77,137 results on '"Phillips P"'
Search Results
202. Influence of Local Aperture Heterogeneity on Invading Fluid Connectivity During Rough Fracture Drainage
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Phillips, Tomos, Bultreys, Tom, Van Stappen, Jeroen, Singh, Kamaljit, Achuo Dze, Sahyuo, Van Offenwert, Stefanie, Callow, Ben, Borji, Mostafa, Boersheim, Erik Clemens, Novak, Vladimir, Schlepütz, Christian M., Cnudde, Veerle, Doster, Florian, and Busch, Andreas
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- 2024
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203. Examining Concordance Between the Clinical Assessment of Attention Deficit-Adult and the Barkley Adult ADHD Rating Scale-IV in a Sample of Adults Referred for ADHD
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Robinson, Anthony D., Finley, John-Christopher A., Phillips, Matthew S., Ulrich, Devin M., Cerny, Brian M., Ovsiew, Gabriel P., Pliskin, Neil H., and Soble, Jason R.
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- 2024
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204. Suprahilar and Retrocrural Domains in RPLND for NSGCT Testis—Going Beyond Where the Light Touches!
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Venkatesh, Shrinivas, Phillips, Malar Raj, Krishnamurthy, Shalini Shree, Suresh, Krishna, Malik, Kanuj, Ramakrishnan, Ayaloor Seshadri, Krishnamurthy, Arvind, Ellusamy, Hemanth Raj, and Raja, Anand
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- 2024
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205. Long-Term Clinical and Radiographic Outcomes of Meniscus Allograft Transplant
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Phillips, Andrew R., Haneberg, Erik C., Boden, Stephanie A., Yanke, Adam B., and Cole, Brian J.
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- 2024
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206. Correlates of Adherence to Oral and Vaginal Pre-exposure Prophylaxis (PrEP) Among Adolescent Girls and Young Women (AGYW) Participating in the MTN-034/REACH Trial
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Ngure, Kenneth, Browne, Erica N., Reddy, Krishnaveni, Friedland, Barbara A., van der Straten, Ariane, Palanee-Phillips, Thesla, Nakalega, Rita, Gati, Brenda, Kalule, Hadijah N., Siziba, Bekezela, Soto-Torres, Lydia, Nair, Gonasagrie, Garcia, Morgan, Celum, Connie, and Roberts, Sarah T.
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- 2024
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207. Plant-based diet adherence is associated with metabolic health status in adults living with and without obesity
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Carey, Mags T., Millar, Seán R., Elliott, Patrick S., Navarro, Pilar, Harrington, Janas M., Perry, Ivan J., and Phillips, Catherine M.
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- 2024
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208. Investigating the influences of precipitation, snowmelt, and freeze-thaw on rockfall in Glenwood Canyon, Colorado using terrestrial laser scanning
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Weidner, Luke, Walton, Gabriel, and Phillips, Cameron
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- 2024
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209. The role of CEUS in the management of biloma
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Marinato, Valentina, Phillips, Alice, Giuliano, Leonardo, Cascella, Tommaso, Greco, Giorgio, and Lanocita, Rodolfo
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- 2024
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210. Platforms and possibilities: a scoping study of curriculum resources for global citizenship education
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Phillips, Louise Gwenneth, de Rivera, Liberty, and Harris, Pauline
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- 2024
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211. Real world study of sacituzumab govitecan in metastatic triple-negative breast cancer in the United Kingdom
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Hanna, Daire, Merrick, Sophie, Ghose, Aruni, Devlin, Michael John, Yang, Dorothy D., Phillips, Edward, Okines, Alicia, Chopra, Neha, Papadimatraki, Elisavet, Ross, Kirsty, Macpherson, Iain, Boh, Zhuang Y., Michie, Caroline O., Swampillai, Angela, Gupta, Sunnia, Robinson, Tim, Germain, Lewis, Twelves, Chris, Atkinson, Charlotte, Konstantis, Apostolos, Riddle, Pippa, Cresti, Nicola, Naik, Jay D., Borley, Annabel, Guppy, Amy, Schmid, Peter, and Phillips, Melissa
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- 2024
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212. Paraprofessionals' Use of Classroom Management in a Small-Group Intervention
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Michael P. Mesa, Beth M. Phillips, and Christopher J. Lonigan
- Abstract
Although previous research suggests the use of classroom management strategies can support student engagement and learning, gaps in the literature still exist including the frequency of classroom management strategies in small-group instruction. The purpose of this descriptive study was to measure the frequency of paraprofessionals' (n = 94) classroom management strategies within the context of a small-group intervention for kindergarteners at-risk of reading difficulties. This study contributes to the field by finding that trends described in previous studies continue to be demonstrated in this targeted instructional setting, in particular, regarding the infrequent use of praise with students at-risk of academic failure. The results of paired-sample sign tests suggest that when providing corrective feedback, paraprofessionals were more likely to specifically label the behavior being reprimanded. However, paraprofessionals infrequently labeled the specific behavior being reinforced when praising students.
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- 2023
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213. Revenues and Expenditures for Public Elementary and Secondary Education: FY 21. Finance Tables. NCES 2023-301
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National Center for Education Statistics (NCES) (ED/IES), US Census Bureau, Cornman, S. Q., Phillips, J. J., and Howell, M. R.
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This set of tables introduces new data for national and state-level public elementary and secondary revenues and expenditures for fiscal year (FY) 2021. Specifically, these tables include the following school finance data: (1) revenue and expenditure totals; (2) revenues by source; (3) expenditures by function and object; (4) current expenditures; (5) revenues and current expenditures per pupil; (6) expenditures from Title I funds; and (7) revenues and expenditures from COVID-19 Federal Assistance Funds. The tables chosen for this report demonstrate the range of information available when using the National Public Education Financial Survey (NPEFS). [For "Revenues and Expenditures for Public Elementary and Secondary Education: FY 20. Finance Tables. NCES 2022-301," see ED619372.]
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- 2023
214. Timer-Based Coverage Control for Mobile Sensors
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Zegers, Federico M., Phillips, Sean, and Hicks, Gregory P.
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Electrical Engineering and Systems Science - Systems and Control - Abstract
This work investigates the coverage control problem over a static, compact, and convex workspace and develops a hybrid extension of the continuous-time Lloyd algorithm. Each agent in a multi-agent system (MAS) is equipped with a timer mechanism that generates intermittent measurement and control update events, which may occur asynchronously between agents. Between consecutive event times, as determined by the corresponding timer mechanism, the controller of each agent is held constant. These controllers are shown to drive the configuration of the MAS into a neighborhood of the set of centroidal Voronoi configurations, i.e., the minimizers of the standard locational cost. The combination of continuous-time dynamics with intermittently updated control inputs is modeled as a hybrid system. The coverage objective is posed as a set attractivity problem for hybrid systems, where an invariance-based convergence analysis yields sufficient conditions that ensure maximal solutions of the hybrid system asymptotically converge to a desired set. A brief simulation example is included to showcase the result.
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- 2024
215. Interferometry of Atomic Matter Waves in the Cold Atom Lab onboard the International Space Station
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Williams, Jason R., Sackett, Charles A., Ahlers, Holger, Aveline, David C., Boegel, Patrick, Botsi, Sofia, Charron, Eric, Elliott, Ethan R., Gaaloul, Naceur, Giese, Enno, Herr, Waldemar, Kellogg, James R., Kohel, James M., Lay, Norman E., Meister, Matthias, Müller, Gabriel, Müller, Holger, Oudrhiri, Kamal, Phillips, Leah, Pichery, Annie, Rasel, Ernst M., Roura, Albert, Sbroscia, Matteo, Schleich, Wolfgang P., Schneider, Christian, Schubert, Christian, Sen, Bejoy, Thompson, Robert J., and Bigelow, Nicholas P.
