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153 results on '"Bryant, David"'

2. ECM dimensionality tunes actin tension to modulate endoplasmic reticulum function and spheroid phenotypes of mammary epithelial cells.

Author

Ou, Guanqing, Tourdot, Richard, Stashko, Connor, Gaietta, Guido, Swift, Mark, Volkmann, Niels, Long, Alexandra, Han, Yulong, Huang, Hector, Leidal, Andrew, Viasnoff, Virgile, Bryant, David, Guo, Wei, Wiita, Arun, Guo, Ming, Hanein, Dorit, Radhakrishnan, Ravi, Weaver, Valerie, Dumont, Sophie, Kai, Fuiboon, and Northey, Jason

Subjects
actin tension, endoplasmic reticulum, extracellular matrix, membrane contact sites, spheroids, Actins, Endoplasmic Reticulum, Endoplasmic Reticulum Stress, Epithelial Cells, Filamins, Phenotype
Abstract

Patient-derived organoids and cellular spheroids recapitulate tissue physiology with remarkable fidelity. We investigated how engagement with a reconstituted basement membrane in three dimensions (3D) supports the polarized, stress resilient tissue phenotype of mammary epithelial spheroids. Cells interacting with reconstituted basement membrane in 3D had reduced levels of total and actin-associated filamin and decreased cortical actin tension that increased plasma membrane protrusions to promote negative plasma membrane curvature and plasma membrane protein associations linked to protein secretion. By contrast, cells engaging a reconstituted basement membrane in 2D had high cortical actin tension that forced filamin unfolding and endoplasmic reticulum (ER) associations. Enhanced filamin-ER interactions increased levels of PKR-like ER kinase effectors and ER-plasma membrane contact sites that compromised calcium homeostasis and diminished cell viability. Consequently, cells with decreased cortical actin tension had reduced ER stress and survived better. Consistently, cortical actin tension in cellular spheroids regulated polarized basement membrane membrane deposition and sensitivity to exogenous stress. The findings implicate cortical actin tension-mediated filamin unfolding in ER function and underscore the importance of tissue mechanics in organoid homeostasis.

Published
2022

4. Parsimony and the rank of a flattening matrix

Author

Snyman, Jandre, Fox, Colin, and Bryant, David

Subjects
Quantitative Biology - Populations and Evolution
Abstract

The standard models of sequence evolution on a tree determine probabilities for every character or site pattern. A flattening is an arrangement of these probabilities into a matrix, with rows corresponding to all possible site patterns for one set $A$ of taxa and columns corresponding to all site patterns for another set $B$ of taxa. Flattenings have been used to prove difficult results relating to phylogenetic invariants and consistency and also form the basis of several methods of phylogenetic inference. We prove that the rank of the flattening equals $r^{\ell_T(A|B)}$, where $r$ is the number of states and $\ell_T(A|B)$ is the parsimony length of the binary character separating $A$ and $B$. This result corrects an earlier published formula and opens up new applications for old parsimony theorems. Since completing this work, we have learnt that an equivalent result has been proved much earlier by Casanellas and Fern\'andez-S\'anchez, using a different proof strategy.

Published
2021

5. Diversities and the Generalized Circumradius

Author

Bryant, David, Huber, Katharina T., Moulton, Vincent, and Tupper, Paul F.

Subjects
Mathematics - Metric Geometry, 52A20, 51F99
Abstract

The generalized circumradius of a set of points $A \subseteq \mathbb{R}^d$ with respect to a convex body $K$ equals the minimum value of $\lambda \geq 0$ such that $A$ is contained in a translate of $\lambda K$. Each choice of $K$ gives a different function on the set of bounded subsets of $\mathbb{R}^d$; we characterize which functions can arise in this way. Our characterization draws on the theory of diversities, a recently introduced generalization of metrics from functions on pairs to functions on finite subsets. We additionally investigate functions which arise by restricting the generalised circumradius to a finite subset of $\mathbb{R}^d$. We obtain elegant characterizations in the case that $K$ is a simplex or parallelotope., Comment: To be published in Discrete and Computational Geometry

Published
2021

7. The Supreme Court Undercuts The SEC

Author

Bryant, David

Subjects
United States. Supreme Court -- Powers and duties, Administrative procedure -- Laws, regulations and rules, Securities fraud -- Cases, Company legal issue, Government regulation, Business, international, Dodd-Frank Wall Street Reform and Consumer Protection Act of 2010, Administrative Procedure Act
Abstract

An increasingly assertive SEC has found itself in uncharted territory, defenestrated. Since the 2008 recession and the subsequent passing of the Dodd-Frank Wall Street Reform and Consumer Protection Act, the [...]

