24,195 results on '"Brubaker A"'
Search Results
2. Efficient Neural Network Encoding for 3D Color Lookup Tables
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Zehtab, Vahid, Lindell, David B., Brubaker, Marcus A., and Brown, Michael S.
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Image and Video Processing ,I.4.0 ,I.4.2 ,I.5.0 ,I.5.1 ,I.5.4 ,I.2.0 ,I.2.6 ,I.2.10 - Abstract
3D color lookup tables (LUTs) enable precise color manipulation by mapping input RGB values to specific output RGB values. 3D LUTs are instrumental in various applications, including video editing, in-camera processing, photographic filters, computer graphics, and color processing for displays. While an individual LUT does not incur a high memory overhead, software and devices may need to store dozens to hundreds of LUTs that can take over 100 MB. This work aims to develop a neural network architecture that can encode hundreds of LUTs in a single compact representation. To this end, we propose a model with a memory footprint of less than 0.25 MB that can reconstruct 512 LUTs with only minor color distortion ($\bar{\Delta}E_M$ $\leq$ 2.0) over the entire color gamut. We also show that our network can weight colors to provide further quality gains on natural image colors ($\bar{\Delta}{E}_M$ $\leq$ 1.0). Finally, we show that minor modifications to the network architecture enable a bijective encoding that produces LUTs that are invertible, allowing for reverse color processing. Our code is available at https://github.com/vahidzee/ennelut., Comment: 14 pages, 13 figures; extended version; to appear in AAAI 2025
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- 2024
3. Quadratic unconstrained binary optimization and constraint programming approaches for lattice-based cyclic peptide docking
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Brubaker, J. Kyle, Booth, Kyle E. C., Arakawa, Akihiko, Furrer, Fabian, Ghosh, Jayeeta, Sato, Tsutomu, and Katzgraber, Helmut G.
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Quantitative Biology - Biomolecules ,Mathematics - Optimization and Control ,Physics - Chemical Physics ,Quantum Physics - Abstract
The peptide-protein docking problem is an important problem in structural biology that facilitates rational and efficient drug design. In this work, we explore modeling and solving this problem with the quantum-amenable quadratic unconstrained binary optimization (QUBO) formalism. Our work extends recent efforts by incorporating the objectives and constraints associated with peptide cyclization and peptide-protein docking in the two-particle model on a tetrahedral lattice. We propose a ``resource efficient'' QUBO encoding for this problem, and baseline its performance with a novel constraint programming (CP) approach. We implement an end-to-end framework that enables the evaluation of our methods on instances from the Protein Data Bank (PDB). Our results show that the QUBO approach, using a classical simulated annealing solver, is able to find feasible conformations for problems with up to 6 peptide residues and 34 target protein residues, but has trouble scaling beyond this problem size. In contrast, the CP approach can solve problems with up to 13 peptide residues and 34 target protein residues. We conclude that while QUBO can be used to successfully tackle this problem, its scaling limitations and the strong performance of the CP method suggest that it may not be the best choice., Comment: 30 pages (9 pages content body, 18 pages appendices), 11 figures, 6 tables
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- 2024
4. RoMo: Robust Motion Segmentation Improves Structure from Motion
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Goli, Lily, Sabour, Sara, Matthews, Mark, Brubaker, Marcus, Lagun, Dmitry, Jacobson, Alec, Fleet, David J., Saxena, Saurabh, and Tagliasacchi, Andrea
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Computer Science - Computer Vision and Pattern Recognition - Abstract
There has been extensive progress in the reconstruction and generation of 4D scenes from monocular casually-captured video. While these tasks rely heavily on known camera poses, the problem of finding such poses using structure-from-motion (SfM) often depends on robustly separating static from dynamic parts of a video. The lack of a robust solution to this problem limits the performance of SfM camera-calibration pipelines. We propose a novel approach to video-based motion segmentation to identify the components of a scene that are moving w.r.t. a fixed world frame. Our simple but effective iterative method, RoMo, combines optical flow and epipolar cues with a pre-trained video segmentation model. It outperforms unsupervised baselines for motion segmentation as well as supervised baselines trained from synthetic data. More importantly, the combination of an off-the-shelf SfM pipeline with our segmentation masks establishes a new state-of-the-art on camera calibration for scenes with dynamic content, outperforming existing methods by a substantial margin.
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- 2024
5. Scalable iterative pruning of large language and vision models using block coordinate descent
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Rosenberg, Gili, Brubaker, J. Kyle, Schuetz, Martin J. A., Zhu, Elton Yechao, Kadıoğlu, Serdar, Borujeni, Sima E., and Katzgraber, Helmut G.
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Computer Science - Machine Learning ,Mathematics - Optimization and Control ,Quantum Physics - Abstract
Pruning neural networks, which involves removing a fraction of their weights, can often maintain high accuracy while significantly reducing model complexity, at least up to a certain limit. We present a neural network pruning technique that builds upon the Combinatorial Brain Surgeon, but solves an optimization problem over a subset of the network weights in an iterative, block-wise manner using block coordinate descent. The iterative, block-based nature of this pruning technique, which we dub ``iterative Combinatorial Brain Surgeon'' (iCBS) allows for scalability to very large models, including large language models (LLMs), that may not be feasible with a one-shot combinatorial optimization approach. When applied to large models like Mistral and DeiT, iCBS achieves higher performance metrics at the same density levels compared to existing pruning methods such as Wanda. This demonstrates the effectiveness of this iterative, block-wise pruning method in compressing and optimizing the performance of large deep learning models, even while optimizing over only a small fraction of the weights. Moreover, our approach allows for a quality-time (or cost) tradeoff that is not available when using a one-shot pruning technique alone. The block-wise formulation of the optimization problem enables the use of hardware accelerators, potentially offsetting the increased computational costs compared to one-shot pruning methods like Wanda. In particular, the optimization problem solved for each block is quantum-amenable in that it could, in principle, be solved by a quantum computer., Comment: 16 pages, 6 figures, 5 tables
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- 2024
6. Advancing Large Language Models for Spatiotemporal and Semantic Association Mining of Similar Environmental Events
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Tian, Yuanyuan, Li, Wenwen, Hu, Lei, Chen, Xiao, Brook, Michael, Brubaker, Michael, Zhang, Fan, and Liljedahl, Anna K.
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Computer Science - Information Retrieval ,Computer Science - Artificial Intelligence - Abstract
Retrieval and recommendation are two essential tasks in modern search tools. This paper introduces a novel retrieval-reranking framework leveraging Large Language Models (LLMs) to enhance the spatiotemporal and semantic associated mining and recommendation of relevant unusual climate and environmental events described in news articles and web posts. This framework uses advanced natural language processing techniques to address the limitations of traditional manual curation methods in terms of high labor cost and lack of scalability. Specifically, we explore an optimized solution to employ cutting-edge embedding models for semantically analyzing spatiotemporal events (news) and propose a Geo-Time Re-ranking (GT-R) strategy that integrates multi-faceted criteria including spatial proximity, temporal association, semantic similarity, and category-instructed similarity to rank and identify similar spatiotemporal events. We apply the proposed framework to a dataset of four thousand Local Environmental Observer (LEO) Network events, achieving top performance in recommending similar events among multiple cutting-edge dense retrieval models. The search and recommendation pipeline can be applied to a wide range of similar data search tasks dealing with geospatial and temporal data. We hope that by linking relevant events, we can better aid the general public to gain an enhanced understanding of climate change and its impact on different communities.
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- 2024
7. A Random-Key Optimizer for Combinatorial Optimization
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Chaves, Antonio A., Resende, Mauricio G. C., Schuetz, Martin J. A., Brubaker, J. Kyle, Katzgraber, Helmut G., de Arruda, Edilson F., and Silva, Ricardo M. A.
