141,211 results on '"Bowman AS"'
Search Results
102. The Impact of Emergency Online Learning on D/Deaf College Students' Experience of Social Isolation, Self-Efficacy, and Well-Being
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Bowman, M. Elizabeth and Crowe, Teresa
- Abstract
During the 2020 COVID-19 pandemic, many universities in the United States converted face-to-face classroom teaching to remote, online based learning formats. Gallaudet University was among these universities and faced particular challenges due to the need for visually accessible classrooms for d/Deaf students. Because college students are primarily made up of early and emerging adults, and d/Deaf college students have been shown to have better academic success when social connection is fostered, the current study sought to determine how d/Deaf students at Gallaudet University were emotionally impacted by the change to online learning during the COVID-19 pandemic in 2020. The research question for this study was: How did the COVID-19 pandemic and subsequent emergency switch to online course participation influence college students' experience of well-being, self-efficacy, and loneliness? Results indicated that overall, d/Deaf students at Gallaudet university had positive emotional adjustment during this transition, despite challenges. Discussion describes within-group differences by age and how the University supported students and the campus community to encourage this positive outcome.
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- 2023
103. The Role of Minoritized Student Representation in Promoting Achievement and Equity within College Stem Courses
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Nicholas Bowman, Christine Logel, Jennifer Lacosse, Elizabeth A. Canning, Katherine T. U. Emerson, and Mary C. Murphy
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In the context of continued equity gaps in student success within and beyond STEM, this paper explored the extent to which the representation of underrepresented racial minority (URM) and first-generation college students predict grades in postsecondary STEM courses. The analyses examined 87,027 grades received by 11,868 STEM-interested students within 8,468 STEM courses at 20 institutions. Cross-classified multilevel models and student fixed effects analyses of these data both support the same conclusion: the proportion of URM and first-generation students within a class is positively associated with STEM grades among all students, and these relationships are stronger among students who are members of the minoritized group. Thus, promoting the representation of students with minoritized identities in STEM courses may lead to greater equity in college outcomes.
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- 2023
104. LGBTQIA+ Inclusive School Library Research: A Systematic Literature Review
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Jenna Spiering, Lucy Santos Green, and Jesselyn Dreeszen Bowman
- Abstract
The current LGBTQIA+-hostile political climate highlights a growing need among school librarians for evidence-based support addressing inclusive professional practices. To establish a baseline of studies providing this evidence and to identify areas where further research is needed, this study used systematic literature review methodology to examine international empirical research in the field of school and youth librarianship published between the years of 2009 and 2021. The study's objectives were to identify and categorize published empirical research on LGBTQIA+ topics in school and youth librarianship and to identify and categorize gaps in that research, proposing focuses for future research studies. Findings determined that little research has been done to examine LGBTQIA+ inclusive school library services for youth. Also revealed was a monolithic approach to the discussion of LGBTQIA+ identities and expressions. More research in this area and the employment of diverse methodologies to uncover a detailed and expansive picture of what LGBTQIA+ inclusive service means are desperately needed.
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- 2023
105. In Need of a Research Base: Evidence-Based Reading Interventions for Elementary Students with Overlapping EBD and LD
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Burke, Mack D., Boon, Richard T., Bowman-Perrott, Lisa, and Hatton, Heather
- Abstract
Students with or at-risk of emotional/behavioral disorders (EBD) often have reading difficulties and/or undiagnosed learning disabilities (LD). Reading challenges among this group of children and youth often exacerbate associated emotional and/or behavioral problems. This systematic review and quantitative synthesis yielded seven studies focused on improving the reading outcomes of students with or at-risk of EBD at the elementary school level. Summarized are participant and reading intervention characteristics across the seven studies. Effect sizes were calculated for each study, and results are reported for both academic and behavioral outcome measures. Implications for research and practice are discussed.
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- 2023
106. Carbon emissions from the 2023 Canadian wildfires
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Byrne, Brendan, Liu, Junjie, Bowman, Kevin W., Pascolini-Campbell, Madeleine, Chatterjee, Abhishek, Pandey, Sudhanshu, Miyazaki, Kazuyuki, van der Werf, Guido R., Wunch, Debra, Wennberg, Paul O., Roehl, Coleen M., and Sinha, Saptarshi
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- 2024
- Full Text
- View/download PDF
107. A physics-informed kernel approach to learning the operator for parametric PDEs
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Kurz, J., Bowman, B., Seman, M., Oian, C., and Khan, T.
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- 2024
- Full Text
- View/download PDF
108. Positive-feedback organic light-emitting diodes and upconverters
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Lampande, Raju, DesOrmeaux, Jon-Paul S., Pizano, Adrian, Schrecengost, Jonathon R., Cawthorn, Robert, Bowman, Hunter, Grede, Alex, Guler, Urcan, Hamer, John W., and Giebink, Noel C.
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- 2024
- Full Text
- View/download PDF
109. Efficacy of a Cognitive-Behavioral Anxiety Management Program Integrated Within a Reading Intervention
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Grills, Amie E., Vaughn, Sharon, Bowman, Chelsey, Capin, Philip, Fall, Anna-Mari, Roberts, Greg, and Barnes, Emily D.
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- 2024
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110. Strategically Diverse: An Intersectional Analysis of Enrollments at U.S. Law Schools
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Bowman, Nicholas A., Fernandez, Frank, Fenton-Miller, Solomon, and Stroup, Nicholas R.
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- 2024
- Full Text
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111. Imaging techniques for diagnosing and managing Peyronie disease
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Pradeep, Aishwarya, Alexander, Lauren F., Padilla-Maldonado, Gary W., Taylor, L. Ian, Bowman, Andrew W., Broderick, Gregory A., and Cernigliaro, Joseph G.
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- 2024
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112. Increasing frequency and intensity of the most extreme wildfires on Earth
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Cunningham, Calum X., Williamson, Grant J., and Bowman, David M. J. S.
