About

John David Polk is an Adjunct Professor in the Biomedical and Translational Sciences department at the Carle Illinois College of Medicine, University of Illinois Urbana-Champaign. His contact email is jdpolk@illinois.edu. The page does not provide specific details about his research focus, background, or key contributions, and no additional biographical information is available from the provided content.

Research topics

• Geometry
• Ecology
• Statistics
• Mathematics
• Biology
• Medicine

Selected publications

• Revised Body Mass Estimates for Extinct Lemurs

  American Journal of Biological Anthropology · 2025-11-01 · 1 citations

  articleOpen access

  ABSTRACT Objectives Body mass estimates for extinct animals are critical for informing hypotheses and analyses related to behavioral ecology, extinction risk, and locomotor modes. These estimates underpin reconstructions of behavioral ecology, especially for Madagascar's extinct subfossil lemurs. Previous estimates, based on femoral and humeral midshaft cortical areas, did not account for phylogenetic relatedness, potentially impacting their accuracy. This study updates body mass estimates for extinct lemurs using phylogenetically informed methods. Materials and Methods We analyzed 64 femora from 10 extinct lemur species. Each specimen was scanned using a Bruker SkyScan 1178 micro‐CT scanner to obtain high‐resolution images of femoral cortical areas. These data were combined to form a dataset comprising more than 125 subfossil lemur specimens across 15 identifiable species. Phylogenetically informed regression models (pGLS) incorporating femoral cortical surface area (FCSA) and femoral length (FL) as predictors were applied. Model fits were evaluated using Akaike information criterion (AIC) and adjusted R 2 values to determine the optimal predictors of body mass (BM). Results Natural log‐transformed FCSA emerged as the best predictor of natural log‐transformed BM among living primates. This pGLS regression equation was used to estimate body mass and lower and upper 95% prediction limits for all subfossil specimens, and weighted average BM estimates were obtained for each species. Our updated body mass estimates are consistently smaller than those previously reported. Discussion These estimates provide a more accurate basis for understanding extinct lemur life history traits, morphometrics, and ecological adaptations. These findings underscore the importance of incorporating evolutionary context in paleontological and ecological research.

  PublisherDOI

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

  PLoS Computational Biology · 2023-01-19 · 14 citations

  articleOpen accessCorresponding

  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. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit.

  PublisherDOI

• Spatial Variation in Young Ovine Cortical Bone Properties

  Journal of Biomechanical Engineering · 2023-01-03 · 5 citations

  article

  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. Three point bending tests were performed to measure the flexural modulus, strength, and post-yield displacement. There was no difference in cortical thickness or density between anterior or posterior quadrants; however, density was consistently higher in the middle diaphysis. Interestingly, bending modulus and strength were higher in anterior quadrants compared to posterior quadrants. Together, our results suggest that there is a differential spatial response of bone in terms of elastic bending modulus and mechanical strength. The origins of this difference may lie within the variation in ongoing mineralization, in combination with the collagen-rich plexiform structure, and whether this is related to strain mode remains to be explored. These data suggest that in young ovine cortical bone, modulation of strength occurs via potentially complex interactions of both mineral and collagen-components that may be different in regions of bone exposed to variable amounts of strain. Further work is needed to confirm the physiological load state of bone during growth to better elucidate the degree to which these variations are a function of the local mechanical environment.