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Computer Science - Artificial Intelligence ,Condensed Matter - Disordered Systems and Neural Networks ,Computer Science - Neural and Evolutionary Computing ,Mathematics - Optimization and Control ,90-02, 90B40, 90C27 ,G.1.6 ,G.2.1 ,I.2.8 - Abstract
This paper presents the Random-Key Optimizer (RKO), a versatile and efficient stochastic local search method tailored for combinatorial optimization problems. Using the random-key concept, RKO encodes solutions as vectors of random keys that are subsequently decoded into feasible solutions via problem-specific decoders. The RKO framework is able to combine a plethora of classic metaheuristics, each capable of operating independently or in parallel, with solution sharing facilitated through an elite solution pool. This modular approach allows for the adaptation of various metaheuristics, including simulated annealing, iterated local search, and greedy randomized adaptive search procedures, among others. The efficacy of the RKO framework, implemented in C++, is demonstrated through its application to three NP-hard combinatorial optimization problems: the alpha-neighborhood p-median problem, the tree of hubs location problem, and the node-capacitated graph partitioning problem. The results highlight the framework's ability to produce high-quality solutions across diverse problem domains, underscoring its potential as a robust tool for combinatorial optimization., Comment: 54 pages, 16 figures, 8 tables
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- 2024
8. A policy toolkit for authorship and dissemination policies may benefit NIH research consortia.
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Bavendam, Tamara, Connett, John, Claussen, Amy, Lewis, Cora, Rudser, Kyle, Sutcliffe, Siobhan, Wyman, Jean, Miller, Janis, Brubaker, Linda, and Nodora, Jesse
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Author contributions ,author responsibilities ,corporate authorship ,external authorship ,guidelines ,publication duplication ,writing teams ,Humans ,Authorship ,Writing ,Language ,Policy - Abstract
Authorship and dissemination policies vary across NIH research consortia. We aimed to describe elements of real-life policies in use by eligible U01 clinical research consortia. Principal investigators of eligible, active U01 clinical research projects identified in the NIH Research Portfolio Online Reporting Tools database shared relevant policies. The characteristics of key policy elements, determined a priori, were reviewed and quantified, when appropriate. Twenty one of 81 research projects met search criteria and provided policies. K elements (e.g., in quotations): manuscript proposals reviewed and approved by committee (90%); guidelines for acknowledgements (86%); writing team formation (71%); process for final manuscript review and approval (71%), responsibilities for lead author (67%), guidelines for other types of publications (67%); draft manuscript review and approval (62%); recommendation for number of members per consortium site (57%); and requirement to identify individual contributions in the manuscript (19%). Authorship/dissemination policies for large team science research projects are highly variable. Creation of an NIH policies repository and accompanying toolkit with model language and recommended key elements could improve comprehensiveness, ethical integrity, and efficiency in team science work while reducing burden and cost on newly funded consortia and directing time and resources to scientific endeavors.
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- 2024
9. Kirillov's conjecture on Hecke-Grothendieck polynomials
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Brubaker, Ben, Dasher, A. Suki, Hu, Michael, Jain, Nupur, Li, Yifan, Lin, Yi, Mihaila, Maria, Tran, Van, and Ünel, I. Deniz
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Mathematics - Combinatorics ,Mathematical Physics ,Mathematics - Representation Theory - Abstract
We use algebraic methods in statistical mechanics to represent a multi-parameter class of polynomials in severable variables as partition functions of a new family of solvable lattice models. The class of polynomials, defined by A.N. Kirillov, is derived from the largest class of divided difference operators satisfying the braid relations of Cartan type $A$. It includes as specializations Schubert, Grothendieck, and dual-Grothendieck polynomials among others. In particular, our results prove positivity conjectures of Kirillov for the subfamily of Hecke--Grothendieck polynomials, while the larger family is shown to exhibit rare instances of negative coefficients.
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- 2024
10. Introduction
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Boyer, T, Blunden, J, Dunn, RJH, Ades, Melanie, Adler, Robert, Adusumilli, Susheel, Agyakwah, W, Ahmadpour, Somayeh, Aldeco, Laura S, Alexander, Michael A, Alexe, Mihai, Alfaro, Eric J, Allan, Richard P, Allgood, Adam, Alves, Lincoln M, Amador, Jorge A, Amaya, Dillon J, Amory, Charles, Anderson, John, Andrade, B, Andreassen, Liss Marie, Anneville, Orlane, Aono, Yasuyuki, Arguez, Anthony, Armenteras Pascual, Dolores, Arosio, Carlo, Asher, Elizabeth, Augustine, John A, Avalos, Grinia, Azorin-Molina, Cesar, Baez-Villanueva, Oscar M, Baiman, Rebecca, Ballinger, Thomas J, Banwell, Alison F, Bardin, M Yu, Barichivich, J, Barreira, Sandra, Beadling, Rebecca L, Beauchemin, Marc, Beck, Hylke E, Becker, Emily J, Beckley, Brian, Bekele, E, Bellouin, Nicolas, Benedetti, Angela, Berne, Christine, Berner, Logan T, Bernhard, Germar H, Bhatt, Uma S, Bigalke, Siiri, Bissolli, Peter, Bjerke, Jarle W, Blake, Eric S, Blannin, Josh, Blenkinsop, Stephen, Bochníček, Oliver, Bock, Olivier, Bodin, Xavier, Bonte, Olivier, Bosilovich, Michael G, Boucher, Olivier, Box, Jason E, Bozkurt, Deniz, Brettschneider, Brian, Bringas, Francis G, Brubaker, Mike, Buehler, Stefan A, Bukunt, Brandon, Burgess, David, Butler, Amy H, Byrne, Michael P, Calderón, Blanca, Camargo, Suzana J, Campbell, Jayaka, Campos, Diego, Cappucci, Fabrizio, Carrea, Laura, Carter, Brendan R, Cerveny, Randall, Cetinić, Ivona, Chambers, Don P, Chan, Duo, Chandler, Elise, Chang, Kai-Lan, Charlton, Candice S, Chen, Jack, Chen, Lin, Cheng, Lijing, Cheng, Vincent YS, Chisholm, Lucy, Christiansen, Hanne H, Christy, John R, Chung, Eui-Seok, Ciasto, Laura M, Clarke, Leonardo, Clem, Kyle R, Clingan, Scott, Coelho, Caio AS, Coldewey-Egbers, Melanie, and Colwell, Steve
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Earth Sciences ,Geology ,Climate Action ,Astronomical and Space Sciences ,Atmospheric Sciences ,Physical Geography and Environmental Geoscience ,Meteorology & Atmospheric Sciences ,Atmospheric sciences ,Climate change science - Abstract
Abstract: —J. Blunden and T. Boyer In 2023, La Niña conditions that generally prevailed in the eastern Pacific Ocean from mid-2020 into early 2023 gave way to a strong El Niño by October. Atmospheric concentrations of Earth’s major greenhouse gases—carbon dioxide, methane, and nitrous oxide—all increased to record-high levels. The annual global average carbon dioxide concentration in the atmosphere rose to 419.3±0.1 ppm, which is 50% greater than the pre-industrial level. The growth from 2022 to 2023 was 2.8 ppm, the fourth highest in the record since the 1960s. The combined short-term effects of El Niño and the long-term effects of increasing levels of heat-trapping gases in the atmosphere contributed to new records for many essential climate variables reported here. The annual global temperature across land and oceans was the highest in records dating as far back as 1850, with the last seven months (June–December) having each been record warm. Over land, the globally averaged temperature was also record high. Dozens of countries reported record or near-record warmth for the year, including China and continental Europe as a whole (warmest on record), India and Russia (second warmest), and Canada (third warmest). Intense and widespread heatwaves were reported around the world. In Vietnam, an all-time national maximum temperature record of 44.2°C was observed at Tuong Duong on 7 May, surpassing the previous record of 43.4°C at Huong Khe on 20 April 2019. In Brazil, the air temperature reached 44.8°C in Araçuaí in Minas Gerais on 20 November, potentially a new national record and 12.8°C above normal. The effect of rising temperatures was apparent in the cryosphere, where snow cover extent by June 2023 was the smallest in the 56-year record for North America and seventh smallest for the Northern Hemisphere overall. Heatwaves contributed to the greatest average mass balance loss for Alpine glaciers around the world since the start of the record in 1970. Due to rapid volume loss beginning in 2021, St. Anna Glacier in Switzerland and Ice Worm Glacier in the United States disappeared completely. In August, as a direct result of glacial thinning over the past 20 years, a glacial lake on a tributary of the Mendenhall Glacier in Alaska burst through its ice dam and caused unprecedented flooding on Mendenhall River near Juneau. Across the Arctic, the annual surface air temperature was the fourth highest in the 124-year record, and summer (July–September) was record warm. Smaller-than-normal snow cover extent in May and June contributed to the third-highest average peak tundra greenness in the 24-year record. In September, Arctic minimum sea ice extent was the fifth smallest in the 45-year satellite record. The 17 lowest September extents have all occurred in the last 17 years. In Antarctica, temperatures for much of the year were up to 6°C above average over the Weddell Sea and along coastal Dronning Maud Land. The Antarctic Peninsula also experienced well-above-average temperatures during the 2022/23 melt season, which contributed to its fourth consecutive summer of above-average surface melt. On 21 February, Antarctic sea ice extent and sea ice area both reached all-time lows, surpassing records set just a year earlier. Over the course of