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PubMed2026

Conference report: the third Bacterial Genome Sequencing Pan-European Network conference.

The third Bacterial Genome Sequencing Pan-European Network conference, held in Engelberg, Switzerland (12-15 January 2026), brought together experts from six European countries to discuss the implementation of bacterial genome sequencing in clinical microbiology and public health. Key themes included regulatory frameworks (In Vitro Diagnostic Regulation, General Data Protection Regulation), standardization, quality control, data sharing, economic evaluation, and the integration of artificial intelligence and long-read sequencing into diagnostic workflows. Across presentations, panel discussions, and workshops, participants emphasized that successful implementation of genome sequencing requires more than technical capacity: it depends on robust validation, sustainable funding, interoperable data standards, ethical governance, and interdisciplinary collaboration. The meeting highlighted that sequencing should remain question-driven and clinically meaningful, balancing cost, turnaround time, and public health impact. Overall, the conference reinforced the need for coordinated European efforts to advance responsible, standardized, and sustainable genomic surveillance and diagnostics.

bacterial genome sequencing↗

PubMed2026

Scalable medium-density genotyping platforms for cultivar identification, pedigree authentication, marker-assisted and genomic selection, and other applications in strawberry.

A broad spectrum of high-density genotyping approaches, including single-nucleotide polymorphism (SNP) arrays, genotyping-by-sequencing, and whole-genome reduced-representation sequencing, have been shown to perform well in strawberry (Fragaria × ananassa), despite the inherent complexity of the octoploid genome. While these approaches are effective, their routine deployment in breeding programs can be constrained by cost, computational requirements, and workflow complexity. In parallel, many breeding programs continue to rely on locus-specific assays for marker-assisted selection, resulting in fragmented and inefficient genotyping strategies. Here, we describe medium-density amplicon-based genotyping platforms for strawberry designed to provide cost-effective, turnkey solutions that integrate markers used for marker-assisted selection with genome-wide markers suitable for genomic prediction in a single laboratory assay. These platforms were developed by targeting 1,650 or 4,811 target SNPs via amplicon sequencing, and are interoperable with existing high-density genotyping resources, including a widely used 50K SNP array, thereby facilitating data integration across platforms. We benchmarked their performance relative to the 50K SNP array across breeding-relevant applications, including identity and purity testing, pedigree authentication, marker-assisted selection, and genomic selection, and further evaluated the feasibility of genotype imputation to enhance genome-wide information content. Across analyses, the 1,650- and 4,811-amplicon platforms produced results comparable to higher-density platforms while substantially reducing genotyping cost and analytical overhead. This work demonstrates that targeted amplicon-based genotyping can support efficient, scalable, and integrated genome-informed breeding, enabling the routine application of both marker-assisted and genomic selection within strawberry breeding workflows. Open-source R workflows are provided to support streamlined analyses in breeding contexts.

Fragaria↗

PubMed2026

KG-Microbe: Building modular and scalable knowledge graphs for microbiome and microbial sciences.

BACKGROUND: The integration of many disparate forms of data is essential for understanding the microbial world and its interaction with the environment and human health. Doing so is particularly challenging in the context of microbe-host and microbe-microbe interactions that contribute to health or environmental outcomes. There are thousands of relevant microbial species, and millions of interactions among those microbes and with their environment or host. Integrated information (e.g., about host and microbial physiology, genetics, and metabolism) facilitates deeper understanding of complex mechanisms and helps interpret correlative results. RESULTS: The KG-Microbe construction framework is a novel approach to harmonizing bacterial and archaeal data in the form of a findable, accessible, interoperable, reusable and AI-ready knowledge graph (KG). Starting from a core KG with organismal traits, environments, and growth preferences and the integration of established ontologies, the framework generates a hierarchy of related KGs targeting specific use cases, including the human microbiome in the context of disease, or environmental microbiomes. The framework supports customizable taxa subsets representing communities or clades of interest. Evaluations of the KG-Microbe KGs through a series of competency questions demonstrate the accuracy and effectiveness of the data harmonization, and the utility of the resulting KGs in studies of inflammatory bowel disease and Parkinson's disease. Finally, the predictive and environmental capabilities of the KGs are demonstrated by predicting growth preferences using graph features. CONCLUSIONS: The KG-Microbe framework unifies microbial contexts in a single resource to support integrative analyses across biomedical, host, and environmental domains. KG-Microbe is a flexible, modular enabling technology for humans and machine learning methods to uncover candidate mechanistic explanations of microbial associations.

