Skyler St. Pierre

All Publications

• The mechanical and sensory signature of plant-based and animal meat. NPJ science of food St Pierre, S. R., Darwin, E. C., Adil, D., Aviles, M. C., Date, A., Dunne, R. A., Lall, Y., Parra Vallecillo, M., Perez Medina, V. A., Linka, K., Levenston, M. E., Kuhl, E. 2024; 8 (1): 94

  Abstract

  Eating less meat is associated with a healthier body and planet. Yet, we remain reluctant to switch to a plant-based diet, largely due to the sensory experience of plant-based meat. Food scientists characterize meat using a double compression test, which only probes one-dimensional behavior. Here we use tension, compression, and shear tests-combined with constitutive neural networks-to automatically discover the behavior of eight plant-based and animal meats across the entire three-dimensional spectrum. We find that plant-based sausage and hotdog, with stiffnesses of 95.9 ± 14.1 kPa and 38.7 ± 3.0 kPa, successfully mimic their animal counterparts, with 63.5 ± 45.7 kPa and 44.3 ± 13.2 kPa, while tofurky is twice as stiff, and tofu is twice as soft. Strikingly, a complementary food tasting survey produces in nearly identical stiffness rankings for all eight products (ρ = 0.833, p = 0.015). Probing the fully three-dimensional signature of meats is critical to understand subtle differences in texture that may result in a different perception of taste. Our data and code are freely available at https://github.com/LivingMatterLab/CANN.

  View details for DOI 10.1038/s41538-024-00330-6

  View details for PubMedID 39548076

  View details for PubMedCentralID PMC11568319

• Mimicking Mechanics: A Comparison of Meat and Meat Analogs. Foods (Basel, Switzerland) St Pierre, S. R., Kuhl, E. 2024; 13 (21)

  Abstract

  The texture of meat is one of the most important features to mimic when developing meat analogs. Both protein source and processing method impact the texture of the final product. We can distinguish three types of mechanical tests to quantify the textural differences between meat and meat analogs: puncture type, rheological torsion tests, and classical mechanical tests of tension, compression, and bending. Here, we compile the shear force and stiffness values of whole and comminuted meats and meat analogs from the two most popular tests for meat, the Warner-Bratzler shear test and the double-compression texture profile analysis. Our results suggest that, with the right fine-tuning, today's meat analogs are well capable of mimicking the mechanics of real meat. While Warner-Bratzler shear tests and texture profile analysis provide valuable information about the tenderness and sensory perception of meat, both tests suffer from a lack of standardization, which limits cross-study comparisons. Here, we provide guidelines to standardize meat testing and report meat stiffness as the single most informative mechanical parameter. Collecting big standardized data and sharing them with the community at large could empower researchers to harness the power of generative artificial intelligence to inform the systematic development of meat analogs with desired mechanical properties and functions, taste, and sensory perception.

  View details for DOI 10.3390/foods13213495

  View details for PubMedID 39517278

• Sex-specific cardiovascular risk factors in the UK Biobank. Frontiers in physiology St Pierre, S. R., Kaczmarski, B., Peirlinck, M., Kuhl, E. 2024; 15: 1339866

  Abstract

  The lack of sex-specific cardiovascular disease criteria contributes to the underdiagnosis of women compared to that of men. For more than half a century, the Framingham Risk Score has been the gold standard to estimate an individual's risk of developing cardiovascular disease based on the age, sex, cholesterol levels, blood pressure, diabetes status, and the smoking status. Now, machine learning can offer a much more nuanced insight into predicting the risk of cardiovascular diseases. The UK Biobank is a large database that includes traditional risk factors and tests related to the cardiovascular system: magnetic resonance imaging, pulse wave analysis, electrocardiograms, and carotid ultrasounds. Here, we leverage 20,542 datasets from the UK Biobank to build more accurate cardiovascular risk models than the Framingham Risk Score and quantify the underdiagnosis of women compared to that of men. Strikingly, for a first-degree atrioventricular block and dilated cardiomyopathy, two conditions with non-sex-specific diagnostic criteria, our study shows that women are under-diagnosed 2× and 1.4× more than men. Similarly, our results demonstrate the need for sex-specific criteria in essential primary hypertension and hypertrophic cardiomyopathy. Our feature importance analysis reveals that out of the top 10 features across three sexes and four disease categories, traditional Framingham factors made up between 40% and 50%; electrocardiogram, 30%-33%; pulse wave analysis, 13%-23%; and magnetic resonance imaging and carotid ultrasound, 0%-10%. Improving the Framingham Risk Score by leveraging big data and machine learning allows us to incorporate a wider range of biomedical data and prediction features, enhance personalization and accuracy, and continuously integrate new data and knowledge, with the ultimate goal to improve accurate prediction, early detection, and early intervention in cardiovascular disease management. Our analysis pipeline and trained classifiers are freely available at https://github.com/LivingMatterLab/CardiovascularDiseaseClassification.