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Physics - Atomic Physics ,Physics - Space Physics ,Quantum Physics - Abstract
Ultracold atomic gases hold unique promise for space science by capitalizing on quantum advantages and extended freefall, afforded in a microgravity environment, to enable next-generation precision sensors. Atom interferometers are a class of quantum sensors which can use freely falling gases of atoms cooled to sub-photon-recoil temperatures to provide unprecedented sensitivities to accelerations, rotations, and gravitational forces, and are currently being developed for space-based applications in gravitational, earth, and planetary sciences, as well as to search for subtle forces that could signify physics beyond General Relativity and the Standard Model. NASA's Cold Atom Lab (CAL) operates onboard the International Space Station as a multi-user facility for studies of ultracold atoms and to mature quantum technologies, including atom interferometry, in persistent microgravity. In this paper, we report on path-finding experiments utilizing ultracold $^{87}$Rb atoms in the CAL atom interferometer, which was enabled by an on-orbit upgrade of the CAL science module: A three-pulse Mach-Zehnder interferometer was studied to understand limitations from the influence of ISS vibrations. Additionally, Ramsey shear-wave interferometry was used to manifest interference patterns in a single run that were observable for over 150 ms free-expansion time. Finally, the CAL atom interferometer was used to remotely measure the photon recoil from the atom interferometer laser as a demonstration of the first quantum sensor using matter-wave interferometry in space., Comment: 14 pages, 5 figures
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- 2024
216. Assessing Correlated Truncation Errors in Modern Nucleon-Nucleon Potentials
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Millican, P. J., Furnstahl, R. J., Melendez, J. A., Phillips, D. R., and Pratola, M. T.
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Nuclear Theory ,High Energy Physics - Phenomenology ,Physics - Data Analysis, Statistics and Probability - Abstract
We test the BUQEYE model of correlated effective field theory (EFT) truncation errors on Reinert, Krebs, and Epelbaum's semi-local momentum-space implementation of the chiral EFT ($\chi$EFT) expansion of the nucleon-nucleon (NN) potential. This Bayesian model hypothesizes that dimensionless coefficient functions extracted from the order-by-order corrections to NN observables can be treated as draws from a Gaussian process (GP). We combine a variety of graphical and statistical diagnostics to assess when predicted observables have a $\chi$EFT convergence pattern consistent with the hypothesized GP statistical model. Our conclusions are: First, the BUQEYE model is generally applicable to the potential investigated here, which enables statistically principled estimates of the impact of higher EFT orders on observables. Second, parameters defining the extracted coefficients such as the expansion parameter $Q$ must be well chosen for the coefficients to exhibit a regular convergence pattern -- a property we exploit to obtain posterior distributions for such quantities. Third, the assumption of GP stationarity across lab energy and scattering angle is not generally met; this necessitates adjustments in future work. We provide a workflow and interpretive guide for our analysis framework, and show what can be inferred about probability distributions for $Q$, the EFT breakdown scale $\Lambda_b$, the scale associated with soft physics in the $\chi$EFT potential $m_{\rm eff}$, and the GP hyperparameters. All our results can be reproduced using a publicly available Jupyter notebook, which can be straightforwardly modified to analyze other $\chi$EFT NN potentials., Comment: 29 pages, 33 figures
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- 2024
217. Dueling Over Dessert, Mastering the Art of Repeated Cake Cutting
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Brânzei, Simina, Hajiaghayi, MohammadTaghi, Phillips, Reed, Shin, Suho, and Wang, Kun
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Computer Science - Computer Science and Game Theory ,Computer Science - Artificial Intelligence ,Economics - Theoretical Economics - Abstract
We consider the setting of repeated fair division between two players, denoted Alice and Bob, with private valuations over a cake. In each round, a new cake arrives, which is identical to the ones in previous rounds. Alice cuts the cake at a point of her choice, while Bob chooses the left piece or the right piece, leaving the remainder for Alice. We consider two versions: sequential, where Bob observes Alice's cut point before choosing left/right, and simultaneous, where he only observes her cut point after making his choice. The simultaneous version was first considered by Aumann and Maschler (1995). We observe that if Bob is almost myopic and chooses his favorite piece too often, then he can be systematically exploited by Alice through a strategy akin to a binary search. This strategy allows Alice to approximate Bob's preferences with increasing precision, thereby securing a disproportionate share of the resource over time. We analyze the limits of how much a player can exploit the other one and show that fair utility profiles are in fact achievable. Specifically, the players can enforce the equitable utility profile of $(1/2, 1/2)$ in the limit on every trajectory of play, by keeping the other player's utility to approximately $1/2$ on average while guaranteeing they themselves get at least approximately $1/2$ on average. We show this theorem using a connection with Blackwell approachability. Finally, we analyze a natural dynamic known as fictitious play, where players best respond to the empirical distribution of the other player. We show that fictitious play converges to the equitable utility profile of $(1/2, 1/2)$ at a rate of $O(1/\sqrt{T})$.
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- 2024
218. Self-stacked 1$\mathrm{T}$-1$\mathrm{H}$ layers in 6$\mathrm{R}$-NbSeTe and the emergence of charge and magnetic correlations due to ligand disorder
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Mahatha, S. K., Phillips, J., Corral-Sertal, J., Subires, D., Korshsunov, A., Kar, A., Buck, J., Diekmann, F., Ivanov, Y. P., Chuvilin, A., Mondal, D., Vobornik, I., Bosak, A., Rossnagel, K., Pardo, V., Fumega, Adolfo O., and Blanco-Canosa, S.
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Condensed Matter - Materials Science ,Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Strongly Correlated Electrons - Abstract
The emergence of correlated phenomena arising from the combination of 1$\mathrm{T}$ and 1$\mathrm{H}$ van der Waals layers is the focus of intense research. Here, we synthesize a novel self-stacked 6$\mathrm{R}$ phase in NbSeTe, showing a perfect alternating 1T and 1H layers that grow coherently along the c-direction, as revealed by scanning transmission electron microscopy. Angle resolved photoemission spectroscopy shows a mixed contribution of the trigonal and octahedral Nb bands to the Fermi level. Diffuse scattering reveals temperature-independent short-range charge fluctuations with propagation vector $\mathrm{q_{CO}}$=(0.25,0), derived from the condensation of a longitudinal mode in the 1T layer. We observe that ligand disorder quenches the formation of a charge density wave. Magnetization measurements suggest the presence of an inhomogeneous, short-range magnetic order, further supported by the absence of a clear phase transition in the specific heat. These experimental analyses in combination with \textit{ab initio} calculations indicate that the ground state of 6$\mathrm{R}$-NbSeTe is described by a statistical distribution of short-range charge-modulated and spin-correlated regions driven by ligand disorder. Our results devise a route to synthesize 1$\mathrm{T}$-1$\mathrm{H}$ self-stacked bulk heterostructures to study emergent phases of matter., Comment: 12 pages, including Supplementary Information. 4 figures + 6 supplementary figures
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- 2024
219. Particle Denoising Diffusion Sampler
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Phillips, Angus, Dau, Hai-Dang, Hutchinson, Michael John, De Bortoli, Valentin, Deligiannidis, George, and Doucet, Arnaud
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Statistics - Machine Learning ,Computer Science - Machine Learning ,Statistics - Computation - Abstract
Denoising diffusion models have become ubiquitous for generative modeling. The core idea is to transport the data distribution to a Gaussian by using a diffusion. Approximate samples from the data distribution are then obtained by estimating the time-reversal of this diffusion using score matching ideas. We follow here a similar strategy to sample from unnormalized probability densities and compute their normalizing constants. However, the time-reversed diffusion is here simulated by using an original iterative particle scheme relying on a novel score matching loss. Contrary to standard denoising diffusion models, the resulting Particle Denoising Diffusion Sampler (PDDS) provides asymptotically consistent estimates under mild assumptions. We demonstrate PDDS on multimodal and high dimensional sampling tasks., Comment: To be published in ICML 2024. 37 pages, 20 figures, 3 tables, 5 algorithms
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- 2024
220. No Dimensional Sampling Coresets for Classification
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Alishahi, Meysam and Phillips, Jeff M.
