Search Results (1,828)

The introduction of multibeam echosounders has marked a turning point in bathymetric data acquisition, providing precise and detailed digital bathymetric models. These instruments not only enhance our understanding of underwater terrain dynamics but also reveal the presence of complex sedimentary structures, such as submarine dunes. Dunes play an important role in the preservation of the environment but can also be obstacles to safe navigation, requiring dragging operations. Hence, it is important to detect them from bathymetric models. Although information about these dunes has numerous applications, their identification methods remain poorly automated. This paper aims to leverage deep learning to develop a segmentation method for submarine dunes. Several challenges must be overcome. Dunes are complex objects with irregular, highly variable shapes, while bathymetric data are noisy and lack detailed information. Furthermore, in the fluvio-marine context, no labeled datasets exist for training purposes. Starting from a small pre-labeled dataset, this paper proposes a systematic approach to train a Mask R-CNN network. First, data augmentation techniques are applied to expand the dataset significantly and introduce meaningful variations. By relying on transfer learning with a carefully selected pre-trained backbone, feature extraction is optimized, reducing training time while enhancing model performance. The adaptation of the Mask R-CNN model to our submarine dune segmentation task has led to a significant improvement in detection performance, with a pixel-level F1-score reaching 89%. Additionally, the mean Average Precision has exceeded 50%, demonstrating the model’s effectiveness in identifying and delineating dunes despite their varied shapes and blurred contours. These results confirm the relevance of our approach for achieving more reliable dune segmentation in a complex fluvio-marine environment. Full article

Lipidomics has emerged as a transformative discipline in biomedical research, providing high-resolution insights into metabolic signaling and disease pathophysiology. The R programming language provides a widely adopted framework for extensible analysis of complex lipidomic datasets due to its robust biostatistical infrastructure. Herein, we present a comprehensive roadmap for lipidomics in R, structured around a standardized analytical lifecycle: from raw data acquisition and preprocessing to structural annotation, statistical modeling and functional interpretation. We critically contextualize and integrate a curated suite of widely adopted R packages (version 4.3.0), including xcms and MSnbase for feature extraction, LipidMS 3.0 for fragmentation-based identification, and lipidr for quality control and normalization. Furthermore, we demonstrate how advanced tools such as mixOmics and clusterProfiler can be integrated to bridge the gap between differential lipid abundance and systems-level biological insights. Particular emphasis is placed on reproducibility, nomenclature standardization and the emerging role of machine learning in biomarker discovery. By synthesizing these resources into a coherent pipeline, this guide provides a structured reference for researchers. Further discussion addresses methodological pitfalls, statistical assumptions and reproducibility constraints that frequently compromise lipidomics studies. Ultimately, this structured approach facilitates systematic tool selection, accelerating the translation of complex lipidomic signatures into reproducible and clinically meaningful discoveries. Full article

The life sciences are currently undergoing a serious transition from the reductive biochemical analysis of dissociated tissues to non-destructive “spatial forensics”. In addition to discovering new molecules, we are moving towards finding out their precise tissue localization and performing in situ interrogation to uncover a biological logic within preserved cellular “neighborhoods”. Our perspective is focused on exploring the spatial imperative, including the structural logic and “neighborhood effects” of the tissue microenvironment, which is a prerequisite to understanding cellular function in normal and in pathological conditions. Beginning with a historical foundation of the origins of histochemistry, dating back to the 19th century with pioneer botanist François-Vincent Raspail, we emphasize the technological metamorphosis, transitioning from classical immunohistochemistry to modern multi- and high-plex spatial multi-omics. A critical evaluation of the current operational landscape has been made, addressing the engineering strategies behind multiplexed immunofluorescence (mIF), the challenges of experimental design in spatial transcriptomics, and the functional symbiosis between targeted and unbiased spatial proteomics. There are many layers of genomic and proteomic information we have to consider in order to unravel the mechanisms underlying body function. If we learn how to combine all this information together, we will be able to better understand how cells communicate with each other and what disrupts their communication, leading to cancer and many other pathologies. It is obvious that by implementing spatial biology tools, it becomes possible to develop new medicines and treat diseases in the most efficient ways. At the same time, we realize that there is an urgent need to learn how to put data pieces together so that they blend seamlessly into a meaningful output, further transitioning spatial biology over time into a routine tool to cure for both common and rare diseases and improve our lives and health. Full article

