Showing papers by "John W. Hutchinson published in 2023"

Quantitative biomechanical assessment of locomotor capabilities of the stem archosaur Euparkeria capensis

Abstract: Birds and crocodylians are the only remaining members of Archosauria (ruling reptiles) and they exhibit major differences in posture and gait, which are polar opposites in terms of locomotor strategies. Their broader lineages (Avemetatarsalia and Pseudosuchia) evolved a multitude of locomotor modes in the Triassic and Jurassic periods, including several occurrences of bipedalism. The exact timings and frequencies of bipedal origins within archosaurs, and thus their ancestral capabilities, are contentious. It is often suggested that archosaurs ancestrally exhibited some form of bipedalism. Euparkeria capensis is a central taxon for the investigation of locomotion in archosaurs due to its phylogenetic position and intermediate skeletal morphology, and is argued to be representative of facultative bipedalism in this group. However, no studies to date have biomechanically tested if bipedality was feasible in Eupakeria. Here, we use musculoskeletal models and static simulations in its hindlimb to test the influences of body posture and muscle parameter estimation methods on locomotor potential. Our analyses show that the resulting negative pitching moments around the centre of mass were prohibitive to sustainable bipedality. We conclude that it is unlikely that Euparkeria was facultatively bipedal, and was probably quadrupedal, rendering the inference of ancestral bipedal abilities in Archosauria unlikely.

Locomotor and postural diversity among reptiles viewed through the prism of femoral microanatomy: Palaeobiological implications for some Permian and Mesozoic taxa

Abstract: The water‐to‐land transition by the first tetrapod vertebrates represents a key stage in their evolution. Selection pressures exerted by this new environment on animals led to the emergence of new locomotor and postural strategies that favoured access to different ecological niches and contributed to their evolutionary success. Today, amniotes show great locomotor and postural diversity, particularly among Reptilia, whose extant representatives include parasagittally locomoting erect and crouched bipeds (birds), sub‐parasagittal ‘semi‐erect’ quadrupeds (crocodylians) and sprawling quadrupeds (squamates and turtles). But the different steps leading to such diversity remain enigmatic and the type of locomotion adopted by many extinct species raises questions. This is notably the case of certain Triassic taxa such as Euparkeria and Marasuchus. The exploration of the bone microanatomy in reptiles could help to overcome these uncertainties. Indeed, this locomotor and postural diversity is accompanied by great microanatomical disparity. On land, the bones of the appendicular skeleton support the weight of the body and are subject to multiple constraints that partly shape their external and internal morphology. Here we show how microanatomical parameters measured in cross‐section, such as bone compactness or the position of the medullocortical transition, can be related to locomotion. We hypothesised that this could be due to variations in cortical thickness. Using statistical methods that take phylogeny into account (phylogenetic flexible discriminant analyses), we develop different models of locomotion from a sample of femur cross‐sections from 51 reptile species. We use these models to infer locomotion and posture in 7 extinct reptile taxa for which they remain debated or not fully clear. Our models produced reliable inferences for taxa that preceded and followed the quadruped/biped and sprawling/erect transitions, notably within the Captorhinidae and Dinosauria. For taxa contemporary with these transitions, such as Terrestrisuchus and Marasuchus, the inferences are more questionable. We use linear models to investigate the effect of body mass and functional ecology on our inference models. We show that body mass seems to significantly impact our model predictions in most cases, unlike the functional ecology. Finally, we illustrate how taphonomic processes can impact certain microanatomical parameters, especially the eccentricity of the section, while addressing some other potential limitations of our methods. Our study provides insight into the evolution of enigmatic locomotion in various early reptiles. Our models and methods could be used by palaeontologists to infer the locomotion and posture in other extinct reptile taxa, especially when considered in combination with other lines of evidence.

Modern three-dimensional digital methods for studying locomotor biomechanics in tetrapods

Abstract: ABSTRACT Here, we review the modern interface of three-dimensional (3D) empirical (e.g. motion capture) and theoretical (e.g. modelling and simulation) approaches to the study of terrestrial locomotion using appendages in tetrapod vertebrates. These tools span a spectrum from more empirical approaches such as XROMM, to potentially more intermediate approaches such as finite element analysis, to more theoretical approaches such as dynamic musculoskeletal simulations or conceptual models. These methods have much in common beyond the importance of 3D digital technologies, and are powerfully synergistic when integrated, opening a wide range of hypotheses that can be tested. We discuss the pitfalls and challenges of these 3D methods, leading to consideration of the problems and potential in their current and future usage. The tools (hardware and software) and approaches (e.g. methods for using hardware and software) in the 3D analysis of tetrapod locomotion have matured to the point where now we can use this integration to answer questions we could never have tackled 20 years ago, and apply insights gleaned from them to other fields.