the year, new daily record-low sea ice extents were set on 278 days. In some instances, these daily records were set by a large margin, for example, the extent on 6 July was 1.8 million km2 lower than the previous record low for that day. Across the global oceans, the annual sea surface temperature was the highest in the 170-year record, far surpassing the previous record of 2016 by 0.13°C. Daily and monthly records were set from March onward, including an historic-high daily global mean sea surface temperature of 18.99°C recorded on 22 August. Approximately 94% of the ocean surface experienced at least one marine heatwave in 2023, while 27% experienced at least one cold spell. Globally averaged ocean heat content from the surface to 2000-m depth was record high in 2023, increasing at a rate equivalent to ∼0.7 Watts per square meter of energy applied over Earth’s surface. Global mean sea level was also record high for the 12th consecutive year, reaching 101.4 mm above the 1993 average when satellite measurements began, an increase of 8.1±1.5 mm over 2022 and the third highest year-over-year increase in the record. A total of 82 named tropical storms were observed during the Northern and Southern Hemispheres’ storm seasons, below the 1991–2020 average of 87. Hurricane Otis became the strongest landfalling hurricane on record for the west coast of Mexico at 140 kt (72 m s−1), causing at least 52 fatalities and $12–16 billion U.S. dollars in damage. Freddy became the world’s longest-lived tropical cyclones on record, developing into a tropical cyclone on 6 February and finally dissipating on 12 March. Freddy crossed the full width of the Indian Ocean and made one landfall in Madagascar and two in Mozambique. In the Mediterranean Sea—outside of traditional tropical cyclone basins—heavy rains and flooding from Storm Daniel killed more than 4300 people and left more than 8000 missing in Libya. The record-warm temperatures in 2023 created conditions that helped intensify the hydrological cycle. Measurements of total-column water vapor in the atmosphere were the highest on record, while the fraction of cloud area in the sky was the lowest since records began in 1980. The annual global mean precipitation total over land surfaces for 2023 was among the lowest since 1979, but global one-day maximum totals were close to average, indicating an increase in rainfall intensity. In July, record-high areas of land across the globe (7.9%) experienced extreme drought, breaking the previous record of 6.2% in July 2022. Overall, 29.7% of land experienced moderate or worse categories of drought during the year, also a record. Mexico reported its driest (and hottest) year since the start of its record in 1950. In alignment with hot and prolonged dry conditions, Canada experienced its worst national wildfire season on record. Approximately 15 million hectares burned across the country, which was more than double the previous record from 1989. Smoke from the fires were transported far into the United States and even to western European countries. August to October 2023 was the driest three-month period in Australia in the 104-year record. Millions of hectares of bushfires burned for weeks in the Northern Territory. In South America, extreme drought developed in the latter half of the year through the Amazon basin. By the end of October, the Rio Negro at Manaus, a major tributary of the Amazon River, fell to its lowest water level since records began in 1902. The transition from La Niña to El Niño helped bring relief to the prolonged drought conditions in equatorial eastern Africa. However, El Niño along with positive Indian Ocean dipole conditions also contributed to excessive rainfall that resulted in devastating floods over southeastern Ethiopia, Somalia, and Kenya during October to December that displaced around 1.5 million people. On 5 September, the town of Zagora, Greece, broke a national record for highest daily rainfall (754 mm in 21 hours, after which the station ceased reporting) due to Storm Daniel; this one-day accumulation was close to Zagora’s normal annual total.
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- 2024
11. CryoSPIN: Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
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Shekarforoush, Shayan, Lindell, David B., Brubaker, Marcus A., and Fleet, David J.
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Cryo-EM is an increasingly popular method for determining the atomic resolution 3D structure of macromolecular complexes (eg, proteins) from noisy 2D images captured by an electron microscope. The computational task is to reconstruct the 3D density of the particle, along with 3D pose of the particle in each 2D image, for which the posterior pose distribution is highly multi-modal. Recent developments in cryo-EM have focused on deep learning for which amortized inference has been used to predict pose. Here, we address key problems with this approach, and propose a new semi-amortized method, cryoSPIN, in which reconstruction begins with amortized inference and then switches to a form of auto-decoding to refine poses locally using stochastic gradient descent. Through evaluation on synthetic datasets, we demonstrate that cryoSPIN is able to handle multi-modal pose distributions during the amortized inference stage, while the later, more flexible stage of direct pose optimization yields faster and more accurate convergence of poses compared to baselines. On experimental data, we show that cryoSPIN outperforms the state-of-the-art cryoAI in speed and reconstruction quality., Comment: NeurIPS 2024, Project webpage: https://shekshaa.github.io/semi-amortized-cryoem
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- 2024
12. Special Functions for Hyperoctahedral Groups Using Bosonic Lattice Models: Special Functions for Hyperoctahedral Groups
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Brubaker, Ben, Grodzicki, Will, and Schultz, Andrew
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- 2024
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13. PolyOculus: Simultaneous Multi-view Image-Based Novel View Synthesis
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Yu, Jason J., Aumentado-Armstrong, Tristan, Forghani, Fereshteh, Derpanis, Konstantinos G., Brubaker, Marcus A., Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Leonardis, Aleš, editor, Ricci, Elisa, editor, Roth, Stefan, editor, Russakovsky, Olga, editor, Sattler, Torsten, editor, and Varol, Gül, editor
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- 2025
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14. Watch Your Steps: Local Image and Scene Editing by Text Instructions
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Mirzaei, Ashkan, Aumentado-Armstrong, Tristan, Brubaker, Marcus A., Kelly, Jonathan, Levinshtein, Alex, Derpanis, Konstantinos G., Gilitschenski, Igor, Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Leonardis, Aleš, editor, Ricci, Elisa, editor, Roth, Stefan, editor, Russakovsky, Olga, editor, Sattler, Torsten, editor, and Varol, Gül, editor
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- 2025
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15. PolyOculus: Simultaneous Multi-view Image-based Novel View Synthesis
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Yu, Jason J., Aumentado-Armstrong, Tristan, Forghani, Fereshteh, Derpanis, Konstantinos G., and Brubaker, Marcus A.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
This paper considers the problem of generative novel view synthesis (GNVS), generating novel, plausible views of a scene given a limited number of known views. Here, we propose a set-based generative model that can simultaneously generate multiple, self-consistent new views, conditioned on any number of views. Our approach is not limited to generating a single image at a time and can condition on a variable number of views. As a result, when generating a large number of views, our method is not restricted to a low-order autoregressive generation approach and is better able to maintain generated image quality over large sets of images. We evaluate our model on standard NVS datasets and show that it outperforms the state-of-the-art image-based GNVS baselines. Further, we show that the model is capable of generating sets of views that have no natural sequential ordering, like loops and binocular trajectories, and significantly outperforms other methods on such tasks.
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- 2024
16. Cruising Queer HCI on the DL: A Literature Review of LGBTQ+ People in HCI
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Taylor, Jordan, Simpson, Ellen, Tran, Anh-Ton, Brubaker, Jed, Fox, Sarah, and Zhu, Haiyi
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Computer Science - Human-Computer Interaction - Abstract
LGBTQ+ people have received increased attention in HCI research, paralleling a greater emphasis on social justice in recent years. However, there has not been a systematic review of how LGBTQ+ people are researched or discussed in HCI. In this work, we review all research mentioning LGBTQ+ people across the HCI venues of CHI, CSCW, DIS, and TOCHI. Since 2014, we find a linear growth in the number of papers substantially about LGBTQ+ people and an exponential increase in the number of mentions. Research about LGBTQ+ people tends to center experiences of being politicized, outside the norm, stigmatized, or highly vulnerable. LGBTQ+ people are typically mentioned as a marginalized group or an area of future research. We identify gaps and opportunities for (1) research about and (2) the discussion of LGBTQ+ in HCI and provide a dataset to facilitate future Queer HCI research.
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- 2024
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17. Microbiologist in the Clinic: Postmenopausal Woman with Chronic OAB and Positive Urine Culture
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Brubaker, Linda, Horsley, Harry, Khasriya, Rajvinder, and Wolfe, Alan J.