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Computer Science - Machine Learning ,Computer Science - Computational Geometry - Abstract
We refine and generalize what is known about coresets for classification problems via the sensitivity sampling framework. Such coresets seek the smallest possible subsets of input data, so one can optimize a loss function on the coreset and ensure approximation guarantees with respect to the original data. Our analysis provides the first no dimensional coresets, so the size does not depend on the dimension. Moreover, our results are general, apply for distributional input and can use iid samples, so provide sample complexity bounds, and work for a variety of loss functions. A key tool we develop is a Radamacher complexity version of the main sensitivity sampling approach, which can be of independent interest., Comment: 42 Pages
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- 2024
221. Standard Gaussian Process Can Be Excellent for High-Dimensional Bayesian Optimization
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Xu, Zhitong, Wang, Haitao, Phillips, Jeff M, and Zhe, Shandian
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
A longstanding belief holds that Bayesian Optimization (BO) with standard Gaussian processes (GP) -- referred to as standard BO -- underperforms in high-dimensional optimization problems. While this belief seems plausible, it lacks both robust empirical evidence and theoretical justification. To address this gap, we present a systematic investigation. First, through a comprehensive evaluation across eleven widely used benchmarks, we found that while the popular Square Exponential (SE) kernel often leads to poor performance, using Matern kernels enables standard BO to consistently achieve top-tier results, frequently surpassing methods specifically designed for high-dimensional optimization. Second, our theoretical analysis reveals that the SE kernels failure primarily stems from improper initialization of the length-scale parameters, which are commonly used in practice but can cause gradient vanishing in training. We provide a probabilistic bound to characterize this issue, showing that Matern kernels are less susceptible and can robustly handle much higher dimensions. Third, we propose a simple robust initialization strategy that dramatically improves the performance of the SE kernel, bringing it close to state of the art methods, without requiring any additional priors or regularization. We prove another probabilistic bound that demonstrates how the gradient vanishing issue can be effectively mitigated with our method. Our findings advocate for a re-evaluation of standard BOs potential in high-dimensional settings.
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- 2024
222. FDNet: Frequency Domain Denoising Network For Cell Segmentation in Astrocytes Derived From Induced Pluripotent Stem Cells
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Li, Haoran, Shi, Jiahua, Chen, Huaming, Du, Bo, Maksour, Simon, Phillips, Gabrielle, Dottori, Mirella, and Shen, Jun
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Artificially generated induced pluripotent stem cells (iPSCs) from somatic cells play an important role for disease modeling and drug screening of neurodegenerative diseases. Astrocytes differentiated from iPSCs are important targets to investigate neuronal metabolism. The astrocyte differentiation progress can be monitored through the variations of morphology observed from microscopy images at different differentiation stages, then determined by molecular biology techniques upon maturation. However, the astrocytes usually ``perfectly'' blend into the background and some of them are covered by interference information (i.e., dead cells, media sediments, and cell debris), which makes astrocytes difficult to observe. Due to the lack of annotated datasets, the existing state-of-the-art deep learning approaches cannot be used to address this issue. In this paper, we introduce a new task named astrocyte segmentation with a novel dataset, called IAI704, which contains 704 images and their corresponding pixel-level annotation masks. Moreover, a novel frequency domain denoising network, named FDNet, is proposed for astrocyte segmentation. In detail, our FDNet consists of a contextual information fusion module (CIF), an attention block (AB), and a Fourier transform block (FTB). CIF and AB fuse multi-scale feature embeddings to localize the astrocytes. FTB transforms feature embeddings into the frequency domain and conducts a high-pass filter to eliminate interference information. Experimental results demonstrate the superiority of our proposed FDNet over the state-of-the-art substitutes in astrocyte segmentation, shedding insights for iPSC differentiation progress prediction., Comment: Accepted by The IEEE International Symposium on Biomedical Imaging (ISBI) 2024
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- 2024
223. The Smoke of Zaanen
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Phillips, Philip W.
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Physics - History and Philosophy of Physics ,Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Superconductivity - Abstract
Theoretical physics suffered a major loss with the death of my dear friend Jan Zaanen on January 18. This note is my remembrance of him.
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- 2024
224. Detailed Error Analysis of the HHL Algorithm
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Phillips, Xinbo Li Christopher
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Quantum Physics ,Mathematics - Numerical Analysis - Abstract
We reiterate the contribution made by Harrow, Hassidim, and Llyod to the quantum matrix equation solver with the emphasis on the algorithm description and the error analysis derivation details. Moreover, the behavior of the amplitudes of the phase register on the completion of the Quantum Phase Estimation is studied. This study is beneficial for the comprehension of the choice of the phase register size and its interrelation with the Hamiltonian simulation duration in the algorithm setup phase.
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- 2024
225. Compton Scattering on 4He with Nuclear One- and Two-Body Densities
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Griesshammer, Harald W., Liao, Junjie, McGovern, Judith A., Nogga, Andreas, and Phillips, Daniel R.
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Nuclear Theory ,Nuclear Experiment - Abstract
We present the first \emph{ab initio} calculation of elastic Compton scattering from 4He. It is carried out to $\mathcal{O}(e^2 \delta^3)$ [N3LO] in the $\delta$ expansion of $\chi$EFT. At this order and for this target, the only free parameters are the scalar-isoscalar electric and magnetic dipole polarisabilities of the nucleon. Adopting current values for these yields a parameter-free prediction. This compares favourably with the world data from HI$\gamma$S, Illinois and Lund for photon energies $50\;\mathrm{MeV}\lesssim\omega\lesssim120\;\mathrm{MeV}$ within our theoretical uncertainties of $\pm10\%$. We predict a cross section up to 7 times that for deuterium. As in 3He, this emphasises and tests the key role of meson-exchange currents between np pairs in Compton scattering on light nuclei. We assess the sensitivity of the cross section and beam asymmetry to the nucleon polarisabilities, providing clear guidance to future experiments seeking to further constrain them. The calculation becomes tractable by use of the Transition Density Method. The one- and two-body densities generated from 5 chiral potentials and the AV18$+$UIX potential are available using the python package provided at \url{https://pypi.org/project/nucdens/}., Comment: 38 pages LaTeX2e (pdflatex) including 13 figures as 14 .pdf files using includegraphics. Minor grammatical/typographical changes, figures 3, 4 and 7 typographically corrected without changes of substance. Text- and figure-identical to published version
- Published
- 2024
226. A survey for variable young stars with small telescopes: VIII -- Properties of 1687 Gaia selected members in 21 nearby clusters
