Biology subjects

Evans, M.

Publications and source records attributed to Evans, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Extrachromosomal Circular DNA Function as Mobile Elements to Alter the Mammalian Germline Genome

The viability of any species including the human requires that the germline genome is kept stable as it is transmitted across generations by the germ cells. Failure to safeguard the genome integrity and stability would lead to inherited diseases and infertility. Thus, a better understanding of the mechanisms that alter the germline genome is crucial to ensure human health and our continuation as a species. Here, we show that the extrachromosomal circular DNA (eccDNA) in the mouse and human male germline represents a new mechanism in altering the mammalian germline genome. To enable the tracking of germline eccDNA in vivo, we established a novel mouse model that allows the generation of a reporter eccDNA in a cell type-specific manner. Using this mouse model, we showed that eccDNA formed in the developing male germ cells can integrate into the germline genome. Using eccDNA-containing sperm for in vitro fertilization led to the eccDNA sequence being inherited by the embryos. By analyzing a large cohort of long-read whole genome sequencing data, we showed that eccDNA-mediated germline genome insertions represent an important source of human genome structural variations. Finally, by leveraging human sperm samples, we found that diabetes induces an increase in sperm eccDNA quantity, which is mediated at least in part through poly (ADP-ribose) polymerases. Together, our results provide new insights into how the mammalian germline genome can be altered, with important implications for human health and genome evolution.

developmental biology↗

bioRxiv2026

Modelling the persistence of post-management disturbance in Calluna vulgaris communities

O_LICalluna vulgaris is often managed in the UK by rotational burning, but this practice has recently been banned on peat with depth greater than 30-40 cm. It is unclear how then to manage the large areas of Calluna on blanket bogs used for sport shooting because without managed burning, fuel loads and wildfire risk will increase as the Calluna ages within the artificially narrow age distributions created by burn management. C_LIO_LIWe developed a model of Calluna mortality and management to understand duration and persistence of post-management effects. This allows us to assess how long it will take to reach a more natural age structure which would allow increased diversity if management ceases. C_LIO_LIOur results show that management effects persist for around 50 years depending on site-specific mortality rates. Active management may therefore be needed either to mitigate the elevated risk of severe wildfire or to speed up this transition. C_LIO_LISome studies have employed, as unmanaged analogues, Calluna stands that were last managed <50 years ago, but such studies may have unintentionally biased their results by observing Calluna still in post-management recovery leading to an over-estimation of wildfire risk associated with more natural blanket bogs. C_LIO_LISynthesis and applications: with the banning of burning as a management tool for Calluna on deep peat, alternative management is now likely needed as our model shows it could take around 50 years for the Calluna to reach a more natural age distribution. Mowing can replicate some of the effects of managed burning but requires repeated intervention and may compress the peat surface from repeated machine tracking. Rewetting and Sphagnum reintroduction may offer a more sustainable management approach to lowering Calluna fuel loads and reducing severe wildfire risk by creating wetter sub-optimal conditions for Calluna growth and thereby altering the competitive balance between Sphagnum and Calluna. Further work is needed to assess the efficacy of rewetting in controlling fuel loads and how this varies with climate and local pressures. More broadly, this work highlights the need to quantify the persistence of past management regimes to understand ecological trajectories. C_LI

ecology↗

bioRxiv2026

Topological Analysis of Multi-Network Threading in the Pancreas

The pancreas is a complex inner organ that develops through the concurrent formation of multiple interacting biological networks, but the geometric principles governing their spatial organization remain poorly understood. Here, we study pancreatic development by analysing loop structures in ductal, neuronal, and vascular networks using tools from topological data analysis. In particular, we employ the application of chromatic persistence, which is designed to detect topological interactions between distinct subsets of a structure; this is used to quantify how loops from different networks become spatially entangled. Our analysis reveals distinct developmental timelines for loop formation, progressive entanglement between ducts and vasculature, and spatial concentration of threading toward the organ interior, providing a geometric characterisation of coordinated network development in the pancreas.

