1,720,974 research outputs found
Data and code for TFlux measurement associated with the publication: PCP-dependent polarized mechanics in the cortex of individual cells during convergent extension
No full textThis dataset contains MATLAB scripts and example demonstration files for the TFlux measurement in the publication: Weng, S., Devitt, C. C., Nyaoga, B. M., Alvarado, J. & Wallingford, J. B. PCP-dependent polarized mechanics in the cortex of individual cells during convergent extension. Dev. Biol. 523, 59–67 (2025). https://doi.org/10.1016/j.ydbio.2025.04.007 </a
TOOLS FOR MESO-SCALE CHARACTERIZATION AND PROCESSING IN BIOLOGICAL TISSUES
Full text linkThe burgeoning focus on engineering transplantable tissues for therapeutic purposes engenders an urgent need for developing a comprehensive framework consisting of diverse tools for both creation and validation of such tissues. The first two pertain to methods for generating physiological mimicking tissues: the fabrication of large-scale aligned collagen matrices with myoblasts and the 3D bioprinting of skin and airway tissues. The final component focuses on the validation of ECM structure and the organization of cells within the tissues. Although there are limitations associated with fabricating larger and complex organ, this paper proposed a novel method to develop large-scale aligned collagen matrices using viscous long-chain polymers to mimic the highly aligned ECM pattern in the body. After mixed with the viscous long-chain polymers, the collagen flowed into the self-made channels. The matrices emulate the highly ordered matrices in humans. C2C12 cells retained a high viability and could align with the collagen fibrils. Additionally, the application of 3D bioprinting in creating intricate tissue architectures holds significant promise in emulating biological tissues. The fibroblasts and epithelial cells showed about 50% viability in 3D bioprinted tissues cultured in the special medium. Moreover, the clear distribution of epithelial cells in the matrix demonstrates possibilities in disease modeling and novel therapy development.
This study extends to the evaluation of tissues obtained from live animals by comparing the collagen remodeling and organization of cells in metastatic and normal lung. By applying the fiber analytic tools, we found that the length of collagen fibers is different between the metastatic lung and normal lung. Additionally, we investigated the potential effects of YAP in the alternation of E-cad and fibronectin due to the acute colitis triggered by colonization with ETBF in mice. Although no difference in the signal of E- cad between YAP and YAP-KO conditions was observed, the method can be used in validating the ECM structure and the organization of cells in artificial tissues. Through these methodologies, this study provides a comprehensive framework for studying both healthy and pathological 3D tissues, thus advancing tissue engineering and its biomedical applications
TOOLS FOR MESO-SCALE CHARACTERIZATION AND PROCESSING IN BIOLOGICAL TISSUES
Full text linkThe burgeoning focus on engineering transplantable tissues for therapeutic purposes engenders an urgent need for developing a comprehensive framework consisting of diverse tools for both creation and validation of such tissues. The first two pertain to methods for generating physiological mimicking tissues: the fabrication of large-scale aligned collagen matrices with myoblasts and the 3D bioprinting of skin and airway tissues. The final component focuses on the validation of ECM structure and the organization of cells within the tissues. Although there are limitations associated with fabricating larger and complex organ, this paper proposed a novel method to develop large-scale aligned collagen matrices using viscous long-chain polymers to mimic the highly aligned ECM pattern in the body. After mixed with the viscous long-chain polymers, the collagen flowed into the self-made channels. The matrices emulate the highly ordered matrices in humans. C2C12 cells retained a high viability and could align with the collagen fibrils. Additionally, the application of 3D bioprinting in creating intricate tissue architectures holds significant promise in emulating biological tissues. The fibroblasts and epithelial cells showed about 50% viability in 3D bioprinted tissues cultured in the special medium. Moreover, the clear distribution of epithelial cells in the matrix demonstrates possibilities in disease modeling and novel therapy development.
This study extends to the evaluation of tissues obtained from live animals by comparing the collagen remodeling and organization of cells in metastatic and normal lung. By applying the fiber analytic tools, we found that the length of collagen fibers is different between the metastatic lung and normal lung. Additionally, we investigated the potential effects of YAP in the alternation of E-cad and fibronectin due to the acute colitis triggered by colonization with ETBF in mice. Although no difference in the signal of E- cad between YAP and YAP-KO conditions was observed, the method can be used in validating the ECM structure and the organization of cells in artificial tissues. Through these methodologies, this study provides a comprehensive framework for studying both healthy and pathological 3D tissues, thus advancing tissue engineering and its biomedical applications
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
To Be, or Not to Be: Cellular Homeostasis to Mechanical Perturbations
Full text linkMechanical homeostasis is an emerging mechanobiology concept that describes the critical biological process to maintain whole-cell/tissue physiology against forces and deformation arising both intra- and extracellularly. Dysregulation of mechanical homeostasis has important implications in pathophysiological conditions such as developmental defect, cardiovascular and pulmonary diseases, and cancer. Mechanical homeostasis has been commonly investigated at molecular, cellular, tissue levels and beyond. However, in mechanical homeostasis collective dynamics at smaller scales and its functional relationship with emergent system-level properties at larger scales remains elusive.