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Froebrich, Dirk, Scholz, Aleks, Campbell-White, Justyn, Vanaverbeke, Siegfried, Herbert, Carys, Eislöffel, Jochen, Urtly, Thomas, Long, Timothy P., Walton, Ivan L., Wiersema, Klaas, Quinn, Nick J., Rodda, Tony, González-Carballo, Juan-Luis, Aimar, Mario Morales, García, Rafael Castillo, Alfaro, Francisco C. Soldán, de la Cuesta, Faustino García, Licchelli, Domenico, Perez, Alex Escartin, González, José Luis Salto, Deldem, Marc, Futcher, Stephen R. L., Nelson, Tim, Dvorak, Shawn, Moździerski, Dawid, Kotysz, Krzysztof, Mikołajczyk, Przemysław, Fleming, George, Phillips, Mark, Vale, Tony, Öğmen, Yenal, Dubois, Franky, Rolfe, Samantha M., Campbell, David A., Eggenstein, Heinz-Bernd, Hambsch, Franz-Josef, Heald, Michael A., Lewin, Pablo, Rose, Adam C., Stone, Geoffrey, Crow, Martin Valentine, Dawes, Simon Francis, OKeeffe, Derek, Popowicz, Adam, Bernacki, Krzysztof, Malcher, Andrzej, Lasota, Slawomir, Fiolka, Jerzy, Dustor, Adam, Vajpayee, Amritanshu, Devine, Pat, Kolb, Matthias, Marquette, Jean-Baptiste, Ruppel, Gregg L., Crowson, Dan R., da Silva, Cledison Marcos, Michaud, Michel, Patel, Aashini L., Dickers, Matthew D., Dover, Lord, Grozdanova, Ivana I., Urquhart, James S., and Lynch, Chris J. R.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Astrophysics of Galaxies - Abstract
The Hunting Outbursting Young Stars (HOYS) project performs long-term, optical, multi-filter, high cadence monitoring of 25 nearby young clusters and star forming regions. Utilising Gaia DR3 data we have identified about 17000 potential young stellar members in 45 coherent astrometric groups in these fields. Twenty one of them are clear young groups or clusters of stars within one kiloparsec and they contain 9143 Gaia selected potential members. The cluster distances, proper motions and membership numbers are determined. We analyse long term (about 7yr) V, R, and I-band light curves from HOYS for 1687 of the potential cluster members. One quarter of the stars are variable in all three optical filters, and two thirds of these have light curves that are symmetric around the mean. Light curves affected by obscuration from circumstellar materials are more common than those affected by accretion bursts, by a factor of 2-4. The variability fraction in the clusters ranges from 10 to almost 100 percent, and correlates positively with the fraction of stars with detectable inner disks, indicating that a lot of variability is driven by the disk. About one in six variables shows detectable periodicity, mostly caused by magnetic spots. Two thirds of the periodic variables with disk excess emission are slow rotators, and amongst the stars without disk excess two thirds are fast rotators - in agreement with rotation being slowed down by the presence of a disk., Comment: accepted for publication in MNRAS, 1 table, 9 figures
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- 2024
227. Embedding Elites: Examining the Use of Tweets Embedded in Online News Articles across Reliable and Fringe Outlets
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Horne, Benjamin D., Phillips, Summer, and Koontz, Nelia
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Computer Science - Computers and Society ,Computer Science - Social and Information Networks - Abstract
This study examines the use of embedded tweets in online news media. In particular, we add to the previous literature by exploring embedded tweets across reliable and unreliable news outlets. We use a mixed-method analysis to examine how the function and frequency of embedded tweets change across outlet reliability and news topic. We find that, no matter the outlet reliability, embedded tweets are most often used to relay the opinions of elites, to syndicate information from another news source, or to self-cite information an outlet previously produced. Our results also show some notable differences between reliable media and fringe media's use of tweets. Namely, fringe media embed tweets more and use those tweets as the source of news more than reliable media. Our work adds to the literature on hybrid media systems and the normalization of social media in journalism., Comment: MeLa Lab Preliminary Findings Report
- Published
- 2024
228. Deciphering regulatory architectures from synthetic single-cell expression patterns
- Author
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Pan, Rosalind Wenshan, Roeschinger, Tom, Faizi, Kian, Garcia, Hernan, and Phillips, Rob
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Quantitative Biology - Genomics ,Quantitative Biology - Quantitative Methods - Abstract
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to physiological and evolutionary adaptation. One category of high-throughput experiments used to understand the sequence-phenotype relationship of the transcriptome is massively parallel reporter assays (MPRAs). However, to improve the versatility and scalability of MPRA pipelines, we need a "theory of the experiment" to help us better understand the impact of various biological and experimental parameters on the interpretation of experimental data. To that end, in this paper we create tens of thousands of synthetic single-cell gene expression outputs using both equilibrium and out-of-equilibrium models. These models make it possible to imitate the summary statistics (information footprints and expression shift matrices) used to characterize the output of MPRAs and from this summary statistic to infer the underlying regulatory architecture. Specifically, we use a more refined implementation of the so-called thermodynamic models in which the binding energies of each sequence variant are derived from energy matrices. Our simulations reveal important effects of the parameters on MPRA data and we demonstrate our ability to optimize MPRA experimental designs with the goal of generating thermodynamic models of the transcriptome with base-pair specificity. Further, this approach makes it possible to carefully examine the mapping between mutations in binding sites and their corresponding expression profiles, a tool useful not only for better designing MPRAs, but also for exploring regulatory evolution.
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- 2024
229. Using the Transition-Density Formalism in the First Computation of 4He Compton Scattering
- Author
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Griesshammer, Harald W., Liao, Junjie, McGovern, Judith A., Nogga, Andreas, and Phillips, Daniel R.
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Nuclear Theory ,Nuclear Experiment - Abstract
The method and results of the first theory description of 4He Compton scattering at nuclear energies is presented, with a focus on figures. An upcoming publication [1] contains details and a comprehensive list of references., Comment: 6 pages LaTeX2e (pdflatex) including 4 figures as 6 .pdf files using includegraphics and webofc class. Contribution to the Proceedings of the 16th International Conference on Meson-Nucleon Physics and the Structure of the Nucleon (MENU 2023), Mainz 16-20 October 2023
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- 2024
230. JWST NIRSpec+MIRI Observations of the nearby Type IIP supernova 2022acko
- Author
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Shahbandeh, M., Ashall, C., Hoeflich, P., Baron, E., Fox, O., Mera, T., DerKacy, J., Stritzinger, M. D., Shappee, B., Law, D., Morrison, J., Pauly, T., Pierel, J., Medler, K., Andrews, J., Baade, D., Bostroem, A., Brown, P., Burns, C., Burrow, A., Cikota, A., Cross, D., Davis, S., de Jaeger, T., Do, A., Dong, Y., Hsiao, E., Dominguez, I., Galbany, L., Janzen, D., Jencson, J., Hoang, E., Karamehmetoglu, E., Khaghani, B., Krisciunas, K., Kumar, S., Lu, J., Mazzali, P., Morrell, N., Patat, F., Pearson, J., Pfeffer, C., Wang, L., Yang, Y., Cai, Y. Z., Camacho-Neves, Y., Elias-Rosa, N., Lundquist, M., Maund, J., Phillips, M., Rest, A., Retamal, N., Stangl, S., Shrestha, M., Stevens, C., Suntzeff, N., Telesco, C., Tucker, M., Foley, R., Jha, S., Kwok, L., Larison, C., LeBaron, N., Moran, S., Rho, J., Salmaso, I., Schmidt, J., and Tinyanont, S.
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Astrophysics - High Energy Astrophysical Phenomena ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We present JWST spectral and photometric observations of the Type IIP supernova (SN) 2022acko at ~50 days past explosion. These data are the first JWST spectral observations of a core-collapse SN. We identify ~30 different H I features, other features associated with products produced from the CNO cycle, and s-process elements such as Sc II and Ba II. By combining the JWST spectra with ground-based optical and NIR spectra, we construct a full Spectral Energy Distribution from 0.4 to 25 microns and find that the JWST spectra are fully consistent with the simultaneous JWST photometry. The data lack signatures of CO formation and we estimate a limit on the CO mass of < 10^{-8} solar mass. We demonstrate how the CO fundamental band limits can be used to probe underlying physics during stellar evolution, explosion, and the environment. The observations indicate little mixing between the H envelope and C/O core in the ejecta and show no evidence of dust. The data presented here set a critical baseline for future JWST observations, where possible molecular and dust formation may be seen.