Decoupling body shape and mass distribution in birds and their dinosaurian ancestors

Abstract: It is accepted that non-avian theropod dinosaurs, with their long muscular tails and small forelimbs, had a centre-of-mass close to the hip, while extant birds, with their reduced tails and enlarged wings have their mass centred more cranially. Transition between these states is considered crucial to two key innovations in the avian locomotor system: crouched bipedalism and powered flight. Here we use image-based models to challenge this dichotomy. Rather than a phylogenetic distinction between 'dinosaurian' and 'avian' conditions, we find terrestrial versus volant taxa occupy distinct regions of centre-of-mass morphospace consistent with the disparate demands of terrestrial bipedalism and flight. We track this decoupled evolution of body shape and mass distribution through bird evolution, including the origin of centre-of-mass positions more advantageous for flight and major reversions coincident with terrestriality. We recover modularity in the evolution of limb proportions and centre-of-mass that suggests fully crouched bipedalism evolved after powered flight.

Multiple equilibrium states of a curved-sided hexagram: Part II-Transitions between states

Abstract: Curved-sided hexagrams with multiple equilibrium states have great potential in engineering applications such as foldable architectures, deployable aerospace structures, and shape-morphing soft robots. In Part I, the classical stability criterion based on energy variation was used to study the elastic stability of the curved-sided hexagram and identify the natural curvature range for stability of each state for circular and rectangular rod cross-sections. Here, we combine a multi-segment Kirchhoff rod model, finite element simulations, and experiments to investigate the transitions between four basic equilibrium states of the curved-sided hexagram. The four equilibrium states, namely the star hexagram, the daisy hexagram, the 3-loop line, and the 3-loop"8", carry uniform bending moments in their initial states, and the magnitudes of these moments depend on the natural curvatures and their initial curvatures. Transitions between these equilibrium states are triggered by applying bending loads at their corners or edges. It is found that transitions between the stable equilibrium states of the curved-sided hexagram are influenced by both the natural curvature and the loading position. Within a specific natural curvature range, the star hexagram, the daisy hexagram, and the 3-loop"8"can transform among one another by bending at different positions. Based on these findings, we identify the natural curvature range and loading conditions to achieve transition among these three equilibrium states plus a folded 3-loop line state for one specific ring having a rectangular cross-section. The results obtained in this part also validate the elastic stability range of the four equilibrium states of the curved-sided hexagram in Part I. We envision that the present work could provide a new perspective for the design of multi-functional deployable and foldable structures.

Curved Ring Origami: Bistable Elastic Folding for Magic Pattern Reconfigurations

Abstract: Ring origami has emerged as a robust strategy for designing foldable and deployable structures due to its impressive packing abilities achieved from the snap-folding mechanism. In general, polygonal rings with rationally designed geometric parameters can fold into compacted three-loop configurations with curved segments, which result from the internal bending moment in the folded state. Inspired by the internal bending moment-induced curvature in the folded state, we explore how this curvature can be tuned by introducing initial natural curvature to the segments of the polygonal rings in their deployed stress-free state, and study how this initial curvature affects their folded configurations. Taking a clue from straight-segmented polygonal rings that fold into overlapping curved loops, we find it is possible to reverse the process by introducing curvature into the ring segments in the stress-free initial state such that the rings fold into a straight-line looped pattern with “zero” area. This realizes extreme packing. In this work, by a combination of experimental observation, finite element analysis, and theoretical modeling, we systematically study the effect of segment curvature on folding behavior, folded configurations, and packing of curved ring origami with different geometries. It is anticipated that curved ring origami can open a new avenue for the design of foldable and deployable structures with simple folded configurations and high packing efficiency.

Evolution of posture in amniotes-Diving into the trabecular architecture of the femoral head.