Microbiota↗

PubMed2026

Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae.

Synthetic biology and metabolic engineering increasingly demand predictable and interoperable gene expression across phylogenetically distant organisms, as the need for portable genetic systems and transferable metabolic pathways continues to grow. However, fundamental differences in promoter architecture and transcriptional logic across kingdoms remain a key bottleneck in developing universal expression platforms. Here, we designed a set of modular hybrid promoters that enable tunable and quantitatively consistent gene expression in both Escherichia coli and Saccharomyces cerevisiae. These promoters integrate bacterial -10/-35 motifs and Shine-Dalgarno sequences with minimal yeast TATA boxes and Kozak sequences to ensure transcriptional and translational compatibility. The promoter set supported weak, moderate, and strong expression with high relative consistency across species. Applied to the biosynthetic pathway for the valuable pigment prodeoxyviolacein, the hybrid promoters enabled coordinated production in both hosts. This work establishes a broadly compatible promoter architecture and provides a foundational toolkit for cross-kingdom, multi-host synthetic biology.

Promoter Regions, Genetic↗

PubMed1990

Reproducibility of radionuclide left ventricular ejection fraction in patients awaiting cardiac transplantation.

Radionuclide-derived left ventricular ejection fraction (LVEF) is used to assess LV systolic function, to follow trends in the natural history of dilated cardiomyopathy, and to prioritize patients waiting for cardiac transplantation. Reproducibility of LVEF at extremely low levels has not, however, been reported. To assess the reproducibility of radionuclide LVEF at levels below 0.30 EF U, 17 highly symptomatic patients (NYHA Class III/IV) with dilated cardiomyopathy were studied on two occasions, 72 hours apart. Sequential scans were analyzed by two independent observers. Mean LVEF was 0.18 +/- 0.06 U (scan 1) and 0.17 +/- 0.06 U (scan 2). Interoperator reproducibility (SD) was 0.03 U (R = 0.76), interscan reproducibility (SD) was 0.03 U (R = 0.62), and overall reproducibility (SD) was 0.04 U (R = 0.50). The interobserver variation of 0.03 (actually 0.027) was just over one half that seen in normal volunteers (variation 0.05, n = 29) studied previously in this department. A change of greater than or equal to 0.08 U (2SD) in either direction is highly likely to represent a real change in LV function in those with LVEF less than or equal to 0.30 units, compared with the change of at least 0.10 units required in those with normal LV function. Lower interobserver and interscan reproducibility should be taken into account when interpreting sequential scans in patients with severe LV dysfunction.

Adolescent↗

PubMed2025

A general strategy for generating expert-guided, simplified views of ontologies.

Annotation of biomedical entities with widely used, well-structured ontologies and ontology-aware tools ensures data and analyses are Findable, Accessible, Interoperable, and Reusable (FAIR). Standardized terms with synonyms support lexical search, while ontology structure enables biologically meaningful grouping of annotations, such as by location and type. However, ontologies serving diverse communities are often more complex than needed for specific applications, creating barriers to adoption by researchers and resource developers. For example, cell atlases often attempt simplifications by manually building term hierarchies linking to cell type and anatomy ontologies, but these may include relationship types unsuitable for grouping annotations. We present tools for validating human expert curated term hierarchies, developed in two human reference atlas projects, against ontology structures. The tools provide tabular statistics plus graphical views of matching and non-matching terms and relationships to support discussion and conflict resolution. The HuBMAP Human Reference Atlas (HRA) effort is used to validate the approach and tools, and the Human Developmental Cell Atlas is featured as a use case.

Journal Article↗

PubMed2026

Antibiotic-impregnated bone graft to prevent infection after total hip arthroplasty (ABOGRAFT): protocol for a randomised, double-blind, placebo-controlled trial.