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- 2024
231. Out-of-Distribution Detection & Applications With Ablated Learned Temperature Energy
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LeVine, Will, Pikus, Benjamin, Phillips, Jacob, Norman, Berk, Gil, Fernando Amat, and Hendryx, Sean
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
As deep neural networks become adopted in high-stakes domains, it is crucial to identify when inference inputs are Out-of-Distribution (OOD) so that users can be alerted of likely drops in performance and calibration despite high confidence -- ultimately to know when networks' decisions (and their uncertainty in those decisions) should be trusted. In this paper we introduce Ablated Learned Temperature Energy (or "AbeT" for short), an OOD detection method which lowers the False Positive Rate at 95\% True Positive Rate (FPR@95) by $43.43\%$ in classification compared to state of the art without training networks in multiple stages or requiring hyperparameters or test-time backward passes. We additionally provide empirical insights as to why our model learns to distinguish between In-Distribution (ID) and OOD samples while only being explicitly trained on ID samples via exposure to misclassified ID examples at training time. Lastly, we show the efficacy of our method in identifying predicted bounding boxes and pixels corresponding to OOD objects in object detection and semantic segmentation, respectively -- with an AUROC increase of $5.15\%$ in object detection and both a decrease in FPR@95 of $41.48\%$ and an increase in AUPRC of $34.20\%$ in semantic segmentation compared to previous state of the art.
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- 2024
232. SleepNet: Attention-Enhanced Robust Sleep Prediction using Dynamic Social Networks
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Khalid, Maryam, Klerman, Elizabeth B., Mchill, Andrew W., Phillips, Andrew J. K., and Sano, Akane
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Computer Science - Social and Information Networks ,Electrical Engineering and Systems Science - Signal Processing - Abstract
Sleep behavior significantly impacts health and acts as an indicator of physical and mental well-being. Monitoring and predicting sleep behavior with ubiquitous sensors may therefore assist in both sleep management and tracking of related health conditions. While sleep behavior depends on, and is reflected in the physiology of a person, it is also impacted by external factors such as digital media usage, social network contagion, and the surrounding weather. In this work, we propose SleepNet, a system that exploits social contagion in sleep behavior through graph networks and integrates it with physiological and phone data extracted from ubiquitous mobile and wearable devices for predicting next-day sleep labels about sleep duration. Our architecture overcomes the limitations of large-scale graphs containing connections irrelevant to sleep behavior by devising an attention mechanism. The extensive experimental evaluation highlights the improvement provided by incorporating social networks in the model. Additionally, we conduct robustness analysis to demonstrate the system's performance in real-life conditions. The outcomes affirm the stability of SleepNet against perturbations in input data. Further analyses emphasize the significance of network topology in prediction performance revealing that users with higher eigenvalue centrality are more vulnerable to data perturbations., Comment: Accepted for publication in Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies (IMWUT), 8 (March 2024)
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- 2024
233. New Approach to Strong Correlation: Twisting Hubbard into the Orbital Hatsugai-Kohmoto Model
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Mai, Peizhi, Zhao, Jinchao, Tenkila, Gaurav, Hackner, Nico A., Kush, Dhruv, Pan, Derek, and Phillips, Philip W.
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Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Superconductivity - Abstract
We present the $n$-orbital extension of the Hatsugai-Kohmoto (HK) model to the orbital HK (OHK) model which obtains by covering the Brillouin zone with $N/n$ Hubbard clusters each containing $n$-sites all connected via twisted boundary conditions. We show that this defines a systematic computational scheme to go from $n=1$ ``band'' HK to the full Hubbard model. Further, through powerful scaling arguments, we show that the convergence to Hubbard goes as $1/n^{2d}$ for $n^d$-orbital HK on a $d$-dimensional system implying that all the fluctuations vanish in $d=\infty$. As evidence for the above, we employ exact diagonalization and DMRG to show that the OHK model matches the exact (from Bethe ansatz) ground state energy of the 1d Hubbard model within 1$\%$ with just $n=10$ orbitals. For a square lattice, we recover an insulating state regardless of the strength of the interactions, double occupancy in agreement with state of the art simulations, dynamical spectral weight transfer, short-range antiferromagnetic correlations and charge neutral excitations leading to the algebraic temperature dependence of the specific heat, all with a fraction of the computational time of more advanced cluster methods and making it possible to obtain analytical insights. The success of OHK and its rapid convergence to the Hubbard model reiterates that a fixed point controls the physics. Consequently, the $n$-orbital HK model offers a new tool for strongly correlated quantum matter., Comment: 7 pages + supplement (greatly expanded revision)
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- 2024
234. Force Propagation in Active Cytoskeletal Networks
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Liu, Shichen, Pan, Rosalind Wenshan, Lee, Heun Jin, Shadkhoo, Shahriar, Yang, Fan, Li, Chunhe, Qu, Zijie, Phillips, Rob, and Thomson, Matt
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Condensed Matter - Soft Condensed Matter - Abstract
In biological systems, molecular-scale forces and motions are pivotal for enabling processes like motility, shape change, and replication. These forces and motions are organized, amplified, and transmitted across macroscopic scales by active materials such as the cytoskeleton, which drives micron-scale cellular movement and re-organization. Despite the integral role of active materials, understanding how molecular-scale interactions alter macroscopic structure and force propagation remains elusive. This knowledge gap presents challenges to the harnessing and regulation of such dynamics across diverse length scales. Here, we demonstrate how mediating the bundling of microtubules can shift active matter between a global force-transmitting phase and a local force-dissipating phase. A fivefold increase in microtubule effective length results in the transition from local to global phase with a hundredfold increase in velocity autocorrelation. Through theory and simulation, we identify signatures of a percolation-driven transition between the two phases. This provides evidence for how force propagation can be generated when local molecular interactions reach a sufficient length scale. We show that force propagation in the active matter system enables material transport. Consequently, we demonstrate that the global phase is capable of facilitating millimeter-scale human cell transport and manipulation, as well as powering the movement of aqueous droplets. These findings underscore the potential for designing active materials capable of force organization and transmission. Our results lay the foundation for further exploration into the organization and propagation of forces/stresses in biological systems, thereby paving the way for the engineering of active materials in synthetic biology and soft robotics., Comment: 15 pages, 4 figrues
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- 2024
235. Topological Phase Transition without Single-Particle-Gap Closing in Strongly Correlated Systems
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Mai, Peizhi, Zhao, Jinchao, Maier, Thomas A., Bradlyn, Barry, and Phillips, Philip W.
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Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Materials Science - Abstract
We show here that numerous examples abound where changing topology does not necessarily close the bulk insulating charge gap as demanded in the standard non-interacting picture. From extensive determinantal and dynamical cluster quantum Monte Carlo simulations of the half-filled and quarter-filled Kane-Mele-Hubbard model, we show that for sufficiently strong interactions at either half- or quarter-filling, a transition between topological and trivial insulators occurs without the closing of a charge gap. To shed light on this behavior, we illustrate that an exactly solvable model reveals that while the single-particle gap remains, the many-body gap does in fact close. These two gaps are the same in the non-interacting system but depart from each other as the interaction turns on. We purport that for interacting systems, the proper probe of topological phase transitions is the closing of the many-body rather than the single-particle gap.