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- 2024
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113. Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity
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Schwede, Matthew, Jahn, Katharina, Kuipers, Jack, Miles, Linde A., Bowman, Robert L., Robinson, Troy, Furudate, Ken, Uryu, Hidetaka, Tanaka, Tomoyuki, Sasaki, Yuya, Ediriwickrema, Asiri, Benard, Brooks, Gentles, Andrew J., Levine, Ross, Beerenwinkel, Niko, Takahashi, Koichi, and Majeti, Ravindra
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- 2024
- Full Text
- View/download PDF
114. The wrap up
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Bowman, Sarah and Lee-Archer, Paul
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- 2024
115. Effect of detachment on Magnum-PSI ELM-like pulses: II. Spectroscopic analysis and role of molecular assisted reactions
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Federici, Fabio, Lipschultz, Bruce, Akkermans, Gijs R. A., Verhaegh, Kevin, Reinke, Matthew L., Chandra, Ray, Bowman, Chris, Classen, Ivo G. J., and Team, the Magnum-PSI
- Subjects
Physics - Plasma Physics - Abstract
The linear plasma machine Magnum-PSI can replicate similar conditions to those found in a tokamak at the end of the divertor leg. A dedicated capacitor bank, in parallel to the plasma source, can release a sudden burst of energy, leading to a rapid increase in plasma temperature and density, resulting in a transient heat flux increase of half of an order of magnitude, a so called ELM-like pulse. Throughout both the steady state and the pulse, the neutral pressure in the target chamber is then increased, causing the target to transition from an attached to a detached state. In the first paper related to this study\cite{Federici} direct measurements of the plasma properties are used to qualitatively determine the effect of detachment on the ELM-like pulse. This is used to show the importance of molecular assisted reactions. Molecular processes, and especially molecular activated dissociation, are found to be important in the exchange of potential energy with the plasma, while less so in radiating the energy from the ELM-like pulse. At low target chamber pressure, the plasma generated via ionisation during the part of the ELM-like pulse with the higher temperature is more than that produced by the plasma source, a unique case in linear machines. At high target chamber pressure molecular activated recombination contributes up to a third of the total recombination rate, contributing to the reduction of the target particle flux. Some metrics that estimate the energy lost by the plasma per interactions with neutrals, potentially relevant for the portion of the tokamak divertor leg below $\sim10eV$, are then tentatively obtained., Comment: 25 pages, 22 figures. To be published in Nuclear Fusion. This paper is the second related to a single experimental session, the first is: "Effect of detachment on Magnum-PSI ELM-like pulses: I. Direct observations and qualitative results", to be published in Nuclear Fusion
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- 2023
116. Observational mapping of the mass discrepancy in eclipsing binaries: Selection of the sample and its photometric and spectroscopic properties
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Tkachenko, A., Pavlovski, K., Serebriakova, N., Bowman, D. M., IJspeert, L., Gebruers, S., and Southworth, J.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
Abridged. Eclipsing spectroscopic double-lined binaries are the prime source of precise and accurate measurements of masses and radii of stars. These measurements provide a stringent test of models of stellar evolution that are persistently reported to contain major shortcomings. The mass discrepancy observed for the eclipsing spectroscopic double-lined binaries is one of the manifestations of shortcomings in stellar evolution models. Our ultimate goal is to provide an observational mapping of the mass discrepancy and propose a recipe for its solution. We initiate a spectroscopic monitoring campaign of 573 candidate eclipsing binaries of which 83 are analysed in this work with the methods of least-squares deconvolution and spectral disentangling. TESS light curves are used to provide photometric classification of the systems according to the type of their intrinsic variability. We confirm 69 systems as either spectroscopic binaries or higher-order multiple systems. Twelve stars are classified as single and two more objects are found at the interface of their line profile variability being interpreted as due to binarity and intrinsic variability of the star. Moreover, 20 eclipsing binaries are found to contain at least one component that exhibits stellar oscillations. The sample presented in this work contains both detached and semi-detached systems and covers a range in the effective temperature and mass of the star of Teff = [7000,30000] K and M = [1.5,15] M_Sun, respectively. We conclude an appreciable capability of the spectral disentangling method to deliver precise and accurate spectroscopic orbital elements from as few as 6-8 orbital phase-resolved spectroscopic observations. Orbital solutions obtained this way are accurate enough to deliver age estimates with accuracy of 10% or better, an important resource for calibration of stellar evolution models., Comment: 18 pages with appendices, 5 figures. Accepted for publication in A&A
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- 2023
117. Symmetry Enforced Fermi Surface Degeneracies Observed in Time-Reversal Symmetry-Breaking Superconductor LaNiGa$_2$
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Staab, Matthew, Prater, Robert, Sreedhar, Sudheer, Byland, Journey, Mann, Eliana, Zackaria, Davis, Shi, Yunshu, Bowman, Henry J., Stephens, Andrew L., Jung, Myung-Chul, Botana, Antia S., Pickett, Warren E., Taufour, Valentin, and Vishik, Inna
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Condensed Matter - Superconductivity - Abstract
LaNiGa$_2$ is superconductor that breaks time-reversal symmetry in the superconducting state without any known nearby magnetism. Recently, single crystals of LaNiGa$_2$ have been synthesized, revealing a nonsymmorphic Cmcm space group. Here, we report measurements of the electronic structure of LaNiGa$_2$ throughout the three-dimensional Brillouin zone (BZ) using angle-resolved photoemission spectroscopy (ARPES). Our findings show broad consistency with density functional theory (DFT) calculations and provide evidence for degeneracies in the electronic structure that are predicted from the space group. The calculations also predict four Fermi surfaces which cross the purported nodal plane and should therefore form two degenerate pairs. We report evidence for those predicted symmetry enforced degeneracies as well as accidental near degeneracies throughout the BZ. These degeneracies and near-degeneracies may play a role in the pairing mechanism of LaNiGa$_2$. Our results provide insight into the interplay between structure, Fermiology, and superconductivity in unconventional superconductors with nonsymmorphic space group., Comment: Main: 8 pages, 6 figures. SI: 6 pages, 8 figures
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- 2023
118. matvis: A matrix-based visibility simulator for fast forward modelling of many-element 21 cm arrays
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Kittiwisit, Piyanat, Murray, Steven G., Garsden, Hugh, Bull, Philip, Cain, Christopher, Parsons, Aaron R., Sipple, Jackson, Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Berkhout, Lindsay M., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Burba, Jacob, Carey, Steven, Carilli, Chris L., Chen, Kai-Feng, Cheng, Carina, Choudhuri, Samir, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Dynes, Scott, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Gehlot, Bharat Kumar, Ghosh, Abhik, Glendenning, Brian, Gorce, Adelie, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Huang, Tian, Jacobs, Daniel C., Josaitis, Alec, Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kim, Honggeun, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, Ma, Yin-Zhe, MacMahon, David H. E., Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Neben, Abraham R., Nikolic, Bojan, Nunhokee, Chuneeta Devi, Nuwegeld, Hans, Pascua, Robert, Patra, Nipanjana, Pieterse, Samantha, Qin, Yuxiang, Rath, Eleanor, Razavi-Ghods, Nima, Riley, Daniel, Robnett, James, Rosie, Kathryn, Santos, Mario G., Sims, Peter, Singh, Saurabh, Storer, Dara, Swarts, Hilton, Tan, Jianrong, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., Xu, Zhilei, and Zheng, Haoxuan
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Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Detection of the faint 21 cm line emission from the Cosmic Dawn and Epoch of Reionisation will require not only exquisite control over instrumental calibration and systematics to achieve the necessary dynamic range of observations but also validation of analysis techniques to demonstrate their statistical properties and signal loss characteristics. A key ingredient in achieving this is the ability to perform high-fidelity simulations of the kinds of data that are produced by the large, many-element, radio interferometric arrays that have been purpose-built for these studies. The large scale of these arrays presents a computational challenge, as one must simulate a detailed sky and instrumental model across many hundreds of frequency channels, thousands of time samples, and tens of thousands of baselines for arrays with hundreds of antennas. In this paper, we present a fast matrix-based method for simulating radio interferometric measurements (visibilities) at the necessary scale. We achieve this through judicious use of primary beam interpolation, fast approximations for coordinate transforms, and a vectorised outer product to expand per-antenna quantities to per-baseline visibilities, coupled with standard parallelisation techniques. We validate the results of this method, implemented in the publicly-available matvis code, against a high-precision reference simulator, and explore its computational scaling on a variety of problems., Comment: 25 pages, 20 figures, submitted to RAS Techniques and Instruments, matvis is publicly available at https://github.com/HERA-Team/matvis
- Published
- 2023
119. Human Perception-Inspired Grain Segmentation Refinement Using Conditional Random Fields
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Aksoy, Doruk, Xin, Huolin L., Rupert, Timothy J., and Bowman, William J.
