued success of the organization. For clinicians, an understanding of and familiarity with technologies can significantly improve workflow, organization, and patient interaction. For the patient, technology can be leveraged as a means to take initiative and responsibility for his/her own health. This article defines e-health and explains the implications and benefits of e-health to nurses and their patients. The article also identifies unique opportunities e-health/e-commerce can provide case managers in promoting patient connectivity, care management, and economy in cost of care.

Case Management↗

PubMed2006

Cost drivers in anesthesia: manpower, technique and other factors.

PURPOSE OF REVIEW: This article reviews the recent literature on cost drivers in anesthesia with respect to staff, techniques and drug costs, and with special focus on anesthesia workflow in the postanesthesia care unit. Moreover, the costs of post-operative pain management provided by an acute pain service are highlighted. RECENT FINDINGS: Staff costs represent the main contributor to anesthesia costs in all studies. Therefore, many studies address the reduction of personnel costs, e.g. by using fast-tracking procedures which allow the patients to bypass the postanesthesia care unit. However, postanesthesia care unit bypassing and replacement of anesthesiologists by certified anesthesia nurses were not able to significantly decrease anesthesia costs. If anesthesiologists are reimbursed by surgically controlled time, this time is the main determinator for anesthesia costs and should be carefully monitored. Regional anesthesia techniques can help to reduce costs in the ambulatory setting because of reduced post-operative side-effects and earlier home readiness of the patients. Low gas flow and modern electroencephalographic monitoring can contribute to decreased drug-related costs. Acute pain services are mainly run by anesthesia staff thus increasing the costs in anesthesia departments. However, an acute pain service can reduce costs of surgical procedures significantly. SUMMARY: Clear definition of the meaning of cost drivers and of criteria which allow assessment of patients' condition, and peri-operative standard operating procedures are warranted to ensure comparability of economic data in anesthesia.

Anesthesia↗

PubMed2006

The drive for operating room efficiency will increase quality of patient care.

PURPOSE OF REVIEW: The public is demanding that medicine both increase its efficiency and lower its costs. 'Watchdog' groups are scrutinizing our performance, publicizing our results, and forcing us to compete. They want doctors first to use evidence-based medicine to identify truly beneficial healthcare interventions and then to use continuous quality improvement to perform those beneficial interventions consistently at lower costs. RECENT FINDINGS: A renaissance is underway in our thinking about quality and efficiency in the operating room. 'Work process redesign' and 'the systems approach' are starting to be more than slogans, as researchers redesign the physical environment of the operating room, along with its 'workflow' and methods of communication. SUMMARY: Soon physicians and hospitals will be receiving 'pay-for-performance', whereby our income will depend on our ability to demonstrate both good patient care processes and good outcomes. Medicine is starting to act like a competitive industry, and this tendency will be good for quality and efficiency in the operating room. Community and academic practitioners need to understand and participate in this transformation in order to be able to influence its evolution and to survive financially.

Appointments and Schedules↗

PubMed2006

Experimental validation of data mined single nucleotide polymorphisms from several databases and consecutive dbSNP builds.

Rapid development in the annotation of human genetic variation has increased the numbers of single nucleotide polymorphisms (SNPs) in candidate genes by several orders of magnitude. The selection of both useful target SNPs for disease-gene association studies and SNPs associated with the treatment response is therefore an increasingly challenging task. We describe a workflow for selecting SNPs based on their putative function and frequency in candidate genes extracted from PubMed resources. The annotation of each SNP and its frequency in a Caucasian population was assessed in several databases. Approximately 4000 SNPs were identified from an initial 233 candidate genes. In a case study, we performed actual genotyping of 1030 of these SNPs in 213 genes and obtained 710 successfully genotyped SNPs. Using the flow-chart outlined here, only 87 SNPs were monomorphic (approximately 12%). This study reports the frequency of SNPs in a Caucasian population, selected in silico, using a candidate gene approach and validated by actually genotyping 193 individuals. The selected genotypes represent a valuable set of verified candidate SNPs for pharmacogenetic studies in Caucasian populations.

Breast Neoplasms↗

PubMed2006

Decreasing errors in pediatric continuous intravenous infusions.