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- 2024
236. New Manual Quantitative Polymerase Chain Reaction Assay Validated on Tongue Swabs Collected and Processed in Uganda Shows Sensitivity That Rivals Sputum-based Molecular Tuberculosis Diagnostics
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Steadman, Amy, Andama, Alfred, Ball, Alexey, Mukwatamundu, Job, Khimani, Khushboo, Mochizuki, Tessa, Asege, Lucy, Bukirwa, Alice, Kato, John Baptist, Katumba, David, Kisakye, Esther, Mangeni, Wilson, Mwebe, Sandra, Nakaye, Martha, Nassuna, Irene, Nyawere, Justine, Nakaweesa, Annet, Cook, Catherine, Phillips, Patrick, Nalugwa, Talemwa, Bachman, Christine M, Semitala, Fred Collins, Weigl, Bernhard H, Connelly, John, Worodria, William, and Cattamanchi, Adithya
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Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Research ,Tuberculosis ,Rare Diseases ,Infectious Diseases ,Emerging Infectious Diseases ,HIV/AIDS ,Vaccine Related ,4.2 Evaluation of markers and technologies ,Detection ,screening and diagnosis ,Infection ,Good Health and Well Being ,Humans ,Female ,Sputum ,Male ,Uganda ,Adult ,Tongue ,Sensitivity and Specificity ,Specimen Handling ,Mycobacterium tuberculosis ,Real-Time Polymerase Chain Reaction ,Molecular Diagnostic Techniques ,Middle Aged ,Young Adult ,Tuberculosis ,Pulmonary ,tuberculosis ,diagnosis ,nonsputum ,tongue swab ,oral swab ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
BackgroundSputum-based testing is a barrier to increasing access to molecular diagnostics for tuberculosis (TB). Many people with TB are unable to produce sputum, and sputum processing increases assay complexity and cost. Tongue swabs are emerging as an alternative to sputum, but performance limits are uncertain.MethodsFrom June 2022 to July 2023, we enrolled 397 consecutive adults with cough >2 weeks at 2 health centers in Kampala, Uganda. We collected demographic and clinical information, sputum for TB testing (Xpert MTB/RIF Ultra and 2 liquid cultures), and tongue swabs for same-day quantitative polymerase chain reaction (qPCR) testing. We evaluated tongue swab qPCR diagnostic accuracy versus sputum TB test results, quantified TB targets per swab, assessed the impact of serial swabbing, and compared 2 swab types (Copan FLOQSWAB and Steripack spun polyester).ResultsAmong 397 participants, 43.1% were female, median age was 33 years, 23.5% were diagnosed with human immunodeficiency virus, and 32.0% had confirmed TB. Sputum Xpert Ultra and tongue swab qPCR results were concordant for 98.2% (95% confidence interval [CI]: 96.2-99.1) of participants. Tongue swab qPCR sensitivity was 92.6% (95% CI: 86.5 to 96.0) and specificity was 99.1% (95% CI: 96.9 to 99.8) versus microbiological reference standard. A single tongue swab recovered a 7-log range of TB copies, with a decreasing recovery trend among 4 serial swabs. Swab types performed equivalently.ConclusionsTongue swabs are a promising alternative to sputum for molecular diagnosis of TB, with sensitivity approaching sputum-based molecular tests. Our results provide valuable insights for developing successful tongue swab-based TB diagnostics.
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- 2024
237. Paving the path for implementation of clinical genomic sequencing globally: Are we ready?
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Marshall, Deborah, Hua, Nicolle, Buchanan, James, Christensen, Kurt, Frederix, Geert, Goranitis, Ilias, Ijzerman, Maarten, Jansen, Jeroen, Lavelle, Tara, Regier, Dean, Smith, Hadley, Ungar, Wendy, Weymann, Deirdre, Wordsworth, Sarah, and Phillips, Kathryn
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clinical genomic sequencing ,genetic testing ,genomic medicine ,global health ,health economics ,precision medicine - Abstract
Despite the emerging evidence in recent years, successful implementation of clinical genomic sequencing (CGS) remains limited and is challenged by a range of barriers. These include a lack of standardized practices, limited economic assessments for specific indications, limited meaningful patient engagement in health policy decision-making, and the associated costs and resource demand for implementation. Although CGS is gradually becoming more available and accessible worldwide, large variations and disparities remain, and reflections on the lessons learned for successful implementation are sparse. In this commentary, members of the Global Economics and Evaluation of Clinical Genomics Sequencing Working Group (GEECS) describe the global landscape of CGS in the context of health economics and policy and propose evidence-based solutions to address existing and future barriers to CGS implementation. The topics discussed are reflected as two overarching themes: (1) system readiness for CGS and (2) evidence, assessments, and approval processes. These themes highlight the need for health economics, public health, and infrastructure and operational considerations; a robust patient- and family-centered evidence base on CGS outcomes; and a comprehensive, collaborative, interdisciplinary approach.
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- 2024
238. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells.
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Rosano, Dalia, Sofyali, Emre, Dhiman, Heena, Ghirardi, Chiara, Ivanoiu, Diana, Heide, Timon, Vingiani, Andrea, Bertolotti, Alessia, Pruneri, Giancarlo, Canale, Eleonora, Dewhurst, Hannah, Saha, Debjani, Barozzi, Iros, Li, Tong, Zemlyanskiy, Grigory, Phillips, Henry, James, Chela, Győrffy, Balázs, Lynn, Claire, Cresswell, George, Rehman, Farah, Noberini, Roberta, Bonaldi, Tiziana, Sottoriva, Andrea, Magnani, Luca, and Slaven, Neil
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Humans ,Breast Neoplasms ,Female ,Epigenesis ,Genetic ,Neoplasm Recurrence ,Local ,Gene Expression Regulation ,Neoplastic - Abstract
UNLABELLED: Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE: This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs. See related commentary by Llinas-Bertran et al., p. 704. This article is featured in Selected Articles from This Issue, p. 695.
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- 2024
239. Storylines of family medicine V: ways of thinking—honing the therapeutic self
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Ventres, William B, Stone, Leslie A, Shapiro, Johanna F, Haq, Cynthia, Leão, Jéssica RB, Nease, Donald E, Grant, Liz, Mercer, Stewart W, Gillies, John CM, Blasco, Pablo González, De Benedetto, Maria Auxiliadora C, Moreto, Graziela, Levites, Marcelo R, DeVoe, Jennifer E, Phillips, William R, Uygur, Jane M, Egnew, Thomas R, and Stanley, Colette S
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Health Services and Systems ,Public Health ,Health Sciences ,Good Health and Well Being ,Humans ,Family Practice ,Physicians ,Family ,Cognitive Reflection ,Emotions ,Humanism ,Family ,Family Medicine ,General Practice ,Health Knowledge ,Attitudes ,Practice ,Illness Behavior ,Health services and systems ,Public health - Abstract
Storylines of Family Medicine is a 12-part series of thematically linked essays with accompanying illustrations that explore the many dimensions of family medicine, as interpreted by individual family physicians and medical educators in the USA and elsewhere around the world. In 'V: ways of thinking-honing the therapeutic self', authors present the following sections: 'Reflective practice in action', 'The doctor as drug-Balint groups', 'Cultivating compassion', 'Towards a humanistic approach to doctoring', 'Intimacy in family medicine', 'The many faces of suffering', 'Transcending suffering' and 'The power of listening to stories.' May readers feel a deeper sense of their own therapeutic agency by reflecting on these essays.
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- 2024
240. Experience With Four-Month Rifapentine and Moxifloxacin-Based Tuberculosis Treatment in San Francisco.
- Author
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Louie, Janice, Agraz-Lara, Rocio, Velásquez, Gustavo, Phillips, Allison, and Szumowski, John
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4-month ,SF ,short-course ,treatment ,tuberculosis - Abstract
BACKGROUND: A multicountry randomized controlled trial has demonstrated that pan-susceptible pulmonary tuberculosis (TB) can be successfully treated with a 4-month regimen of daily isoniazid, rifapentine, moxifloxacin, and pyrazinamide (HPMZ). We piloted HPMZ in San Francisco (SF) using a modified version of the US Centers for Disease Control and Prevention HPMZ treatment guidelines. METHODS: In this retrospective cohort, patients consecutively referred to SF TB clinic were evaluated for HPMZ eligibility based on preestablished inclusion/exclusion criteria. All underwent evaluation and management according to national recommendations. We reviewed the medical records of those initiated on HPMZ. RESULTS: From August 2021 to December 2023, 30 (18.8%) of 160 patients diagnosed with active TB met HPMZ inclusion criteria; of these, 22 (13.8%) started HPMZ. The median age (range) was 32.5 (14-86) years, 17 (77.3%) were otherwise healthy, and 19 (86.4%) had pulmonary TB, including 7 (36.8%) with cavitary disease. Eighteen (81.8%) patients had an adverse event, with 11 (50%) prematurely discontinuing HPMZ; the most common adverse events were vomiting, elevated transaminases, and rash. To date, 9 (40.9%) have completed treatment, with most achieving criteria for cure. One patient was diagnosed with possible TB recurrence and restarted standard TB treatment. CONCLUSIONS: Our experience, with half of patients to date prematurely discontinuing HPMZ, illustrates the challenge of extrapolating findings from TB clinical trials commonly conducted in high-incidence, non-US settings to US clinical practice. Further experience may help identify best practices for implementing HPMZ, including identifying predictors of which patients may be most likely to benefit from and tolerate this regimen.
