Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.

The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias.

Spatial Variation in Young Ovine Cortical Bone Properties.

Significant effort continues to be made to understand whether differences exist in the structural, compositional, and mechanical properties of cortical bone subjected to different strain modes or magnitudes. We evaluated juvenile sheep femora (age = 4 months) from the anterior and posterior quadrants at three points along the diaphysis as a model system for variability in loading. Micro-CT scans (50 micron) were used to measure cortical thickness and mineral density.

Scaling of linear anthropometric dimensions in living humans.

Objectives: Some previous studies suggest that humans do not conform to geometric similarity (isometry) in anthropometric dimensions of the upper and lower limbs. Researchers often rely on a single statistical approach to the study of scaling patterns, and it is unclear whether these methods produce similar results and are equally robust. This study used one bivariate and one multivariate method to examine how linear anthropometric dimensions scale in a sample of adult humans.

Temporal and spatial changes in bone accrual, density, and strain energy density in growing foals.

Bone adaptation is in part driven by mechanical loading, and exercise during youth has been shown to have life-long benefits for bone health. However, the development of early exercise-based interventions that reduce the incidence of fractures in racing horses is limited by the lack of characterization of normal development in growing bone. Previous efforts to quantify bone development in the horse have relied on repeated radiographs or peripheral quantitative computed tomography scans, which are limited in their assessment of the entire bone.

Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features.

Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act, is still an open question in evolutionary developmental biology. We use high-resolution quantitative trait locus (QTL) mapping in the F generation of an advanced intercross experiment (LG,SM-G ) to characterize the genetic architecture of the mouse pelvis.

Rat bone properties and their relationship to gait during growth.

Allometric relationships have been studied over different Orders of mammals to understand how bone accommodates the mechanical demands associated with increasing mass. However, less attention has been given to the scaling of bone within a single lifetime. We aimed to determine how bone morphology and tissue density are related to (1) bending and compressive strength, and (2) gait dynamics.

An Algorithm for Automated Separation of Trabecular Bone From Variably Thick Cortices in High-Resolution Computed Tomography Data.

Objective: Structural measurements after separation of cortical from trabecular bone are of interest to a wide variety of communities but are difficult to obtain because of the lack of accurate automated techniques.

Methods: We present a structure-based algorithm for separating cortical from trabecular bone in binarized images. Using the thickness of the cortex as a seed value, bone connected to the cortex within a spatially local threshold value is identified and separated from the remaining bone.

BDNF, endurance activity, and mechanisms underlying the evolution of hominin brains.

Objectives: As a complex, polygenic trait, brain size has likely been influenced by a range of direct and indirect selection pressures for both cognitive and non-cognitive functions and capabilities. It has been hypothesized that hominin brain expansion was, in part, a correlated response to selection acting on aerobic capacity (Raichlen & Polk, 2013). According to this hypothesis, selection for aerobic capacity increased the activity of various signaling molecules, including those involved in brain growth.

Limb dominance, foot orientation and functional asymmetry during walking gait.

While healthy gait is often characterized as, or assumed to be symmetric, consistent asymmetries often exist. In this study, we test the hypotheses that asymmetries in lower limb function, as measured by ground reaction force characteristics, may be explained by differences in foot orientation or limb dominance. Peak ground reaction force (GRF) measurements, and impulses were obtained for thirty-six healthy subjects with simultaneous kinematic estimates of foot posture.

Ontogenetic scaling of fore limb and hind limb joint posture and limb bone cross-sectional geometry in vervets and baboons.

Objectives: Previous studies suggest that the postures habitually adopted by an animal influence the mechanical loading of its long bones. Relatively extended limb postures in larger animals should preferentially reduce anteroposterior (A-P) relative to mediolateral (M-L) bending of the limb bones and therefore decrease A-P/M-L rigidity. We test this hypothesis by examining growth-related changes in limb bone structure in two primate taxa that differ in ontogenetic patterns of joint posture.

Exercise-induced bone formation is poorly linked to local strain magnitude in the sheep tibia.

Functional interpretations of limb bone structure frequently assume that diaphyses adjust their shape by adding bone primarily across the plane in which they are habitually loaded in order to minimize loading-induced strains. Here, to test this hypothesis, we characterize the in vivo strain environment of the sheep tibial midshaft during treadmill exercise and examine whether this activity promotes bone formation disproportionately in the direction of loading in diaphyseal regions that experience the highest strains. It is shown that during treadmill exercise, sheep tibiae were bent in an anteroposterior direction, generating maximal tensile and compressive strains on the anterior and posterior shaft surfaces, respectively.

The primate vaginal microbiome: comparative context and implications for human health and disease.

The primate body hosts trillions of microbes. Interactions between primate hosts and these microbes profoundly affect primate physiology, reproduction, health, survival, and ultimately, evolution. It is increasingly clear that primate health cannot be understood fully without knowledge of host-microbial interactions.

The evolution of locomotor rhythmicity in tetrapods.