OBJECTIVE: To evaluate the effect of a Web-based calculator and decision-support system on infusion ordering errors and to estimate error frequency in pharmacy infusion preparation. DESIGN: Data on ordering error frequency and typology were collected before and after implementation of an online infusion ordering system. Data on pharmacy preparation errors of infusions were collected. SETTING: A children's hospital at an academic medical center. PATIENTS: None. Data were abstracted from infusion orders. INTERVENTIONS: Introduction of a voluntary-use Web-based calculator into infusion ordering workflow. Observation only. MAIN OUTCOME MEASURES: Number and type of errors in handwritten and calculator-generated orders. Number and type of errors in pharmacy infusion preparation. RESULTS: Before calculator deployment, 129 sequential handwritten infusion orders were collected over 5 weeks. After deployment, of 162 sequential infusion orders, 88% (142) were calculator-generated. Calculator-generated infusion orders contained 83% fewer (p < .001) orders containing one or more errors than handwritten orders. Calculator-generated orders contained no high-risk errors (incorrect decimal, dose, or unit of measure) when compared with handwritten orders and were associated with fewer pharmacy interventions. In 118 sequential pharmacy infusion preparations over 4 wks, there were no errors observed. CONCLUSION: A Web-based calculator reduced significantly the total number of errors and eliminated all high-risk errors in the prescribing process for continuous pediatric infusions. With no observed errors in pharmacy preparation, this study provides data to support the use of computerized ordering as an independent safe and viable method for ordering continuous pediatric infusions.

Chi-Square Distribution↗

PubMedDate not supplied

Registration and fusion of CT and MRI of the temporal bone.

OBJECTIVE: To present and evaluate a registration method to fuse complementary information of CT and MRI of the temporal bone. METHODS: CT and MRI of the temporal bone of 26 patients were independently registered 4 times. A manual, iterative, intrinsic, rigid, and retrospective registration method was used. Mean CREm (consistency registration error) was calculated as a reproducibility measurement. RESULTS: CREm was 0.6 mm (95% CI = 0.52-0.68 mm). T-test revealed no difference between pathologic and normal cases (t[102] = -1.71; P = 0.09). Time needed: 13 minutes. In the registered and fused datasets, important bony surgical landmarks (eg, facial nerve canal, inner ear) could be assessed in 3 dimensions relatively to tumor tissue (eg, acoustic schwannoma). Fluid distribution within partially obliterated cochleae could be assigned to either scalae. CONCLUSION: An accurate, reproducible registration and fusion method that improves tumor surgery and cochlea implantation planning with only minor changes to the clinical workflow was presented and described. We suggest this method in selected cases.

Adolescent↗

PubMed2006

Analysis of simulated angiographic procedures: part 1--capture and presentation of audio and video recordings.

PURPOSE: To assess different methods of recording angiographic simulations and to determine how such recordings might be used for training and research. MATERIALS AND METHODS: Two commercially available high-fidelity angiography simulations, the Mentice Vascular Interventional Simulation Trainer and the Simbionix AngioMentor, were used for data collection. Video and audio records of simulated procedures were created by different methods, including software-based screen capture, video splitters and converters, and external cameras. Recording parameters were varied, and the recordings were transferred to computer workstations for postprocessing and presentation. RESULTS: The information displayed on the simulators' computer screens could be captured by each method. Although screen-capture software provided the highest resolution, workflow considerations favored a hardware-based solution that duplicated the video signal and recorded the data stream(s) at lower resolutions. Additional video and audio recording devices were used to monitor the angiographer's actions during the simulated procedures. The multiple audio and video files were synchronized and composited with personal computers equipped with commercially available video editing software. Depending on the needs of the intended audience, the resulting files could be distributed and displayed at full or reduced resolutions. CONCLUSIONS: The capture, editing, presentation, and distribution of synchronized multichannel audio and video recordings holds great promise for angiography training and simulation research. To achieve this potential, technical challenges will need to be met, and content will need to be tailored to suit the needs of trainees and researchers.

Angiography↗

PubMed2024

Value of HCC surveillance in a landscape of emerging surveillance options: Perspectives of a multi-stakeholder modified Delphi panel.