Abstract: Extant amniotes show remarkable postural diversity. Broadly speaking, limbs with erect (strongly adducted, more vertically oriented) posture are found in mammals that are particularly heavy (graviportal) or show good running skills (cursorial), while crouched (highly flexed) limbs are found in taxa with more generalized locomotion. In Reptilia, crocodylians have a "semi-erect" (somewhat adducted) posture, birds have more crouched limbs and lepidosaurs have sprawling (well-abducted) limbs. Both synapsids and reptiles underwent a postural transition from sprawling to more erect limbs during the Mesozoic Era. In Reptilia, this postural change is prominent among archosauriforms in the Triassic Period. However, limb posture in many key Triassic taxa remains poorly known. In Synapsida, the chronology of this transition is less clear, and competing hypotheses exist. On land, the limb bones are subject to various stresses related to body support that partly shape their external and internal morphology. Indeed, bone trabeculae (lattice-like bony struts that form the spongy bone tissue) tend to orient themselves along lines of force. Here, we study the link between femoral posture and the femoral trabecular architecture using phylogenetic generalized least squares. We show that microanatomical parameters measured on bone cubes extracted from the femoral head of a sample of amniote femora depend strongly on body mass, but not on femoral posture or lifestyle. We reconstruct ancestral states of femoral posture and various microanatomical parameters to study the "sprawling-to-erect" transition in reptiles and synapsids, and obtain conflicting results. We tentatively infer femoral posture in several hypothetical ancestors using phylogenetic flexible discriminant analysis from maximum likelihood estimates of the microanatomical parameters. In general, the trabecular network of the femoral head is not a good indicator of femoral posture. However, ancestral state reconstruction methods hold great promise for advancing our understanding of the evolution of posture in amniotes.

EUCLID: A New Approach to Constrain Nuclear Data via Optimized Validation Experiments using Machine Learning

Abstract: Compensating errors between several nuclear data observables in a library can adversely impact application simulations. The EUCLID project (Experiments Underpinned by Computational Learning for Improvements in Nuclear Data) set out to first identify where compensating errors could be hiding in our libraries, and then design validation experiments optimized to reduce compensating errors for a chosen set of nuclear data. Adjustment of nuclear data will be performed to assess whether the new experimental data—spanning measurements from multiple responses—successfully reduced compensating errors. The specific target nuclear data for EUCLID are 239Pu fission, inelastic scattering, elastic scattering, capture, nu-bar, and prompt fission neutron spectrum (PFNS). A new experiment has been designed, which will be performed at the National Criticality Experiments Research Center (NCERC).

Functional Annotation Routines Used by ABRF Bioinformatics Core Facilities - Observations, Comparisons, and Considerations.

Abstract: The functional annotation of gene lists is a common analysis routine required for most genomics experiments, and bioinformatics core facilities must support these analyses. In contrast to methods such as the quantitation of RNA-Seq reads or differential expression analysis, our research group noted a lack of consensus in our preferred approaches to functional annotation. To investigate this observation, we selected 4 experiments that represent a range of experimental designs encountered by our cores and analyzed those data with 6 tools used by members of the Association of Biomolecular Resource Facilities (ABRF) Genomic Bioinformatics Research Group (GBIRG). To facilitate comparisons between tools, we focused on a single biological result for each experiment. These results were represented by a gene set, and we analyzed these gene sets with each tool considered in our study to map the result to the annotation categories presented by each tool. In most cases, each tool produces data that would facilitate identification of the selected biological result for each experiment. For the exceptions, Fisher's exact test parameters could be adjusted to detect the result. Because Fisher's exact test is used by many functional annotation tools, we investigated input parameters and demonstrate that, while background set size is unlikely to have a significant impact on the results, the numbers of differentially expressed genes in an annotation category and the total number of differentially expressed genes under consideration are both critical parameters that may need to be modified during analyses. In addition, we note that differences in the annotation categories tested by each tool, as well as the composition of those categories, can have a significant impact on results.

Multiple equilibrium states of a curved-sided hexagram:Part I-Stability of states

Abstract: The stability of the multiple equilibrium states of a hexagram ring with six curved sides is investigated. Each of the six segments is a rod having the same length and uniform natural curvature. These rods are bent uniformly in the plane of the hexagram into equal arcs of 120deg or 240deg and joined at a cusp where their ends meet to form a 1-loop planar ring. The 1-loop rings formed from 120deg or 240deg arcs are inversions of one another and they, in turn, can be folded into a 3-loop straight line configuration or a 3-loop ring with each loop in an"8"shape. Each of these four equilibrium states has a uniform bending moment. Two additional intriguing planar shapes, 6-circle hexagrams, with equilibrium states that are also uniform bending, are identified and analyzed for stability. Stability is lost when the natural curvature falls outside the upper and lower limits in the form of a bifurcation mode involving coupled out-of-plane deflection and torsion of the rod segments. Conditions for stability, or lack thereof, depend on the geometry of the rod cross-section as well as its natural curvature. Rods with circular and rectangular cross-sections will be analyzed using a specialized form of Kirchhoff rod theory, and properties will be detailed such that all four of the states of interest are mutually stable. Experimental demonstrations of the various states and their stability are presented. Part II presents numerical simulations of transitions between states using both rod theory and a three-dimensional finite element formulation, includes confirmation of the stability limits established in Part I, and presents additional experimental demonstrations and verifications.