Biology subjects

Begon, M.

Publications and source records attributed to Begon, M..

10 recordsLinked to original sources

bioRxiv2025

Refined shoulder kinematics via markerless bony landmark detection and acromial 3D shape using an RGB-D camera during hand-cycling

Biomechanical biofeedback has the potential to enhance rehabilitation by providing clinicians with objective evaluation of patient performances. As feedback systems often depend on expensive and sophisticated motion capture technologies, researchers explore computer vision-based alternatives. Existing methods suffer from substantial joint angle errors, particularly in the upper limb, and neglect the scapular movements. We developed an approach for detecting bony landmarks and performing refined upper-limb kinematics assessments using a single consumer-grade depth-sensing camera. Unlike other markerless methods, our model incorporates the scapula, offering comprehensive shoulder joint kinematics. Annotated images from eight participants were used to fine-tune a convolutional neural network, which was subsequently evaluated on a hand-cycling motion. Our method showed a strong agreement with a reference marker-based system, with 3D bony landmark detection errors averaging 5 mm. The resulting kinematics closely aligned with the reference system, maintaining acceptable joint angle errors ([~]6.3{degrees}). Furthermore, the algorithm could provide real-time bony landmark positions and joint kinematics at a rate of 50 Hz. This study highlights the potential of using a single consumer-grade depth-sensing camera combined with an acromial 3D-shape to accurately estimate upper-limb kinematics through bony landmark detection, paving the way for more accessible clinical assessments.

bioengineering↗

bioRxiv2025

Seroprevalence and risk factors for Toxoplasma gondii transmission in wild, domestic and companion animals in urban informal settlements from Salvador, Brazil

Toxoplasma gondii is a globally neglected zoonotic parasite, particularly prevalent in socioeconomically vulnerable areas. Various animal species serve as reservoirs for T. gondii across different regions, including domestic cats, livestock, and a variety of wild and synanthropic animals. In urban areas, especially informal settlements, the close coexistence of humans, domestic animals, and wildlife may influence local transmission dynamics. This study evaluated the seroprevalence and associated risk factors for T. gondii infection in domestic and synanthropic animals from two low-income communities in Salvador, Brazil. A cross-sectional study was conducted in the neighborhoods of Marechal Rondon and Pau da Lima from October 2021 to February 2023. Blood samples were collected from domestic animals (288 dogs, 112 cats, 27 chickens, and six horses) and synanthropic species (54 brown rats and 75 big-eared opossums). Serological tests were performed using an indirect immunofluorescence antibody test. Questionnaires were used to collect environmental, demographic, and socioeconomic data from households where sampling took place. Generalized linear mixed models were applied to identify predictors of exposure. Seroprevalence was highest in chickens (66.7%), followed by dogs (37.2%), rats (24.1%), cats (22.3%), opossums (20%), and horses (16.7%). No significant factors were found to be associated with T. gondii seroprevalence in chickens, horses, rats, or opossums. Nevertheless, in dogs and cats, homemade diets increased the odds of infection by nearly six times compared to commercial feeding. Dogs from Pau da Lima were twice as likely to be infected as those from Marechal Rondon. These findings underscore the importance of promoting safe pet management, improving sanitation, and monitoring sentinel species to mitigate zoonotic risks in urban informal settlements. Author summaryToxoplasma gondii is a parasite that infects humans and animals worldwide, significantly impacting impoverished areas. In this study, we investigated the prevalence and factors associated with T. gondii infection in domestic and urban wildlife from two low-income communities in Salvador (BA, Brazil). We collected blood samples from dogs, cats, chickens, horses, rats, and opossums to test for antibodies against the parasite and analyzed environmental and lifestyle factors that might influence infection risk. Chickens showed the highest infection rates (67%), followed by dogs (37%), rats (24%), cats (22%), opossums (20%), and horses (17%). We found that homemade diets significantly increased the likelihood of infection in dogs and cats compared to commercial pet food. Additionally, dogs from one neighborhood were twice as likely to be infected as those from the other, likely due to environmental conditions. These findings highlight how diet, environment, and urban living conditions affect the spread of T. gondii. By improving sanitation, promoting responsible pet care, and monitoring animals that share human environments, we can reduce the risk of this parasite in vulnerable communities.

ecology↗

bioRxiv2024

Superspreaders have lower gut microbial alpha-diversity and distinct gut microbial composition in a natural rodent population