Published
2024

30. Deciphering maternal-fetal cross-talk in the human placenta during parturition using single-cell RNA sequencing

Author

Garcia-Flores, Valeria, primary, Romero, Roberto, additional, Tarca, Adi L., additional, Peyvandipour, Azam, additional, Xu, Yi, additional, Galaz, Jose, additional, Miller, Derek, additional, Chaiworapongsa, Tinnakorn, additional, Chaemsaithong, Piya, additional, Berry, Stanley M., additional, Awonuga, Awoniyi O., additional, Bryant, David R., additional, Pique-Regi, Roger, additional, and Gomez-Lopez, Nardhy, additional

Published
2024
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35. WIRE-21 Sensor Irradiation Experiment Ready for HFIR Insertion

Author

Petrie, Christian, primary, Chapel, Shay, additional, Mulligan, Padhraic, additional, Bryant, David, additional, Sweeney, Dan, additional, James, Adam, additional, Ezell, N Dianne, additional, Smith, Kurt, additional, Godsey, Kara, additional, Searles, Maureen, additional, Stafford, Shawn, additional, Arndt, Jeff, additional, and Carvajal, Jorge, additional

Published
2022
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36. Acoustic surveys improve landscape-scale detection of a critically endangered Australian bird, the plains-wanderer (Pedionomus torquatus).

Author

Rowe, Karen M. C., Selwood, Katherine E., Bryant, David, and Baker-Gabb, David

Abstract

Context. Monitoring the population dynamics of threatened species requires a landscape-scale understanding of their distribution over time. However, detectability is inherently low for rare, widely dispersed, and cryptic species. For animals that vocalise, passive acoustic recorders allow for efficient and repeated surveys over a large geographic area, increasing inference in relation to detectability and occupancy. Aims. Our aim was to determine how well acoustic surveys, combined with automated species detection, identified the presence of the critically endangered plains-wanderer (Pedionomus torquatus) relative to a traditional method of nocturnal spotlighting surveys at sites across the Northern Plains of Victoria, Australia. Methods. Using Hidden Markov Models, we created 17 different plains-wanderer call recognisers by varying input parameters and assessed their performance on the same training and testing audio dataset. We then applied our best-performing recogniser to a field audio dataset to estimate detectability and compared the presence of plains-wanderers at sites paired with nocturnal surveys. Key results. Recognisers varied in their overall performance in detecting individual plains-wanderer calls but were equally effective at determining whether any plains-wanderer calls were detected at a site within ourtraining and testing datasets. Although survey effort was not standardised across field survey methods, we found audio surveys and nocturnal spotlight surveys were equally successful at establishing site-level occupancy; however, acoustic surveys provide the potential to survey more sites over a given time period. Conclusions. We suggest acoustic surveys can be an effective and efficient means to document occupancy at the landscape scale, facilitating prioritisation of nocturnal surveys to assess population demographic parametersincluding abundance and breeding status. Implications.Acoustic surveys can provide a complementary method to establish occupancy for cryptic, vocally active, threatened species. We provide recommendations on ways to develop an effective acoustic monitoring program workflow, from data collection to acoustic analysis, that can be used by different user groups. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Immunosequencing and Profiling of T Cells at the Maternal–Fetal Interface of Women with Preterm Labor and Chronic Chorioamnionitis

Author

Miller, Derek, primary, Romero, Roberto, additional, Myers, Luke, additional, Xu, Yi, additional, Arenas-Hernandez, Marcia, additional, Galaz, Jose, additional, Soto, Cinque, additional, Done, Bogdan, additional, Quiroz, Angelica, additional, Awonuga, Awoniyi O., additional, Bryant, David R., additional, Tarca, Adi L., additional, and Gomez-Lopez, Nardhy, additional