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Condensed Matter - Materials Science ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Accurate segmentation of interconnected line networks, such as grain boundaries in polycrystalline material microstructures, poses a significant challenge due to the fragmented masks produced by conventional computer vision algorithms, including convolutional neural networks. These algorithms struggle with thin masks, often necessitating intricate post-processing for effective contour closure and continuity. Addressing this issue, this paper introduces a fast, high-fidelity post-processing technique, leveraging domain knowledge about grain boundary connectivity and employing conditional random fields and perceptual grouping rules. This approach significantly enhances segmentation mask accuracy, achieving a 79% segment identification accuracy in validation with a U-Net model on electron microscopy images of a polycrystalline oxide. Additionally, a novel grain alignment metric is introduced, showing a 51% improvement in grain alignment, providing a more detailed assessment of segmentation performance for complex microstructures. This method not only enables rapid and accurate segmentation but also facilitates an unprecedented level of data analysis, significantly improving the statistical representation of grain boundary networks, making it suitable for a range of disciplines where precise segmentation of interconnected line networks is essential.
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- 2023
120. Making waves in massive star asteroseismology
- Author
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Bowman, Dominic M.
- Subjects
Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Massive stars play a major role not only in stellar evolution but also galactic evolution theory. This is because of their dynamical interaction with binary companions, and because their strong winds and explosive deaths as supernovae provide chemical, radiative and kinematic feedback to their environments. Yet this feedback strongly depends on the physics of the supernova progenitor star. It is only in recent decades that asteroseismology - the study of stellar pulsations - has developed the necessary tools to a high level of sophistication to become a prime method at the forefront of astronomical research for constraining the physical processes at work within stellar interiors. For example, precise and accurate asteroseismic constraints on interior rotation, magnetic field strength and geometry, mixing and angular momentum transport processes of massive stars are becoming increasingly available across a wide range of masses. Moreover, ongoing large-scale time-series photometric surveys with space telescopes have revealed a large diversity in the variability of massive stars, including widespread coherent pulsations across a large range in mass and age, and the discovery of ubiquitous stochastic low-frequency (SLF) variability in their light curves. In this invited review, I discuss the progress made in understanding the physical processes at work within massive star interiors thanks to modern asteroseismic techniques, and conclude with a future outlook., Comment: Author accepted version of Invited Review for 2023 Astronomy Awardees Prize Collection of Astrophysics and Space Science journal
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- 2023
121. TESS Cycle 2 observations of roAp stars with 2-min cadence data
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Holdsworth, D. L., Cunha, M. S., Lares-Martiz, M., Kurtz, D. W., Antoci, V., Forteza, S. Barceló, De Cat, P., Derekas, A., Kayhan, C., Ozuyar, D., Skarka, M., Hey, D. R., Shi, F., Bowman, D. M., Kobzar, O., Gómez, A. Ayala, Bognár, Zs., Buzasi, D. L., Ebadi, M., Fox-Machado, L., Hernández, A. García, Ghasemi, H., Guzik, J. A., Handberg, R., Handler, G., Hasanzadeh, A., Jayaraman, R., Khalack, V., Kochukhov, O., Lovekin, C. C., Mikołajczyk, P., Mkrtichian, D., Murphy, S. J., Niemczura, E., Olafsson, B. G., Pascual-Granado, J., Paunzen, E., Posiłek, N., Safari, A. Ramón-Ballesta H., Samadi-Ghadim, A., Smalley, B., Sódor, Á., Stateva, I., Suárez, J. C., Szabó, R., Wu, T., Ziaali, E., Zong, W., and Seager, S.
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Astrophysics - Solar and Stellar Astrophysics - Abstract
We present the results of a systematic search of the Transiting Exoplanet Survey Satellite (TESS) 2-min cadence data for new rapidly oscillating Ap (roAp) stars observed during the Cycle 2 phase of its mission. We find seven new roAp stars previously unreported as such and present the analysis of a further 25 roAp stars that are already known. Three of the new stars show multiperiodic pulsations, while all new members are rotationally variable stars, leading to almost 70 per cent (22) of the roAp stars presented being $\alpha^2$ CVn-type variable stars. We show that targeted observations of known chemically peculiar stars are likely to overlook many new roAp stars, and demonstrate that multi-epoch observations are necessary to see pulsational behaviour changes. We find a lack of roAp stars close to the blue edge of the theoretical roAp instability strip, and reaffirm that mode instability is observed more frequently with precise, space-based observations. In addition to the Cycle 2 observations, we analyse TESS data for all known roAp stars. This amounts to 18 further roAp stars observed by TESS. Finally, we list six known roAp stars that TESS is yet to observe. We deduce that the incidence of roAp stars amongst the Ap star population is just 5.5 per cent, raising fundamental questions about the conditions required to excite pulsations in Ap stars. This work, coupled with our previous work on roAp stars in Cycle 1 observations, presents the most comprehensive, homogeneous study of the roAp stars in the TESS nominal mission, with a collection of 112 confirmed roAp stars in total., Comment: Accepted for publication in MNRAS. 32 Pages, 2 Tables, 77 Figures
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- 2023
122. Bayesian estimation of cross-coupling and reflection systematics in 21cm array visibility data
- Author
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Murphy, Geoff G., Bull, Philip, Santos, Mario G., Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee, Bowman, Judd D., Bradley, Richard F., Burba, Jacob, Cain, Christopher, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Dillon, Joshua S., Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hazelton, Bryna J., Hewitt, Jacqueline N., Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kern, Nicholas S., Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Liu, Adrian, Loots, Anita, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Martinot, Zachary E., Mesinger, Andrei, Molewa, Mathakane, Morales, Miguel F., Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Sipple, Jackson, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan
- Subjects
Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
Observations with radio arrays that target the 21-cm signal originating from the early Universe suffer from a variety of systematic effects. An important class of these are reflections and spurious couplings between antennas. We apply a Hamiltonian Monte Carlo sampler to the modelling and mitigation of these systematics in simulated Hydrogen Epoch of Reionisation Array (HERA) data. This method allows us to form statistical uncertainty estimates for both our models and the recovered visibilities, which is an important ingredient in establishing robust upper limits on the Epoch of Reionisation (EoR) power spectrum. In cases where the noise is large compared to the EoR signal, this approach can constrain the systematics well enough to mitigate them down to the noise level for both systematics studied. Where the noise is smaller than the EoR, our modelling can mitigate the majority of the reflections with there being only a minor level of residual systematics, while cross-coupling sees essentially complete mitigation. Our approach performs similarly to existing filtering/fitting techniques used in the HERA pipeline, but with the added benefit of rigorously propagating uncertainties. In all cases it does not significantly attenuate the underlying signal., Comment: 19 pages, 14 figures, submitted to MNRAS
- Published
- 2023
123. GPQA: A Graduate-Level Google-Proof Q&A Benchmark
- Author
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Rein, David, Hou, Betty Li, Stickland, Asa Cooper, Petty, Jackson, Pang, Richard Yuanzhe, Dirani, Julien, Michael, Julian, and Bowman, Samuel R.
