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At least 19 recordsLinked to original sources
PubMed2026

A Critical Assessment of Evidence-Based Design's Knowledge Base and Inspiration: A Systematic Review.

PurposeThis study examines Evidence-Based Design (EBD) as an epistemological framework for guiding design research and practice, with a particular focus on its reliance on Evidence-Based Medicine (EBM) as a source of methodological inspiration.BackgroundOver the past two decades, EBD has been promoted as a way to strengthen design processes through the systematic use of scientific evidence. Its relationship to EBM, however, remains conceptually ambiguous: EBD draws legitimacy from EBM's hierarchical conception of "best evidence" while at the same time acknowledging the specificities of design practice, which do not easily fit such a model.MethodologyA systematic review was conducted on 31 publications in the design research literature that explicitly address the tension surrounding EBD's conception of "best evidence." The criticisms raised were coded and analyzed by main topics and subtopics.ResultsThe review highlights several reasons why EBM's hierarchical view of "best evidence" is an unsuitable epistemological foundation for EBD. It imposes scientifically inappropriate and practically ineffective methodological standards, devalues important sources of design knowledge, and fails to address central epistemic challenges intrinsic to design processes.ConclusionsBy bringing together critical yet fragmented insights from the literature, this study argues for the development of an updated epistemological framework for EBD. Constructing this framework will require sustained interdisciplinary dialogue between design research and philosophy of science.

Humans↗
PubMed2025

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases.

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples generated from templates and grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

Journal Article↗
PubMed1978

Knowledge-based computer-assisted diagnosis of chest radiographs.

The computer can produce structured radiologic content which can potentially keep the radiologists current in radiology literature. As the radiologist continues to make observations and uses the available information, he has at his fingertips with the computer the current information to offer appropriate differential diagnosis and suggest appropriate patient follow up. The computer allows the radiologist to learn and grow rather than guess and hope.

Diagnosis, Computer-Assisted↗
PubMed2026

The musculoskeletal pain literacy questionnaire (MSK-PLq) - Part 1: Development of a preliminary version through a systematic review and Delphi consensus.

OBJECTIVE: Chronic musculoskeletal (MSK) pain is a leading cause of disability worldwide, and self-management is a first-line approach recommended by international clinical guidelines. Access to evidence-based information that enhances health literacy may support patients' engagement in their self-management and treatment decision-making, potentially reducing disease burden and pain. However, no tool currently exists to assess health literacy specifically in MSK pain. This study aimed to develop and describe the preliminary version of a knowledge-based questionnaire to evaluate MSK pain literacy, the Musculoskeletal Pain-Literacy questionnaire (MSK-PLq). METHODS: A systematic literature review identified existing health literacy instruments and generated a preliminary list of domains. A two-round Delphi study with 22 panellists (19 experts and three people living with chronic MSK pain), followed by consensus meetings, was used to refine domains and items (≥70% agreement). Readability was assessed using the Flesch Reading Ease (FRE) score and three stakeholders were consulted to review the questionnaire for comprehensibility, clarity, and face validity. RESULTS: Six domains were retained (Understand, Access, Appraise, Apply, Digital, Beliefs), comprising 20 items in the preliminary version of MSK-PLq. Readability was acceptable (mean FRE 74, indicating fairly easy reading), and subject feedback supported the questionnaire's clarity and face validity. CONCLUSIONS: The preliminary version of the MSK-PLq is proposed as the first knowledge-based tool to assess functional, interactive, and critical aspects of MSK pain literacy. It may have applications in clinical practice, research, education, and digital health, by informing tailored patient education and supporting self-management strategies, although further psychometric validation is required.

Humans↗
PubMed2026

Margin Adequacy in Phyllodes Tumors Revisited: Reappraisal of the Evidence Base and Knowledge Gaps.