Background/Objectives: To develop and assess the feasibility of a natural language processing (NLP) framework for automated assessment of radiology–pathology concordance in breast biopsy using machine learning-based analysis of unstructured reports. Methods: This retrospective study included 766 paired radiology and pathology reports from ultrasound- or mammography-guided breast biopsies (August 2020–May 2024). Reports underwent translation, normalization, tokenization, lemmatization, and synonym expansion, followed by structured encoding of BI-RADS and pathology categories. Three models were trained: a Decision Tree, a LightGBM classifier, and a fine-tuned BioBERT model. Concordance labels were defined by multidisciplinary consensus. Performance metrics included accuracy, sensitivity, specificity, F1-score, area under the curve (AUC), and Cohen’s kappa. SHapley Additive exPlanations (SHAP) analysis was used to identify influential features. Results: Among 766 cases, 707 (92.3%) were concordant and 59 (7.7%) were initially discordant. After excluding B3 lesions (n = 46), 13 true discordant cases remained (1.7%). Including B3 lesions increased clinically non-concordant or indeterminate cases from 1.7% to 7.7%, indicating that the apparent performance of the models is likely sensitive to case definition and dataset composition. BI-RADS 4a was the most common category (31.3%), and benign pathology (B2) accounted for 64.4% of biopsies. Within this dataset, LightGBM yielded the highest apparent AUC (0.999) (however, given the extremely small number of true discordant cases, this estimate is likely unstable and should be interpreted with caution), while BioBERT showed the strongest agreement with expert consensus (κ = 0.89). SHAP analysis identified clinically meaningful terms such as calcification, hypoechoic, ductal, and carcinoma as key contributors to model predictions. Given the very limited number of true discordant cases, these performance estimates are likely unstable and should be regarded as preliminary, requiring validation in larger, multi-center cohorts. Conclusions: This study presents a proof-of-concept NLP-based framework for radiology–pathology concordance assessment. The models showed promising performance in identifying potentially discordant cases; however, given the limited number of true discordant samples, these findings should be considered preliminary and require further validation in larger, multi-center datasets before clinical implementation. Full article

The combination of Fourier-transform infrared (FTIR) spectroscopy and machine learning gives a promising result in wheat variety classification. This study aimed to evaluate the contributions of distinct spectral regions and their combinations to classification performance. Out of the full raw spectra of four bread wheat varieties, namely Altindane, Cavus, Flamura-85, and Nevzatbey, 15 spectral datasets were prepared. Artificial Neural Networks (ANN), Support Vector Machines (SVM), Random Forest (RF), and K-Nearest Neighbor (KNN) models were trained and analyzed. The highest classification performance was obtained using spectral regions associated with protein and lipid bands. The highest average accuracy of 0.9895 was shown by the SVM model, while the ANN produced comparable results with lower variability. Additionally, Variable Importance in Projection (VIP) analysis identified the most influential spectral bands in the protein (Amide II, ~1542 cm⁻¹) and carbonyl (1744–1715 cm⁻¹) regions. These findings indicate that classification is driven by chemically meaningful features rather than purely statistical patterns. The approach followed in this study provides an insight that, in FTIR-based classification, when rigorously evaluated using nested cross-validation, spectral region selection can outweigh model complexity. This approach demonstrates strong potential for rapid and non-destructive assessment, especially for real-time applications in grain processing and automated sorting systems. Full article

Background: Accurate differentiation of kidney diseases such as cysts, tumors, stones, and normal tissue from computed tomography (CT) images remains challenging due to overlapping visual characteristics and variability in data distributions. While deep learning approaches have shown promising results, many existing studies rely on image-level data splitting and focus primarily on accuracy, which may lead to overly optimistic performance and limited clinical reliability. Methods: This study proposes KDH-Net (Kidney Disease Hybrid Network), a hybrid deep learning framework for multiclass kidney disease characterization that integrates EfficientNetB0, ResNet50, and MobileNetV2 through feature-level fusion. A two-stage training strategy is adopted to enhance optimization stability. To ensure realistic performance assessment, experiments on the primary dataset are conducted under a patient-level evaluation protocol, eliminating potential data leakage. The framework further incorporates calibration analysis, statistical validation, and explainable artificial intelligence to evaluate prediction reliability and interpretability. Results: On the patient-level dataset, KDH-Net achieves an overall accuracy of 0.93 with a macro-average F1-score of 0.91, demonstrating balanced performance across all classes. Confidence analysis indicates meaningful alignment between prediction confidence and correctness, while Grad-CAM visualizations highlight anatomically relevant regions associated with each class. Conclusions: The results demonstrate that KDH-Net provides a stable, reliable, and interpretable framework for kidney CT characterization. The proposed system is designed to support clinical decision-making by offering trustworthy predictions under realistic evaluation conditions, rather than replacing clinical expertise. Full article