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Computer Science - Artificial Intelligence ,Computer Science - Computation and Language - Abstract
We present GPQA, a challenging dataset of 448 multiple-choice questions written by domain experts in biology, physics, and chemistry. We ensure that the questions are high-quality and extremely difficult: experts who have or are pursuing PhDs in the corresponding domains reach 65% accuracy (74% when discounting clear mistakes the experts identified in retrospect), while highly skilled non-expert validators only reach 34% accuracy, despite spending on average over 30 minutes with unrestricted access to the web (i.e., the questions are "Google-proof"). The questions are also difficult for state-of-the-art AI systems, with our strongest GPT-4 based baseline achieving 39% accuracy. If we are to use future AI systems to help us answer very hard questions, for example, when developing new scientific knowledge, we need to develop scalable oversight methods that enable humans to supervise their outputs, which may be difficult even if the supervisors are themselves skilled and knowledgeable. The difficulty of GPQA both for skilled non-experts and frontier AI systems should enable realistic scalable oversight experiments, which we hope can help devise ways for human experts to reliably get truthful information from AI systems that surpass human capabilities., Comment: 28 pages, 5 figures, 7 tables
- Published
- 2023
124. Direct Optimal Mapping Image Power Spectrum and its Window Functions
- Author
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Xu, Zhilei, Kim, Honggeun, Hewitt, Jacqueline N., Chen, Kai-Feng, Kern, Nicholas S., Rath, Eleanor, Byrne, Ruby, Gorce, Adélie, Pascua, Robert, Martinot, Zachary E., Dillon, Joshua S., Hazelton, Bryna J., Liu, Adrian, Morales, Miguel F., Abdurashidova, Zara, Adams, Tyrone, Aguirre, James E., Alexander, Paul, Ali, Zaki S., Baartman, Rushelle, Balfour, Yanga, Beardsley, Adam P., Bernardi, Gianni, Billings, Tashalee S., Bowman, Judd D., Bradley, Richard F., Bull, Philip, Burba, Jacob, Carey, Steven, Carilli, Chris L., Cheng, Carina, DeBoer, David R., Acedo, Eloy de Lera, Dexter, Matt, Eksteen, Nico, Ely, John, Ewall-Wice, Aaron, Fagnoni, Nicolas, Fritz, Randall, Furlanetto, Steven R., Gale-Sides, Kingsley, Glendenning, Brian, Gorthi, Deepthi, Greig, Bradley, Grobbelaar, Jasper, Halday, Ziyaad, Hickish, Jack, Jacobs, Daniel C., Julius, Austin, Kariseb, MacCalvin, Kerrigan, Joshua, Kittiwisit, Piyanat, Kohn, Saul A., Kolopanis, Matthew, Lanman, Adam, La Plante, Paul, Loots, Anita, MacMahon, David Harold Edward, Malan, Lourence, Malgas, Cresshim, Malgas, Keith, Marero, Bradley, Mesinger, Andrei, Molewa, Mathakane, Mosiane, Tshegofalang, Murray, Steven G., Neben, Abraham R., Nikolic, Bojan, Nuwegeld, Hans, Parsons, Aaron R., Patra, Nipanjana, Pieterse, Samantha, Razavi-Ghods, Nima, Robnett, James, Rosie, Kathryn, Sims, Peter, Smith, Craig, Swarts, Hilton, Thyagarajan, Nithyanandan, van Wyngaarden, Pieter, Williams, Peter K. G., and Zheng, Haoxuan
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Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Cosmology and Nongalactic Astrophysics - Abstract
The key to detecting neutral hydrogen during the epoch of reionization (EoR) is to separate the cosmological signal from the dominating foreground radiation. We developed direct optimal mapping (DOM) to map interferometric visibilities; it contains only linear operations, with full knowledge of point spread functions from visibilities to images. Here, we demonstrate a fast Fourier transform-based image power spectrum and its window functions computed from the DOM images. We use noiseless simulation, based on the Hydrogen Epoch of Reionization Array Phase I configuration, to study the image power spectrum properties. The window functions show $<10^{-11}$ of the integrated power leaks from the foreground-dominated region into the EoR window; the 2D and 1D power spectra also verify the separation between the foregrounds and the EoR., Comment: Published in ApJ
- Published
- 2023
125. Debate Helps Supervise Unreliable Experts
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Michael, Julian, Mahdi, Salsabila, Rein, David, Petty, Jackson, Dirani, Julien, Padmakumar, Vishakh, and Bowman, Samuel R.
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Computer Science - Artificial Intelligence ,Computer Science - Computation and Language ,I.2.0 - Abstract
As AI systems are used to answer more difficult questions and potentially help create new knowledge, judging the truthfulness of their outputs becomes more difficult and more important. How can we supervise unreliable experts, which have access to the truth but may not accurately report it, to give answers that are systematically true and don't just superficially seem true, when the supervisor can't tell the difference between the two on their own? In this work, we show that debate between two unreliable experts can help a non-expert judge more reliably identify the truth. We collect a dataset of human-written debates on hard reading comprehension questions where the judge has not read the source passage, only ever seeing expert arguments and short quotes selectively revealed by 'expert' debaters who have access to the passage. In our debates, one expert argues for the correct answer, and the other for an incorrect answer. Comparing debate to a baseline we call consultancy, where a single expert argues for only one answer which is correct half of the time, we find that debate performs significantly better, with 84% judge accuracy compared to consultancy's 74%. Debates are also more efficient, being 68% of the length of consultancies. By comparing human to AI debaters, we find evidence that with more skilled (in this case, human) debaters, the performance of debate goes up but the performance of consultancy goes down. Our error analysis also supports this trend, with 46% of errors in human debate attributable to mistakes by the honest debater (which should go away with increased skill); whereas 52% of errors in human consultancy are due to debaters obfuscating the relevant evidence from the judge (which should become worse with increased skill). Overall, these results show that debate is a promising approach for supervising increasingly capable but potentially unreliable AI systems., Comment: 84 pages, 13 footnotes, 5 figures, 4 tables, 28 debate transcripts; data and code at https://github.com/julianmichael/debate/tree/2023-nyu-experiments
- Published
- 2023
126. Using Old Laboratory Equipment with Modern Web-of-Things Standards: a Smart Laboratory with LabThings Retro
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McDermott, Samuel, Kotar, Jurij, Collins, Joel, Mancini, Leonardo, Bowman, Richard, and Cicuta, Pietro
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Physics - Instrumentation and Detectors - Abstract
There has been an increasing, and welcome, Open Hardware trend towards science teams building and sharing their designs for new instruments. These devices, often built upon low-cost microprocessors and micro-controllers, can be readily connected to enable complex, automated, and smart experiments. When designed to use open communication web standards, devices from different laboratories and manufacturers can be controlled using a single protocol, and even communicate with each other. However, science labs still have a majority of old, perfectly functional, equipment which tends to use older, and sometimes proprietary, standards for communications. In order to encourage the continued and integrated use of this equipment in modern automated experiments, we develop and demonstrate LabThings Retro. This allows us to retrofit old instruments to use modern web-of-things standards, which we demonstrate with closed-loop feedback involving an optical microscope, digital imaging and fluid pumping., Comment: Supplementary material - video demonstration available at https://zenodo.org/doi/10.5281/zenodo.10123735
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- 2023
127. The partition algebra and the plethysm coefficients II: ramified plethysm
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Bowman, Chris, Paget, Rowena, and Wildon, Mark
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Mathematics - Representation Theory ,Mathematics - Combinatorics - Abstract
The plethysm coefficient $p(\nu, \mu, \lambda)$ is the multiplicity of the Schur function $s_\lambda$ in the plethysm product $s_\nu \circ s_\mu$. In this paper we use Schur--Weyl duality between wreath products of symmetric groups and the ramified partition algebra to interpret an arbitrary plethysm coefficient as the multiplicity of an appropriate composition factor in the restriction of a module for the ramified partition algebra to the partition algebra. This result implies new stability phenomenon for plethysm coefficients when the first parts of $\nu$, $\mu$ and $\lambda$ are all large. In particular, it gives the first positive formula in the case when $\nu$ and $\lambda$ are arbitrary and $\mu$ has one part. Corollaries include new explicit positive formulae and combinatorial interpretations for the plethysm coefficients $p((n-b,b), (m), (mn-r,r))$, and $p((n-b,1^b), (m), (mn-r,r))$ when $m$ and $n$ are large.