HCC surveillance is recommended by liver professional societies but lacks broad acceptance by several primary care and cancer societies due to limitations in the existing data. We convened a diverse multidisciplinary group of cancer screening experts to evaluate current and future paradigms of HCC prevention and early detection using a rigorous Delphi panel approach. The experts had high agreement on 21 statements about primary prevention, HCC surveillance benefits, HCC surveillance harms, and the evaluation of emerging surveillance modalities. The experts agreed that current data have methodologic limitations as well as unclear generalizability to Western populations. Although a randomized clinical trial of surveillance versus no surveillance is unlikely feasible, they concurred that alternative designs, such as a comparison of 2 surveillance modalities, could provide indirect evidence of surveillance efficacy. The panel acknowledged the presence of surveillance harms, but concurred the overall value of surveillance appears high, particularly given a greater emphasis on benefits over harms by both patients and clinicians. The experts underscored the importance of a framework for measuring both benefits and harms when evaluating emerging surveillance strategies. The panel acknowledged performance metrics of emerging methods may differ from other cancer screening programs given differences in populations, including higher risk of cancer development and competing risk of morality, and differences in diagnostic workflow in patients at risk of HCC. These data provide insights into the perceived value of HCC surveillance in an era of emerging blood- and imaging-based surveillance strategies.

Humans↗

PubMed2026

Artificial intelligence in kidney cancer: a review of clinical applications across the disease spectrum.

PURPOSE OF REVIEW: This review examines recent advances (2024-2025) in the application of artificial intelligence (AI) to kidney cancer diagnosis, prognosis, and treatment planning. It categorizes studies across 13 clinical scenarios to assess where AI offers the most clinical utility. RECENT FINDINGS: AI models have demonstrated strong performance in a range of tasks including tumor grading, subtype classification, survival prediction, and risk stratification. Integration of radiomics, genomics, and histopathology has enabled personalized, noninvasive, and timely decision-making. The highest-performing models used CT-based radiomics, particularly for predicting progression-free and recurrence-free survival. However, performance varies across tasks and tumor subtypes, with lower accuracy in detecting oncocytomas or benign vs. malignant differentiation. AI applications in metastatic and nonresected cases remain underexplored, and ultrasound remains a largely under researched modality. While some models improve diagnostic accuracy and workflow efficiency, broader validation across diverse populations is still needed. SUMMARY: AI is transforming kidney cancer care across multiple clinical stages. Although promising, real-world implementation demands ongoing validation and postdeployment monitoring to prevent performance degradation due to distributional drift. AI's integration with multimodal data offers substantial potential to improve outcomes and reduce overtreatment.

Humans↗

PubMed2005

WEDS: a Web services-based environment for distributed simulation.

Web services have the potential to radically enhance the ability of researchers to make use of distributed computing resources, but jargon and a plethora of standards make their use almost impossible for the scientist without prior experience of the necessary technologies. A powerful and simple WSRF-based middleware scheme is presented, designed to let scientists remotely deploy single or multiple instances of a pre-existing code across multiple resources, and giving steering, visualization and workflow functionality with only simple modifications to program code. It is hoped that the development and implementation of such a toolkit will be relevant not only to the problem of deploying workstation-class codes in real time, but also the move towards more tractable alternatives to the Globus toolkit for deployment of processes in a high-performance computing environment.

Computer Simulation↗

PubMed2016

DNA barcoding in diverse educational settings: five case studies.

Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5-18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.This article is part of the themed issue 'From DNA barcodes to biomes'.

Biodiversity↗

PubMed2025

Dual RNA isolation from blood: an optimized protocol for host and bacterial RNA purification for dual RNA-sequencing analysis in whole blood sepsis samples.

Dual RNA-sequencing (dual RNA-seq) holds significant promise for deciphering bacterial virulence mechanisms during systemic infections. However, its application in sepsis research is hindered by technical challenges, including a low bacterial burden in blood and limited sample volumes and RNA yield from vulnerable populations, such as neonates. We developed an optimized protocol [dual RNA isolation from blood (DRIB)] for simultaneous stabilization, isolation and purification of high-quality host leukocyte and bacterial RNA from low-volume whole blood samples (0.5 ml). This protocol is compatible with clinical sample collection workflows and high-throughput RNA sequencing. The feasibility of DRIB for dual RNA-seq was validated using a pilot cohort of clinical adult sepsis samples, enabling the investigation of host-bacterial gene expression during sepsis. The DRIB protocol yielded 2.10-6.91 µg of total RNA per clinical sample in our pilot cohort. Dual-species ribosomal RNA (rRNA) depletion and RNA-seq generated 16.6-24.8 million filtered reads per sample, with 63±7% of reads uniquely mapped to host or bacterial sequences. Host genes accounted for 51-68% (8.4-10.9 million) reads, while 0.5-6.7% (79,496-789,808 reads) mapped to bacterial genomes. Bioinformatic analysis revealed that both shared and individual transcriptional patterns were identified in host and bacterial responses, including pathways related to immune metabolism and metal-ion binding. Our optimized DRIB protocol and RNA-seq pipeline effectively captured both host and bacterial RNA transcription in clinical sepsis samples. Expanding this approach to larger cohorts and varying disease timepoints will provide crucial new insights into host-bacterial gene co-expression dynamics in sepsis progression and outcomes.