The major contribution of this dissertation is to provide a detailed picture of the functional link between molecular and subcellular events and apparent cellular behaviors under mechanical perturbations. A novel suite of technologies, involving microfabrication, live-cell imaging, high-throughput and multidimensional image processing, and mechanical characterization, have been developed and implemented in this research for the live-cell study of both subcellular and cellular aspects of mechanical homeostasis. By utilizing these techniques, we performed cell stretch experiments and quantitative measurements of biomechanical and biochemical responses with a spatiotemporal resolution to examine cell behaviors upon mechanical perturbation. Our data have revealed that cellular mechanical homeostasis is an emergent phenomenon driven by collective and graduated, yet non-homeostatic, subcellular behaviors (“subcellular rheostasis”) that follow distinct mechanosensitive compensatory paths. We have for the first time shown that subcellular dynamics would observe patterns different from that at the single-cell level. Further investigations have revealed that impairment to the extracellular matrix (ECM) – focal adhesion (FA) – cytoskeleton (CSK) mechanical linkage can lead to an effective exit from cellular mechanical homeostasis by skewing the subcellular rheostasis pattern of FAs, which might be a sensitive gating mechanism of cellular homeostasis. Lastly, a mechano-biophysical model has been constructed in this work to quantitatively recapitulate experimental observations of subcellular rheostasis and its perturbation by different drug treatments. Cross-examination of experimental and theoretical modeling results has unveiled the regulatory roles of different mechanosensitive machineries including catch-slip bonds and myosin motor activity in governing the emergence of cellular mechanical homeostasis.PhDMechanical EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/135780/1/shinuow_1.pd
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
ADVANCING CELLULAR IMAGING AND ANALYSIS: UNVEILING ADIPOCYTE AND ASTROCYTE DYNAMICS WITH OPTICAL DIFFRACTION TOMOGRAPHY
No full textCells are highly dynamic, constantly reshaping their morphology and function in response to intrinsic signals and external stimuli. Capturing these transformations in a quantitative, label-free manner is essential to advancing our understanding of cellular processes. Traditional imaging techniques, such as fluorescence microscopy, require labels that can alter cellular function and limit long-term studies. Optical Diffraction Tomography (ODT) addresses these challenges by providing a label-free, three-dimensional imaging approach capable of quantitatively analyzing cellular morphology and biophysical properties. ODT reconstructs the refractive index (RI) distribution of a sample by capturing multiple holographic images at varying illumination angles. This enables the retrieval of key cellular parameters, including volume, dry mass, and RI variations, which reflect intracellular composition and density. Since phase shifts in light correspond to differences in optical path length, ODT allows for the measurement of subtle structural and compositional changes without the need for exogenous labels. Beyond morphological characterization, ODT quantifies biophysical properties that are critical for understanding cellular function. The RI of a cell is directly linked to its macromolecular content, including proteins, lipids, and nucleic acids. By analyzing RI variations, ODT provides insights into intracellular heterogeneity. Its high-resolution, quantitative nature makes it particularly useful for studying dynamic processes such as differentiation and cellular adaptation to microenvironmental cues.
This dissertation utilizes ODT to investigate the morphological and biophysical dynamics of human adipocytes and rat cortical astrocytes. First, ODT was used to study human white and brown preadipocyte differentiation, revealing distinct lipid accumulation patterns and fluctuations in cell dry mass during early adipogenesis. Next, the impact of metabolic microenvironments was examined by exposing brown preadipocytes to glucose and fructose, showing that fructose impairs lipid accumulation and morphology. Expanding beyond adipocytes, ODT was applied to study astrocyte morphology, uncovering distinct structural adaptations and demonstrating that nanostructured glass substrates induce in vivo-like astrocyte morphology with enhanced process branching. By integrating ODT across these diverse cellular systems, this dissertation highlights the influence of microenvironmental factors on cellular morphology and function. These findings underscore the potential of ODT as a transformative tool for studying cellular dynamics in metabolic and neurobiological research
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Modeling Cell Motility: From Single Cells in Confinement to Collective Behaviors in Tissues
No full textCell motility is crucial for physiological processes such as development, tissue repair, and cancer metastasis. In this dissertation, I employ theoretical and data-driven models to elucidate the physical principles underlying cell motility, aiming to enhance our understanding of cell movement and interactions in various confining environments.
The motility of eukaryotic cells is significantly influenced by their environment. Confined cells exhibit different motility patterns compared to those on simple two-dimensional substrates, with variations also observed between different cell types. This work explores how cells respond to environmental constraints and models these behaviors using computational phase field approaches. Notably, I develop a unified cell model that captures diverse experimental behaviors with the assumption that contact with non-adhesive substrates inhibits cell movement. Integrating data-driven techniques with simulations, I also reveal how simple quantitative changes in cell properties can lead to dramatic qualitative changes in cell behavior.
In addition to moving as single entities, cells can move together as a collective. This dissertation examines collective cell migration at two levels: cell-cell interactions in colliding cell pairs and the morphogenesis of branching tips in large cell clusters. Using a phase field model, I highlight two predictors of collision outcome -- relative cell speed or contact angle -- that remain robust to perturbations. These predictors depend on the chosen assumption of how cells select their preferred direction of motion, and since they are experimentally measurable, they can provide insights into cell decision-making processes. Additionally, by simulating branching morphogenesis in cell clusters, I suggest that cells with lower surface tension or higher sensitivity to external chemical cues can drive the formation of and localize to branching tips. These models align with recent experimental observations and offer a framework for understanding how cells navigate and interact in crowded environments
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