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- 2023
128. Gap structure of the non-symmorphic superconductor LaNiGa2 probed by muSR
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Sundar, Shyam, Yakovlev, M., Azari, N., Abedi, M., Broun, D. M., Ozdemir, H. U., Dunsiger, S. R., Zackaria, D., Bowman, H., Klavins, P., Shi, Y., Taufour, V., and Sonier, J. E.
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Condensed Matter - Superconductivity - Abstract
We report muon spin rotation (muSR) measurements of the temperature dependence of the absolute value of the magnetic penetration depth and the magnetic field dependence of the vortex core size in the mixed state of the non-symmorphic superconductor LaNiGa2. The temperature dependence of the normalized superfluid density is shown to be well described by a two-band model with strong interband coupling. Consistent with a strong coupling of the superconducting condensates in two different bands, we show that the field dependence of the vortex core size resembles that of a single-band superconductor. Our results lend support to the proposal that LaNiGa2 is a fully-gapped, internally antisymmetric nonunitary spin-triplet superconductor., Comment: 11 pages, 7 figures
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- 2023
129. Predicting recovery following stroke: deep learning, multimodal data and feature selection using explainable AI
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White, Adam, Saranti, Margarita, Garcez, Artur d'Avila, Hope, Thomas M. H., Price, Cathy J., and Bowman, Howard
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Computer Science - Artificial Intelligence ,Computer Science - Computers and Society ,Computer Science - Machine Learning - Abstract
Machine learning offers great potential for automated prediction of post-stroke symptoms and their response to rehabilitation. Major challenges for this endeavour include the very high dimensionality of neuroimaging data, the relatively small size of the datasets available for learning, and how to effectively combine neuroimaging and tabular data (e.g. demographic information and clinical characteristics). This paper evaluates several solutions based on two strategies. The first is to use 2D images that summarise MRI scans. The second is to select key features that improve classification accuracy. Additionally, we introduce the novel approach of training a convolutional neural network (CNN) on images that combine regions-of-interest extracted from MRIs, with symbolic representations of tabular data. We evaluate a series of CNN architectures (both 2D and a 3D) that are trained on different representations of MRI and tabular data, to predict whether a composite measure of post-stroke spoken picture description ability is in the aphasic or non-aphasic range. MRI and tabular data were acquired from 758 English speaking stroke survivors who participated in the PLORAS study. The classification accuracy for a baseline logistic regression was 0.678 for lesion size alone, rising to 0.757 and 0.813 when initial symptom severity and recovery time were successively added. The highest classification accuracy 0.854 was observed when 8 regions-of-interest was extracted from each MRI scan and combined with lesion size, initial severity and recovery time in a 2D Residual Neural Network.Our findings demonstrate how imaging and tabular data can be combined for high post-stroke classification accuracy, even when the dataset is small in machine learning terms. We conclude by proposing how the current models could be improved to achieve even higher levels of accuracy using images from hospital scanners.
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- 2023
130. Towards Understanding Sycophancy in Language Models
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Sharma, Mrinank, Tong, Meg, Korbak, Tomasz, Duvenaud, David, Askell, Amanda, Bowman, Samuel R., Cheng, Newton, Durmus, Esin, Hatfield-Dodds, Zac, Johnston, Scott R., Kravec, Shauna, Maxwell, Timothy, McCandlish, Sam, Ndousse, Kamal, Rausch, Oliver, Schiefer, Nicholas, Yan, Da, Zhang, Miranda, and Perez, Ethan
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Statistics - Machine Learning ,I.2.6 - Abstract
Human feedback is commonly utilized to finetune AI assistants. But human feedback may also encourage model responses that match user beliefs over truthful ones, a behaviour known as sycophancy. We investigate the prevalence of sycophancy in models whose finetuning procedure made use of human feedback, and the potential role of human preference judgments in such behavior. We first demonstrate that five state-of-the-art AI assistants consistently exhibit sycophancy across four varied free-form text-generation tasks. To understand if human preferences drive this broadly observed behavior, we analyze existing human preference data. We find that when a response matches a user's views, it is more likely to be preferred. Moreover, both humans and preference models (PMs) prefer convincingly-written sycophantic responses over correct ones a non-negligible fraction of the time. Optimizing model outputs against PMs also sometimes sacrifices truthfulness in favor of sycophancy. Overall, our results indicate that sycophancy is a general behavior of state-of-the-art AI assistants, likely driven in part by human preference judgments favoring sycophantic responses., Comment: 32 pages, 20 figures
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- 2023
131. Detection of Accretion Shelves Out to the Virial Radius of a Low-Mass Galaxy with JWST
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Conroy, Charlie, Johnson, Benjamin D., van Dokkum, Pieter, Deason, Alis, Tacchella, Sandro, Belli, Sirio, Bowman, William P., Naidu, Rohan P., Park, Minjung, Abraham, Roberto, and Emami, Razieh
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Astrophysics - Astrophysics of Galaxies - Abstract
We report the serendipitous discovery of an extended stellar halo surrounding the low-mass galaxy Ark 227 ($M_\ast=5\times10^9 M_\odot$; d=35 Mpc) in deep JWST NIRCam imaging from the Blue Jay Survey. The F200W-F444W color provides robust star-galaxy separation, enabling the identification of stars at very low density. By combining resolved stars at large galactocentric distances with diffuse emission from NIRCam and Dragonfly imaging at smaller distances, we trace the surface brightness and color profiles of this galaxy over the entire extent of its predicted dark matter halo, from 0.1-100 kpc. Controlled N-body simulations have predicted that minor mergers create "accretion shelves" in the surface brightness profile at large radius. We observe such a feature in Ark 227 at 10-20 kpc, which, according to models, could be caused by a merger with total mass ratio 1:10. The metallicity declines over this radial range, further supporting the minor merger scenario. There is tentative evidence of a second shelf at $\mu_V\approx 35$ mag arcsec$^{-2}$ extending from 50-100 kpc, along with a corresponding drop in metallicity. The stellar mass in this outermost envelope is $\approx10^7M_\odot$. These results suggest that Ark 227 experienced multiple mergers with a spectrum of lower-mass galaxies -- a scenario that is broadly consistent with the hierarchical growth of structure in a cold dark matter-dominated universe. Finally, we identify an ultra-faint dwarf associated with Ark 227 with $M_\ast\approx10^5 M_\odot$ and $\mu_{V,e}=28.1$ mag arcsec$^{-2}$, demonstrating that JWST is capable of detecting very low-mass dwarfs to distances of at least ~30 Mpc., Comment: 10 pages, 9 figures, submitted to ApJ