developmental biology↗

bioRxiv2026

In vitro sexual dimorphism establishment in schistosomes

Schistosomes are parasitic flatworms that cause Schistosomiasis, a major Neglected Tropical Disease (NTD) that affects more than 250 million people worldwide. With two morphologically distinct sexes, a heterogametic female (ZW) and a homogametic male (ZZ), schistosomes are an exception among flatworms, which are largely hermaphroditic. Sexual dimorphism in schistosomes only becomes apparent by adulthood within the mammalian host. The cellular and molecular mechanisms underlying the sexual differentiation of these parasites are poorly understood, partly due to intrinsic challenges in assessing parasite development in vivo. Therefore, robust and reproducible approaches for maintaining and developing parasites in vitro are needed to overcome these difficulties. However, to date, only a few studies have focused on protocols that allow cultured parasites to reach sexual dimorphic stages, and none have been reproduced, limiting the ability to understand the unique sexual biology of this major human parasite. Here, we refine a protocol for long-term culture of newly transformed cercariae that developed in vitro into sexually dimorphic forms. We assessed the effect of two different sera, Foetal Bovine Serum (FBS) and Human Serum (HS), added to the culture medium supplemented with human red blood cells. We found that in contrast to FBS-cultured worms, HS-cultured parasites digested red blood cells, a crucial step for long term parasite development. Additionally, while most FBS-cultured parasites did not progress beyond an early liver stage, sexual dimorphism was clearly established in the HS-cultured worms, albeit delayed compared to in vivo development. Moreover, EdU pulse experiments revealed a continuous proliferation of cells over time in HS-cultured parasites, while a significantly lower number of proliferating cells were detected in FBS-cultured worms. This protocol paves the way to study parasite development in vitro, positively impacting the principles of the 3Rs (Replacement, Reduction and Refinement) for animal research, and allowing for in-depth studies of sexual dimorphism establishment as well as in vitro screening for novel control strategies across the life cycle of these major human parasites.

developmental biology↗

bioRxiv2025

Use of a cytochrome P450 humanised mouse model to refine schistosomiasis drug discovery.

Control of schistosomiasis, a neglected tropical disease caused by infection with Schistosoma spp., remains reliant on a single chemotherapy, praziquantel (PZQ). This strategy presents a risk to global health should PZQ-resistant schistosomes establish in endemic areas and justifies the search for new drugs. However, species-specific metabolic differences between humans and preclinical models hinder the optimisation of next-generation anti-schistosomal therapeutics. Here, to bypass these species-specific limitations, we exploited a humanised mouse model, 8HUM, engineered to express the principal human Phase I cytochrome P450 enzymes (CYP1A1/2, CYP2C9, CYP2D6, CYP3A4/7) as well as the transcription factors constitutive androstane receptor (CAR) and pregnane X receptor (PXR) in place of 35 murine orthologues. We characterised S. mansoni development, immunopathology, hepatic transcriptomic responses, intestinal microbiome changes and PZQ metabolism as well as PZQ efficacy in 8HUM versus wild-type (WT) mice. 8HUM mice supported normal S. mansoni maturation, infection-associated microbiome dysbiosis, Th2-dominant immune responses and characteristic hepatic pathology. PZQ intrinsic clearance in 8HUM hepatic microsomes mirrored human levels and was >10-fold lower than that found for WT microsomes. Oral dosing revealed human-like PZQ exposures of (R)-PZQ and 4OH-PZQ in 8HUM mice at 25 mg/kg bodyweight and >90% reductions in worm burdens at 100 mg/kg bodyweight (equivalent to that seen in WT mice administered PZQ at 400 mg/kg bodyweight). Our results revealed that 8HUM mice recapitulate key features of murine schistosomiasis while exhibiting human-relevant drug metabolism. These findings establish 8HUM as a refined translational platform for anti-schistosomal drug development, improving predictive accuracy and accelerating therapeutic discovery. One Sentence SummaryA cytochrome P450 humanised mouse model is used to study Schistosoma mansoni development, schistosomiasis, drug metabolism and drug efficacy.

pharmacology and toxicology↗

bioRxiv2025

Preclinical efficacy of combinatorial B7-H3 CAR T cells and ONC206 against diffuse intrinsic pontine glioma

BackgroundDiffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor affecting over 300 children annually in the United States. Chimeric antigen receptor (CAR) T cells are a targeted immune effector cell therapy with substantial clinical benefit against hematologic cancers. Against CNS tumors, CAR T cells targeting B7-H3, a protein highly expressed on DIPG, have rapidly advanced from preclinical studies to clinical trials. BrainChild-03 (NCT04185038), a phase 1 trial of repeatedly delivered intracerebroventricular (ICV) B7-H3-targeting CAR T cells (B7-H3 CAR T cells), demonstrated tolerability and potential efficacy for children and young adults with DIPG. However, clinical benefits were not uniformly seen, and multi-agent treatment strategies may be required against such an aggressive disease. Here, we combined B7-H3 CAR T cells with ONC206, an imipridone molecule also under clinical investigation. MethodsWe tested B7-H3 CAR T cells combined with ONC206 across multiple DIPG cell cultures and orthotopic xenograft mouse models. ResultsB7-H3 CAR T cell monotherapy induced robust cytotoxicity while ONC206 treatment resulted in significant mitochondrial dysfunction against DMG/DIPG cells. The combination of low effector-to-target ratios of B7-H3 CAR T cells and IC50 concentrations of ONC206 led to significantly enhanced cytotoxicity in vitro (p<0.003) and increased IL-2, IL-29, VEGF-A, and Granzyme B levels. In vivo combinatorial studies of ONC206 and a single ICV dose of B7-H3 CAR T cells significantly extended survival in multiple DIPG xenograft mouse models (p<0.05). ConclusionsB7-H3 CAR T cells combined with ONC206 is a feasible and efficacious multi-agent approach against multiple DIPG models. Importance of the studyDiffuse intrinsic pontine glioma (DIPG) is a fatal pediatric brain tumor. While B7-H3 CAR T cells have shown tolerability and potential benefit in early trials, combinatorial regimens may be required for consistent cures against this aggressive disease. This study demonstrates that a preclinical therapeutic regimen of B7-H3 CAR T cells with ONC206, a second-generation imipridone, increases anti-tumor efficacy in vitro and in orthotopic DIPG mouse models. To our knowledge, this is the first study to evaluate ONC206 in combination with CAR T cells. Our findings provide a preclinical roadmap for evaluating small molecules with CAR T cells to interrogate both their combined benefit and the effect of small molecules on T cells themselves. This work offers a biologically-informed, clinically translatable strategy integrating small molecule therapeutics with CAR T cell therapy and support the development of multi-agent immunotherapy trials for children with DIPG and other high-grade brain and spinal cord tumors. Key PointsO_LIB7-H3 CAR T cells are cytotoxic against preclinical DMG models. C_LIO_LIONC206 causes metabolic apoptosis in preclinical DMG models. C_LIO_LIB7-H3 CAR T cells and ONC206 have combinatorial efficacy against DMG. C_LI

cancer biology↗

bioRxiv2025

RUNX2 inhibition disrupts a PAX3::FOXO1-RUNX2 feed-forward loop and dismantles oncogenic gene programs in fusion-positive rhabdomyosarcoma

Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer of skeletal muscle lineage, with a 5-year overall survival of <30% for high-risk disease, and <8% when metastatic. The PAX3::FOXO1 fusion gene, resulting from t(2:13), is a signature driver of fusion-positive rhabdomyosarcoma, but similar to other transcription-factor based fusion genes in other cancers, not currently pharmacologically tractable. To identify novel druggable proteins in fusion-positive rhabdomyosarcoma tumor tissue and cell lines, we performed mRNA-seq of RMS patient tumors and utilizing the human FP-RMS cell lines Rh30 and Rh4, found that the RUNX2 transcription factor was the top druggable dependency. In vitro loss of function studies using genetic (RNAi) or pharmacologic (small molecule CADD522) inhibition showed that RUNX2 suppression inhibited FP-RMS cell growth, induced myogenic differentiation and apoptosis, and phenocopied PAX3::FOXO1 suppression. In vivo loss of function studies using conditional (dox-inducible) or pharmacologic (small molecule CADD522) blockade of tumor growth in a xenograft model system showed that RUNX2 suppression inhibited tumor growth. Mechanistically, we identify a PAX3::FOXO1 feed-forward loop whereby PAX3::FOXO1 binds a RUNX2 enhancer to upregulate gene expression alongside MYOD1, while RUNX2 expression supports the expression of PAX3::FOXO1 at the mRNA and protein level. SignificanceRUNX2 inhibition reduces PAX3::FOXO1 expression and signaling, which impairs fusion-positive rhabdomyosarcoma oncogenic phenotypes. In vivo treatment with CADD522 decreased tumor growth and increased survival, indicating that RUNX2 is a promising therapeutic target.