  View details for DOI 10.3389/fphys.2024.1339866

  View details for PubMedID 39165282

  View details for PubMedCentralID PMC11333928

• On sparse regression, Lp regularization, and automated model discovery International Journal for Numerical Methods in Engineering McCulloch, J. A., St. Pierre, S. R., Linka, K., Kuhl, E. 2024

  View details for DOI 10.1002/nme.7481

• Discovering the mechanics of artificial and real meat COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING St Pierre, S. R., Rajasekharan, D., Darwin, E. C., Linka, K., Levenston, M. E., Kuhl, E. 2023; 415

  View details for DOI 10.1016/j.cma.2023.116236

  View details for Web of Science ID 001047757200001

• Principal-stretch-based constitutive neural networks autonomously discover a subclass of Ogden models for human brain tissue Brain Multiphysics St. Pierre, S. R., Linka, K., Kuhl, E. 2023; 4

  View details for DOI 10.1016/j.brain.2023.100066

• Automated model discovery for human brain using Constitutive Artificial Neural Networks Acta Biomaterialia Linka, K., St. Pierre, S. R., Kuhl, E. 2023

  View details for DOI 10.1016/j.actbio.2023.01.055

• Sex Matters: A Comprehensive Comparison of Female and Male Hearts. Frontiers in physiology St Pierre, S. R., Peirlinck, M., Kuhl, E. 2022; 13: 831179

  Abstract

  Cardiovascular disease in women remains under-diagnosed and under-treated. Recent studies suggest that this is caused, at least in part, by the lack of sex-specific diagnostic criteria. While it is widely recognized that the female heart is smaller than the male heart, it has long been ignored that it also has a different microstructural architecture. This has severe implications on a multitude of cardiac parameters. Here, we systematically review and compare geometric, functional, and structural parameters of female and male hearts, both in the healthy population and in athletes. Our study finds that, compared to the male heart, the female heart has a larger ejection fraction and beats at a faster rate but generates a smaller cardiac output. It has a lower blood pressure but produces universally larger contractile strains. Critically, allometric scaling, e.g., by lean body mass, reduces but does not completely eliminate the sex differences between female and male hearts. Our results suggest that the sex differences in cardiac form and function are too complex to be ignored: the female heart is not just a small version of the male heart. When using similar diagnostic criteria for female and male hearts, cardiac disease in women is frequently overlooked by routine exams, and it is diagnosed later and with more severe symptoms than in men. Clearly, there is an urgent need to better understand the female heart and design sex-specific diagnostic criteria that will allow us to diagnose cardiac disease in women equally as early, robustly, and reliably as in men.Systematic Review Registration: https://livingmatter.stanford.edu/.

  View details for DOI 10.3389/fphys.2022.831179

  View details for PubMedID 35392369

• Condensation tendency and planar isotropic actin gradient induce radial alignment in confined monolayers ELIFE Xie, T., St Pierre, S. R., Olaranont, N., Brown, L. E., Wu, M., Sun, Y. 2021; 10

  Abstract

  A monolayer of highly motile cells can establish long-range orientational order, which can be explained by hydrodynamic theory of active gels and fluids. However, it is less clear how cell shape changes and rearrangement are governed when the monolayer is in mechanical equilibrium states when cell motility diminishes. In this work, we report that rat embryonic fibroblasts (REF), when confined in circular mesoscale patterns on rigid substrates, can transition from the spindle shapes to more compact morphologies. Cells align radially only at the pattern boundary when they are in the mechanical equilibrium. This radial alignment disappears when cell contractility or cell-cell adhesion is reduced. Unlike monolayers of spindle-like cells such as NIH-3T3 fibroblasts with minimal intercellular interactions or epithelial cells like Madin-Darby canine kidney (MDCK) with strong cortical actin network, confined REF monolayers present an actin gradient with isotropic meshwork, suggesting the existence of a stiffness gradient. In addition, the REF cells tend to condense on soft substrates, a collective cell behavior we refer to as the 'condensation tendency'. This condensation tendency, together with geometrical confinement, induces tensile prestretch (i.e. an isotropic stretch that causes tissue to contract when released) to the confined monolayer. By developing a Voronoi-cell model, we demonstrate that the combined global tissue prestretch and cell stiffness differential between the inner and boundary cells can sufficiently define the cell radial alignment at the pattern boundary.

  View details for DOI 10.7554/eLife.60381.sa2

  View details for Web of Science ID 000703105000001

  View details for PubMedID 34542405

  View details for PubMedCentralID PMC8478414

• Patterning Neuroepithelial Cell Sheet via a Sustained Chemical Gradient Generated by Localized Passive Diffusion Devices ACS BIOMATERIALS SCIENCE & ENGINEERING Li, N., Yang, F., Parthasarathy, S., St Pierre, S., Hong, K., Pavon, N., Pak, C., Sun, Y. 2021; 7 (4): 1713-1721

  Abstract

  Recent advances in human pluripotent stem cells (hPSCs)-derived in vitro models open a new avenue for studying early stage human development. While current approaches leverage the self-organizing capability of hPSCs, it remains unclear whether extrinsic morphogen gradients are sufficient to pattern neuroectoderm tissues in vitro. While microfluidics or hydrogel-based approaches to generate chemical gradients are well-established, these systems either require continuous pumping or encapsulating cells in gels, making it difficult for adaptation in standard biology laboratories and downstream analysis. In this work, we report a new device design that leverages localized passive diffusion, or LPaD for short, to generate a stable chemical gradient in an open environment. As LPaD is operated simply by media changing, common issues for microfluidic systems such as leakage, bubble formation, and contamination can be avoided. The device contains a slit carved in a film filled with solid gelatin and connected to a static aqueous morphogen reservoir. Concentration gradients generated by the device were visualized via DAPI fluorescent intensity and were found to be stable for up to 168 h. Using this device, we successfully induced cellular response of Madin-Darby canine kidney (MDCK) cells to the concentration gradient of a small-molecule drug, cytochalasin D. Furthermore, we efficiently patterned the dorsal-ventral axis of hPSC-derived forebrain neuroepithelial cells with the sonic hedgehog (Shh) signal gradient generated by the LPaD devices. Together, LPaD devices are powerful tools to control the local chemical microenvironment for engineering organotypic structures in vitro.

  View details for DOI 10.1021/acsbiomaterials.0c01365

  View details for Web of Science ID 000640306300036

  View details for PubMedID 33751893