INTRODUCTION: Studies have shown promising results using bone graft as a carrier for local administration of antibiotics to reduce the risk of prosthetic joint infection (PJI). The objective of this clinical trial is to determine if tobramycin and vancomycin-impregnated bone graft is safe and effective in reducing the rate of PJI after total hip arthroplasty (THA). METHODS AND ANALYSIS: This study is an international, randomised, double-blinded, placebo-controlled clinical drug trial. Patients scheduled for THA (n=1100) requiring bone grafting (excluding revisions due to an ongoing infection) are randomised in a 1:1 ratio to prophylactic treatment with tobramycin and vancomycin or placebo-impregnated bone graft.The primary outcome is the time to reoperation due to infection or diagnosis of PJI, expressed as a relative risk difference between the two groups. A risk reduction of at least 50% is considered clinically relevant. Secondary outcomes are time to and reason for reoperation and implant revision, type of micro-organism and antibiotic susceptibility pattern within 2 and 5 years after surgery. Safety outcomes are the number of adverse events and revision rate due to aseptic loosening. The primary analysis will be performed using proportional hazard models. ETHICS AND DISSEMINATION: The study has been approved under the Clinical Trial Regulation No 536/2014 (EU CT; 2024-510921-25-00). Results will be published in open-access peer-reviewed journals and disseminated to patient organisations and the media, and de-identified individual participant data will be curated and shared on reasonable request in accordance with the Findability, Accessibility, Interoperability and Reuse principles, subject to the laws and regulations governing data protection in each participating country. TRIAL REGISTRATION NUMBER: NCT05169229.

Humans↗

PubMed1992

PACS mini refresher course. Network and ACR-NEMA protocols.

The backbone of the picture archiving and communication system (PACS) is the electronic network used to move information. Communications networks require electronic rules of operation or protocols so that a set of data being transmitted reaches the intended destination and does not collide with another set of transmitted data. The most efficient protocol is flexible and can respond to the fluctuations in volume of data transmitted via the network. Successful network connection of PACS devices requires standardized interfaces so that equipment from multiple vendors can use the network protocol. The American College of Radiology (ACR) and the National Electrical Manufacturers Association (NEMA) have developed a standard for imaging equipment interfaces: DICOM (Digital Imaging and Communications in Medicine). The DICOM standard allows interoperability among different computers and operating systems. It is flexible and will allow modification and expansions as new imaging techniques evolve. The authors and the ACR-NEMA committee believe that the DICOM standard represents an important choice for radiologists, since it was developed with their interests in mind.

Computer Communication Networks↗

PubMed2026

The Network of National COVID-19 Data Portals: public health equity through collaboration.

The network of the national COVID-19 Data Portals was developed and linked to the COVID-19 Data Portal (https://www.covid19dataportal.org/)inresponsetothe need for rapid data sharing and analysis during the 2020-2022 SARS-CoV-2 pandemic. Built on open-source code developed by the Swedish COVID-19 Data Portal (now the Swedish Pathogens Portal, www.pathogens.se) the network included 12 national portals addressing demand for local open data sharing and access, across data types and resources. It provides a robust case study of national initiatives for FAIR (Findable, Accessible, Interoperable and Reusable) resources and a foundation for future pandemic preparedness across pathogens globally. In this paper we outline the structure of the origins of the network of National COVID-19 Datal Portals, the technical aspects and code originating from the Swedish Portal and provide an overview of the services and tools offered by each Portal. The paper showcases the process and operation of four Portals: Sweden, Poland, Spain, Norway and The Netherlands. In this study, we observe that pandemic response greatly benefits from an established infrastructure that can be quickly mobilised, developed and extended. Collaborations and preparation built on solid foundations over several years, supported by investment in the form of national and international research grants, is key for sustainability, continuation and readiness to deploy such efforts.

COVID-19↗

PubMed2025

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines.

As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud-based research continue to expand. Besides the potential for accelerated and diverse biomedical discovery that comes from a harmonized data ecosystem, the cloud also presents a shift away from the standard practice of duplicating data to computational clusters or local computers for analysis. However, despite these benefits, researcher migration to the cloud has lagged, in part due to insufficient educational resources to train biomedical scientists on cloud infrastructure. There exists a conceptual lack especially around the crafting of custom analytic pipelines that require software not pre-installed by cloud analysis platforms. We here present three fundamental concepts necessary for custom pipeline creation in the cloud. These overarching concepts are workflow and cloud provider agnostic, extending the utility of this education to serve as a foundation for any computational analysis running any dataset in any biomedical cloud platform. We illustrate these concepts using one of our own custom analyses, a study using the case-parent trio design to detect sex-specific genetic effects on orofacial cleft (OFC) risk, which we crafted in the biomedical cloud analysis platform CAVATICA.

