Heterogeneity Profoundly Alters Emergent Stress Fields in Constrained Multicellular Systems.

Stress fields emerging from the transfer of forces between cells within multicellular systems are increasingly being recognized as major determinants of cell fate. Current analytical and numerical models used for the calculation of stresses within cell monolayers assume homogeneous contractile and mechanical cellular properties; however, cell behavior varies by region within constrained tissues. Here, we show the impact of heterogeneous cell properties on resulting stress fields that guide cell phenotype and apoptosis. Using circular micropatterns, we measured biophysical metrics associated with cell mechanical stresses. We then computed cell-layer stress distributions using finite element contraction models and monolayer stress microscopy. In agreement with previous studies, cell spread area, alignment, and traction forces increase, whereas apoptotic activity decreases, from the center of cell layers to the edge. The distribution of these metrics clearly indicates low cell stress in central regions and high cell stress at the periphery of the patterns. However, the opposite trend is predicted by computational models when homogeneous contractile and mechanical properties are assumed. In our model, utilizing heterogeneous cell-layer contractility and elastic moduli values based on experimentally measured biophysical parameters, we calculate low cell stress in central areas and high anisotropic stresses in peripheral regions, consistent with the biometrics. These results clearly demonstrate that common assumptions of uniformity in cell contractility and stiffness break down in postconfluence confined multicellular systems. This work highlights the importance of incorporating regional variations in cell mechanical properties when estimating emergent stress fields from collective cell behavior.

A certified de-identification system for all clinical text documents for information extraction at scale.

Objectives: Clinical notes are a veritable treasure trove of information on a patient's disease progression, medical history, and treatment plans, yet are locked in secured databases accessible for research only after extensive ethics review. Removing personally identifying and protected health information (PII/PHI) from the records can reduce the need for additional Institutional Review Boards (IRB) reviews. In this project, our goals were to: (1) develop a robust and scalable clinical text de-identification pipeline that is compliant with the Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule for de-identification standards and (2) share routinely updated de-identified clinical notes with researchers. Materials and Methods: Building on our open-source de-identification software called Philter, we added features to: (1) make the algorithm and the de-identified data HIPAA compliant, which also implies type 2 error-free redaction, as certified via external audit; (2) reduce over-redaction errors; and (3) normalize and shift date PHI. We also established a streamlined de-identification pipeline using MongoDB to automatically extract clinical notes and provide truly de-identified notes to researchers with periodic monthly refreshes at our institution. Results: To the best of our knowledge, the Philter V1.0 pipeline is currently the first and only certified, de-identified redaction pipeline that makes clinical notes available to researchers for nonhuman subjects' research, without further IRB approval needed. To date, we have made over 130 million certified de-identified clinical notes available to over 600 UCSF researchers. These notes were collected over the past 40 years, and represent data from 2757016 UCSF patients.

Anisotropy profoundly alters stress fields within contractile cells and cell aggregates.

Many biological phenomena such as cell proliferation and death are correlated with stress fields within cells. Stress fields are quantified using computational methods which rely on fundamental assumptions about local mechanical properties. Most existing methods such as Monolayer Stress Microscopy assume isotropic properties, yet experimental observations strongly suggest anisotropy. We first model anisotropy in circular cells analytically using Eshelby's inclusion method. Our solution reveals that uniform anisotropy cannot exist in cells due to the occurrence of substantial stress concentration in the central region. A more realistic non-uniform anisotropy model is then introduced based on experimental observations and implemented numerically which interestingly clears out stress concentration. Stresses within the entire aggregate also drastically change compared to the isotropic case, resulting in better agreement with observed biomarkers. We provide a physics-based mechanism to explain the low alignment of stress fibers in the center of cells, which might explain certain biological phenomena e.g., existence of disrupted rounded cells, and higher apoptosis rate at the center of circular aggregates.

Laser-induced heating of polydimethylsiloxane-magnetite nanocomposites for hyperthermic inhibition of triple-negative breast cancer cell proliferation.

This paper presents the results of an experimental and computational study of the effects of laser-induced heating provided by magnetite nanocomposite structures that are being developed for the localized hyperthermic treatment of triple-negative breast cancer. Magnetite nanoparticle-reinforced polydimethylsiloxane (PDMS) nanocomposites were fabricated with weight percentages of 1%, 5%, and 10% magnetite nanoparticles. The nanocomposites were exposed to incident Near Infrared (NIR) laser beams with well-controlled powers. The laser-induced heating is explored in: (i) heating liquid media (deionized water and cell growth media [Leibovitz L15+]) to characterize the photothermal properties of the nanocomposites, (ii) in vitro experiments that explore the effects of localized heating on triple-negative breast cancer cells, and (iii) experiments in which the laser beams penetrate through chicken tissue to heat up nanocomposite samples embedded at different depths beneath the chicken skin. The resulting plasmonic laser-induced heating is explained using composite theories and heat transport models. The results show that the laser/nanocomposite interactions decrease the viability of triple-negative breast cancer cells (MDA-MB-231) at temperatures in the hyperthermia domain between 41 and 44°C. Laser irradiation did not cause any observed physical damage to the chicken tissue. The potential in vivo performance of the PDMS nanocomposites was also investigated using computational finite element models of the effects of laser/magnetite nanocomposite interactions on the temperatures and thermal doses experienced by tissues that surround the nanocomposite devices. The implications of the results are then discussed for the development of implantable nanocomposite devices for localized treatment of triple-negative breast cancer tissue via hyperthermia.