Biology subjects

Cunha, I.

Publications and source records attributed to Cunha, I..

5 recordsLinked to original sources

bioRxiv2026

Mapping bioimage-analysis software adoption in microscopy

Most quantitative microscopy measurements pass through image-analysis software, and different programs can return different measurements from the same images. Which programs researchers rely on therefore matters for reproducibility; however, this information lies scattered across the methods sections of the microscopy literature. In this analysis, we show how mentions of 30 software packages changed across 1.7 million full-text microscopy papers published between 2010 and 2025. In 2010, 12% of these papers mentioned at least one of the 22 analysis packages we tracked; by 2025, 30% did. Mentions stayed concentrated on a few general-purpose platforms, led by ImageJ/Fiji. Newer packages are mentioned more often in particular fields, such as QuPath in pathology and napari in electron microscopy. Deep-learning methods are usually mentioned alongside an established platform; papers often run StarDist inside Fiji and Cellpose on its own. Many papers mention a package without citing it, so citation counts understate how often packages appear in published work; authors should make that use visible by citing each package and reporting how they ran it.

bioinformatics↗

bioRxiv2026

SMLMFlow: Improving Structural Resolution in Single Molecule Localization Microscopy with Flow Matching

While Single Molecule Localization Microscopy (SMLM) aims to generate precise coordinates of molecular targets in cells, the resulting point clouds are inherently blurred by additive noise sources across the experimental, imaging, and processing workflow. This blurring often limits SMLMs ability to accurately quantify complex assembled structures required to address biological issues, despite reported localization precision down to a couple of nanometers. Here, we present SMLMFlow, a machine learning framework for improving structural resolution in SMLM datasets that combines a graph neural network and a hierarchical transformer with flow matching. We show that SMLMFlow improves structural resolution and downstream quantification across different structures, including filaments and protein nano-clusters, and generalizes to new unseen photophysics models.

bioinformatics↗

bioRxiv2025

AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI

Live-cell imaging provides a unique insight into complex cellular processes including single cell fate, but remains limited by both low-throughput and the lack of generalisable analytics for the multidimensional datasets it produces. This work introduces AI4CellFate, an interpretable and data-driven machine learning framework for predicting cell fate from microscopy timelapses, applied here to cancer therapy. By integrating generative AI and contrastive learning, AI4CellFate enables early fate prediction as well as visualisation of biologically relevant features, with limited annotation.

bioinformatics↗

bioRxiv2024

Small non-coding RNA content in plasma-derived extracellular vesicles distinguish ataxic SCA3 mutation carriers from pre-ataxic and control subjects

Spinocerebellar ataxia type 3 (SCA3), a neurodegenerative disorder caused by a CAG expansion in the ATXN3 gene, is the most common spinocerebellar ataxia subtype worldwide. Currently, there is no therapy to stop or prevent disease progression. Promising therapeutic strategies are emerging, but their translation into clinical practice requires sensitive and reliable biomarkers. Blood circulating extracellular vesicles constitute a promising source of biomarkers with potential to track alterations of the central nervous system due to their ability to cross the blood brain barrier. Here, we perform sequencing analysis of small RNAs from plasma-derived extracellular vesicles from SCA3 mutation carriers (10 pre-ataxic and 10 ataxic) and 12 control subjects to identify potential RNA biomarker candidates for this disease. Data showed that plasma-derived extracellular vesicles from ataxic SCA3 mutation carriers are enriched in mitochondrial, nuclear, and nucleolar RNA biotypes compared to pre-ataxic and control subjects. Moreover, ataxic mutation carriers could be discriminated from control and pre-ataxic subjects based on the miRNAs or piRNAs content, but not tRNA. Furthermore, we identified a subset of differentially expressed miRNAs and piRNAs that clearly differentiate ataxic mutation carriers from pre-ataxic and control subjects. These findings open new avenues for further investigation on the role of these RNAs in the pathogenesis of SCA3 and their potential as biomarkers for this disease.

neuroscience↗

bioRxiv2019

DENTAL CARIES AND ORAL HEALTH BEHAVIOR ASSESSMENT AMONG PORTUGUESE ADOLESCENTS

IntroductionIt is during the school phase that children and adolescents consolidate healthy behaviors, which will contribute to the decrease of diseases, especially in the reduction of dental caries. The main objective of the present study was to assess the decayed, missing and filled deciduous and permanent teeth index and oral health behaviors among Portuguese adolescents.\n\nMaterials and methodsAn observational cross-sectional study was designed including a sample of 694 adolescents between the ages of 12 and 18 years old from five public schools in the Viseu and Guarda districts, Portugal. After a self-administered questionnaire was filled out by the participants, a clinical examination was carried out in order to assess oral status and dental caries identification. A descriptive analysis of the variables was performed using the Chi-square, Mann-Whitney and Kruskal-Wallis tests (p<0.05).\n\nResultsThe decayed, missing and filled permanent teeth index was 2.91{+/-}2.9 and the decayed, missing and filled deciduous teeth index was 1.10{+/-}1.4. Of the total sample, 73% consumed sugary food on a daily basis, 54.7% drank bottled water, 50.1% considered oral health good, 70.8% did not report pain in the last 12 months, but noticed gingival bleeding (51.5%). Most adolescents (79.4%) brushed their teeth daily and 60% did not use dental floss. Of the total sample, 96.4% had a dental appointment in the last 12 months, being 46.4% due to prevention treatments. The high decayed, missing and filled deciduous teeth index was associated with low maternal scholarship, male gender and living in a rural residence area (p<0.05). Adolescents who brush their teeth daily presented a good perception about their oral health (p<0.001).\n\nConclusionsPortuguese adolescents presented a low decayed, missing and filled deciduous and permanent teeth index index. The decayed, missing and filled deciduous teeth index was associated with sociodemographic factors. Oral hygiene habits were associated with self-perception of oral health. It is suggested that oral health promotion and prevention programs should be improved in schools in order to reduce the risks of oral disease development.

scientific communication and education↗