cancer biology↗

bioRxiv2025

The De-Modifier: a tool for screening modification-induced alternate peptide taxonomy in palaeoproteomics

In palaeoproteomic research, the accuracy of taxonomic matches is crucial, as research questions frequently hinge on which species were utilised by ancient people. However, protein modifications including deamidation of glutamine and asparagine, and conversion of glutamine or glutamic acid to pyroglutamic acid, can change the sequence of peptides, leading to spurious taxonomic detections and potentially inaccurate archaeological interpretations. While a handful of examples of this phenomenon have been reported in the literature, the issue is potentially much wider reaching than currently realised. In reality, any time a peptide containing a deamidated glutamine or asparagine residue, an unmodified glutamic acid or aspartic acid residue, or a pyroglutamic acid modification is detected by proteomic search software, the sequence, and therefore potentially its taxonomy, may be incorrect, which could potentially lead to unsound archaeological interpretations. The Demodifier is a fast, open source tool which solves this issue by screening for modification-induced alternate peptide taxonomy, enabling archaeologists to make informed interpretations of the taxonomies of peptides detected in ancient samples. To assess its utility, the Demodifier is tested against an archaeological dataset containing all unique peptides reported in palaeoproteomic studies of dental calculus and vessels. The results reveal that modification-induced alternate peptide taxonomies are severely under-reported, occurring 15% more frequently than previously understood. Modifications were found to produce three different types of inaccurate taxonomic matches: those which yielded completely different taxonomic lowest common ancestors to the input peptide, those which were more taxonomically specific than the input peptide, and those which were less taxonomically specific than the input peptide. The Demodifier therefore enables the rapid detection of potentially inaccurate peptide taxonomies, avoiding spurious archaeological interpretations in future studies.

bioinformatics↗

bioRxiv2024

Functional and Clinical Implications of Extrachromosomal Circular DNA in the Human Germline

Extrachromosomal circular DNA (eccDNA) originates from linear chromosomal DNA and can be found in various human cell types including the male germline. However, the functional effects and biogenesis mechanisms of the eccDNA in the human male germline are not well understood. Here, we developed a sequencing approach to extract eccDNA sequence information and the paired transcriptome information from the same cells. By applying this approach to human samples, we found evidence of transcriptional activities of germline eccDNAs. We also showed that patients with chronic diseases such as hypertension and diabetes had a significantly higher number of eccDNAs in the sperm than their healthy counterparts. This was, at least partly, due to an increased apoptosis signaling in the germline. Analysis of single cell RNA sequencing data of spermatogenic cells from diabetic patients vs. healthy individuals suggested that a dysregulation in the expression levels of multiple poly (ADP-ribose) polymerases may contribute to the increased amount of germline eccDNAs in diseased patients. In addition, we identified a potential horizontal transfer mechanism through which healthy sperm can take up eccDNAs from their surrounding microenvironment. Together, our results suggest that eccDNA may have functional effects on the germline, and it may serve as a non-invasive clinical biomarker for human health.

genomics↗

bioRxiv2024

The impact of cooking and burial on proteins: a characterisation of experimental foodcrusts and ceramics