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- 2023
132. Spatially resolved photoluminescence analysis of Se passivation and defect formation in CdSe$_{x}$Te$_{1-x}$ thin films
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Bowman, Alan R, Leaver, Jacob J, Frohna, Kyle, Stranks, Samuel D, Tagliabue, Giulia, and Major, Jon D
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Condensed Matter - Materials Science ,Physics - Applied Physics ,Physics - Optics - Abstract
CdTe is the most commercially successful thin-film photovoltaic technology to date. The recent development of Se-alloyed CdSe$_{x}$Te$_{1-x}$ layers in CdTe solar cells has led to higher device efficiencies, due to a lowered bandgap improving the photocurrent, improved voltage characteristics and longer carrier lifetimes. Evidence from cross-sectional electron microscopy is widely believed to indicate that Se passivates defects in CdSe$_{x}$Te$_{1-x}$ solar cells, and that this is the reason for better lifetimes and voltages in these devices. Here, we utilise spatially resolved photoluminescence measurements of CdSe$_{x}$Te$_{1-x}$ thin films on glass to study the effects of Se on carrier recombination in the material, isolated from the impact of conductive interfaces and without the need to prepare cross-sections through the samples. We find further evidence to support Se passivation of grain boundaries, but also identify an associated increase in below-bandgap photoluminescence that indicates the presence of Se-enhanced luminescent defects. Our results show that Se treatment, in tandem with Cl passivation, does increase radiative efficiencies. However, the simultaneous enhancement of defects within the grain interiors suggests that although it is overall beneficial, Se incorporation may still ultimately limit the maximum attainable efficiency of CdSe$_{x}$Te$_{1-x}$ solar cells.
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- 2023
133. A Review of Infrasound and Seismic Observations of Sample Return Capsules since the End of the Apollo Era in Anticipation of the OSIRIS-REx Arrival
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Silber, Elizabeth A., Bowman, Daniel C., and Albert, Sarah
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Astrophysics - Earth and Planetary Astrophysics ,Physics - Geophysics - Abstract
Advancements in space exploration and sample return technology present a unique opportunity to leverage sample return capsules (SRCs) towards studying atmospheric entry of meteoroids and asteroids. Specifically engineered for the secure transport of valuable extraterrestrial samples from interplanetary space to Earth, SRCs offer unexpected benefits that reach beyond their intended purpose. As SRCs enter the Earth's atmosphere at hypervelocity, they are analogous to naturally occurring meteoroids and thus, for all intents and purposes, can be considered artificial meteors. Furthermore, SRCs are capable of generating shockwaves upon reaching the lower transitional flow regime, and thus can be detected by strategically positioned geophysical instrumentation. NASA's OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, and Security-Regolith Explorer) SRC is one of only a handful of artificial objects to re-enter the Earth's atmosphere from interplanetary space since the end of the Apollo era and it will provide an unprecedented observational opportunity. This review summarizes past infrasound and seismic observational studies of SRC re-entries since the end of the Apollo era and presents their utility towards the better characterization of meteoroid flight through the atmosphere., Comment: 20 pages, 12 figures
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- 2023
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134. Pathogenesis of Sjögren syndrome
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Dumusc, Alexandre, primary, Nayar, Saba, additional, Fisher, Benjamin A., additional, and Bowman, Simon, additional
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- 2025
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135. Influenza D virus utilizes both 9-O-acetylated N-acetylneuraminic and 9-O-acetylated N-glycolylneuraminic acids as functional entry receptors.
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Liu, Yunpeng, Bowman, Andrew, Martinez-Sobrido, Luis, Parrish, Colin, Melikyan, Gregory, Wang, Dan, Li, Feng, Uprety, Tirth, Yu, Jieshi, Nogales, Aitor, Naveed, Ahsan, Yu, Hai, and Chen, Xi
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CASD1 ,Neu5 ,9Ac2 ,Neu5Gc9Ac ,influenza D ,receptor ,Animals ,Cattle ,Cell Membrane ,Deltainfluenzavirus ,N-Acetylneuraminic Acid ,Neuraminic Acids ,Orthomyxoviridae ,Receptors ,Virus ,Sialic Acids - Abstract
Influenza D virus (IDV) utilizes bovines as a primary reservoir with periodical spillover to other hosts. We have previously demonstrated that IDV binds both 9-O-acetylated N-acetylneuraminic acid (Neu5,9Ac2) and 9-O-acetylated N-glycolylneuraminic acid (Neu5Gc9Ac). Bovines produce both Neu5,9Ac2 and Neu5Gc9Ac, while humans are genetically unable to synthesize Neu5Gc9Ac. 9-O-Acetylation of sialic acids is catalyzed by CASD1 via a covalent acetyl-enzyme intermediate. To characterize the role of Neu5,9Ac2 and Neu5Gc9Ac in IDV infection and determine which form of 9-O-acetylated sialic acids drives IDV entry, we took advantage of a CASD1 knockout (KO) MDCK cell line and carried out feeding experiments using synthetic 9-O-acetyl sialic acids in combination with the single-round and multi-round IDV infection assays. The data from our studies show that (i) CASD1 KO cells are resistant to IDV infection and lack of IDV binding to the cell surface is responsible for the failure of IDV replication; (ii) feeding CASD1 KO cells with Neu5,9Ac2 or Neu5Gc9Ac resulted in a dose-dependent rescue of IDV infectivity; and (iii) diverse IDVs replicated robustly in CASD1 KO cells fed with either Neu5,9Ac2 or Neu5Gc9Ac at a level similar to that in wild-type cells with a functional CASD1. These data demonstrate that IDV can utilize Neu5,9Ac2- or non-human Neu5Gc9Ac-containing glycan receptor for infection. Our findings provide evidence that IDV has acquired the ability to infect and transmit among agricultural animals that are enriched in Neu5Gc9Ac, in addition to posing a zoonotic risk to humans expressing only Neu5,9Ac2.IMPORTANCEInfluenza D virus (IDV) has emerged as a multiple-species-infecting pathogen with bovines as a primary reservoir. Little is known about the functional receptor that drives IDV entry and promotes its cross-species spillover potential among different hosts. Here, we demonstrated that IDV binds exclusively to 9-O-acetylated N-acetylneuraminic acid (Neu5,9Ac2) and non-human 9-O-acetylated N-glycolylneuraminic acid (Neu5Gc9Ac) and utilizes both for entry and infection. This ability in effective engagement of both 9-O-acetylated sialic acids as functional receptors for infection provides an evolutionary advantage to IDV for expanding its host range. This finding also indicates that IDV has the potential to emerge in humans because Neu5,9Ac2 is ubiquitously expressed in human tissues, including lung. Thus, results of our study highlight a need for continued surveillance of IDV in humans, as well as for further investigation of its biology and cross-species transmission mechanism.
