Research Appraisals
Evidence-based critical appraisals of the latest medical research, systematically evaluated using Oxford CEBM methodology.
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Cell reports methods
Spatial multi-omics imputation and embedding with SpaMIE
SpaMIE is a deep graph neural network framework designed to tackle the challenge of multi-section integration in spatial multi-omics (SMO) datasets with systematic missing modalities. Current SMO platforms face limitations such as high cost and limited throughput, leading to many large-scale spatial atlases relying on cost-effective mono-omics measurements while only a few sections are profiled with full multi-omics technologies. This results in heterogeneous modality coverage across tissue sections. SpaMIE offers a two-stage solution. In the first stage, it performs spatially informed cross-modal imputation, enabling accurate inference of missing modalities from mono-omics data. In the second stage, it integrates measured and imputed spatial multi-omics profiles across multiple tissue sections to learn a unified embedding. Benchmarking on simulated and experimental datasets shows that SpaMIE achieves accurate cross-modal imputation, robust multi-section integration, and improved spatial domain identification, providing a flexible and scalable solution for constructing and analyzing SMO atlases.
22 July 2026
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Retrofitting a clinical pencil beam scanning proton therapy unit for 2D ultra-high dose rate scanning
Purpose.This work aimed to demonstrate how existing clinical infrastructure can be adapted to enable ultra-high dose rate (UHDR) pencil beam scanning (PBS) for FLASH research. Leveraging available hardware and minimizing modifications, we extended the capabilities of PSI Gantry 1, previously used as a flexible UHDR fixed-beam delivery platform, by enabling true 2D PBS for UHDR small-field irradiations through the addition of a second scanning direction and multiple gantry angles.Methods.A second (vertical) scanning direction was implemented by repurposing an existing steering magnet and integrating it into the control system. Inter-spot dead times were minimized through software optimizations that synchronized control processes and magnet settling times, optimizing the local average dose rate. A precise spot map acquisition process ensured accurate dose delivery across different gantry angles. Additionally, a1kHzlogging system was introduced, enabling the reconstruction of lateral dose and dose-rate distributions from recorded beam parameters.Results.Gantry 1 was successfully commissioned for 2D scanning of small fields (100×24mm2) at gantry angles from 0∘(beam towards floor) to-120∘. Dose-uniform field deliveries were achieved at local average dose rates up to75Gys-1. The reconstructed lateral dose distributions were in good agreement with CCD measurements regarding the90%iso-dose contour, while the dose-rate distributions were validated againstmicro-Diamonddetector measurements, confirming the precision of the recalculated dose rates.Conclusions.By repurposing existing hardware and optimizing beam delivery, Gantry 1 has been upgraded to a true 2D PBS UHDR scanning system, capable of delivering fields at local average dose rates exceeding70Gys-1. The high-frequency logging system enables future reanalysis of data as the mechanisms underlying the FLASH effect become clearer. This transformation makes Gantry 1 a versatile platform for preclinical research and small animal irradiation, advancing the investigation of the FLASH effect.
27 May 2026
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