Foodcrusts have received relatively little attention in the burgeoning field of proteomic analysis of ancient cuisine. We remain ignorant of how cooking and burial impacts protein survival, and crucially, the extent to which the extractome reflects the composition of input ingredients. Therefore, through experimental analogues we explore the extent of protein survival in unburied and buried foodcrusts and ceramics using typical Mesolithic ingredients (red deer, Atlantic salmon and sweet chestnut). We then explore a number of physiochemical properties theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, input ingredient strongly influences protein preservation, and that degradation is not universal nor linear between proteins, indicating that multiple protein physiochemical properties are at play. While certain properties such as hydrophobicity apparently aid protein preservation, none single-handedly explain why particular proteins/peptides survive in buried foodcrusts: this complex interplay requires further investigation. The findings demonstrate that proteins indicative of the input ingredient can be identifiable in foodcrust, but that the full proteome is unlikely to preserve. While this shows promise for the survival of proteins in archaeological foodcrust, further research is needed to accurately interpret foodcrust extractomes.

biochemistry↗

bioRxiv2023

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of good practice to interrogate our data. However, there is a lack of a systematic exploration of how these affect the identification of peptides, post-translational modifications (PTMs), proteins and their significance (through the False Discovery Rate) and correctness. We systematically investigated the performance of a wide range of sequencing tools and search engines in a controlled system: the experimental degradation of the single purified bovine {beta}-lactoglobulin (BLG), heated at 95 {degrees}C and pH 7 for 0, 4 and 128 days. We target BLG since it is one of the most robust and ubiquitous proteins in the archaeological record. We tested different reference database choices, a targeted dairy protein one, and the whole bovine proteome and the three digestion options (tryptic-, semi-tryptic- and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. We also explored alternative strategies, including open search that allows for the global identification of PTMs based upon wide precursor mass tolerance and de novo sequencing to boost sequence coverage. We analysed the samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe and DeNovoGUI (pepNovo+, DirecTag, Novor), benchmarked these tools and discuss the optimal strategy for the characterisation of ancient proteins. We also studied physicochemical properties of the BLG that correlate with bias in the identification coverage.

bioinformatics↗

bioRxiv2023

Mouse Model of Heart Attack and Stroke Shows Improved Survival with MPO Inhibition

Thromboembolic events, including myocardial infarction (MI) or stroke, caused by the rupture or erosion of unstable atherosclerotic plaques are the leading cause of death worldwide1. Unfortunately, the lack of a mouse model that develops advanced coronary atherosclerosis and that exhibits a high incidence of spontaneous plaque rupture with MI or stroke has greatly stymied development of more effective therapeutic approaches for reducing these events beyond what has been achieved with aggressive lipid lowering. Herein, we describe a novel mouse model that develops widespread advanced atherosclerosis including in coronary, brachiocephalic, and carotid arteries. These mice show high mortality following Western Diet feeding with clear evidence of plaque rupture, MI, and stroke. To validate the utility of this model, mice were treated with the drug candidate AZM198, which inhibits myeloperoxidase, an enzyme primarily produced by activated neutrophils and predictive of rupture of human atherosclerotic lesions2-7. AZM198 treatment resulted in marked improvements in survival with a greater than 60% decrease in the incidence of plaque rupture, MI, and stroke. In summary, our work describes a novel mouse model that closely replicates late-stage clinical events of advanced human atherosclerotic disease and evidence that this model can be used to identify and test potential new therapeutic agents to prevent major adverse cardiac events.

physiology↗

bioRxiv2023

Enhanced Deep Convolutional Neural Network for SARS-CoV-2 Variants Classification

High-throughput sequencing techniques and sequence analysis have enabled the taxonomic classification of pathogens present in clinical samples. Sequencing provides an unbiased identification and systematic classification of pathogens and this is generally achieved by comparing novel sequences to pre-existing annotated reference databases. However, this approach is limited by large-scale reference databases which require considerable computational resources and skills to compare against. Alternative robust methods such as machine learning are currently employed in genome sequence analysis and classification, and it can be applied in classifying SARS-CoV-2 variants, whose continued evolution has resulted in the emergence of multiple variants. We developed a deep learning Convolutional Neural Networks-Long Short Term Memory (CNN-LSTM) model to classify dominant SARS-CoV-2 variants (omicron, delta, beta, gamma and alpha) based on gene sequences from the surface glycoprotein (spike gene). We trained and validated the model using > 26,000 SARS-CoV-2 sequences from the GISAID database. The model was evaluated using unseen 3,057 SARS-CoV-2 sequences. The model was compared to existing molecular epidemiology tool, nextclade. Our model achieved an accuracy of 98.55% on training, 99.19% on the validation and 98.41% on the test dataset. Comparing the proposed model to nextclade, the model achieved significant accuracy in classifying SARS-CoV-2 variants from unseen data. Nextclade identified the presence of recombinant strains in the evaluation data, a mechanism that the proposed model did not detect. This study provides an alternative approach to pre-existing methods employed in the classification of SARS-CoV-2 variants. Timely classification will enable effective monitoring and tracking of SARS-CoV-2 variants and inform public health policies in the control and management of the COVID-19 pandemic.