Differences in rhythmicity (relative variance in cycle period) among mammal, fish, and lizard feeding systems have been hypothesized to be associated with differences in their sensorimotor control systems. We tested this hypothesis by examining whether the locomotion of tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of bradymetabolic tetrapods (lizards, alligators, turtles, salamanders). Species averages of intraindividual coefficients of variation in cycle period were compared while controlling for gait and substrate.

Linking brains and brawn: exercise and the evolution of human neurobiology.

The hunting and gathering lifestyle adopted by human ancestors around 2 Ma required a large increase in aerobic activity. High levels of physical activity altered the shape of the human body, enabling access to new food resources (e.g.

Parallel Factor Analysis of gait waveform data: A multimode extension of Principal Component Analysis.

Gait data are typically collected in multivariate form, so some multivariate analysis is often used to understand interrelationships between observed data. Principal Component Analysis (PCA), a data reduction technique for correlated multivariate data, has been widely applied by gait analysts to investigate patterns of association in gait waveform data (e.g.

Divergent patterns of integration and reduced constraint in the human hip and the origins of bipedalism.

When compared to other hominids--great apes including humans--the human pelvis reveals a fundamental reorganization of bony morphology comprised of multiple trait-level changes, many of which are associated with bipedal locomotion. Establishing how patterns of integration--correlations and covariances among traits--within the pelvis have evolved in concert with morphology is essential to explaining this evolutionary transition because integration may facilitate or constrain morphological evolution. Here, we show that the human hip bone has significantly lower levels of integration and constraint overall when compared to other hominids, that the focus of these changes is on traits hypothesized to play major functional roles in bipedalism, and we provide evidence that the human hip was reintegrated in a pattern distinct from other members of this group.

Methods to temporally align gait cycle data.

The need for the temporal alignment of gait cycle data is well known; however, there is little consensus concerning which alignment method to use. In this paper, we discuss the pros and cons of some methods commonly applied to temporally align gait cycle data (normalization to percent gait cycle, dynamic time warping, derivative dynamic time warping, and piecewise alignment methods). In addition, we empirically evaluate these different methods' abilities to produce successful temporal alignment when mapping a test gait cycle trajectory to a target trajectory.

Quantifying complexity and variability in phase portraits of gait.

Background: Injuries to the lower extremity often cause limitations to joint motion and alter movement patterns of limb segments during gait. We hypothesized that complexity and variability of limb segment motion during gait would increase in both limbs due to unilateral injury. Using simulated injury to generate asymmetric gait, we developed new methods to quantify changes in the complexity and variability of limb segment angular phase portraits.

Body size and joint posture in primates.

Body mass has been shown in experimental and comparative morphological studies to have a significant effect on joint posture in major limb joints. The generalizability of experimental studies is limited by their use of small sample sizes and limited size ranges. In contrast, while comparative morphological studies often have increased sample sizes, the connection between joint posture and morphological variables is often indirect.

Differences in gait complexity and variability between children with and without developmental coordination disorder.

We used elliptical Fourier analysis (EFA) to examine potential differences in the complexity and variability of gait of children with (N=10) and without (N=10) Developmental Coordination Disorder (DCD). Children with DCD generated movement patters with larger variability and complexity than typically developing (TD) children. In addition, children with DCD exhibited greater asymmetry in their movement patterns compared to TD children.

Knee posture predicted from subchondral apparent density in the distal femur: an experimental validation.

Spatial patterning in the apparent density of subchondral bone can be used to discriminate between species that differ in their joint loading conditions. This study provides an experimental test of two hypotheses that relate aspects of subchondral apparent density patterns to joint loading conditions. First, the region of maximum subchondral apparent density (RMD) will correspond to differences in joint posture at the time of peak locomotor loads; and second, differences in maximum density between individuals will correspond to differences in exercise level.

A new approach to detecting asymmetries in gait.

Background: Traditional parameters used to assess gait asymmetries, e.g., joint range of motion or symmetry indices, fail to provide insight regarding timing and magnitude of movement deviations among lower limb joints during the gait cycle.

Quantifying variability in phase portraits: application to gait ontogeny.

We describe new Fourier- and shape-based methods for quantifying variation in phase-portraits, and re-analyze previously-published ontogenetic and adult data [Clark, J. E., & Phillips, S.

Sampling frequencies and measurement error for linear and temporal gait parameters in primate locomotion.

Quantitative analyses of animal motion are increasingly easy to conduct using simple video equipment and relatively inexpensive software packages. With careful use, such analytical tools have the potential to quantify differences in movement between individuals or species and to allow insights into the behavioral consequences of morphological differences between taxa. However, as with any other type of measurement, there are errors associated with kinematic measurements.

Predicting long bone loading from cross-sectional geometry.

Long bone loading histories are commonly evaluated using a beam model by calculating cross-sectional second moments of areas (SMAs). Without in vivo strain data, SMA analyses commonly make two explicit or implicit assumptions. First, while it has long been known that axial compression superimposed on bending shifts neutral axes away from cross-sectional area centroids, most analyses assume that cross-sectional properties calculated through the area centroid approximate cross-sectional strength.