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- 2024
241. Digital activism to achieve meaningful institutional change: A bricolage of crowdsourcing, social media, and data analytics
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Mindel, Vitali, Overstreet, Robert E, Sternberg, Henrik, Mathiassen, Lars, and Phillips, Nelson
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Economics ,Applied Economics ,Commerce ,Management ,Tourism and Services ,Strategy ,Management and Organisational Behaviour ,Institutional change ,Crowdsourcing ,Resource bricolage ,Institutional theory ,Science -activist collaboration ,Case study ,Business and Management ,Marketing ,Science Studies ,Strategy ,management and organisational behaviour ,Applied economics - Published
- 2024
242. Estimands for clinical endpoints in tuberculosis treatment randomized controlled trials: a retrospective application in a completed trial.
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Weir, Isabelle, Dufault, Suzanne, and Phillips, Patrick
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Clinical trials ,Estimands ,Tuberculosis ,Humans ,Data Interpretation ,Statistical ,Randomized Controlled Trials as Topic ,Retrospective Studies ,Tuberculosis - Abstract
BACKGROUND: Randomized trials for the treatment of tuberculosis (TB) rely on a composite primary outcome to capture unfavorable treatment responses. However, variability between trials in the outcome definition and estimation methods complicates across-trial comparisons and hinders the advancement of treatment guidelines. The International Council for Harmonization (ICH) provides international regulatory standards for clinical trials. The estimand framework outlined in the recent ICH E9(R1) addendum offers a timely opportunity for randomized trials of TB treatment to adopt broadly standardized outcome definitions and analytic approaches. We previously proposed and defined four estimands for use in this context. Our objective was to evaluate how the use of these estimands and choice of estimation method impacts results and interpretation of a large phase III TB trial. METHODS: We reanalyzed participant-level data from the REMoxTB trial. We applied four estimands and various methods of estimation to assess non-inferiority of both novel 4-month treatment regimens against standard of care. RESULTS: With each of the four estimands, we reached the same conclusion as the original trial analysis that the novel regimens were not non-inferior to standard of care. Each estimand and method of estimation gave similar estimates of the treatment effect with fluctuations in variance and differences driven by the methods applied for handling intercurrent events. CONCLUSIONS: Our application of estimands defined by the ICH E9 (R1) addendum offers a formalized framework for addressing the primary TB treatment trial objective and can promote uniformity in future trials by limiting heterogeneity in trial outcome definitions. We demonstrated the utility of our proposal using data from the REMoxTB randomized trial. We outlined methods for estimating each estimand and found consistent conclusions across estimands. We recommend future late-phase TB treatment trials to implement some or all of our estimands to promote rigorous outcome definitions and reduce variability between trials. TRIAL REGISTRATION: ClinicalTrials.gov NCT00864383. Registered on March 2009.
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- 2024
243. Exploring the incidence and risk factors of reoperation for symptomatic adjacent segment disease following cervical decompression and fusion.
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Shahzad, Hania, Alvarez, Paul, Pallumeera, Mustaqueem, Bhatti, Nazihah, Yu, Elizabeth, Phillips, Frank, Khan, Safdar, and Singh, Varun
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Adjacent segment disease ,Cervical disc disorder ,Cervical fusion ,Cervical spondylosis ,Postoperative complication ,Revision surgery - Abstract
BACKGROUND: Patients with long-term follow-up after cervical decompression and fusion have often been noted to have development of adjacent segment degeneration with a smaller subset of these patients progressing to adjacent segment disease (ASD), which results in the development of new symptomatic radiculopathy or myelopathy referable to a site either directly above or below a prior fused segment. The cause of ASD is multifactorial often involving natural age-related progression of spondylosis, accelerated progression following cervical decompression and fusion, operative technique, and patient-related factors. The effect of age at the time of index cervical decompression and fusion on the need for reoperation for ASD is not fully understood. This study aims to establish underlying risk factors for the development of symptomatic cervical ASD following cervical decompression and fusion requiring reoperation in patients of various age groups. METHODS: A retrospective database review of patients aged 20 or greater with insurance claims of primary cervical decompression and fusion over the course of 11 years and 10 months (January 01, 2010-October 31, 2022) was conducted using an insurance claims database. The primary outcome was to evaluate the incidence of cervical ASD requiring reoperation amongst patients stratified by age at the time of their primary procedure. Secondary outcomes included an evaluation of various risk factors for ASD following cervical decompression and fusion including surgeon-controlled factors such as the number of levels fused and approach taken, patient cervical pathology including cervical disc disorder and cervical spondylosis, and underlying patient medical comorbidities including osteoporosis and vitamin D deficiency, and substance use. RESULTS: A total of 60,292 patient records were analyzed, where the overall reoperation incidence for symptomatic ASD was 6.57%, peaking at 8.12% among those aged 30 to 39 and decreasing with age. Regression analysis revealed ages lower than 50 years as more predictive for the development of symptomatic ASD requiring reoperation. Multivariate regression analysis identified predictive factors for reoperation, including age, Elixhauser Comorbidity Index (ECI), multiple-level surgery, cervical spondylosis, cervical disc disorder, osteoporosis, and vitamin D deficiency. Notably, these factors had a variable impact across various age groups, as revealed by subgroup analysis. CONCLUSIONS: The incidence of reoperation secondary to symptomatic ASD is 6.57%, highest in those aged 30 to 39. The surgical approach had no significant impact on the need for reoperation, but multiple-level fusions posed a consistent risk in the development of symptomatic ASD requiring reoperation. Patient factors like degenerative disc disease, spondylosis, osteoporosis, and vitamin D deficiency were associated, urging further age-specific risk assessment and nonoperative intervention exploration.
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- 2024
244. Predictive factors of symptomatic lumbar pseudoarthrosis following multilevel primary lumbar fusion.
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Shahzad, Hania, Ahmad, Moizzah, Singh, Varun, Bhatti, Nazihah, Yu, Elizabeth, Phillips, Frank, and Khan, Safdar
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Comorbidities ,Lumbar pseudoarthrosis ,Predictive factors ,Spinal fusion ,Substance use disorders ,Surgical approaches - Abstract
BACKGROUND: Lumbar spinal fusion surgery is a well-established treatment for various spinal disorders. However, one of its complications, pseudoarthrosis, poses a significant concern. This study aims to explore the incidence, time and predictive factors contributing to pseudoarthrosis in patients who have undergone lumbar fusion surgery over a 10-year period. METHODS: Data for this research was sourced from the PearlDiver database where insurance claims of patients who underwent multilevel lumbar spinal fusion between 01/01/2010 and 10/31/2022 were examined for claims of pseudoarthrosis within the 10 years of their index procedure. A variety of demographic, comorbid, and surgical factors were assessed, including age, gender, Elixhauser Comorbidity Index (ECI), surgical approach, substance use disorders and history of spinal disorders. Statistical analyses, including chi-squared tests, multivariate analysis, and cox survival analysis were employed to determine significant associations. RESULTS: Among the 76,337 patients included in this retrospective study, 2.70% were diagnosed with symptomatic lumbar pseudoarthrosis at an average of 7.38 years in a 10-year follow-up. Multivariate and Cox hazard analyses revealed that significant predictors of symptomatic pseudoarthrosis development following multilevel primary lumbar fusion include vitamin D deficiency, osteoarthritis, opioid and NSAID use, tobacco use, and a prior history of congenital spine disorders. CONCLUSIONS: In summary, this study revealed a 2.70% incidence of symptomatic lumbar pseudoarthrosis within 10 years of the index procedure. It highlighted several potential predictive factors, including comorbidities, surgical approaches, and substance use disorders, associated with the development of symptomatic pseudoarthrosis. Future research should focus on refining our understanding of these factors to improve patient outcomes and optimize healthcare resource allocation.