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- 2024
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18. The 'Colonial Impulse' of Natural Language Processing: An Audit of Bengali Sentiment Analysis Tools and Their Identity-based Biases
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Das, Dipto, Guha, Shion, Brubaker, Jed, and Semaan, Bryan
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Computer Science - Computation and Language ,Computer Science - Computers and Society ,Computer Science - Human-Computer Interaction ,Computer Science - Machine Learning - Abstract
While colonization has sociohistorically impacted people's identities across various dimensions, those colonial values and biases continue to be perpetuated by sociotechnical systems. One category of sociotechnical systems--sentiment analysis tools--can also perpetuate colonial values and bias, yet less attention has been paid to how such tools may be complicit in perpetuating coloniality, although they are often used to guide various practices (e.g., content moderation). In this paper, we explore potential bias in sentiment analysis tools in the context of Bengali communities that have experienced and continue to experience the impacts of colonialism. Drawing on identity categories most impacted by colonialism amongst local Bengali communities, we focused our analytic attention on gender, religion, and nationality. We conducted an algorithmic audit of all sentiment analysis tools for Bengali, available on the Python package index (PyPI) and GitHub. Despite similar semantic content and structure, our analyses showed that in addition to inconsistencies in output from different tools, Bengali sentiment analysis tools exhibit bias between different identity categories and respond differently to different ways of identity expression. Connecting our findings with colonially shaped sociocultural structures of Bengali communities, we discuss the implications of downstream bias of sentiment analysis tools.
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- 2024
19. Generative Ghosts: Anticipating Benefits and Risks of AI Afterlives
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Morris, Meredith Ringel and Brubaker, Jed R.
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Computer Science - Computers and Society ,Computer Science - Artificial Intelligence - Abstract
As AI systems quickly improve in both breadth and depth of performance, they lend themselves to creating increasingly powerful and realistic agents, including the possibility of agents modeled on specific people. We anticipate that within our lifetimes it may become common practice for people to create custom AI agents to interact with loved ones and/or the broader world after death; indeed, the past year has seen a boom in startups purporting to offer such services. We call these generative ghosts, since such agents will be capable of generating novel content rather than merely parroting content produced by their creator while living. In this paper, we reflect on the history of technologies for AI afterlives, including current early attempts by individual enthusiasts and startup companies to create generative ghosts. We then introduce a novel design space detailing potential implementations of generative ghosts, and use this analytic framework to ground discussion of the practical and ethical implications of various approaches to designing generative ghosts, including potential positive and negative impacts on individuals and society. Based on these considerations, we lay out a research agenda for the AI and HCI research communities to better understand the risk/benefit landscape of this novel technology so as to ultimately empower people who wish to create and interact with AI afterlives to do so in a beneficial manner., Comment: version 4, updated to include new references and examples
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- 2024
20. Efficient high-resolution refinement in cryo-EM with stochastic gradient descent
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Toader, Bogdan, Brubaker, Marcus A., and Lederman, Roy R.
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Mathematics - Numerical Analysis ,Quantitative Biology - Biomolecules - Abstract
Electron cryomicroscopy (cryo-EM) is an imaging technique widely used in structural biology to determine the three-dimensional structure of biological molecules from noisy two-dimensional projections with unknown orientations. As the typical pipeline involves processing large amounts of data, efficient algorithms are crucial for fast and reliable results. The stochastic gradient descent (SGD) algorithm has been used to improve the speed of ab initio reconstruction, which results in a first, low-resolution estimation of the volume representing the molecule of interest, but has yet to be applied successfully in the high-resolution regime, where expectation-maximization algorithms achieve state-of-the-art results, at a high computational cost. In this article, we investigate the conditioning of the optimization problem and show that the large condition number prevents the successful application of gradient descent-based methods at high resolution. Our results include a theoretical analysis of the condition number of the optimization problem in a simplified setting where the individual projection directions are known, an algorithm based on computing a diagonal preconditioner using Hutchinson's diagonal estimator, and numerical experiments showing the improvement in the convergence speed when using the estimated preconditioner with SGD. The preconditioned SGD approach can potentially enable a simple and unified approach to ab initio reconstruction and high-resolution refinement with faster convergence speed and higher flexibility, and our results are a promising step in this direction., Comment: 22 pages, 7 figures
- Published
- 2023
21. Harnessing the power within: engineering the microbiome for enhanced gynecologic health
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Brennan, Caitriona, Chan, Kristina, Kumar, Tanya, Maissy, Erica, Brubaker, Linda, Dothard, Marisol I, Gilbert, Jack A, Gilbert, Katharine E, Lewis, Amanda L, Thackray, Varykina G, Zarrinpar, Amir, and Knight, Rob
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Microbiology ,Biological Sciences ,Biomedical and Clinical Sciences ,Biotechnology ,Microbiome ,Women's Health ,Dietary Supplements ,Complementary and Integrative Health ,Contraception/Reproduction ,Prevention ,Nutrition ,1.1 Normal biological development and functioning ,Oral and gastrointestinal ,Good Health and Well Being ,Female ,Humans ,Animals ,Microbiota ,Gastrointestinal Microbiome ,Probiotics ,Prebiotics ,Reproduction ,microbiome manipulation ,gynecologic health ,polycystic ovary syndrome ,bacterial vaginosis ,endometriosis - Abstract
AbstractAlthough numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome's influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiomes for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working toward making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions.Lay summaryManipulating the microbiome has recently entered popular culture, with various diets thought to aid the microbes that live within us. These microbes live in different locations of our body and accordingly help us digest food, modulate our immune system, and influence reproductive health. The role of the microbes living in and influencing the female reproductive tract remains understudied despite known roles in common conditions such as vulvovaginal candidiasis (affecting 75% of females in their lifetime), bacterial vaginosis (25% of females in their lifetime), cervical HPV infection (80% of females in their lifetime), endometriosis (6-10% of females of reproductive age), and polycystic ovary syndrome (10-12% of females of reproductive age). Here, we review four different approaches used to manipulate the female reproductive tract and gastrointestinal system microbiomes: microbiota transplants, probiotics, prebiotics, and dietary interventions, and the use of engineered microbial strains. In doing so, we aim to stimulate discussion on new ways to understand and treat female reproductive health conditions.
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- 2024
22. Sedentary behaviour may cause differences in physical outcomes and activities of daily living in older cardiovascular disease patients participating in phase I cardiac rehabilitation
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Izawa, Kazuhiro P., Ishihara, Kodai, Kanejima, Yuji, Kitamura, Masahiro, Ogura, Asami, Kubo, Ikko, Oka, Koichiro, Brubaker, Peter H., Nagashima, Hitomi, Tawa, Hideto, Matsumoto, Daisuke, and Shimizu, Ikki
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- 2024
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23. Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer’s disease-associated metabolites
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Ball, Brendan K., Kuhn, Madison K., Fleeman Bechtel, Rebecca M., Proctor, Elizabeth A., and Brubaker, Douglas K.
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- 2024
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24. Reconstructive Latent-Space Neural Radiance Fields for Efficient 3D Scene Representations
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Aumentado-Armstrong, Tristan, Mirzaei, Ashkan, Brubaker, Marcus A., Kelly, Jonathan, Levinshtein, Alex, Derpanis, Konstantinos G., and Gilitschenski, Igor
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Computer Science - Computer Vision and Pattern Recognition ,I.2.10 - Abstract
Neural Radiance Fields (NeRFs) have proven to be powerful 3D representations, capable of high quality novel view synthesis of complex scenes. While NeRFs have been applied to graphics, vision, and robotics, problems with slow rendering speed and characteristic visual artifacts prevent adoption in many use cases. In this work, we investigate combining an autoencoder (AE) with a NeRF, in which latent features (instead of colours) are rendered and then convolutionally decoded. The resulting latent-space NeRF can produce novel views with higher quality than standard colour-space NeRFs, as the AE can correct certain visual artifacts, while rendering over three times faster. Our work is orthogonal to other techniques for improving NeRF efficiency. Further, we can control the tradeoff between efficiency and image quality by shrinking the AE architecture, achieving over 13 times faster rendering with only a small drop in performance. We hope that our approach can form the basis of an efficient, yet high-fidelity, 3D scene representation for downstream tasks, especially when retaining differentiability is useful, as in many robotics scenarios requiring continual learning.
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- 2023
25. Characterization of a SiPM-based monolithic neutron scatter camera using dark counts
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Balajthy, J., Brown, J., Brubaker, E., Cabrera-Palmer, B., Cates, J., Goldblum, B. L., Folsom, M., Hausladen, P., Keefe, K., Nattress, J., Negut, V., Nishimura, K., Steele, J., and Ziock, K.