  PublisherDOI

• Variation in young ovine cortical bone properties in regions habitually exposed to tension versus compression

  2022-06-07

  preprintOpen access
  PublisherDOI

• Effects of Body Mass on Leg and Vertical Stiffness in Running Humans

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-05-05 · 3 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Numerous cross-species comparisons have examined the scaling of gait parameters with respect to body mass (i.e., allometry), but few have done so within humans. This study examined how leg and vertical stiffness, force, displacement, and leg spring angle scaled in 64 healthy adults of varying body masses during slow and fast leg-length-adjusted running speeds. We calculated scaling patterns for stiffness and its components via kinematic and kinetic data using log-log regressions with 95% confidence/highest density intervals. To determine if the chosen statistical method influenced conclusions about scaling patterns, we compared regression results across three statistical methods, ordinary least squares (OLS) regression, linear mixed models (LMM), and Bayesian linear mixed models (BLMM). We also performed sex-specific analyses to determine if each sex revealed similar scaling patterns as the pooled sample. In the pooled sample, all variables scaled according to the isometric expectations, suggesting that different-sized humans move in a similar manner. Sex-specific analyses revealed similar patterns of isometry in all variables, except for vertical stiffness, which displayed slight negative allometry (i.e., lower than expected stiffness) in both sexes at the slow speed and negative allometry in females during fast running. Model choice did not significantly affect results, and scaling patterns were the same regardless of the statistical method employed.

  PublisherOA PDFDOI

• Educating students while recruiting underrepresented populations for Alzheimer’s disease research: the Student Ambassador Program

  BMC Medical Education · 2022-10-05 · 11 citations

  articleOpen access

  BACKGROUND: Increasing numbers of patients with Alzheimer's Disease and related disorders (ADRD) necessitates increasing numbers of clinicians to care for them. Educational programming related to community outreach with older adults may help inspire interest in future ADRD clinical careers, while increasing awareness of ADRD in the community and aiding recruitment of underrepresented participants into research studies. METHOD: The Boston University Alzheimer's Disease Research Center (BU ADRC) created the BU ADRC Student Ambassador Program, where medical students, graduate students, and undergraduates interested in medicine completed a curriculum during the academic year that included six educational and three outreach events, including monthly dementia-focused didactic meetings and outreach focusing on Black participant recruitment. A pre-post program survey design was implemented to assess changes in students' knowledge of and attitudes toward dementia and related disorders. RESULTS: Between September 2015 and May 2020, thirty-seven students completed the program. Following program completion, students demonstrated increased knowledge of dementia and willingness to work with patients with dementia, as well as more positive attitudes toward patients and the role of empathy in physician practice. In terms of recruitment benefits, the students helped the BU ADRC reach older adults from underrepresented groups who could serve as participants in future research studies. CONCLUSIONS: The BU ADRC Student Ambassador Program can serve as a model for other clinical research programs who wish to encourage students to consider a career in a specific field. In addition, this model has the potential to increase enrollment of participants to research studies. We discuss limitations of our initial efforts and directions for future work to quantify the anticipated benefits for student education and participant recruitment.

  PublisherOA PDFDOI

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2021-05-18 · 2 citations

  preprintOpen access

  Abstract 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. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit. Author summary The quantification of biological shape variation has relied on expert placement of relatively small subsets of landmarks and their analysis using tools of geometric morphometrics (GM). This paper introduces morphVQ, a novel, automated, learning-based approach to shape analysis that approximates the non-rigid correspondence between surface models of bone. With accurate functional correspondence between bones, we can characterize the shape variation within a dataset. Our results demonstrate that morphVQ performs similarly to manual digitization and to an existing automated phenotyping approach, auto3DGM. morphVQ has the advantages of greater computational efficiency and while capturing shape variation directly from surface model representations of bone. We can classify biological shapes to the Genus level with comparable accuracy to previous approaches, and we can demonstrate which aspects of bone shape differ most between groups. The ability to provide comparable accuracy in a Genus level classification with features extracted from morphVQ further guarantees the validity of this approach.