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- 2024
136. PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.
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Smith, Louis, Novak, Borna, Osato, Meghan, Bowman, Gregory, and Mobley, David
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Protein Binding ,Ligands ,Proteins ,Entropy ,Protein Conformation ,Thermodynamics ,Binding Sites - Abstract
Obtaining accurate binding free energies from in silico screens has been a long-standing goal for the computational chemistry community. However, accuracy and computational cost are at odds with one another, limiting the utility of methods that perform this type of calculation. Many methods achieve massive scale by explicitly or implicitly assuming that the target protein adopts a single structure, or undergoes limited fluctuations around that structure, to minimize computational cost. Others simulate each protein-ligand complex of interest, accepting lower throughput in exchange for better predictions of binding affinities. Here, we present the PopShift framework for accounting for the ensemble of structures a protein adopts and their relative probabilities. Protein degrees of freedom are enumerated once, and then arbitrarily many molecules can be screened against this ensemble. Specifically, we use Markov state models (MSMs) as a compressed representation of a proteins thermodynamic ensemble. We start with a ligand-free MSM and then calculate how addition of a ligand shifts the populations of each protein conformational state based on the strength of the interaction between that protein conformation and the ligand. In this work we use docking to estimate the affinity between a given protein structure and ligand, but any estimator of binding affinities could be used in the PopShift framework. We test PopShift on the classic benchmark pocket T4 Lysozyme L99A. We find that PopShift is more accurate than common strategies, such as docking to a single structure and traditional ensemble docking─producing results that compare favorably with alchemical binding free energy calculations in terms of RMSE but not correlation─and may have a more favorable computational cost profile in some applications. In addition to predicting binding free energies and ligand poses, PopShift also provides insight into how the probability of different protein structures is shifted upon addition of various concentrations of ligand, providing a platform for predicting affinities and allosteric effects of ligand binding. Therefore, we expect PopShift will be valuable for hit finding and for providing insight into phenomena like allostery.
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- 2024
137. Parental emotionality is related to preschool children’s neural responses to emotional faces
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Xia, Ruohan, Heise, Megan J, and Bowman, Lindsay C
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Biological Psychology ,Psychology ,Behavioral and Social Science ,Clinical Research ,Mental Health ,Pediatric ,Neurosciences ,Basic Behavioral and Social Science ,Mind and Body ,Mental health ,Humans ,Child ,Preschool ,Emotions ,Parents ,Anger ,Fear ,Brain ,Evoked Potentials ,Facial Expression ,emotion perception ,parental emotionality ,event-related potentials ,neural correlates ,children ,Cognitive Sciences ,Experimental Psychology ,Biological psychology ,Clinical and health psychology - Abstract
The ability to accurately decode others' facial expressions is essential for successful social interaction. Previous theories suggest that aspects of parental emotionality-the frequency, persistence and intensity of parents' own emotions-can influence children's emotion perception. Through a combination of mechanisms, parental emotionality may shape how children's brains specialize to respond to emotional expressions, but empirical data are lacking. The present study provides a direct empirical test of the relation between the intensity, persistence and frequency of parents' own emotions and children's neural responses to perceiving emotional expressions. Event-related potentials (ERPs) were recorded as typically developing 3- to 5-year-old children (final Ns = 59 and 50) passively viewed faces expressing different emotional valences (happy, angry and fearful) at full and reduced intensity (100% intense expression and 40% intense expression). We examined relations between parental emotionality and children's mean amplitude ERP N170 and negative central responses. The findings demonstrate a clear relation between parental emotionality and children's neural responses (in the N170 mean amplitude and latency) to emotional expressions and suggest that parents may influence children's emotion-processing neural circuitry.
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- 2024
138. Overcoming resolution attenuation during tilted cryo-EM data collection.
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Aiyer, Sriram, Baldwin, Philip, Tan, Shi, Shan, Zelin, Oh, Juntaek, Mehrani, Atousa, Bowman, Marianne, Louie, Gordon, Passos, Dario, Đorđević-Marquardt, Selena, Mietzsch, Mario, Hull, Joshua, Hoshika, Shuichi, Barad, Benjamin, Grotjahn, Danielle, McKenna, Robert, Agbandje-McKenna, Mavis, Benner, Steven, Noel, Joseph, Wang, Dong, Tan, Yong, and Lyumkis, Dmitry
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Cryoelectron Microscopy ,Anisotropy ,Benchmarking ,Computer Systems ,Data Collection - Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting preferred orientations on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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- 2024
139. Microbial community composition predicts bacterial production across ocean ecosystems.
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Connors, Elizabeth, Dutta, Avishek, Trinh, Rebecca, Erazo, Natalia, Dasarathy, Srishti, Ducklow, Hugh, Weissman, J, Yeh, Yi-Chun, Schofield, Oscar, Steinberg, Deborah, Fuhrman, Jed, and Bowman, Jeff
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bacterial production ,community structure ,microbial ecological function ,random forest regression ,Antarctic Regions ,Bacteria ,Microbiota ,California ,Ecosystem ,Seawater ,Oceans and Seas - Abstract
Microbial ecological functions are an emergent property of community composition. For some ecological functions, this link is strong enough that community composition can be used to estimate the quantity of an ecological function. Here, we apply random forest regression models to compare the predictive performance of community composition and environmental data for bacterial production (BP). Using data from two independent long-term ecological research sites-Palmer LTER in Antarctica and Station SPOT in California-we found that community composition was a strong predictor of BP. The top performing model achieved an R2 of 0.84 and RMSE of 20.2 pmol L-1 hr-1 on independent validation data, outperforming a model based solely on environmental data (R2 = 0.32, RMSE = 51.4 pmol L-1 hr-1). We then operationalized our top performing model, estimating BP for 346 Antarctic samples from 2015 to 2020 for which only community composition data were available. Our predictions resolved spatial trends in BP with significance in the Antarctic (P value = 1 × 10-4) and highlighted important taxa for BP across ocean basins. Our results demonstrate a strong link between microbial community composition and microbial ecosystem function and begin to leverage long-term datasets to construct models of BP based on microbial community composition.