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Physics - Instrumentation and Detectors - Abstract
We report on the design and characterization of a prototype monolithic neutron scatter camera that is intended to significantly improve upon the geometrical shortcomings of conventional neutron cameras. The detector consists of a 50 mm $\times$ 56 mm $\times$ 60 mm monolithic block of EJ-204 plastic scintillator instrumented on two faces with arrays of 64 Hamamatsu S13360-6075PE silicon photomultipliers (SiPMs). The electronic crosstalk is limited to < 5% between adjacent channels and < 0.1% between all other channel pairs. SiPMs introduce a significantly elevated dark count rate over PMTs, as well as correlated noise from after-pulsing and optical crosstalk. In this article, we characterize the dark count rate and optical crosstalk and present a modified event reconstruction likelihood function that accounts for them. We find that the average dark count rate per SiPM is 4.3 MHz with a standard deviation of 1.5 MHz among devices. The analysis method we employ to measure internal optical crosstalk also naturally yields the mean and width of the single-electron pulse height. We calculate separate contributions to the width of the single-electron pulse-height from electronic noise and avalanche fluctuations. We demonstrate a timing resolution for a single-photon pulse to be 128 ($\pm$4) ps. Finally, coincidence analysis is employed to measure external (pixel-to-pixel) optical crosstalk. We present a map of the average external crosstalk probability between 2-by-4 groups of SiPMs, as well as the in-situ timing characteristics extracted from the coincidence analysis. Further work is needed to characterize the performance of the camera at reconstructing single- and double-site interactions, as well as image reconstruction.
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- 2023
26. Dual-Camera Joint Deblurring-Denoising
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Shekarforoush, Shayan, Walia, Amanpreet, Brubaker, Marcus A., Derpanis, Konstantinos G., and Levinshtein, Alex
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Recent image enhancement methods have shown the advantages of using a pair of long and short-exposure images for low-light photography. These image modalities offer complementary strengths and weaknesses. The former yields an image that is clean but blurry due to camera or object motion, whereas the latter is sharp but noisy due to low photon count. Motivated by the fact that modern smartphones come equipped with multiple rear-facing camera sensors, we propose a novel dual-camera method for obtaining a high-quality image. Our method uses a synchronized burst of short exposure images captured by one camera and a long exposure image simultaneously captured by another. Having a synchronized short exposure burst alongside the long exposure image enables us to (i) obtain better denoising by using a burst instead of a single image, (ii) recover motion from the burst and use it for motion-aware deblurring of the long exposure image, and (iii) fuse the two results to further enhance quality. Our method is able to achieve state-of-the-art results on synthetic dual-camera images from the GoPro dataset with five times fewer training parameters compared to the next best method. We also show that our method qualitatively outperforms competing approaches on real synchronized dual-camera captures., Comment: Project webpage: http://shekshaa.github.io/Joint-Deblurring-Denoising/
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- 2023
27. Watch Your Steps: Local Image and Scene Editing by Text Instructions
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Mirzaei, Ashkan, Aumentado-Armstrong, Tristan, Brubaker, Marcus A., Kelly, Jonathan, Levinshtein, Alex, Derpanis, Konstantinos G., and Gilitschenski, Igor
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Denoising diffusion models have enabled high-quality image generation and editing. We present a method to localize the desired edit region implicit in a text instruction. We leverage InstructPix2Pix (IP2P) and identify the discrepancy between IP2P predictions with and without the instruction. This discrepancy is referred to as the relevance map. The relevance map conveys the importance of changing each pixel to achieve the edits, and is used to to guide the modifications. This guidance ensures that the irrelevant pixels remain unchanged. Relevance maps are further used to enhance the quality of text-guided editing of 3D scenes in the form of neural radiance fields. A field is trained on relevance maps of training views, denoted as the relevance field, defining the 3D region within which modifications should be made. We perform iterative updates on the training views guided by rendered relevance maps from the relevance field. Our method achieves state-of-the-art performance on both image and NeRF editing tasks. Project page: https://ashmrz.github.io/WatchYourSteps/, Comment: Project page: https://ashmrz.github.io/WatchYourSteps/
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- 2023
28. Effects of variation in sample storage conditions and swab order on 16S vaginal microbiome analyses.
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Kumar, Tanya, Bryant, MacKenzie, Cantrell, Kalen, Song, Se, McDonald, Daniel, Tubb, Helena, Farmer, Sawyer, Lewis, Amanda, Lukacz, Emily, Brubaker, Linda, and Knight, Robin
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16S ,microbiome ,preservation method ,sample collection ,sample storage ,vaginal microbiome - Abstract
The composition of the human vaginal microbiome has been linked to a variety of medical conditions including yeast infection, bacterial vaginosis, and sexually transmitted infection. The vaginal microbiome is becoming increasingly acknowledged as a key factor in personal health, and it is essential to establish methods to collect and process accurate samples with self-collection techniques to allow large, population-based studies. In this study, we investigate if using AssayAssure Genelock, a nucleic acid preservative, introduces microbial biases in self-collected vaginal samples. To our knowledge, we also contribute some of the first evidence regarding the impacts of multiple swabs taken at one time point. Vaginal samples have relatively low biomass, so the ability to collect multiple swabs from a unique participant at a single time would greatly improve the replicability and data available for future studies. This will hopefully lay the groundwork to gain a more complete and accurate understanding of the vaginal microbiome.
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- 2024
29. Association Between Maternal Depression and Lower Urinary Tract Symptoms in Their Primary School-Age Daughters: A Birth Cohort Study.
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Cunningham, Shayna, Lindberg, Sarah, Joinson, Carol, Shoham, David, Chu, Haitao, Newman, Diane, Epperson, Neill, Brubaker, Linda, Low, Lisa, Camenga, Deepa, LaCoursiere, D, Meister, Melanie, Kenton, Kimberly, Sutcliffe, Siobhan, Markland, Alayne, Gahagan, Sheila, Coyne-Beasley, Tamera, and Berry, Amanda
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Pregnancy ,Child ,Female ,Humans ,Cohort Studies ,Depression ,Postpartum ,Longitudinal Studies ,Depression ,Nuclear Family ,Nocturia ,Lower Urinary Tract Symptoms ,Schools - Abstract
PURPOSE: Although maternal depression is associated with adverse outcomes in women and children, its relationship with lower urinary tract symptoms (LUTS) in offspring is less well-characterized. We examined the association between prenatal and postpartum maternal depression and LUTS in primary school-age daughters. DESIGN: Observational cohort study. SUBJECTS AND SETTING: The sample comprised 7148 mother-daughter dyads from the Avon Longitudinal Study of Parents and Children. METHOD: Mothers completed questionnaires about depressive symptoms at 18 and 32 weeks gestation and 21 months postpartum and their childrens LUTS (urinary urgency, nocturia, and daytime and nighttime wetting) at 6, 7, and 9 years of age. Multivariable logistic regression models were used to estimate the association between maternal depression and LUTS in daughters. RESULTS: Compared to daughters of mothers without depression, those born to mothers with prenatal and postpartum depression had higher odds of LUTS, including urinary urgency (adjusted odds ratio [aOR] range = 1.99-2.50) and nocturia (aOR range = 1.67-1.97) at 6, 7, and 9 years of age. Additionally, daughters born to mothers with prenatal and postpartum depression had higher odds of daytime wetting (aOR range = 1.81-1.99) and nighttime wetting (aOR range = 1.63-1.95) at 6 and 7 years of age. Less consistent associations were observed for depression limited to the prenatal or postpartum periods only. CONCLUSIONS: Exposure to maternal depression in the prenatal and postpartum periods was associated with an increased likelihood of LUTS in daughters. This association may be an important opportunity for childhood LUTS prevention. Prevention strategies should reflect an understanding of potential biological and environmental mechanisms through which maternal depression may influence childhood LUTS.
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- 2024
30. “So Just with every Facet, Every Side of this Journey, They Have Somebody Walking alongside with Them”: Practitioners’ Perspectives of the Lethality Assessment Program as a Collaborative Model
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Goodson, Amanda and Brubaker, Sarah Jane
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- 2024
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31. The Association between Psychosocial Stressors and Gestational Weight Gain: Analysis of the National Pregnancy Risk Assessment Monitoring System (PRAMS) Results from 2012 to 2015
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Mehta-Lee, Shilpi S., Echevarria, Ghislaine C., Brubaker, Sara G., Yaghoubian, Yasaman, Long, Sara E., and Dolin, Cara D.
