Biology subjects

Stark, A. W.

Publications and source records attributed to Stark, A. W..

4 recordsLinked to original sources

bioRxiv2026

UV photogrammetry for transparent and composite surfaces

Transparent and composite surfaces pose a fundamental challenge for stereo photogrammetry: optically smooth glass produces no detectable surface features under visible illumination, making three-dimensional reconstruction impossible without surface preparation. This excludes optical components such as lenses and cover glasses, composite assemblies, and semi-translucent biological specimens from non-contact geometric measurement. Here we show that coherent speckle illumination at 266 nm overcomes this limitation by exploiting wavelength-dependent scatter enhancement, generating sufficient backscattered signal on surfaces that are entirely invisible under visible illumination. We developed a multispectral stereo system and evaluated three illumination modalities under identical acquisition conditions. On transparent glass, both visible modalities produce complete reconstruction failure, recovering only non-transparent holder structures. Ultraviolet speckle illumination at 266 nm enables dense reconstruction of the same surfaces. We demonstrate recovery of an uncoated plano-convex lens with a fitted radius of 30.946 mm and point-cloud standard deviation of 106.5 {micro}m, defect detection on a transparent cover glass without surface preparation, and reconstruction of a semi-translucent biological specimen. On metrology-grade reference objects, ultraviolet speckle achieves a standard deviation of 116 {micro}m and completeness exceeding 93%, approaching the performance of optimised visible structured illumination. These results establish ultraviolet speckle photogrammetry as an enabling approach of optical metrology to otherwise uncooperative surfaces, with relevance to optical manufacturing inspection and biological surface analysis.

biophysics↗

bioRxiv2025

Applying telecentric stereo 3D-measurement to small Lepidopterans - bridging the macro and the microscale with isotropic micrometer resolution

We present a straightforward, application-driven telecentric stereo 3D-measurement system for high-precision measurements, designed for applications ranging from industrial quality control to biological research including scanning of Lepidoptera moths. Utilizing a dual-camera setup with telecentric lenses and structured illumination, our system achieves lateral resolution of 8.0 m and axial resolution of 4.46 m in a measurement volume of 11 mm x 11 mm x 6 mm. We address challenges typically encountered when using standard libraries like OpenCV, e.g. in extrinsic parameter estimation using a dedicated calibration method that corrects for a potential model mismatch due to telecentricity. Our approach adapts existing methods, such as telecentric stereo vision and structured illumination, into an optimized, user-friendly system tailored for life science research, enabling detailed 3D reconstructions of scattering objects, such as small moths, with isotropic micrometer accuracy. This work presents an application-driven approach for biological 3D metrology by integrating existing technologies (telecentric stereo vision, structured illumination) into a specialized imaging platform suitable for non-invasive morphological studies. Unlike conventional CT or microscopic approaches, our method provides a balance of precision, scalability, and practical usability for non-expert users with the aim to study developmental changes in species under varying environmental conditions, while also methodically bridging the gap between macroscopic and microscopic resolution in biological imaging.

biophysics↗

bioRxiv2022

A primary sensory cortical interareal feedforward inhibitory circuit for tacto-visual integration

Tactile sensation and vision are often both utilized for the exploration of objects that are within reach though it is not known whether or how these two distinct sensory systems might combine such information. Here in mice we find that stimulation of the contralateral whisker array suppresses visually evoked activity in a subarea of primary visual cortex (VISp) whose visual space covers the whisker search space. This is mediated by local fast spiking interneurons that receive a direct cortico-cortical input predominantly from layer 6 of the primary somatosensory barrel cortex (SSp-bfd). These data demonstrate functional convergence within and between two primary sensory cortical areas for multisensory object detection and recognition.

neuroscience↗

bioRxiv2016

Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions

Part 1Development and calibration of suitably accurate functional assays for BRCA1 RING domain and BRCT domain missense substitutions could dramatically accelerate clinical classification of rare missense substitutions observed in that gene. Leveraging data from 68,000 full sequence tests of BRCA1 and BRCA2, plus data from the limited number of already classified BRCA1 RING domain missense substitutions, we used logistic regression and related techniques to evaluate three BRCA1 RING domain assays. These were recently described high throughput yeast 2-hybrid and E3 ubiquitin ligase assays, plus a newly developed mammalian 2-hybrid assay. While there were concerns about the accuracy of the yeast 2-hybrid assay and the indirect nature of the ubiquitin ligase assay, the mammalian 2-hybrid assay had excellent correlation with existing missense substitution classifications. After calibration, this assay contributed to classification of one newly reported BRCA1 missense substitution. In principal, the mammalian 2-hybrid assay could be converted to a high-throughput format that would likely retain suitable accuracy. Part 2How does one achieve clinically applicable classification of the vast majority of all possible sequence variants in disease susceptibility genes? BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a Mammalian 2-hybrid (M2H) assay. Downstream of the M2H laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that about 20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of about 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 47 with concordant computational and functional assay evidence in favor of pathogenicity; these are particularly likely to be classified as Likely Pathogenic once human observational data become available.

genetics↗