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- 2024
140. Bridging Gaps in Urology Training
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Bowman, Max, Breyer, Benjamin N, and Hampson, Lindsay A
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Public Health ,Biomedical and Clinical Sciences ,Clinical Sciences ,Health Sciences ,Humans ,Urology ,Education ,Medical ,Graduate ,Internship and Residency ,Urologic Diseases ,leadership ,academic training ,residency ,graduate medical education ,Clinical sciences ,Public health - Published
- 2024
141. Early snowmelt advances flowering phenology and disrupts the drivers of pollinator visitation in an alpine ecosystem
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Rose-Person, Annika, Spasojevic, Marko J, Forrester, Chiara, Bowman, William D, Suding, Katharine N, Oldfather, Meagan F, and Rafferty, Nicole E
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Climate Change Impacts and Adaptation ,Agricultural ,Veterinary and Food Sciences ,Biological Sciences ,Ecology ,Environmental Sciences ,Crop and Pasture Production ,Climate change ,Flowering time ,Plant-pollinator interactions ,Topography - Abstract
Abstract: Climate change is altering interactions among plants and pollinators. In alpine ecosystems, where snowmelt timing is a key driver of phenology, earlier snowmelt may generate shifts in plant and pollinator phenology that vary across the landscape, potentially disrupting interactions. Here we ask how experimental advancement of snowmelt timing in a topographically heterogeneous alpine-subalpine landscape impacts flowering, insect pollinator visitation, and pathways connecting key predictors of plant-pollinator interaction. Snowmelt was advanced by an average of 13.5 days in three sites via the application of black sand over snow in manipulated plots, which were paired with control plots. For each forb species, we documented flowering onset and counted flowers throughout the season. We also performed pollinator observations to measure visitation rates. The majority (79.3%) of flower visits were made by dipteran insects. We found that plants flowered earlier in advanced snowmelt plots, with the largest advances in later-flowering species, but flowering duration and visitation rate did not differ between advanced snowmelt and control plots. Using piecewise structural equation models, we assessed the interactive effects of topography on snowmelt timing, flowering phenology, floral abundance, and pollinator visitation. We found that these factors interacted to predict visitation rate in control plots. However, in plots with experimentally advanced snowmelt, none of these predictors explained a significant amount of variation in visitation rate, indicating that different predictors are needed to understand the processes that directly influence pollinator visitation to flowers under future climate conditions. Our findings demonstrate that climate change-induced early snowmelt may fundamentally disrupt the predictive relationships among abiotic and biotic drivers of plant-pollinator interactions in subalpine-alpine environments.
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- 2024
142. Using low volume eDNA methods to sample pelagic marine animal assemblages.
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Dan, Michelle E, Portner, Elan J, Bowman, Jeff S, Semmens, Brice X, Owens, Sarah M, Greenwald, Stephanie M, and Choy, C Anela
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Animals ,Fishes ,Invertebrates ,Zooplankton ,Ecosystem ,Biodiversity ,Seawater ,Aquatic Organisms ,DNA ,Environmental ,General Science & Technology - Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
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- 2024
143. Topical netarsudil for the treatment of primary corneal endothelial degeneration in dogs
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Casanova, M Isabel, Park, Sangwan, Mayes, Melaney A, Roszak, Karolina, Ferneding, Michelle, Echeverria, Nayeli, Bowman, Morgan AW, Michalak, Sarah R, Ardon, Monica, Wong, Sydni, Le, Sophie M, Daley, Nicole, Leonard, Brian C, Good, Kathryn L, Li, Jennifer Y, and Thomasy, Sara M
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Biomedical and Clinical Sciences ,Ophthalmology and Optometry ,Eye Disease and Disorders of Vision ,Evaluation of treatments and therapeutic interventions ,6.1 Pharmaceuticals ,Eye ,Animals ,Dogs ,Benzoates ,beta-Alanine ,Corneal Dystrophies ,Hereditary ,Corneal Edema ,Disease Progression ,Isoquinolines ,Ophthalmic Solutions ,Prospective Studies ,Sulfonamides - Abstract
This study evaluated the tolerability and efficacy of the topical rho-kinase inhibitor netarsudil for canine primary corneal endothelial degeneration (PCED). Twenty-six eyes of 21 client-owned dogs with PCED were enrolled in a prospective, randomized, vehicle control clinical trial and received topical netarsudil 0.02% (Rhopressa®) or vehicle control twice daily (BID) for the first 4 months. Then, all patients received netarsudil for the next 4 or 8 months. Complete ophthalmic examination, ultrasonic pachymetry, Fourier-domain optical coherence tomography, and in vivo confocal microscopy were performed at baseline and 1, 2, 4, 6, 8 and 12 months. Effect of netarsudil on central corneal thickness (CCT), percentage of cornea with edema, and endothelial cell density (ECD) were evaluated by repeated measures ANOVA. Kaplan-Meier curves and log-rank test were used to compare corneal edema and clinical progression of eyes in netarsudil versus vehicle control groups. All dogs developed conjunctival hyperemia in at least one eye while receiving netarsudil. Unilateral transient reticulated intraepithelial bullae and stromal hemorrhage were observed respectively in 2 dogs in the netarsudil group. Two dogs showed persistently decreased tear production while receiving netarsudil, requiring topical immunomodulatory treatment. No significant differences in CCT, ECD, corneal edema or clinical progression were observed between netarsudil or vehicle treated eyes. When comparing efficacy of topical netarsudil BID and topical ripasudil 0.4% administered four times daily from our previous study, dogs receiving ripasudil had significantly less progression than those receiving netarsudil.
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- 2024
144. Emotional auditory stimuli influence step initiation in Parkinson’s disease with freezing of gait
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Lencioni, Tiziana, Meloni, Mario, Bowman, Thomas, Carpinella, Ilaria, Gower, Valerio, Mezzarobba, Susanna, Cosentino, Carola, Bonassi, Gaia, Putzolu, Martina, Ferrarin, Maurizio, Avanzino, Laura, and Pelosin, Elisa
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- 2024
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145. A cross-sectional study of stigma towards opioid users among rural law enforcement and community members in tennessee
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Stone, Kahler W., Chesak, Gabrielle M., Bowman, Angela S., Ayalon, Michael, and Chafin, Cynthia
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- 2024
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146. Effects of aspirin and omega-3 fatty acids on composite and subdomain scores from the NEI-VFQ-25 questionnaire: the ASCEND-Eye randomized controlled trial
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Sammons, Emily L., Buck, Georgina, Bowman, Louise J., Stevens, William M., Hammami, Imen, Parish, Sarah, and Armitage, Jane
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- 2024
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147. On the nature of hydrogen bonding in the H2S dimer
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Jäger, Svenja, Khatri, Jai, Meyer, Philipp, Henkel, Stefan, Schwaab, Gerhard, Nandi, Apurba, Pandey, Priyanka, Barlow, Kayleigh R., Perkins, Morgan A., Tschumper, Gregory S., Bowman, Joel M., van der Avoird, Ad, and Havenith, Martina
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- 2024
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148. Phospho-signaling couples polar asymmetry and proteolysis within a membraneless microdomain in Caulobacter crescentus
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Ahmed, Yasin M., Brown, Logan M., Varga, Krisztina, and Bowman, Grant R.
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- 2024
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149. Innate immune control of influenza virus interspecies adaptation via IFITM3
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Denz, Parker J., Speaks, Samuel, Kenney, Adam D., Eddy, Adrian C., Papa, Jonathan L., Roettger, Jack, Scace, Sydney C., Rubrum, Adam, Hemann, Emily A., Forero, Adriana, Webby, Richard J., Bowman, Andrew S., and Yount, Jacob S.
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- 2024
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150. Ecological implications of row width and cultivar selection on rice (Oryza sativa) and barnyardgrass (Echinochloa crus-galli)
- Author
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Reed, Noah H., Butts, Thomas R., Norsworthy, Jason K., Hardke, Jarrod T., Barber, L. Tom, Bond, Jason A., Bowman, Hunter D., Bateman, Nick R., Poncet, Aurelie M., and Kouame, Koffi B. J.
- Published
- 2024
- Full Text
- View/download PDF
Catalog
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