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- 2024
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32. Prenatal phthalate exposure and fetal penile length and width
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Salvi, Nicole B., Ghassabian, Akhgar, Brubaker, Sara G., Liu, Hongxiu, Kahn, Linda G., Trasande, Leonardo, and Mehta-Lee, Shilpi S.
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- 2024
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33. Explainable AI using expressive Boolean formulas
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Rosenberg, Gili, Brubaker, J. Kyle, Schuetz, Martin J. A., Salton, Grant, Zhu, Zhihuai, Zhu, Elton Yechao, Kadıoğlu, Serdar, Borujeni, Sima E., and Katzgraber, Helmut G.
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Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Mathematics - Optimization and Control ,Quantum Physics - Abstract
We propose and implement an interpretable machine learning classification model for Explainable AI (XAI) based on expressive Boolean formulas. Potential applications include credit scoring and diagnosis of medical conditions. The Boolean formula defines a rule with tunable complexity (or interpretability), according to which input data are classified. Such a formula can include any operator that can be applied to one or more Boolean variables, thus providing higher expressivity compared to more rigid rule-based and tree-based approaches. The classifier is trained using native local optimization techniques, efficiently searching the space of feasible formulas. Shallow rules can be determined by fast Integer Linear Programming (ILP) or Quadratic Unconstrained Binary Optimization (QUBO) solvers, potentially powered by special purpose hardware or quantum devices. We combine the expressivity and efficiency of the native local optimizer with the fast operation of these devices by executing non-local moves that optimize over subtrees of the full Boolean formula. We provide extensive numerical benchmarking results featuring several baselines on well-known public datasets. Based on the results, we find that the native local rule classifier is generally competitive with the other classifiers. The addition of non-local moves achieves similar results with fewer iterations, and therefore using specialized or quantum hardware could lead to a speedup by fast proposal of non-local moves., Comment: 28 pages, 16 figures, 4 tables
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- 2023
34. Designing Quantum Annealing Schedules using Bayesian Optimization
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Finžgar, Jernej Rudi, Schuetz, Martin J. A., Brubaker, J. Kyle, Nishimori, Hidetoshi, and Katzgraber, Helmut G.
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Quantum Physics - Abstract
We propose and analyze the use of Bayesian optimization techniques to design quantum annealing schedules with minimal user and resource requirements. We showcase our scheme with results for two paradigmatic spin models. We find that Bayesian optimization is able to identify schedules resulting in fidelities several orders of magnitude better than standard protocols for both quantum and reverse annealing, as applied to the $p$-spin model. We also show that our scheme can help improve the design of hybrid quantum algorithms for hard combinatorial optimization problems, such as the maximum independent set problem, and illustrate these results via experiments on a neutral atom quantum processor available on Amazon Braket., Comment: 20 pages, 15 figures
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- 2023
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35. Colored vertex models and Iwahori Whittaker functions
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Brubaker, Ben, Buciumas, Valentin, Bump, Daniel, and Gustafsson, Henrik P. A.
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- 2024
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36. The impact of non- and anthracycline-based chemotherapy on fatigue in breast cancer survivors: results from WF-97415
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Avis, Nancy E., Levine, Beverly J., Klepin, Heidi D., Mihalko, Shannon L., Brubaker, Peter H., Moore, Tonya, Ladd, Amy C., Dent, Susan F., Hackney, Mary Helen, Ky, Bonnie, Ntim, William O., Wagner, Lynne I., Weaver, Kathryn E., and Hundley, W. Gregory
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- 2024
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37. Long-Term Photometric Consistent Novel View Synthesis with Diffusion Models
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Yu, Jason J., Forghani, Fereshteh, Derpanis, Konstantinos G., and Brubaker, Marcus A.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Novel view synthesis from a single input image is a challenging task, where the goal is to generate a new view of a scene from a desired camera pose that may be separated by a large motion. The highly uncertain nature of this synthesis task due to unobserved elements within the scene (i.e. occlusion) and outside the field-of-view makes the use of generative models appealing to capture the variety of possible outputs. In this paper, we propose a novel generative model capable of producing a sequence of photorealistic images consistent with a specified camera trajectory, and a single starting image. Our approach is centred on an autoregressive conditional diffusion-based model capable of interpolating visible scene elements, and extrapolating unobserved regions in a view, in a geometrically consistent manner. Conditioning is limited to an image capturing a single camera view and the (relative) pose of the new camera view. To measure the consistency over a sequence of generated views, we introduce a new metric, the thresholded symmetric epipolar distance (TSED), to measure the number of consistent frame pairs in a sequence. While previous methods have been shown to produce high quality images and consistent semantics across pairs of views, we show empirically with our metric that they are often inconsistent with the desired camera poses. In contrast, we demonstrate that our method produces both photorealistic and view-consistent imagery., Comment: Project page: https://yorkucvil.github.io/Photoconsistent-NVS/
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- 2023
38. Reference-guided Controllable Inpainting of Neural Radiance Fields
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Mirzaei, Ashkan, Aumentado-Armstrong, Tristan, Brubaker, Marcus A., Kelly, Jonathan, Levinshtein, Alex, Derpanis, Konstantinos G., and Gilitschenski, Igor
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Computer Science - Computer Vision and Pattern Recognition - Abstract
The popularity of Neural Radiance Fields (NeRFs) for view synthesis has led to a desire for NeRF editing tools. Here, we focus on inpainting regions in a view-consistent and controllable manner. In addition to the typical NeRF inputs and masks delineating the unwanted region in each view, we require only a single inpainted view of the scene, i.e., a reference view. We use monocular depth estimators to back-project the inpainted view to the correct 3D positions. Then, via a novel rendering technique, a bilateral solver can construct view-dependent effects in non-reference views, making the inpainted region appear consistent from any view. For non-reference disoccluded regions, which cannot be supervised by the single reference view, we devise a method based on image inpainters to guide both the geometry and appearance. Our approach shows superior performance to NeRF inpainting baselines, with the additional advantage that a user can control the generated scene via a single inpainted image. Project page: https://ashmrz.github.io/reference-guided-3d, Comment: Project Page: https://ashmrz.github.io/reference-guided-3d
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- 2023
39. Inertia suppresses signatures of activity of active Brownian particles in a harmonic potential
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Arredondo, Angelica, Calavitta, Catania, Gomez, Mauricio, Mendez-Villanueva, Jose, Ahmed, Wylie W., and Brubaker, Nicholas D.
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Condensed Matter - Soft Condensed Matter - Abstract
A harmonically trapped active Brownian particle exhibits two types of positional distributions -- one has a single peak, the other has a single well -- that signify steady-state dynamics with low and high activity, respectively. Adding inertia to the translational motion preserves this strict single peak/well classification of the densities but shifts the dividing boundary between the states in the parameter space. We characterize this shift for the dynamics in one spatial dimension using the static Fokker--Planck equation for the full joint distribution of the state space. We derive local results analytically with a perturbation method for a small rotational velocity and then extend them globally with a numerical approach, Comment: 21 pages, 5 figures
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- 2023
40. Reply to: Inability of a graph neural network heuristic to outperform greedy algorithms in solving combinatorial optimization problems
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Schuetz, Martin J. A., Brubaker, J. Kyle, and Katzgraber, Helmut G.
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Computer Science - Machine Learning ,Condensed Matter - Disordered Systems and Neural Networks ,Computer Science - Artificial Intelligence ,Mathematics - Optimization and Control ,Quantum Physics - Abstract
We provide a comprehensive reply to the comment written by Stefan Boettcher [arXiv:2210.00623] and argue that the comment singles out one particular non-representative example problem, entirely focusing on the maximum cut problem (MaxCut) on sparse graphs, for which greedy algorithms are expected to perform well. Conversely, we highlight the broader algorithmic development underlying our original work, and (within our original framework) provide additional numerical results showing sizable improvements over our original data, thereby refuting the comment's original performance statements. Furthermore, it has already been shown that physics-inspired graph neural networks (PI-GNNs) can outperform greedy algorithms, in particular on hard, dense instances. We also argue that the internal (parallel) anatomy of graph neural networks is very different from the (sequential) nature of greedy algorithms, and (based on their usage at the scale of real-world social networks) point out that graph neural networks have demonstrated their potential for superior scalability compared to existing heuristics such as extremal optimization. Finally, we conclude highlighting the conceptual novelty of our work and outline some potential extensions., Comment: Manuscript: 2 pages, 1 figure. arXiv admin note: substantial text overlap with arXiv:2302.03602
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- 2023
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41. Reply to: Modern graph neural networks do worse than classical greedy algorithms in solving combinatorial optimization problems like maximum independent set
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Schuetz, Martin J. A., Brubaker, J. Kyle, and Katzgraber, Helmut G.