Humans↗

PubMed2024

An Orthogonal T7 Replisome for Continuous Hypermutation and Accelerated Evolution in E. coli.

Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can dramatically accelerate the evolution of new or enhanced protein functions. We describe an orthogonal DNA replication system in E. coli based on the controlled expression of the replisome of bacteriophage T7. The system replicates circular plasmids that enable high transformation efficiencies and seamless integration into standard molecular biology workflows. Engineering of T7 DNA polymerase yielded variant proteins with mutation rates of 1.7 × 10 -5 substitutions per base in vivo - 100,000-fold above the genomic mutation rate. Continuous evolution using the mutagenic T7 replisome was demonstrated by expanding the substrate scope of TEM-1 β-lactamase and increase activity 1,000-fold against clinically relevant monobactam and cephalosporin antibiotics in less than one week.

Journal Article↗

PubMed2025

Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.

We introduce blend-seq, a workflow for combining data from traditional short-read sequencing pipelines with low-coverage long reads, to improve variant discovery for single samples without the full cost of high-coverage long reads. We demonstrate that with only 4x long-read coverage augmenting 30x short reads, we can improve SNP discovery across the genome, exceeding performance beyond even high-coverage short reads (60x). For genotype-agnostic discovery of structural variants, we see a threefold improvement in recall while maintaining precision by using the low-coverage long reads on their own, and show how we can improve genotyping accuracy by adding in the short-read data. In addition, we demonstrate how the long reads can better phase these variants, incorporating long-context information in the genome to substantially outperform phasing with short reads alone. Our experiments highlight the complementary nature of short- and long-read technologies: the former contributing higher depth for genotyping and the latter better resolution of larger events or those in difficult regions.

cost optimization↗

PubMed2024

Integration of Imaging-based and Sequencing-based Spatial Omics Mapping on the Same Tissue Section via DBiTplus.

Spatially mapping the transcriptome and proteome in the same tissue section can significantly advance our understanding of heterogeneous cellular processes and connect cell type to function. Here, we present Deterministic Barcoding in Tissue sequencing plus (DBiTplus), an integrative multi-modality spatial omics approach that combines sequencing-based spatial transcriptomics and image-based spatial protein profiling on the same tissue section to enable both single-cell resolution cell typing and genome-scale interrogation of biological pathways. DBiTplus begins with in situ reverse transcription for cDNA synthesis, microfluidic delivery of DNA oligos for spatial barcoding, retrieval of barcoded cDNA using RNaseH, an enzyme that selectively degrades RNA in an RNA-DNA hybrid, preserving the intact tissue section for high-plex protein imaging with CODEX. We developed computational pipelines to register data from two distinct modalities. Performing both DBiT-seq and CODEX on the same tissue slide enables accurate cell typing in each spatial transcriptome spot and subsequently image-guided decomposition to generate single-cell resolved spatial transcriptome atlases. DBiTplus was applied to mouse embryos with limited protein markers but still demonstrated excellent integration for single-cell transcriptome decomposition, to normal human lymph nodes with high-plex protein profiling to yield a single-cell spatial transcriptome map, and to human lymphoma FFPE tissue to explore the mechanisms of lymphomagenesis and progression. DBiTplusCODEX is a unified workflow including integrative experimental procedure and computational innovation for spatially resolved single-cell atlasing and exploration of biological pathways cell-by-cell at genome-scale.

Journal Article↗

PubMed2025

Iterative, multimodal, and scalable single-cell profiling for discovery and characterization of signaling regulators.