The microbiome is well-known to drive variation in host states (e.g., behaviour, or immunity) that would be expected to modulate the spread of infectious disease - but the role of microbiotal interactions in promoting superspreading by individuals is poorly understood. Superspreaders are individuals with a strongly disproportionate contribution to pathogen transmission, and they come in two forms. Supershedders transmit infection to more individuals because they shed higher levels of a pathogen. Supercontacters transmit infection to more individuals because they have a larger number of social contacts. We explore associations between the gut microbiota and these two forms of superspreading in a wild rodent model - Bartonella spp. bacteraemia in the field vole (Microtus agrestis). We find evidence that, first, individuals fall into distinct shedding and contacting clusters, and second, that higher-contacters have lower and more variable gut microbial alpha-diversity than lower-contacters. We also show evidence that both higher-shedders and higher-contacters have distinct gut microbial composition, and identify OTUs which are differentially abundant in the gut microbiota of these two classes of individuals when compared to lower-shedders and lower-contacters respectively. We find that the Muribaculaceae are associated with differences in both shedding and contacting, and discuss potential mechanisms by which they may be acting on these host traits.

ecology↗

bioRxiv2024

Knee Biomechanics during Walking in Individuals with Anterior Cruciate Ligament Repair: The Role of a Custom 3D Printed Knee Brace

BackgroundAnterior cruciate ligament (ACL) injuries frequently lead to altered gait biomechanics and muscle activation patterns, increasing the risk of osteoarthritis. Knee braces are commonly used to address these issues although a lack of consensus remains regarding their clinical benefits. The recent emergence of 3D-printed braces, lighter and personalized, could improve rehabilitation. ObjectivesTo evaluate the effect of a novel custom-made 3D-printed knee brace (Provoke) in individuals after unilateral ACL reconstruction during walking. The brace incorporates an asymmetrical hinge system aimed at stabilizing the knee joint while minimizing compensatory movements. MethodsFourteen participants with unilateral ACL reconstruction wore the Provoke brace while walking at comfortable and fast paces. Knee kinematics and kinetics, and muscular activity (rectus femoris, vastus medialis, and semitendinosus) were assessed with and without the brace. Two-tailed non-parametric paired T-tests were used to assess the biomechanical effect of the brace. Results and conclusionsThe Provoke brace improved knee kinematics, facilitating a more neutral knee position by reducing valgus angles (-1.95{degrees}), and increasing flexion angles (+1.14{degrees}). Additionally, it enhanced muscle activation, particularly of the rectus femoris, suggesting improved quadriceps function. Overall, the Provoke brace effectively improves knee function and reduces muscle imbalances in individuals undergoing ACL reconstruction. It may help prevent further injury and reduce the risk of post-traumatic osteoarthritis development. The long-term effects of brace use in ACL rehabilitation must be investigated. Key PointsO_LIWalking while wearing Provoke brace allow to reduce knee valgus angles which could counteract the development of post-traumatic osteoarthritis. C_LIO_LIBraced walking may mitigate the stiffened knee gait strategy by increasing the peak knee flexion angle during the stance phase of the gait. C_LIO_LIIncreased rectus femoris activation during early stance phase could improve knee function and stability, acting against quadriceps weakness often observed after anterior cruciate ligament reconstruction. C_LI

bioengineering↗

bioRxiv2024

Density-dependent network structuring within and across wild animal systems

High population density should drive individuals to more frequently share space and interact, producing better-connected spatial and social networks [1-4]. Although this theory is fundamental to our understanding of disease dynamics [2,5-8], it remains unconfirmed how local density generally drives individuals positions within their networks, which reduces our ability to understand and predict density-dependent processes [4,9,10]. Here we provide the first general evidence that density drives greater network connectedness at fine spatiotemporal scales, at the scale of individuals within wild animal populations. We analysed 36 datasets of simultaneous spatial and social behaviour in >58,000 individual animals, spanning 30 species of fish, reptiles, birds, mammals, and insects. 80% of systems exhibited strong positive relationships between local density and network centrality. However, >80% of relationships were nonlinear and 75% became shallower at higher values, signifying that demographic and behavioural processes counteract densitys effects, thereby producing saturating trends [11-15]. Densitys effect was much stronger and less saturating for spatial than social networks, such that individuals become disproportionately spatially connected rather than socially at higher densities. Consequently, ecological processes that depend on spatial connections (e.g. indirect pathogen transmission, resource competition, and territory formation) are likely more density-dependent than those involving social interactions (e.g. direct pathogen transmission, aggression, and social learning). These findings reveal fundamental ecological rules governing societal structuring, with widespread implications. Identifying scaling rules based on processes that generalise across systems, such as these patterns of density dependence, might provide the ability to predict network structures in novel systems.

ecology↗

bioRxiv2022

An innovative 2D-mesh model to improve deltoid moment arms, muscle forces and glenohumeral joint reaction force estimations

We proposed a 2D-mesh representation of the deltoid muscle to improve a realism of forces and moments predictions in a multibody shoulder model. Our 2D-mesh model was qualitatively compared to a commonly used via-point model during an arm elevation in the scapular plane and to previous in-vitro studies in terms of deltoid moment arms. The most notable improvement was observed for the moment arms of the anterior deltoid, which shows better agreement with in-vitro studies. Consequently, joint reaction force above 90{degrees} of arm elevation was more consistent with in-vivo data, validating the 2D-mesh representation of the deltoid muscle.