Published
2023
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40. PTEN deficiency exposes a requirement for an ARF GTPase module for integrin‐dependent invasion in ovarian cancer

Author

Nikolatou, Konstantina, primary, Sandilands, Emma, additional, Román‐Fernández, Alvaro, additional, Cumming, Erin M, additional, Freckmann, Eva, additional, Lilla, Sergio, additional, Buetow, Lori, additional, McGarry, Lynn, additional, Neilson, Matthew, additional, Shaw, Robin, additional, Strachan, David, additional, Miller, Crispin, additional, Huang, Danny T, additional, McNeish, Iain A, additional, Norman, James C, additional, Zanivan, Sara, additional, and Bryant, David M, additional

Published
2023
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45. Author Reply to Peer Reviews of PTEN deficiency exposes a requirement for an ARF GTPase module in integrin-dependent invasion in ovarian cancer.

Author

Nikolatou, Konstantina, primary, Sandilands, Emma, additional, Roman-Fernandez, Alvaro, additional, Cumming, Erin M., additional, Freckmann, Eva C., additional, Lilla, Sergio, additional, Buetow, Lori, additional, McGarry, Lynn, additional, Neilson, Matthew, additional, Shaw, Robin, additional, Strachan, David, additional, Miller, Crispin, additional, Huang, Danny T, additional, McNeish, Ian, additional, Norman, James C., additional, Zanivan, Sara, additional, and Bryant, David M, additional

Published
2023
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46. The small GTPase ARF3 controls invasion modality and metastasis by regulating N-cadherin levels

Author

Sandilands, Emma, primary, Freckmann, Eva C., additional, Cumming, Erin M., additional, Román-Fernández, Alvaro, additional, McGarry, Lynn, additional, Anand, Jayanthi, additional, Galbraith, Laura, additional, Mason, Susan, additional, Patel, Rachana, additional, Nixon, Colin, additional, Cartwright, Jared, additional, Leung, Hing Y., additional, Blyth, Karen, additional, and Bryant, David M., additional

Published
2023
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47. Analysis of concordance between microsatellite instability by next generation sequencing (NGS-MSI) and mismatch repair deficiency by immunohistochemistry (IHC-MMR) in >28,000 colorectal tumors.

Author

Ali-Fehmi, Rouba, primary, Oberley, Matthew James, additional, Kraus, Harris, additional, Herzog, Thomas J, additional, Karnezis, Anthony, additional, Antonarakis, Emmanuel S., additional, Kasi, Pashtoon Murtaza, additional, Farrell, Alex Patrick, additional, Xiu, Joanne, additional, Swensen, Jeffrey, additional, Spetzler, David, additional, Abraham, Jim, additional, Korn, Wolfgang Michael, additional, and Bryant, David, additional

Published
2023
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48. Spatial regulation of the glycocalyx component podocalyxin is a switch for prometastatic function

Author

Román-Fernández, Alvaro, primary, Mansour, Mohammed A., additional, Kugeratski, Fernanda G., additional, Anand, Jayanthi, additional, Sandilands, Emma, additional, Galbraith, Laura, additional, Rakovic, Kai, additional, Freckmann, Eva C., additional, Cumming, Erin M., additional, Park, Ji, additional, Nikolatou, Konstantina, additional, Lilla, Sergio, additional, Shaw, Robin, additional, Strachan, David, additional, Mason, Susan, additional, Patel, Rachana, additional, McGarry, Lynn, additional, Katoch, Archana, additional, Campbell, Kirsteen J., additional, Nixon, Colin, additional, Miller, Crispin J., additional, Leung, Hing Y., additional, Le Quesne, John, additional, Norman, James C., additional, Zanivan, Sara, additional, Blyth, Karen, additional, and Bryant, David M., additional

Published
2023
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49. Dimorphic glioblastoma with glial and epithelioid phenotypes: Clonal evolution and immune selection

Author

Mondia, Mark Willy L., primary, Kritselis, Michael A., additional, Donahue, John E., additional, Elinzano, Heinrich, additional, Sarangi, Sasmit, additional, Bryant, David, additional, Capelletti, Marzia, additional, Korn, W. Michael, additional, Yu, Esther, additional, Yan, Sherry, additional, Toms, Steven A., additional, and Wong, Eric T., additional

Published
2023
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