Cell signaling plays a critical role in regulating cellular state, yet uncovering regulators of signaling pathways and understanding their molecular consequences remains challenging. Here, we present an iterative experimental and computational framework to identify and characterize regulators of signaling proteins, using the mTOR marker phosphorylated RPS6 (pRPS6) as a case study. We present a customized workflow that uses the 10x Flex assay to jointly profile intracellular protein levels, transcriptomes, and CRISPR perturbations in single cells. We use this to generate a "glossary" dataset of paired protein-RNA measurements across targeted perturbations, which we leverage to train a predictive model of pRPS6 levels based solely on transcriptomic data. Applying this model to a genome-wide Perturb-seq dataset enables in silico screening for pRPS6 and nominates novel regulators of mTOR signaling. Experimental validation confirms these predictions and reveals mechanistic diversity among hits, including changes in signaling output driven by anabolic activity, cellular proliferation and multiple stress pathways. Our work demonstrates how integrated experimental and computational approaches provide a scalable framework for multimodal phenotyping and discovery.

Journal Article↗

PubMed2025

MetaChrome: An Open-Source, User-Friendly Tool for Automated Metaphase Chromosome Analysis.

DNA Fluorescence In Situ Hybridization (FISH) is an essential technique to study chromosome biology and genetics, enabling precise visualization of specific genomic loci to study structural abnormalities, gene mapping, and chromosomal rearrangements. High-Throughput Imaging (HTI) can automate the analysis of DNA-FISH chromosome images, but the accurate and automated segmentation of mitotic chromosomes and simultaneous colocalization of FISH signals remains a challenge. While several commercial automated karyotyping tools partially solve these issues, open-source software that effectively combines robust chromosome segmentation with comprehensive colocalization analysis capabilities remains necessary. To address this unmet need, we developed MetaChrome, an open-source software platform built around a graphical user interface and explicitly designed for automated metaphase chromosome analysis. MetaChrome leverages fine-tuned deep learning models to automate metaphase chromosome segmentation, together with colocalization analysis of chromosome-specific FISH probes and immunofluorescent-labeled proteins. Importantly, MetaChrome achieves enhanced segmentation accuracy compared to traditional image processing methods by adopting a Cellpose segmentation model fine-tuned with manually annotated metaphase chromosome datasets. The fine-tuned model ensures precise assignment of DNA-FISH spots to individual chromosomes in an automated manner. This facilitates rapid identification of chromosomal abnormalities, reduces human error, and advances high-throughput chromosome analysis workflows, addressing a key bottleneck in chromosome biology research.

Chromosome segmentation↗

PubMed2025

ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration.

BACKGROUND: In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making integration, cohort selection, and downstream analysis cumbersome. While structured barcoding systems exist in large consortia (e.g., TCGA, GTEx) or domain-specific contexts (e.g., SPREC, GOLD), no unified, extensible framework currently spans both subjects and biosamples in a human- and machine-readable way. METHODS: We developed ClarID, a domain-agnostic specification that supports two identifier formats: (i) a human-readable form (e.g., 'CNAG_Test-HomSap-00001-LIV-TUM-RNA-C22.0-TRT-P1W' that encodes key metadata such as project, species, subject_id, tissue, assay, disease, timepoint and duration (from that event); and (ii) a compact version named 'stub' (e.g., 'CT01001LTR0N401T1W') optimized for filenames, pipelines, and labeling.ClarID is implemented through an open-source command-line tool, ClarID-Tools, which processes tabular metadata files (CSV/TSV) and uses a YAML-based codebook to generate, decode, and validate identifiers, as well as to create and read QR codes. The tool supports bulk and single-sample processing and allows easy integration with institutional workflows. RESULTS: To demonstrate ClarID's utility, we applied it to datasets from the Genomic Data Commons (GDC), generating interpretable identifiers for more than 113,000 clinical records (subjects) and 4,255 biospecimen records. All materials, including pre-processing scripts, input and encoded data, are publicly available and fully reproducible via the accompanying GitHub repository and Google Colab. CONCLUSIONS: ClarID fills a critical gap between opaque accession numbers and rich metadata schemas by embedding key context directly into structured identifiers. It enhances traceability, facilitates downstream analysis, and remains adaptable to project-specific needs through a configurable codebook. The accompanying ClarID-Tools software is freely available, together with full documentation and reproducible pipelines, at https://github.com/CNAG-Biomedical-Informatics/clarid-tools.

Biosample identifiers↗