bioinformatics↗

bioRxiv2021

Early-life immune expression profiles predict later life health and fitness in a wild rodent

Individuals differ in the nature of the immune responses they produce, affecting disease susceptibility and ultimately health and fitness. These differences have been hypothesised to have an origin in events experienced early in life that then affect trajectories of immune development and responsiveness. Here we investigate early life influences on immune expression profiles using a natural population of field voles, Microtus agrestis, in which we are able to monitor variation between and within individuals though time by repeat (longitudinal) sampling of individually marked animals. We analysed the co-expression of 20 immune genes in early life to create a correlational network consisting of three main clusters, one of which (containing Gata3, Il10 and Il17) was associated with later life reproductive success and susceptibility to chronic bacterial (Bartonella) infection. More detailed analyses supported associations between early life expression of Il17 and reproductive success later in life, and of increased Il10 expression early in life and later infection with Bartonella. We also found significant association between an Il17 genotype and the early life expression of Il10. Our results demonstrate that immune expression profiles can be manifested during early life with effects that persist through adulthood and that shape the variability among individuals in susceptibility to infection and fitness widely seen in natural populations.

ecology↗

bioRxiv2021

Bioptim, a Python framework for Musculoskeletal Optimal Control in Biomechanics

Musculoskeletal simulations are useful in biomechanics to investigate the causes of movement disorder, to estimate non-measurable physiological quantities or to study the optimality of human movement. We introduce Bioptim, an easy-to-use Python framework for biomechanical optimal control, handling musculoskeletal models. Relying on algorithmic differentiation and the multiple shooting formulation, Bioptim interfaces nonlinear solvers to quickly provide dynamically consistent optimal solutions. The software is both computationally efficient (C++ core) and easily customizable, thanks to its Python interface. It allows to quickly define a variety of biomechanical problems such as motion tracking/prediction, muscle-driven simulations, parameters optimization, multiphase problems, etc. It is also intended for real-time applications such as moving horizon estimation and model predictive control. Six contrasting examples are presented, comprising various models, dynamics, objective functions and constraints. They include data-driven simulations (i.e., a multiphase muscle driven gait cycle and an upper-limb real-time moving horizon estimation of muscle forces) and predictive simulations (i.e., a muscle-driven pointing task, a twisting somersault with a quaternion-based model, a position controller using external forces, and a multiphase torque-driven maximum-height jump motion).

bioengineering↗

bioRxiv2019

IgE receptor polymorphism predicts divergent, sex-specific inflammatory modes and fitness costs in a wild rodent

The genotype of an individual is an important predictor of their immune function, and subsequently, their ability to control or avoid infection and ultimately contribute offspring to the next generation. However, the same genotype, subjected to different intrinsic and/or extrinsic environments can also result in different phenotypic outcomes, which can be missed in controlled laboratory studies. Natural wildlife populations, which capture both genotypic and environmental variability, provide an opportunity to more fully understand the phenotypic expression of genetic variation. We identified a synonymous polymorphism in the high-affinity Immunoglobulin E (IgE) receptor (GC and non-GC haplotypes) that has sex-dependent effects on immune gene expression, susceptibility to infection and reproductive success of individuals in a natural population of field voles (Microtus agrestis). We found that the effect of the GC haplotype on the expression of immune genes differed between sexes. While males with the GC haplotype had upregulated more pro-inflammatory genes, including the cytokine Il33, females had upregulated more anti-inflammatory genes, including the cytokine inhibitor Socs3. Furthermore we found an effect of the GC haplotype on the probability of infection with a common microparasite, Babesia microti, in females - with females carrying the GC haplotype being more likely to be infected. Finally, we found an effect of the GC haplotype on reproductive success in males - with males carrying the GC haplotype having a lower reproductive success. This is a rare example of a polymorphism whose consequences we are able to follow across immunity, infection and reproduction for both males and females in a natural population.

ecology↗

bioRxiv2019

Decomposing variation in immune response in a wild rodent population

Individuals vary in their immune response and, as a result, some are more susceptible to infectious disease than others. Little is known about which components of immune pathways are responsible for this variation, but understanding these underlying processes could allow us to predict the outcome of infection for an individual, and to manage their health more effectively. In this study, we describe transcriptome-wide variation in immune response (to a standardised challenge) in a wild population of field voles (Microtus agrestis). We find that this variation can be categorised into three main types. We also identify markers, across these three categories, which display particularly strong individual variation in response. This work shows how a simple standardised challenge performed on a natural population can reveal complex patterns of natural variation in immune response.

ecology↗