The return to in-person classes after the COVID-19 pandemic revealed an increase in physical violence among students of secondary school. This article examines the role of the school as a setting that enables students to learn how to coexist with others. Based on an educational qualitative research study conducted in two state-run schools in the Metropolitan Area of Buenos Aires, located in urban poverty contexts, it investigates the effects of COVID-19-induced isolation on school coexistence. The fieldwork involved participant observation, interviews, and analysis of student productions during school workshops. Students and teachers were selected through purposive sampling. The working hypothesis posits that learning to coexist involves not only dealing with conflicting situations but also the need to verbalize them, a practice that schools actively foster. The findings show that, by providing a place where time and space are shared, the school acts as a key mediator, where students’ physical and verbal interactions become essential to reconfiguring relationships among classmates. The study concludes that the school plays a decisive role in transforming conflict into voiced experience, replacing physical aggression with meaningful narratives. Full article

Inclusive education (IE) aims to promote meaningful participation and a sense of belonging for all learners. However, limited research has examined how students with learning difficulties (LDs) experience inclusion in everyday school life. This study explored how primary school students with mild LDs perceive their participation, relationships with teachers and peers, and the role of inclusive classes (ICs) within mainstream Greek primary education. A qualitative design was adopted, and data were collected through semi-structured interviews with ten Grade 6 students receiving support through ICs. Transcripts were analyzed using thematic analysis. Findings indicated that participation was associated with perceived competence in academic tasks, with language-based activities frequently described as cognitively demanding and stressful. Belonging was predominantly felt through peer acceptance and supportive teacher practices rather than solely through classroom placement. The ICs were perceived as providing individualized support and emotional safety, although some ambivalence regarding withdrawal from the mainstream classroom was reported. Students stressed the need for flexible assessment and clearer instructional guidance to enhance fairness and participation. Overall, the findings show that inclusion is experienced as a dynamic interaction between academic accessibility, interpersonal relationships, and supportive learning environments. They also underline the importance of incorporating student voice into inclusive practice. Full article

This study introduces a novel unsupervised framework, ICR-LLS, for detecting pathological gait patterns using instantaneous center of rotation (ICR) trajectories of the shank in the sagittal plane. ICR trajectories were computed from two-dimensional kinematic data captured at the lateral femoral epicondyle and lateral malleolus for both shanks, producing four-dimensional multivariate time series for each gait trial. Pairwise trajectory dissimilarities were quantified using circularly aligned Dynamic Time Warping (DTW), preserving temporal and spatial structure. The resulting dissimilarity matrix was embedded into a three-dimensional space using a force-directed network layout, enabling intuitive visualization of inter-subject gait relationships. Density-based clustering (DBSCAN), enhanced with a consensus-based ensemble approach, was employed to automatically identify clusters representing typical (healthy) gait patterns and outliers corresponding to pathological deviations. The framework is evaluated on a public dataset comprising individuals with Parkinson’s disease (PD) and healthy controls, achieving a normalized mutual information (NMI) of 0.449 and a Separation-to-Compactness Ratio (SCR) of 6.754, indicating a meaningful cluster structure. In addition, classification-oriented metrics yield an accuracy of 90%, sensitivity of 70%, and specificity of 96.7%, supporting the method’s effectiveness in distinguishing pathological gait. By combining minimal 2D kinematic inputs with unsupervised learning, ICR-LLS provides an interpretable framework for the exploratory analysis of gait variability, and although further validation is required, the findings suggest that ICR trajectories may serve as a meaningful biomechanical descriptor for characterizing pathological locomotion. Full article

