Biology subjects

Forbes, S.

Publications and source records attributed to Forbes, S..

4 recordsLinked to original sources

bioRxiv2026

Random-forest segmentation and spatial analysis of injected cardiac spheroids in optically cleared myocardium

Accurate quantification of transplanted cardiac spheroids requires three-dimensional localisation within intact myocardium, yet this remains technically challenging. Optical clearing and light-sheet microscopy enable volumetric imaging of injection sites, but automated segmentation is difficult when transplanted spheroids and host tissue are labelled with the same fluorescent markers and cannot be separated by simple thresholding. We developed a random forest based pixel classification workflow for 3D detection of injected hiPSC derived cardiomyocyte and H9c2 spheroids in optically cleared rabbit myocardium. A supervised classifier trained on intensity, edge, and texture features generated a segmentation then grouped pixels via connected component analysis to reconstruct individual spheroids. The method showed good agreement with manual annotation and enabled automated extraction of spheroid size and spatial metrics. This accessible workflow enables reproducible three-dimensional quantification of transplanted spheroids in large light-sheet microscopy datasets and provides a practical route from volumetric imaging to spatial metrics in cardiac regeneration studies.

biophysics↗

bioRxiv2026

DUCK-Net: Automated deep learning segmentation of Ductular Reaction in murine liver injury captures multicellular niche dynamics from H&E morphology

Ductular Reactions (DRs) are dynamic and complex multicellular responses that occur as a result of various hepatic injuries. Precise identification and quantification of the extent of DRs is a cornerstone of pre-clinical modelling of liver disease, with links to inflammation, fibrosis, regeneration, and disease severity. Here, we apply a deep learning model, Deep Understanding Convolutional Kernel or DUCK-Net, to the automated detection and segmentation of DRs in whole-slide histopathological images of murine models of liver damage. Following annotation of a training dataset by a specialist liver histopathologist, we demonstrate accelerated performance and accurate detection, achieving a mean Dice coefficient (model-expert segmentation overlap) of 85.4% and a specificity of 98%, indicating minimal false positives. Evaluation of model validity and utility was achieved with a histological time course of cholestatic injury and recovery using 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine diet (DDC) in mice. When assessed against a multiple linear regression model incorporating core epithelial and stromal components of the DR as quantified using IHC, DUCK-Net predicted the spatiotemporal response to injury and repair/resolution with a coefficient of determination (R2) of 0.88. Moreover, DUCK-Net kinetics strongly correlated with published spatial transcriptomic (Stereo-seq) analysis of the DDC model, demonstrating that H&E-based segmentation captures molecular DR dynamics comparable to, or exceeding that of individual IHC markers without the need for immunostaining. DUCK-Net provides a novel and accessible platform for rapid, accurate histological quantification of liver injury reflective of the matrix-rich, multicellular regenerative niche observed in DRs.

cell biology↗

bioRxiv2025

Mink by mink: stitching together signatures of subspecies adaptation through a pangenome of threatened mustelids

The American mink (Neogale vison), a semi-aquatic Mustelidae carnivoran with broad ecological range across North America, includes several putative subspecies of conservation concern. To investigate the evolutionary history and adaptive signatures of mink subspecies, chromosome-scale genome assemblies were generated for six individuals representing three southern subspecies: N. vison evergladensis, N. vison vulgivaga, and N. vison lutensis. Genomes were assembled using Illumina short reads, scaffolded with Oxford Nanopore long reads, and aligned to the phased N. vison reference genome. Assemblies ranged from 75.9% to 97.8% completeness, with five meeting thresholds for pangenome construction. A reference-free pangenome revealed an open architecture, highlighting considerable subspecies diversity. Subspecies-specific gene enrichment reflected adaptation: N. vison evergladensis showed enrichment in traits related to reproduction and sensory function; N. vison vulgivaga in cytoskeletal remodeling and oxidative stress; and N. vison lutensis in neuronal development, synaptic plasticity and cellular stress pathways. Assessment of the mitogenomes resolved N. vison lutensis as a distinct lineage, while nuclear data supported broader subspecies divergence but lacked fine scale resolution. N. vison evergladensis showed multiple signatures of small population size, including inbreeding coefficients (FROH) above 0.5, and displayed consistent population decline over time via demographic inference. Our findings support evergladensis as a distinct subspecies, supported by both the mitogenome phylogeny, and significant functional differentiation. As the first pangenome for Mustelidae, this study demonstrates the power of integrating cross-platform sequencing with natural history specimens to improve the resolution on signatures of adaptation and inform conservation policy and management of threatened populations.

genomics↗

bioRxiv2022

Hypoxia shapes the immune landscape in lung injury promoting inflammation persistence

Acute Respiratory Distress Syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, has no cure. Hypoxemia is a defining feature, yet its impact on inflammation is often neglected. Patients with ARDS are monocytopenic early in the onset of the disease. Endotoxin or Streptococcus pneumoniae acute lung injury (ALI) in the context of hypoxia replicates this finding, through hypoxia-driven suppression of type I interferon signalling. This results in failed lung monocyte-derived interstitial macrophages (IM) niche expansion and unchecked neutrophilic inflammation. Administration of colony stimulating factor 1 (CSF1) rescues the monocytopenia, alters the circulating classical monocyte phenotype in hypoxic endotoxin-driven ALI and enables lung IM population expansion, thus limiting lung injury in endotoxin- and virally-induced hypoxic ALI. Hypoxia directly alters immune dynamics to the detriment of the host and manipulation of this aberrant response offers new therapeutic strategies for ARDS.

cell biology↗