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Condensed Matter - Disordered Systems and Neural Networks ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Mathematics - Optimization and Control ,Quantum Physics - Abstract
We provide a comprehensive reply to the comment written by Chiara Angelini and Federico Ricci-Tersenghi [arXiv:2206.13211] and argue that the comment singles out one particular non-representative example problem, entirely focusing on the maximum independent set (MIS) on sparse graphs, for which greedy algorithms are expected to perform well. Conversely, we highlight the broader algorithmic development underlying our original work, and (within our original framework) provide additional numerical results showing sizable improvements over our original results, thereby refuting the comment's performance statements. We also provide results showing run-time scaling superior to the results provided by Angelini and Ricci-Tersenghi. Furthermore, we show that the proposed set of random d-regular graphs does not provide a universal set of benchmark instances, nor do greedy heuristics provide a universal algorithmic baseline. Finally, we argue that the internal (parallel) anatomy of graph neural networks is very different from the (sequential) nature of greedy algorithms and emphasize that graph neural networks have demonstrated their potential for superior scalability compared to existing heuristics such as parallel tempering. We conclude by discussing the conceptual novelty of our work and outline some potential extensions., Comment: Manuscript: 3 pages, 2 figures
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- 2023
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42. The aging lung
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Lowery EM, Brubaker AL, Kuhlmann E, and Kovacs EJ
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Aging ,Lung ,pulmonary immunology ,COPD ,Geriatrics ,RC952-954.6 - Abstract
Erin M Lowery,1 Aleah L Brubaker,2 Erica Kuhlmann,1 Elizabeth J Kovacs31Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine at Loyola University Medical Center, 2Loyola University Stritch School of Medicine, 3Department of Surgery, Loyola University Medical Center, Maywood, IL, USAAbstract: There are many age-associated changes in the respiratory and pulmonary immune system. These changes include decreases in the volume of the thoracic cavity, reduced lung volumes, and alterations in the muscles that aid respiration. Muscle function on a cellular level in the aging population is less efficient. The elderly population has less pulmonary reserve, and cough strength is decreased in the elderly population due to anatomic changes and muscle atrophy. Clearance of particles from the lung through the mucociliary elevator is decreased and associated with ciliary dysfunction. Many complex changes in immunity with aging contribute to increased susceptibility to infections including a less robust immune response from both the innate and adaptive immune systems. Considering all of these age-related changes to the lungs, pulmonary disease has significant consequences for the aging population. Chronic lower respiratory tract disease is the third leading cause of death in people aged 65 years and older. With a large and growing aging population, it is critical to understand how the body changes with age and how this impacts the entire respiratory system. Understanding the aging process in the lung is necessary in order to provide optimal care to our aging population. This review focuses on the nonpathologic aging process in the lung, including structural changes, changes in muscle function, and pulmonary immunologic function, with special consideration of obstructive lung disease in the elderly.Keywords: aging, lung, pulmonary immunology, COPD
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- 2013
43. Abscesses and Fistulas of the Anorectum
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Haubert, Lisa M., primary and Brubaker, Lisa S., additional
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- 2024
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44. Updated review on contaminant communication experiences in the circumpolar Arctic
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Eva M. Krümmel, Amanda D. Boyd, Danielle Brandow, Michael Brubaker, Chris M. Furgal, Robert Gerlach, Brian D. Laird, Mélanie Lemire, Lisa L. Loseto, Gert Mulvad, Shannon P. O’Hara, Kristin Olafsdottir, Jennifer F. Provencher, Mylène Ratelle, Arja Rautio, Kelly Skinner, Pál Weihe, and Maria Wennberg
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Contaminants ,persistent organic pollutants ,mercury ,Indigenous Peoples ,Arctic ,dietary advice ,Arctic medicine. Tropical medicine ,RC955-962 - Abstract
Arctic populations are amongst the highest exposed populations to long-range transported contaminants globally, with the main exposure pathway being through the diet. Dietary advice is an important immediate means to address potential exposure and help minimize adverse health effects. The objective of this work is to enable easier access to dietary advice and communication guidance on contaminants with a focus on the Arctic. This manuscript is part of a special issue summarizing the Arctic Monitoring and Assessment Programme’s Assessment 2021: Human Health in the Arctic. The information was derived with internet searches, and by contacting relevant experts directly. Results include risk communication efforts in European Arctic countries, effectiveness evaluation studies for several Arctic countries, experience of social media use, and the advantages and challenges of using social media in risk communication. We found that current risk communication activities in most Arctic countries emphasize the importance of a nutritious diet. Contaminant-related restrictions are mostly based on mercury; a limited amount of dietary advice is based on other contaminants. While more information on effectiveness evaluation was available, specific information, particularly from Arctic countries other than Canada, is still very limited.
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- 2024
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45. Partnerships Compass: Guiding Questions for Equitable and Impactful Engineering Community-Engaged Learning
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Brubaker, Eric Reynolds, Trego, Marsie, Cohen, Shoshanah, and Taha, Kofi
- Abstract
Campus-community partnerships are integral to community-engaged learning, service-learning and similar pedagogies that extend project-based learning beyond the classroom into "real world" communities. Community-engaged courses have increased in prevalence in engineering education. Evidence suggests that they are effective at connecting engineering theory to practice, engaging students motivated to "make an impact," and preparing students for global and multicultural collaboration. In community-engaged courses, campus partners (students, faculty, staff) and community partners (individuals or organizations from non-academic communities) collaborate on an engineering project that, if successful, benefits community members and contributes to student learning. However, partner relations are not always a primary focus, and partnerships can flounder and fail resulting in limited or imbalanced outcomes, dissatisfaction among partners, or even harm. Building upon documented principles for community engagement and frameworks such as critical service-learning, this paper directs attention to the relationships between campus and community partners as a crucial yet under-studied aspect of engineering community-engaged learning. We interviewed 22 campus and community partners involved in engineering projects spanning seven engineering colleges and five continents. The findings are presented in the form of a Partnerships Compass with guiding questions for nurturing partnerships that are both impactful (in achieving partners' collective goals) and equitable (in attenuating power imbalances, unequal risks of harm, and outcome disparities between partners). Ultimately, the paper aims to provide a timely perspective and actionable tool for engineering instructors, students, and community partners who aim to jointly build enduringly equitable and impactful partnerships.
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- 2022
46. New Results from HAYSTAC's Phase II Operation with a Squeezed State Receiver
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HAYSTAC Collaboration, Jewell, M. J., Leder, A. F., Backes, K. M., Bai, Xiran, van Bibber, K., Brubaker, B. M., Cahn, S. B., Droster, A., Esmat, Maryam H., Ghosh, Sumita, Graham, Eleanor, Hilton, Gene C., Jackson, H., Laffan, Claire, Lamoreaux, S. K., Lehnert, K. W., Lewis, S. M., Malnou, M., Maruyama, R. H., Palken, D. A., Rapidis, N. M., Ruddy, E. P., Simanovskaia, M., Singh, Sukhman, Speller, D. H., Vale, Leila R., Wang, H., and Zhu, Yuqi
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High Energy Physics - Experiment ,Physics - Instrumentation and Detectors - Abstract
A search for dark matter axions with masses $>10 \mu eV/c^{2}$ has been performed using the HAYSTAC experiment's squeezed state receiver to achieve sub-quantum limited noise. This report includes details of the design and operation of the experiment previously used to search for axions in the mass ranges $16.96-17.12$ and $17.14-17.28 \mu eV/c^{2}$($4.100-4.140$GHz) and $4.145-4.178$GHz) as well as upgrades to facilitate an extended search at higher masses. These upgrades include improvements to the data acquisition routine which have reduced the effective dead time by a factor of 5, allowing for the new region to be scanned $\sim$1.6 times faster with comparable sensitivity. No statistically significant evidence of an axion signal is found in the range $18.44-18.71\mu eV/c^{2}$($4.459-4.523$GHz), leading to an aggregate upper limit exclusion at the $90\%$ level on the axion-photon coupling of $2.06\times g_{\gamma}^{KSVZ}$., Comment: 20 pages, 16 figures
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- 2023
47. Semiconductor thermal and electrical properties decoupled by localized phonon resonances
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Spann, Bryan T., Weber, Joel C., Brubaker, Matt D., Harvey, Todd E., Yang, Lina, Honarvar, Hossein, Tsai, Chia-Nien, Treglia, Andrew C., Lee, M., Hussein, Mahmoud I., and Bertness, Kris A.