Cloud Computing↗

PubMed2026

The SARS-CoV-2 Integrated Genomic Epidemiology Database (IGED): Linking viral genomes with patient-level metadata to advance statewide genomic surveillance in California.

In July 2021, the California Code of Regulations Title 17 required all laboratories performing SARS‑CoV‑2 whole genome sequencing (WGS) to report their sequencing results to the California Department of Public Health (CDPH). These viral genomic data and patient metadata were compiled into the Integrated Genomic Epidemiology Database (IGED). Linking anonymized viral sequences with patient‑level information enabled monitoring of infectiousness, pathogenicity, transmission dynamics, evolution, and vaccine evasion among emerging SARS‑CoV‑2 lineages. Laboratories performing SARS-CoV-2 WGS transmitted sequencing results to CDPH through Electronic Laboratory Reporting (ELR) and non-ELR pathways. CDPH applied uniform reporting requirements but allowed flexibility in specific data formats to accommodate diverse data systems. To preserve data quality and interoperability across heterogeneous sources, CDPH implemented standardization, validation, and deduplication protocols. Snowflake, a cloud‑based data storage and analytics platform, and Posit Connect, a cloud deployment and automation platform, supported the management, processing, and integration of data within the IGED. The IGED established links between SARS‑CoV‑2 WGS data and epidemiologic metadata for 801,418 sequences, representing 81.7% of all sequences reported in California. Lineages reported to the IGED showed strong concordance with lineage proportions in GISAID. Sequences reported to the IGED had average turnaround times longer than one month, and the majority of sequencing was performed in Southern California and Los Angeles. The IGED enhanced genomic surveillance through predictive modeling and monitoring concerning evolutionary trends such as recombination and saltations in persistent infections. Development of the IGED highlighted the need for standardized data requirements, sustained funding for sequencing, incentives for data submission, and interdisciplinary collaboration to build an effective genomic surveillance system. This framework for linking genomic and epidemiologic data has not only generated critical insights for SARS‑CoV‑2 but also provided the foundation for CDPH and other public health organizations to develop similar IGED‑like systems for other priority pathogens as genomic surveillance expands.

Journal Article↗

PubMed2026

Digital and computational morphology in hematology: current platforms, clinical evidence, and future requirements.

INTRODUCTION: Morphologic examination of peripheral blood and bone marrow remains central to the diagnosis and classification of hematologic disorders. Conventional optical microscopy, however, is labor-intensive, dependent on operator expertise, and affected by interobserver variability. Digital morphology has developed from automated image acquisition and cell pre-classification into a broader field that includes whole-slide imaging, remote review, quantitative morphometry, and artificial intelligence-based analysis. CONTENT: This review examines current applications of digital morphology in peripheral blood, bone marrow aspirates, malaria detection, and body-fluid analysis. Commercial platforms are evaluated with particular attention to the distinction between raw automated pre-classification, expert digital post-classification, and comparison with independent optical microscopy. Digital systems generally perform well for common mature leukocyte populations but remain less reliable for rare or diagnostically critical cells, including blasts, abnormal lymphoid cells, plasma cells, and intermediate maturation stages. Research systems increasingly extend analysis from individual-cell classification to whole-slide, specimen-level, and patient-level assessment. SUMMARY: Digital morphology can improve standardization, image traceability, remote consultation, education, proficiency testing, quality assurance, and selected aspects of laboratory workflow. Its clinical value depends on appropriate validation, transparent reporting of reference methods, recognition of algorithm-specific failure modes, and clearly defined criteria for expert review and conventional microscopy. Human expertise remains essential not only for validating results but also for adapting cell taxonomies and interpretive rules to evolving classifications of hematologic diseases. OUTLOOK: Future progress will require representative multicenter datasets, harmonized morphologic terminology, external validation, interoperability with laboratory information systems, and continuous monitoring after software or hardware updates. Integration of morphology with quantitative hematology, flow cytometry, cytogenetics, genomics, and clinical data may support more comprehensive computational diagnosis. Digital platforms may also broaden access to specialist expertise, training, and quality programs in resource-limited institutions and regions, provided that infrastructure, governance, and professional competency are adequately supported.

artificial intelligence↗

PubMed2026

PheBee: A Graph-Aware System for Scalable, Traceable, and Semantic Phenotyping.