bioinformatics↗

bioRxiv2023

Chemoenzymatic syntheses of fluorine-18-labeled disaccharides from FDG yield potent sensors of living bacteria in vivo

Chemoenzymatic techniques have been applied extensively to pharmaceutical development, most effectively when routine synthetic methods fail. The regioselective and stereoselective construction of structurally complex glycans is an elegant application of this approach, that is seldom applied to positron emission tomography (PET) tracers. We sought a method to dimerize 2-deoxy-[18F]-fluoro-D-glucose ([18F]FDG), the most common tracer used in clinical imaging, to form [18F]-labeled disaccharides for detecting microorganisms in vivo based on their bacteria-specific glycan incorporation. When [18F]FDG was reacted with {beta}-D-glucose-1-phosphate in the presence of maltose phosphorylase, both the -1,4 and -1,3-linked products 2-deoxy-[18F]-fluoro-maltose ([18F]FDM) and 2-deoxy-2-[18F]-fluoro-sakebiose ([18F]FSK) were obtained. This method was further extended with the use of trehalose (,-1,1), laminaribiose ({beta}-1,3), and cellobiose ({beta}-1,4) phosphorylases to synthesize 2-deoxy-2-[18F]fluoro-trehalose ([18F]FDT), 2-deoxy-2-[18F]fluoro-laminaribiose ([18F]FDL), and 2-deoxy-2-[18F]fluoro-cellobiose ([18F]FDC). We subsequently tested [18F]FDM and [18F]FSK in vitro, showing accumulation by several clinically relevant pathogens including Staphylococcus aureus and Acinetobacter baumannii, and demonstrated their specific uptake in vivo. The lead sakebiose-derived tracer [18F]FSK was stable in human serum and showed high uptake in preclinical models of myositis and vertebral discitis-osteomyelitis. Both the synthetic ease, and high sensitivity of [18F]FSK to S. aureus including methicillin-resistant (MRSA) strains strongly justify clinical translation of this tracer to infected patients. Furthermore, this work suggests that chemoenzymatic radiosyntheses of complex [18F]FDG-derived oligomers will afford a wide array of PET radiotracers for infectious and oncologic applications.

microbiology↗

bioRxiv2023

Neutrophilic Inflammation in Models of Bronchopulmonary Dysplasia and Chronic Obstructive Pulmonary Disease is Rescued by a Lactobacilli Based Live Biotherapeutic

Bronchopulmonary dysplasia (BPD) is a chronic lung disease of prematurity. Exposure to noxious stimuli such as hyperoxia, volutrauma, and infection in infancy can have long-reaching impacts on lung health and predispose towards the development of conditions such as chronic obstructive pulmonary disease (COPD) in adulthood. BPD and COPD are both marked by lung tissue degradation, neutrophil influx, and decreased lung function. Both diseases also express a change in microbial signature dominated by Proteobacteria abundance and Lactobacillus scarcity. However, the relationship between pulmonary microbial dysbiosis and the mechanisms of downstream disease development has yet to be elucidated. We hypothesized that a double-hit hyperoxia and LPS murine model of BPD would show heightened Ac-PGP pathway and neutrophil activity. Through gain- and loss-of-function studies in the same model we showed that Ac-PGP plays a critical role in driving BPD development. We tested a novel inhaled live biotherapeutic using active Lactobacillus strains to counteract lung dysbiosis in in vitro and in vivo models of BPD and COPD. The Lactobacillus LBP is effective in improving lung structure and function, reducing neutrophil influx, and reducing a broad swath of pro-inflammatory markers in these models of chronic pulmonary disease. Live inhaled microbiome-based therapeutics show promise in addressing common pathways of disease progression that in the future can be targeted in a variety of chronic lung diseases.

