Biology subjects

Bray, A.

Publications and source records attributed to Bray, A..

4 recordsLinked to original sources

bioRxiv2026

Deep-learning based 3D segmentation of heterogeneous lizard claw tissue from CT data

The accurate segmentation of lizard claws is important as they are materially heterogeneous, comprising both bone and keratinous tissue. This study presents a deep learning framework for the automated segmentation of lizard claw tissues, specifically bone and keratin, from CT imaging data. A dataset comprising 14 lizard claws was used in this work, with annotations generated through a superpixel based labeling approach to provide ground truth reference segmentations. To evaluate the effect of spatial context on segmentation performance, both 2D and 2.5D CNN architectures using DeepLabV3 with ResNet-50, ResNet-101, and Inception-ResNet-v2 backbones were investigated, with predictions subsequently reconstructed into three-dimensional volumes for analysis. Performance was assessed using a leave one out cross validation (LOOCV) strategy and evaluated with 3D Dice Similarity Coefficient (DSC), Intersection over Union (IoU), Sensitivity (Recall), 95th Percentile Hausdorff Distance (HD95), and Relative Volume Error (RVE). Experimental results demonstrate that 2.5D CNN architectures consistently outperform their 2D counterparts across all evaluation metrics, highlighting the importance of incorporating inter-slice contextual information for volumetric tissue segmentation. From amongst the models, the 2.5D Inception-ResNet-v2 achieved the best overall performance, reaching a validation accuracy of 97.5% and producing segmentation results that closely align with ground-truth tissue structures. Our findings demonstrate the effectiveness of 2.5D deep learning approaches for the high accuracy segmentation of heterogeneous lizard claw tissues from CT data, whilst providing a robust framework for automated morphological analysis in comparative anatomical studies.

zoology↗

bioRxiv2025

Grip and grasp: lizard claw inspired robotic manipulators

This paper considers the selection of a lizard claw to apply as an end effector on a bioinspired robotic manipulator, to improve grasping efficiency. Our work draws on morphological parameters that influence mechanical grip. By considering geometrical ratios that are built on parameters such as the arm-to-tip angle, the claw inner radius, and the slip distance, our research identifies optimal parameters that influence grip strength and stability. We demonstrate that these parameters, when combined to form two specific indices (the geometric mean, IGM, and the arithmetic mean of deviations, IAMD), provide a basis for more extensive comparisons between the different claw morphologies researched. The claw of Crotaphytus collaris is deduced as being the most suitable candidate for application as a bioinspired end effector in a robotic manipulator used for grasping objects, as it closely aligns with our optimal design criteria. To practically demonstrate gripping and grasping, we use a lightweight ping pong ball as well as larger and heavier objects such as an abalone shell, boxing mitts and a printer spool. Our robotic manipulator integrates dual grasping strategies. These include pinching for delicate objects and scooping for larger, irregular objects, thus enhancing its versatility across different environments and for different applications. Overall, this paper offers valuable new insights into biomimetic manipulator design using claws as end effectors, highlighting the importance of lizard claw selection based on morphology.

bioengineering↗

bioRxiv2020

Radiotherapy and chemotherapy alter migration of brain cancer cells before cell death

Although radiotherapy and most cancer drugs target the proliferation of cancer cells, it is metastasis, the complex process by which cancer cells spread from the primary tumor to other tissues and organs of the body where they form new tumors, that leads to over 90% of all cancer deaths. Thus, there is an urgent need for anti-metastasis strategies alongside chemotherapy and radiotherapy. An important step in the metastatic cascade is migration. It is the first step in metastasis via local invasion. Here we address the question whether ionizing radiation and/or chemotherapy might inadvertently promote metastasis and/or invasiveness by enhancing cell migration. We used a standard laboratory irradiator, Faxitron CellRad, to irradiate both non-cancer (HCN2 neurons) and cancer cells (T98G glioblastoma) with 2 Gy, 10 Gy and 20 Gy of X-rays. Paclitaxel (5 M) was used for chemotherapy. We then measured the attachment and migration of the cells using an electric cell substrate impedance sensing device. Both the irradiated HCN2 cells and T98G cells showed significantly (p < 0.01) enhanced migration compared to non-irradiated cells, within the first 20 to 40 hours following irradiation with 20 Gy. Our results suggest that cell migration should be a therapeutic target in anti-metastasis/anti-invasion strategies for improved radiotherapy and chemotherapy outcomes.

cancer biology↗

bioRxiv2019

Phlebotomus papatasi sand fly salivary protein diversity and immune response potential in Egypt and Jordan populations

Phlebotomus papatasi sand flies inject their hosts with a myriad of pharmacologically active salivary proteins to assist with blood feeding and to modulate host defenses. These salivary proteins have been studied for their role in cutaneous leishmaniasis disease outcome with different salivary proteins attenuating or exacerbating lesion size. Studies have shown that while co-administered sand fly saliva exacerbates Leishmania major infections in naive mice, animals pre-exposed to saliva are protected, with the infection attenuated via a delayed-type hypersensitivity immune reaction. These studies highlight the potential of the salivary components to be used as a vaccine. One protein in particular, P. papatasi salivary protein 15 (PpSP15) has been intensively studied because of its ability to protect mice against Le. major challenge. The number of antigenic molecules included in vaccines is restricted thus emphasizing the role of population genetics to identify molecules, like PpSP15, that are functionally significant, conserved across populations and do not experience selection. Three distinct ecotope study sites, one in Egypt (Aswan) and two in Jordan (Swaimeh and Malka), were chosen based on their elevation, rainfall, vegetation, differing reservoir species, and the presence or absence of Le. major. The objective of this work was to analyze the genetic variability of nine of the most abundantly expressed salivary proteins including PpSP12, PpSP14, PpSP28, PpSP29, PpSP30, PpSP32, PpSP36, PpSP42, and PpSP44 and to predict their ability to elicit an immune response. Two proteins, PpSP12 and PpSP14, demonstrated low genetic variability across the three sand fly populations represented in this study, with multiple predicted MHCII epitope binding sites, identified by alleles present in the human populations from the study sites. The other seven salivary proteins revealed greater allelic variation across the same sand fly populations indicating that their use as vaccine targets may prove to be challenging.

genetics↗