OBJECTIVES: Phenotype-driven workflows in clinical and translational research require standardized ontology-based representation, ontology-aware cohort discovery, and provenance inspection for each assertion. Existing approaches optimize either for semantic traversal or scalable batch analytics, but not both. We describe PheBee, a hybrid system that links semantic assertions to scalable evidence storage via a deterministic identifier, preserving provenance while supporting ontology-aware discovery at cohort scale. MATERIALS AND METHODS: PheBee represents phenotype assertions in a knowledge graph as ontology-linked nodes with clinical modifier context (e.g., negated, family history), and stores supporting evidence records in a scalable row-oriented evidence table for cohort-scale access. The two layers are connected by a deterministic identifier enabling stable joins across repeated ingestions without duplicating high-volume evidence in the graph. We evaluated PheBee using synthetic datasets designed to exercise end-to-end ingestion and query workflows. RESULTS: Functional evaluation validated hierarchical term expansion, qualifier-aware retrieval, duplicate-free assertion handling under re-ingestion, and privacy-conscious management of subjects shared across multiple research projects. At scale (10,000 subjects producing 12M evidence records) PheBee completed ingestion in ~30 minutes and responded to interactive queries within 6 seconds under concurrent load. DISCUSSION: PheBee exposes a unified API for ontology-aware cohort discovery with hierarchical term expansion, subject-centric retrieval of phenotypes and clinical modifiers, and evidence and provenance queries. Its data model aligns with GA4GH Phenopackets, facilitating interoperability with phenotype exchange standards. CONCLUSION: By combining ontology-aware semantics with scalable, provenance-bearing evidence storage, PheBee provides a practical open-source foundation for phenotype-driven research workflows that demand both semantic precision and cohort-scale traceability.

cohort studies↗

PubMed2026

OmicsPred as a centralised resource for genetic prediction of multi-omic traits.

Genetic prediction of multi-omic data has emerged as a cost-effective alternative to direct omics profiling, particularly useful for identifying molecular features associated with disease susceptibility. However, despite its popularity, multi-omic imputation models are fragmented across studies, hindering findability, accessibility, interoperability and re-use. To address this, we developed OmicsPred (https://www.omicspred.org), a centralised platform for the deposition and dissemination of genetic prediction models of multi-omic traits. OmicsPred unifies the most commonly used molecular imputation models (e.g. from PredictDB) and other published studies totalling 3,339,469 prediction models spanning transcriptomic, proteomic, and metabolomic traits (as of May 2026). Each model is accompanied by metadata describing score development and predictive performance, and distributed in formats compatible with popular analytic tools, such as PGS Catalog Calculator and MetaXcan. To demonstrate the utility of the resource for systematic target discovery, we perform a multi-omic phenome-wide association analysis in Million Veterans Program data.

Journal Article↗

PubMed2026

From Infection Control to Healthcare System Resilience: Lessons Learned from SARS-CoV-2 Research in Healthcare Workers.