microbiology↗

bioRxiv2023

Examination of 2D frontal and sagittal markerless motion capture: Implications for 2D and 3D markerless applications

This study examined if occluded joint locations from markerless motion capture produced 2D joint angles with reduced accuracy compared to visible joints, and if 2D frontal plane joint angles were usable for practical applications. Fifteen healthy participants performed over-ground walking whilst recorded by fifteen marker-based cameras and two machine vision cameras (frontal and sagittal plane). Repeated measures Bland-Altman analysis illustrated that markerless standard deviation of bias (random differences) for the occluded-side hip and knee joint angles in the sagittal plane were double that of the camera-side (visible) hip and knee. Camera-side sagittal plane knee and hip angles were near or within marker-based error values previously observed. While frontal plane random differences accounted for 35-46% of total range of motion at the hip and knee, systematic and random differences (-4.6-1.6 {+/-} 3.7-4.2{degrees}) were actually similar to previously reported marker-based error values. This was not true for the ankle, where random difference ({+/-}12{degrees}) was still too high for practical applications. Our results add to previous literature, highlighting shortcomings of current pose estimation algorithms and labelled datasets. As such, this paper finishes by reviewing marker-based methods for creating anatomically accurate markerless training data.

bioengineering↗

bioRxiv2022

The Development and Evaluation of a Fully Automated Markerless Motion Capture Workflow

This study presented a fully automated deep learning based markerless motion capture workflow and evaluated its performance against marker-based motion capture during overground running, walking and counter movement jumping. Multi-view high speed (200 Hz) image data were collected concurrently with marker-based motion capture (criterion data), permitting a direct comparison between methods. Lower limb kinematic data for 15 participants were computed using 2D pose estimation, our 3D fusion process and OpenSim based inverse kinematics modelling. Results demonstrated high levels of agreement for lower limb joint angles, with mean differences ranging between 0.1{degrees} - 10.5{degrees} for 6 DoF hip joint rotations, and 0.7{degrees} - 3.9{degrees} for knee and ankle rotations. These differences generally fall within the documented uncertainties of marker-based motion capture, suggesting that our markerless approach could be used for appropriate biomechanics applications. We used an open-source, modular and customisable workflow, allowing for integration with other popular biomechanics tools such as OpenSim. By developing open-source tools, we hope to facilitate the democratisation of markerless motion capture technology and encourage the transparent development of markerless methods. This presents exciting opportunities for biomechanics researchers and practitioners to capture large amounts of high quality, ecologically valid data both in the laboratory and in the wild.

bioengineering↗

bioRxiv2021

Human Movement Science in The Wild: Can Current Deep-Learning Based Pose Estimation Free Us from The Lab?

Human movement researchers are often restricted to laboratory environments and data capture techniques that are time and/or resource intensive. Markerless pose estimation algorithms show great potential to facilitate large scale movement studies in the wild, i.e., outside of the constraints imposed by marker-based motion capture. However, the accuracy of such algorithms has not yet been fully evaluated. We computed 3D joint centre locations using several deep-learning based pose estimation methods (OpenPose, AlphaPose, DeepLabCut) and compared to marker-based motion capture. Participants performed walking, running and jumping activities while marker-based motion capture data and multi-camera high speed images (200 Hz) were captured. The pose estimation algorithms were applied to 2D image data and 3D joint centre locations were reconstructed. Pose estimation derived joint centres demonstrated systematic differences at the hip and knee (~30 - 50 mm), most likely due to mislabeling of ground truth data in the training datasets. Where systematic differences were lower, e.g., the ankle, differences of 1 - 15 mm were observed depending on the activity. Markerless motion capture represents a highly promising emerging technology that could free movement scientists from laboratory environments. We provide recommendations relating to domain specific datasets and benchmarks, which will be vital to realising this goal.

bioengineering↗