The optimal surgical margin for minimizing local recurrence (LR) and distant metastasis in phyllodes tumors (PTs) remains controversial. Despite multiple observational cohorts, variation among studies limits the interpretation of margin-outcome associations. We therefore performed a structured critical interpretative synthesis (CIS) to evaluate whether the current evidence supports specific margin thresholds. The CIS incorporated a systematic review, random-effects meta-analysis, an appraisal of existing meta-analyses and guidelines, and an expert interpretative analysis of 40 single-cohort studies from 2015 to 2025 evaluating surgical margin width and outcomes in PTs. Authors' recommendations regarding margin adequacy were extracted as interpretative "author conclusions." In parallel, LR and distant metastasis outcomes were pooled by tumor grade using random-effects models with prediction intervals. Final margin recommendations were derived by integrating CIS findings and multidisciplinary expert judgment. Current management guidelines do not recommend re-excision for positive or close margins in benign PTs. Contemporary guidelines are also concordant in advising negative margins for borderline and malignant PTs, although the specified margin width ranges from 1 to 10 mm. Within this range, no association has been established between increasing margin width and the risk of LR or malignant transformation upon LR. The estimated LR rates are 12.5% for borderline and 16.5% for malignant PTs. Malignant transformation on recurrence occurred in only 1% and 3% of all benign and borderline PTs, respectively. Approximately 14% of malignant PT metastasize, often without LR. Current heterogeneous evidence does not show lower recurrence with margins wider than a negative (≥1 mm) margin in PTs. For borderline and malignant PTs, a mandatory 10-mm threshold is insufficiently supported, as narrower negative margins may be adequate in selected cases. However, an optimal margin threshold cannot be defined from current data. These conclusions are practice-supporting rather than guideline-defining and reinforce the need for high-quality evidence to establish harmonized, grade-specific margin recommendations.

Humans↗
PubMed2025

Tribus: semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomic data.

MOTIVATION: Multiplexed imaging and single-cell analysis are increasingly applied to investigate the tissue spatial ecosystems in cancer and other complex diseases. Accurate single-cell phenotyping based on marker combinations is a critical but challenging task due to (i) low reproducibility across experiments with manual thresholding, and, (ii) labor-intensive ground-truth expert annotation required for learning-based methods. RESULTS: We developed Tribus, an interactive knowledge-based classifier for multiplexed images and proteomic datasets that avoids hard-set thresholds and manual labeling. We demonstrated that Tribus recovers fine-grained cell types, matching the gold standard annotations by human experts. Additionally, Tribus can target ambiguous populations and discover phenotypically distinct cell subtypes. Through benchmarking against three similar methods in four public datasets with ground truth labels, we show that Tribus outperforms other methods in accuracy and computational efficiency, reducing runtime by an order of magnitude. Finally, we demonstrate the performance of Tribus in rapid and precise cell phenotyping with two large in-house whole-slide imaging datasets. AVAILABILITY AND IMPLEMENTATION: Tribus is available at https://github.com/farkkilab/tribus as an open-source Python package.

Proteomics↗
PubMed1977

Foundations of medical librarianship.

The development of medical librarianship during the last forty years is examined as reflected in the changes of its resources, technology, education, and knowledge base. A shift from historical to scientific inquiry constitutes the direction of medical librarianship. Its nexus is the gathering of information and the transfer of knowledge. The social and human resources for this ongoing change and the basis for a quest for excellence is seen in the pool of talent represented by hospital librarians and the aspirations of the women's movement for equality.

Bibliographies as Topic↗
PubMed1977

The clouded crystal ball and the library profession.

Growing awareness of the transition from an industrial age to a communication- and knowledge-based economy appears reflected in some changing directions in libraries. Major trends include (1) a change in management practices, (2) a realignment of operational goals away from technical processing activities to client-oriented outreach services, and (3) the identification of educational functions as a primary professional role. The twin concepts of knowledge utilization and information brokering are beginning to have an impact on the definition of the librarian's role.

Computer-Assisted Instruction↗