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Condensed Matter - Mesoscale and Nanoscale Physics - Abstract
Thermoelectric materials convert heat into electricity through thermally driven charge transport in solids, or vice versa for cooling. To be competitive with conventional energy-generation technologies, a thermoelectric material must possess the properties of both an electrical conductor and a thermal insulator. However, these properties are normally mutually exclusive because of the interconnection of the scattering mechanisms for charge carriers and phonons. Recent theoretical investigations on sub-device scales have revealed that silicon membranes covered by nanopillars exhibit a multitude of local phonon resonances, spanning the full spectrum, that couple with the heat-carrying phonons in the membrane and collectively cause a reduction in the in-plane thermal conductivity$-$while, in principle, not affecting the electrical properties because the nanopillars are external to the pathway of voltage generation and charge transport. Here this effect is demonstrated experimentally for the first time by investigating device-scale suspended silicon membranes with GaN nanopillars grown on the surface. The nanopillars cause up to 21 % reduction in the thermal conductivity while the electrical conductivity and the Seebeck coefficient remain unaffected, thus demonstrating an unprecedented decoupling in the semiconductor's thermoelectric properties. The measured thermal conductivity behavior for coalesced nanopillars and corresponding lattice-dynamics calculations provide further evidence that the reductions are mechanistically tied to the phonon resonances. This finding breaks a longstanding trade-off between competing properties in thermoelectricity and paves the way for engineered high-efficiency solid-state energy recovery and cooling.
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- 2023
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48. The RISE FOR HEALTH study: Methods for in-person assessment and biospecimen collection.
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Brubaker, Linda, Barthold, Julia, Fitzgerald, Colleen, Kenton, Kimberly, Lewis, Cora, Lowder, Jerry, Lukacz, Emily, Markland, Alayne, Meister, Melanie, Miller, Janis, Mueller, Elizabeth, Rudser, Kyle, Smith, Ariana, and Newman, Diane
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bladder ,microbiome ,musculoskeletal assessment ,pelvic floor ,women ,Adult ,Humans ,Female ,Prospective Studies ,Pelvic Floor ,Urinary Bladder ,Lower Urinary Tract Symptoms ,Pain - Abstract
OBJECTIVES: To describe the methods for the in-person assessment of the RISE FOR HEALTH (RISE) study, a population-based multicenter prospective cohort study designed to identify factors that promote bladder health and/or prevent lower urinary tract symptoms in adult women, conducted by the Prevention of Lower Urinary Tract Symptoms Research Consortium (PLUS). METHODS AND RESULTS: A subset of RISE participants who express interest in the in-person assessment will be screened to ensure eligibility (planned n = 525). Eligible consenting participants are asked to complete 15 physical assessments in addition to height and weight, to assess pelvic floor muscle function, musculoskeletal (MSK) status, and pain, and to provide urogenital microbiome samples. Pelvic floor muscle assessments include presence of prolapse, strength, levator attachment integrity (tear) and myofascial pain. MSK tests evaluate core stability, lumbar spine, pelvic girdle and hip pain and function. Participants are asked to complete the Short Physical Performance Battery to measure balance, lower extremity strength, and functional capacity. All participants are asked to provide a voided urine sample and a vaginal swab for microbiome analyses; a subset of 100 are asked to contribute additional samples for feasibility and validation of a home collection of urinary, vaginal, and fecal biospecimens. RESULTS: Online and in-person training sessions were used to certify research staff at each clinical center before the start of RISE in-person assessments. Standardized protocols and data collection methods are employed uniformly across sites. CONCLUSIONS: The RISE in-person assessment is an integral portion of the overall population-based RISE study and represents an innovative approach to assessing factors hypothesized to promote bladder health and/or prevent lower urinary tract symptoms. Data collected from this assessment will be used to prioritize future research questions and prevention strategies and interventions. This description of the assessment methods is intended to provide methodologic transparency and inform other researchers who join efforts to understand and improve bladder health.
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- 2023
49. RISE FOR HEALTH: Rationale and protocol for a prospective cohort study of bladder health in women.
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Smith, Ariana, Rudser, Kyle, Harlow, Bernard, McGwin, Gerald, Barthold, Julia, Brady, Sonya, Brubaker, Linda, Cunningham, Shayna, Griffith, James, Kenton, Kim, Klusaritz, Heather, Lewis, Cora, Maki, Julia, Markland, Alayne, Mueller, Elizabeth, Newman, Diane, Rickey, Leslie, Rockwood, Todd, Simon, Melissa, Wyman, Jean, Sutcliffe, Siobhan, Lukacz, Emily, and Nodora, Jesse
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bladder health ,epidemiology ,health promotion ,longitudinal study ,lower urinary tract symptoms ,social ecological framework ,womens health ,Adult ,Humans ,Female ,Urinary Bladder ,Prospective Studies ,Longitudinal Studies ,Lower Urinary Tract Symptoms ,Surveys and Questionnaires ,Multicenter Studies as Topic - Abstract
INTRODUCTION: The spectrum of bladder health and the factors that promote bladder health and prevent lower urinary tract symptoms (LUTS) among women are not well understood. This manuscript describes the rationale, aims, study design, sampling strategy, and data collection for the RISE FOR HEALTH (RISE) study, a novel study of bladder health in women conducted by the Prevention of Lower Urinary Tract Symptom (PLUS) Research Consortium. METHODS AND RESULTS: RISE is a population-based, multicenter, prospective longitudinal cohort study of community-dwelling, English- and Spanish-speaking adult women based in the United States. Its goal is to inform the distribution of bladder health and the individual factors (biologic, behavioral, and psychosocial) and multilevel factors (interpersonal, institutional, community, and societal) that promote bladder health and/or prevent LUTS in women across the life course. Key study development activities included the: (1) development of a conceptual framework and philosophy to guide subsequent activities, (2) creation of a study design and sampling strategy, prioritizing diversity, equity, and inclusion, and (3) selection and development of data collection components. Community members and cross-cultural experts shaped and ensured the appropriateness of all study procedures and materials. RISE participants will be selected by simple random sampling of individuals identified by a marketing database who reside in the 50 counties surrounding nine PLUS clinical research centers. Participants will complete self-administered surveys at baseline (mailed paper or electronic) to capture bladder health and LUTS, knowledge about bladder health, and factors hypothesized to promote bladder health and prevent LUTS. A subset of participants will complete an in-person assessment to augment data with objective measures including urogenital microbiome specimens. Initial longitudinal follow-up is planned at 1 year. DISCUSSION: Findings from RISE will begin to build the necessary evidence base to support much-needed, new bladder health promotion and LUTS prevention interventions in women.
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- 2023
50. Solving the n-color ice model
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Addona, Patrick, Bockenhauer, Ethan, Brubaker, Ben, Cauthorn, Michael, Conefrey-Shinozaki, Cianan, Donze, David, Dudarov, William, Dukes, Jessamyn, Hardt, Andrew, Li, Cindy, Li, Jigang, Liu, Yanli, Puthanveetil, Neelima, Qudsi, Zain, Simons, Jordan, Sullivan, Joseph, and Young, Autumn
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Mathematical Physics ,Mathematics - Combinatorics ,Mathematics - Representation Theory ,16T25 (Primary), 82B23, 20G42, 05E10 (secondary) - Abstract
Given an arbitrary choice of two sets of nonzero Boltzmann weights for $n$-color lattice models, we provide explicit algebraic conditions on these Boltzmann weights which guarantee a solution (i.e., a third set of weights) to the Yang-Baxter equation. Furthermore we provide an explicit one-dimensional parametrization of all solutions in this case. These $n$-color lattice models are so named because their admissible vertices have adjacent edges labeled by one of $n$ colors with additional restrictions. The two-colored case specializes to the six-vertex model, in which case our results recover the familiar quadric condition of Baxter for solvability. The general $n$-color case includes important solutions to the Yang-Baxter equation like the evaluation modules for the quantum affine Lie algebra $U_q(\hat{\mathfrak{sl}}_n)$. Finally, we demonstrate the invariance of this class of solutions under natural transformations, including those associated with Drinfeld twisting., Comment: 39 pages, 8 figures
- Published
- 2022
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