The COVID-19 pandemic placed unprecedented pressure on healthcare systems and exposed healthcare workers (HCWs) to biological hazards, organizational pressures, and psychological strain. Evidence generated during the emergency shows that HCW protection cannot rely on isolated measures, but requires an integrated framework combining epidemiological surveillance, contact tracing, infection prevention and control, vaccination, occupational health, and workforce support. Contact tracing helped identify occupational exposures and clarify how duration, proximity, and inadequate use of personal protective equipment jointly shaped infection risk. Subsequent studies of reinfection showed that susceptibility reflected the interaction of viral circulation, individual immunity, and vaccination status. Vaccination reduced the clinical impact of SARS-CoV-2 and supported service continuity, although uptake depended on trust, communication, and management of adverse event concerns. The pandemic also highlighted substantial economic consequences and a high burden of psychological distress and burnout among HCWs. Building on this evidence, future preparedness should translate these lessons into permanent, adaptable infrastructure rather than temporary emergency arrangements, integrating interoperable, AI-assisted surveillance capable of combining occupational, diagnostic, vaccination, and genomic data to detect emerging risks early, while ensuring robust data governance and human oversight. Equally central is the need to address long-term workforce vulnerabilities, including Long COVID, attrition, and burnout, through early identification, rehabilitation, flexible return-to-work models, and sustained psychosocial support. Achieving this requires structured multidisciplinary collaboration among occupational medicine, infection control, epidemiology, mental health, and digital health specialists, moving from fragmented infection-control protocols to an integrated, proactive, and learning-oriented preparedness strategy. Protecting HCWs is therefore not only an occupational safety priority but a foundational prerequisite for safe, equitable, and sustainable healthcare delivery during future infectious threats.

Humans↗

PubMed1988

Cardiac output determinations in the newborn. Reproducibility of the pulsed Doppler velocity measurement.

Cardiac output (QAo) can be estimated noninvasively by pulsed Doppler (PD) ultrasonographic determination of mean ascending aortic blood flow velocity (VAo) combined with M-mode echocardiographic determination of ascending aortic cross sectional area (AAo). Cardiac output is calculated from the volumetric flow equation (QAo) = (VAo) X (AAo). Pulsed Doppler measurements are known to correlate well with Fick and thermodilution methods; however, inter- and intraoperator variability of the velocity component of the PD method has not been determined in newborns. We did three repeated PD measures of mean aortic flow velocity in ten term infants (using four trained operators) to determine inter- and intraoperator reproducibility. The coefficient of variation for intraoperator variability (random error) for a single measurement of VAo was 11.7%. If three repeated measures by a single operator were averaged, the random error was 7.0%. There was little interoperator variability found.

Aorta↗

PubMed1992

Single-operator comparison of early and mid-second-trimester amniocentesis.

We sought to determine whether early amniocentesis is a safe and acceptable method of genetic evaluation in early pregnancy. During the 54-month period from September 1986 to February 1991, 300 consecutive early second-trimester amniocenteses were performed transabdominally at 13-14 weeks' gestation and 567 consecutive mid-second-trimester transabdominal amniocenteses were performed at 16-18 weeks. Group assignment was nonrandomized, interoperator-dependent variables were eliminated, and analysis was performed in one cytogenetics laboratory. The median maternal age and indications for the procedure were similar in both groups. There were no significant differences between the early- and mid-second-trimester amniocenteses in failed sampling, ambiguous results, pregnancy loss from 4 weeks after the procedure to 28 weeks' gestation, preterm birth, or perinatal death rate. Pregnancy loss within 4 weeks of amniocentesis was more frequent in early- than in mid-second-trimester amniocenteses. We conclude that early amniocentesis is a safe and acceptable method of genetic evaluation.

Adult↗

PubMed1990

A study of variance in densitometry of retinal nerve fiber layer photographs in normals and glaucoma suspects.

The main object of this research was to develop a reliable method of screening glaucoma suspects and patients for early loss of or changes in the retinal nerve fiber layer (RNFL). This study quantifies the variances due to photography, digitizing, and analysis of red-free photographs of the RNFL. The influence of pupil size, optic disc position and eye movements, film processing, digitizing, and intra- and interphotographic-session and intra- and interoperator variances were established. It was found that pupils needed to be dilated to at least 6 mm, that the optic disc had to be positioned in a standardized area in the negative, that the head of the subject had to remain still during photography, and that film processing and digitizing of the negative needed to be strictly controlled to minimize the variance in collection of densitometry data from RNFL red-free photographs. It was established that focusing of the negatives during digitization was not crucial. Criteria were defined for acceptable negatives. Interphotographic-session and intraoperator variances were not significant in most cases when negatives were digitized to these criteria. Analysis of interphotographic-session variance showed that there were still some factors in photography, film processing, and/or image digitizing that were not sufficiently controlled for long-term follow-up without normalization of the data. Densitometry data gathered using the established protocol, from negatives of 71 subjects were analyzed; best sensitivity and specificity rates of 80% and 100%, respectively, were achieved for the diagnosis of glaucoma.

Adult↗