  PublisherOA PDFDOI

• Humans Crawl: Species Atypical Movement

  2021-01-01

  book-chapterSenior author
  PublisherDOI

• Scaling of linear anthropometric dimensions in living humans

  American Journal of Physical Anthropology · 2021 · 5 citations

  Senior authorCorresponding
  • Statistics
  • Mathematics
  • Biology

  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. MATERIALS AND METHODS: Motion capture marker data from 104 adults of varying height and mass were used to calculate anthropometric dimensions. We analyzed scaling patterns in pooled and separate sexes with two methods: (1) bivariate log-log regression and (2) multivariate principal component analysis (PCA). We calculated 95% highest density/confidence intervals for each method and defined positive/negative allometry as estimates lying outside those intervals. RESULTS: Results identified isometric scaling of the upper arm, thigh, and shoulder, positive allometry of the forearm and shank, and negative allometry of the pelvis in the pooled sample using both statistical methods. Patterns of allometry in the pooled sample were similar between methods but differed in magnitude. Sex-specific results differed in both pattern and magnitude between log-log regression and PCA. Only one measurement (shoulder width) departed from isometry in the sex-specific log-log regressions. DISCUSSION: Our findings suggest that especially in sex-specific analyses, the pattern and magnitude of allometry are sensitive to statistical methodology. When body mass was selected as the size variable, most human linear anthropometric dimensions in this sample scaled isometrically and were therefore geometrically similar within sexes.

  PublisherDOI

• Subchondral and Trabecular Bone Respond Differently to Exercise in Juvenile Sheep

  The FASEB Journal · 2020-04-01

  article1st authorCorresponding

  Evaluating the responses of subchondral and underlying trabecular bone properties to exercise interventions have implications for understanding normal developmental processes as well as the etiology of diseases affecting these tissues. We hypothesized that exercise would result in (1) increased subchondral and trabecular thickness and density, and increased bone volume fraction, (2) the distribution of increased bone properties would reflect experimentally induced postural differences, and (3) shallower trabecular bone would show a greater response to exercise than deeper trabecular bone. To evaluate these hypotheses we randomly assigned thirty juvenile sheep to flat exercise (n=11), inclined exercise (15% grade; n=11) which used more flexed knee postures, and non‐exercised control (n=8) groups. Exercise was conducted on motorized treadmills twice daily for 20 min at 1.12m/s for 60 days. Distal femora were micro‐CT‐scanned at 50μm resolution. Trabecular thickness, apparent density, bone volume fraction, anisotropy, as well as subchondral thickness and apparent density were measured using custom algorithms in AMIRA, ImageJ and MATLAB. Subchondral thickness showed significant and predictable response to exercise and with approximately 20% thicker bone in both exercise groups compared to controls, and postural changes with increased thickness toward the posterior side of the condyle in the incline group. Subchondral density did not increase substantially with exercise. In contrast trabecular density was increased slightly with exercise (~5%) but the response did not correspond to incline‐exercised and control groups. These results suggest a greater responsiveness to exercise in subchondral than trabecular bone, and imply that increases in stiffness in these tissues may be achieved through modulation of different tissue properties. Support or Funding Information National Science Foundation 1638756

  PublisherDOI

Recent grants

• Reconstructing individual posture and movement patterns from subchondral and trabecular bone structure

  NSF · $441k · 2017–2022

• Doctoral Dissertation Improvement: Morphological Integration and Evolution of the Hominoid Vertebral Column

  NSF · $11k · 2009–2011

• Comparative analyses of femoral subchondral bone density in primates

  NSF · $37k · 2007–2009

Frequent coauthors

• Mariana E. Kersh

  17 shared

• Daniel E. Lieberman

  Harvard University

  12 shared

• William E. H. Harcourt‐Smith

  New York Consortium in Evolutionary Primatology

  12 shared

• Brigitte Demes

  Stony Brook University

  11 shared

• Ryan L. Raaum

  9 shared

• Karl S. Rosengren

  University of Rochester

  9 shared

• Elizabeth T. Hsiao‐Wecksler

  University of Illinois Urbana-Champaign

  8 shared

• Scott A. Williams

  United Nations Economic and Social Commission for Asia and the Pacific

  7 shared

Education

• PhD

  Stony Brook University

  2001

Awards & honors

• Carle Illinois College of Medicine Professorships, Awards, a…