Unmanned aerial vehicles (UAVs) have become indispensable tools in precision agriculture and plant phenotyping, enabling the rapid, non-destructive assessment of crop traits across space and time. Equipped with RGB, multispectral, thermal, and other sensors, UAVs provide detailed information on canopy structure, physiology, and stress responses that can guide management decisions and accelerate breeding programs. Despite these advances, the downstream processing of UAV imagery remains technically demanding. Converting orthomosaics into standardized, biologically meaningful data often requires a combination of photogrammetry, geospatial analysis, and custom scripting, which can limit reproducibility and accessibility across research groups. We present drone2report, an open-source python-based software that processes orthomosaics from UAV flights to generate vegetation indices, summary statistics, derived subimages, and text (html) reports, supporting both research and applied crop breeding needs. Alongside the basic structure and functioning of drone2report, we also present five case studies that illustrate practical applications common in UAV-/drone-phenotyping of plants: (i) thresholding to remove background noise and highlight regions of interest; (ii) monitoring plant phenotypes over time; (iii) extracting information on plant height to detect events like lodging or the falling over of spikes; (iv) integrating multiple sensors (cameras) to construct and optimize new synthetic indices; (v) integrate a trained deep learning network to implement a classification task. These examples demonstrate the tool’s ability to automate analysis, integrate heterogeneous data and models, and support reproducible computation of agronomically relevant traits. drone2report streamlines orthorectified UAV-image processing for precision agriculture by linking orthomosaics to standardized, plot-level outputs. Its modular, configuration-driven design allows transparent workflows, easy customization, and integration of multiple sensors within a unified analytical framework. By facilitating reproducible, multi-modal image analysis, drone2report lowers technical barriers to UAV-based phenotyping and opens the way to robust, data-driven crop monitoring and breeding applications. Full article

Objective: To evaluate overall survival and to identify clinical, pathological, and demographic factors associated with survival in patients with stage III colon cancer. Methods: This retrospective cross-sectional study included 452 patients with stage III colon cancer who were followed at Ankara Bilkent City Hospital between 2005 and 2025. Patient data, including age, sex, ECOG performance status, comorbidities, tumor characteristics, treatment-related toxicities, and recurrence, were analyzed using PASW Statistics 18.0 (SPSS Inc., Chicago, IL, USA). Kaplan–Meier and log-rank tests were used for survival analysis. Prognostic factors, survival, mortality, and recurrence predictions were evaluated using machine learning algorithms, including coarse tree, bagged trees, support vector machines, and k-nearest neighbors. Furthermore, an explainable artificial intelligence framework was incorporated to improve model transparency and reveal clinically meaningful feature contributions. Model performance was assessed using accuracy, sensitivity, specificity, and F-score. Results: According to statistical analyses, older age, ECOG performance score ≥ 2, stage IIIC disease, N2-level lymph node metastasis, and the presence of comorbidities—particularly diabetes mellitus—were significantly associated with worse survival (p < 0.05). Machine learning analyses identified key prognostic factors, including positive surgical margins, rash, mucositis, thrombocytopenia, number of chemotherapy cycles, pathological tumor subtype, diarrhea, age at diagnosis, and anemia. SHAP analysis further demonstrated that treatment-related variables, particularly surgical margin positivity and chemotherapy-associated toxicities, were among the most influential predictors of survival. Several machine learning models outperformed traditional statistical methods in predicting mortality and recurrence, with the highest accuracy observed in ensemble methods such as coarse tree (87%) and bagged trees. Conclusions: This study identifies key prognostic factors influencing survival in stage III colon cancer and demonstrates that machine learning-based approaches can complement conventional statistical methods. The integration of clinical and treatment-related variables may improve individualized risk stratification and support clinical decision-making. These findings may also guide future large-scale, multicenter, and prospective studies. Full article

Cardiovascular disease (CVD) risk assessment in older adults requires models that are accurate, clinically interpretable, and able to retain performance in independent populations. This study developed an interpretable machine-learning framework for CVD risk stratification in individuals aged 65 years and older using routinely available clinical factors and a selected biochemical extension and then evaluated its performance in a substantially larger independent external cohort. Model development used a development cohort of 100 patients (Almaty, age ≥ 65) with leakage-free nested cross-validation and out-of-fold (OOF) probabilities. Three internally evaluated configurations were compared: a clinical logistic regression baseline (LR clinical), a biomarker-augmented logistic regression (LR selected), and a nonlinear random forest on the selected feature set (RF selected). Discrimination was assessed using ROC-AUC and PR-AUC; probabilistic accuracy using Brier score and log loss. Calibration was examined using OOF calibration curves with sigmoid calibration for selected models. Decision-analytic utility and exploratory operational thresholds were assessed using Decision Curve Analysis (DCA), yielding a three-tier scale with thresholds t__low = 0.23 and t__high = 0.40. In nested cross-validation, LR clinical achieved ROC-AUC 0.9425 ± 0.0188 and PR-AUC 0.9574 ± 0.0092 with Brier 0.1004 ± 0.0215 and log loss 0.3634 ± 0.0652; LR selected performed worse, while RF selected showed competitive discrimination. External validation on an independent cohort (n = 695) showed retained discrimination (ROC-AUC 0.8355; PR-AUC 0.9376) with acceptable probabilistic accuracy (Brier 0.1131; log loss 0.3760), and recalibration (intercept + slope) slightly improved probability metrics. Explainability analyses (odds ratios, permutation importance, SHAP) consistently identified heredity, BMI, physical activity, and diabetes as influential model-associated factors, with clinically plausible directionality. The results suggest that an interpretable model trained on a small geriatric cohort can retain meaningful predictive performance on a substantially larger external cohort, supporting the potential value of transparent risk stratification in older adults, while broader prospective and multi-center validation remains necessary before routine clinical implementation. Full article