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- 2024
245. Latitudinal patterns in stabilizing density dependence of forest communities.
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Holík, Jan, Howe, Robert, Hubbell, Stephen, Itoh, Akira, Johnson, Daniel, Kenfack, David, Král, Kamil, Larson, Andrew, Lutz, James, Makana, Jean-Remy, Malhi, Yadvinder, McMahon, Sean, McShea, William, Mohamad, Mohizah, Nasardin, Musalmah, Nathalang, Anuttara, Norden, Natalia, Oliveira, Alexandre, Parmigiani, Renan, Perez, Rolando, Phillips, Richard, Pongpattananurak, Nantachai, Sun, I-Fang, Swanson, Mark, Tan, Sylvester, Thomas, Duncan, Thompson, Jill, Uriarte, Maria, Wolf, Amy, Yao, Tze, Zimmerman, Jess, Zuleta, Daniel, Hartig, Florian, Hülsmann, Lisa, Chisholm, Ryan, Comita, Liza, Visser, Marco, de Souza Leite, Melina, Aguilar, Salomon, Anderson-Teixeira, Kristina, Bourg, Norman, Brockelman, Warren, Bunyavejchewin, Sarayudh, Castaño, Nicolas, Chang-Yang, Chia-Hao, Chuyong, George, Clay, Keith, Davies, Stuart, Duque, Alvaro, Ediriweera, Sisira, Ewango, Corneille, and Gilbert, Gregory|Greg
- Subjects
Seedlings ,Tropical Climate ,Forests ,Trees ,Biodiversity ,Ecosystem - Abstract
Numerous studies have shown reduced performance in plants that are surrounded by neighbours of the same species1,2, a phenomenon known as conspecific negative density dependence (CNDD)3. A long-held ecological hypothesis posits that CNDD is more pronounced in tropical than in temperate forests4,5, which increases community stabilization, species coexistence and the diversity of local tree species6,7. Previous analyses supporting such a latitudinal gradient in CNDD8,9 have suffered from methodological limitations related to the use of static data10-12. Here we present a comprehensive assessment of latitudinal CNDD patterns using dynamic mortality data to estimate species-site-specific CNDD across 23 sites. Averaged across species, we found that stabilizing CNDD was present at all except one site, but that average stabilizing CNDD was not stronger toward the tropics. However, in tropical tree communities, rare and intermediate abundant species experienced stronger stabilizing CNDD than did common species. This pattern was absent in temperate forests, which suggests that CNDD influences species abundances more strongly in tropical forests than it does in temperate ones13. We also found that interspecific variation in CNDD, which might attenuate its stabilizing effect on species diversity14,15, was high but not significantly different across latitudes. Although the consequences of these patterns for latitudinal diversity gradients are difficult to evaluate, we speculate that a more effective regulation of population abundances could translate into greater stabilization of tropical tree communities and thus contribute to the high local diversity of tropical forests.
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- 2024
246. A view of the pan‐genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)
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Liang, Qihua, Muñoz‐Amatriaín, María, Shu, Shengqiang, Lo, Sassoum, Wu, Xinyi, Carlson, Joseph W, Davidson, Patrick, Goodstein, David M, Phillips, Jeremy, Janis, Nadia M, Lee, Elaine J, Liang, Chenxi, Morrell, Peter L, Farmer, Andrew D, Xu, Pei, Close, Timothy J, and Lonardi, Stefano
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Aetiology ,2.1 Biological and endogenous factors ,Zero Hunger ,Vigna ,Genome ,Plant ,Genes ,Plant ,Fabaceae ,Quantitative Trait Loci ,Plant Biology ,Crop and Pasture Production ,Crop and pasture production ,Plant biology - Abstract
Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.
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- 2024
247. Hausdorff measure of zeros of polynomials
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Murdza, Andrew, Nguyen, Khai T., and Phillips, Etienne
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Mathematics - Classical Analysis and ODEs ,Mathematics - Algebraic Geometry - Abstract
The paper provides an elementary proof establishing a sharp universal bound on the $(d-1)$-Hausdorff measure of the zeros of any nontrivial multivariable polynomial $p:\mathbb{R}^d\to\mathbb{R}$ within a $d$-dimensional cube of size $r$. This bound depends solely on the parameter $r$, the dimension $d$, and the degrees of $p$.
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- 2023
248. Formation of Mn-rich interfacial phases in Co2FexMn1-xSi thin films
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Law, Ka Ming, Thind, Arashdeep S., Pendharkar, Mihir, Patel, Sahil J., Phillips, Joshua J., Palmstrom, Chris J., Gazquez, Jaume, Borisevich, Albina, Mishra, Rohan, and Hauser, Adam J.
- Subjects
Condensed Matter - Materials Science - Abstract
We report the formation of Mn-rich regions at the interface of Co2FexMn1-xSi thin films grown on GaAs substrates by molecular beam epitaxy (MBE). Scanning transmission electron microscopy (STEM) with electron energy loss (EEL) spectrum imaging reveals that each interfacial region: (1) is 1-2 nm wide, (2) occurs irrespective of the Fe/Mn composition ratio and in both Co-rich and Co-poor films, and (3) displaces both Co and Fe indiscriminately. We also observe a Mn-depleted region in each film directly above each Mn-rich interfacial layer, roughly 3 nm in width in the x = 0 and x = 0.3 films, and 1 nm in the x = 0.7 (less Mn) film. We posit that growth energetics favor Mn diffusion to the interface even when there is no significant Ga interdiffusion into the epitaxial film. Element-specific X-ray magnetic circular dichroism (XMCD) measurements show larger Co, Fe, and Mn orbital to spin magnetic moment ratios compared to bulk values across the Co2FexMn1-xSi compositional range. The values lie between reported values for pure bulk and nanostructured Co, Fe, and Mn materials, corroborating the non-uniform, layered nature of the material on the nanoscale. Finally, SQUID magnetometry demonstrates that the films deviate from the Slater-Pauling rule for uniform films of both the expected and the measured composition. The results inform a need for care and increased scrutiny when forming Mn-based magnetic thin films on III-V semiconductors like GaAs, particularly when films are on the order of 5 nm or when interface composition is critical to spin transport or other device applications.
- Published
- 2023
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249. Simple AH algebras with the same Elliott invariant and radius of comparison
- Author
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Hirshberg, Ilan and Phillips, N. Christopher
- Subjects
Mathematics - Operator Algebras ,Primary 46L35, Secondary 46L80 - Abstract
We construct an uncountable family of pairwise nonisomorphic AH algebras with the same Elliott invariant and same radius of comparison. They can be distinguished by a local radius of comparison function, naturally defined on the positive cone of the K_0 group., Comment: 34 pages; added some details and corrected misprints
- Published
- 2023
250. Loops with universal and semi-universal flexibility
- Author
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Britten, Riley, Kinyon, Michael, Kunen, Kenneth, and Phillips, J. D.
- Subjects
Mathematics - Group Theory ,20N05 - Abstract
We study loops which are universal (that is, isotopically invariant) with respect to the property of flexibility ($xy\cdot x = x\cdot yx$). We also weaken this to semi-universality, that is, loops in which every left and right isotope is flexible, but not necessarily every isotope. One of our main results is that universally flexible, inverse property loops are Moufang loops. On the other hand, semi-universally flexible, inverse property loops are diassociative. We also examine the relationship between universally flexible loops and middle Bol loops. The paper concludes with some open problems., Comment: 13pp
- Published
- 2023
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