In recent years, Visual Education has emerged as an innovative and interdisciplinary teaching approach aimed at promoting meaningful learning through the conscious use of visual tools and languages. This educational paradigm helps to facilitate the understanding of complex concepts, translating them into clear and intuitive visual representations, while enhancing memorisation skills, critical information processing and the practical application of acquired knowledge. This systematic review, conducted according to the PRISMA (2020) protocol, analyses the most recent empirical evidence on the effectiveness of Visual Education in educational contexts. The main objective is to assess how the intentional use of visual tools—images, concept maps, educational videos, interactive digital materials, and virtual manipulatives—contributes to enhancing learning processes and developing transversal skills. Through a comparative analysis of fourteen international contributions published between 2020 and 2025, selected from the Scopus, Web of Science and EBSCO databases, the research highlights how Visual Education significantly influences the improvement of academic performance, motivation and cognitive and emotional engagement of students. The results also confirm the inclusive function of visual teaching, which can encourage participation, self-esteem and cooperation even in individuals with special educational needs. The discussion emphasises the need for the systematic integration of Visual Education into school curricula as a strategy to enhance soft skills and promote more equitable, effective learning geared towards the integral development of the individual. Full article

Background: Sexual health research with migrant and refugee communities presents unique challenges, shaped by cultural sensitivities, stigma, and the under-representation of these populations in health research. However, lived experiences insights are essential for the development of appropriate and useful research and health initiatives. It is important to learn from researchers’ experiences to expand the representation of migrant and refugee community voices. Method: This paper draws on two qualitative studies conducted in South Australia: one exploring the sexual and reproductive health perspectives of refugee and migrant women, and the other of men. We reflect upon the methodological and ethical considerations in conducting research in this sensitive field and provide recommendations for future researchers and healthcare providers when working with migrant and refugee communities. Results: Both studies encountered difficulties in relation to participant recruitment, cross-cultural communication, and addressing taboos surrounding sexual health. At the same time, they highlighted opportunities for generating meaningful insights through culturally safe, gender-sensitive approaches and collaboration with community stakeholders. Conclusions: By synthesising experiences from both projects, we identify practical strategies for building trust, overcoming linguistic and cultural barriers, and creating supportive environments for discussing sensitive topics. These reflections offer guidance for researchers and clinicians aiming to advance culturally responsive sexual health research and strengthen healthcare provision for migrant and refugee populations. Full article

Background/Context: Creating instructional materials that authentically meet the needs of marginalized learner groups such as student veterans, multilingual adult learners, and first-generation doctoral students demands consistent application of Universal Design for Learning (UDL) principles coupled with meaningful content expertise about those learners’ traits, access needs, and lived experiences. Faculty at teaching-intensive institutions face persistent constraints of time, knowledge, and course load that make systematic UDL implementation difficult. Objective: This practitioner-scholar case study examines whether HAIST-structured agentic LLM-assisted instructional design can produce UDL-aligned materials for student veterans and multilingual learners at a quality level and time frame realistic for under-resourced faculty. Methodology: Drawing from the Human-AI Symbiotic Theory (HAIST) and UDL guidelines, we document four AI-assisted cycles of instructional design at a Hispanic-Serving Institution. Outcomes related to UDL alignment were measured using a rubric adapted from CAST Guidelines 2.2. Results: Across four materials, initial AI generation averaged 61.4% UDL alignment (SD = 8.7%); following iterative calibration, this rose to 84.2% (SD = 5.3%). The largest gains occurred in the Engagement category. Conclusions: These descriptive findings, interpreted as exploratory rather than inferential given the single-site case study design and n = 4 materials, suggest that HAIST-structured AI-assisted design has the potential to produce accessible materials for underserved learner populations in time frames feasible for working faculty. Learner outcome data were not collected in this study; future quasi-experimental work is needed to assess the effectiveness of these materials with target learner populations. Full article