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1. CyVerse: Cyberinfrastructure for open science.

Author: Tyson L Swetnam, Parker B Antin, Ryan Bartelme, Alexander Bucksch, David Camhy, Greg Chism, Illyoung Choi, Amanda M Cooksey, Michele Cosi, Cindy Cowen, Michael Culshaw-Maurer, Robert Davey, Sean Davey, Upendra Devisetty, Tony Edgin, Andy Edmonds, Dmitry Fedorov, Jeremy Frady, John Fonner, Jeffrey K Gillan, Iqbal Hossain, Blake Joyce, Konrad Lang, Tina Lee, Shelley Littin, Ian McEwen, Nirav Merchant, David Micklos, Andrew Nelson, Ashley Ramsey, Sarah Roberts, Paul Sarando, Edwin Skidmore, Jawon Song, Mary Margaret Sprinkle, Sriram Srinivasan, Dan Stanzione, Jonathan D Strootman, Sarah Stryeck, Reetu Tuteja, Matthew Vaughn, Mojib Wali, Mariah Wall, Ramona Walls, Liya Wang, Todd Wickizer, Jason Williams, John Wregglesworth, and Eric Lyons
Subjects: Biology (General), QH301-705.5
Abstract: CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 124,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in three countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.
Published: 2024
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2. Reduction of coastal lighting decreases seabird strandings

Author: Tori V. Burt, Sydney M. Collins, Sherry Green, Parker B. Doiron, Sabina I. Wilhelm, and William A. Montevecchi
Subjects: Medicine, Science
Published: 2024

3. Antidotal treatment of botulism in rats by continuous infusion with 3,4-diaminopyridine

Author: James B. Machamer, Edwin J. Vazquez-Cintron, Sean W. O’Brien, Kyle E. Kelly, Amber C. Altvater, Kathleen T. Pagarigan, Parker B. Dubee, Celinia A. Ondeck, and Patrick M. McNutt
Subjects: Botulinum neurotoxin, Botulism, 3,4-diaminopyridine, Neuromuscular junction, Endplate recordings, Preclinical models, Therapeutics. Pharmacology, RM1-950, Biochemistry, QD415-436
Abstract: Abstract Botulinum neurotoxins (BoNTs) are highly potent, select agent toxins that inhibit neurotransmitter release at motor nerve terminals, causing muscle paralysis and death by asphyxiation. Other than post-exposure prophylaxis with antitoxin, the only treatment option for symptomatic botulism is intubation and supportive care until recovery, which can require weeks or longer. In previous studies, we reported the FDA-approved drug 3,4-diaminopyridine (3,4-DAP) reverses early botulism symptoms and prolongs survival in lethally intoxicated mice. However, the symptomatic benefits of 3,4-DAP are limited by its rapid clearance. Here we investigated whether 3,4-DAP could sustain symptomatic benefits throughout the full course of respiratory paralysis in lethally intoxicated rats. First, we confirmed serial injections of 3,4-DAP stabilized toxic signs and prolonged survival in rats challenged with 2.5 LD50 BoNT/A. Rebound of toxic signs and death occurred within hours after the final 3,4-DAP treatment, consistent with the short half-life of 3,4-DAP in rats. Based on these data, we next investigated whether the therapeutic benefits of 3,4-DAP could be sustained throughout the course of botulism by continuous infusion. To ensure administration of 3,4-DAP at clinically relevant doses, three infusion dose rates (0.5, 1.0 and 1.5 mg/kg∙h) were identified that produced steady-state serum levels of 3,4-DAP consistent with clinical dosing. We then compared dose-dependent effects of 3,4-DAP on toxic signs and survival in rats intoxicated with 2.5 LD50 BoNT/A. In contrast to saline vehicle, which resulted in 100% mortality, infusion of 3,4-DAP at ≥ 1.0 mg/kg∙h from 1 to 14 d after intoxication produced 94.4% survival and full resolution of toxic signs, without rebound of toxic signs after infusion was stopped. In contrast, withdrawal of 3,4-DAP infusion at 5 d resulted in re-emergence of toxic sign and death within 12 h, confirming antidotal outcomes require sustained 3,4-DAP treatment for longer than 5 d after intoxication. We exploited this novel survival model of lethal botulism to explore neurophysiological parameters of diaphragm paralysis and recovery. While neurotransmission was nearly eliminated at 5 d, neurotransmission was significantly improved at 21 d in 3,4-DAP-infused survivors, although still depressed compared to naïve rats. 3,4-DAP is the first small molecule to reverse systemic paralysis and promote survival in animal models of botulism, thereby meeting a critical treatment need that is not addressed by post-exposure prophylaxis with conventional antitoxin. These data contribute to a growing body of evidence supporting the use of 3,4-DAP to treat clinical botulism.
Published: 2022
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4. Variation in resource use between adult and juvenile Semipalmated Sandpipers (Calidris pusilla) and use of physiological indicators for movement decisions highlights the importance of small staging sites during southbound migration in Atlantic Canada

Author: Rebeca C. Linhart, Diana J. Hamilton, Julie Paquet, Sara C. Bellefontaine, Siena Davis, Parker B. Doiron, and Cheri L. Gratto-Trevor
Subjects: Semipalmated Sandpiper, Calidris pusilla, migratory physiology, habitat selection, shorebird conservation, automated radio-telemetry, Evolution, QH359-425, Ecology, QH540-549.5
Abstract: Semipalmated Sandpipers (Calidris pusilla) are Arctic-breeding shorebirds that use staging sites in Atlantic Canada during their annual migration to South America. The Bay of Fundy has long been recognized as a critical staging site for migrating Semipalmated Sandpipers and supports a large prey base. The diet of adult sandpipers in the Bay is flexible but the diet of juveniles, which arrive later, is not well documented. Comparatively little is known about the prey base and how it is utilized by sandpipers at sites in Atlantic Canada outside the Bay. Plasma metabolite measures can provide useful insight to assess habitat quality for sandpipers and have not yet been measured in Semipalmated Sandpipers in Atlantic Canada. To address these knowledge gaps we sampled shorebird habitat to estimate invertebrate availability in the Bay of Fundy and the Northumberland Strait. Concurrently, we collected blood samples from adult and juvenile sandpipers for analysis of plasma metabolite levels and isotopic estimates of dietary niche in both regions. We found that sites on the Northumberland Strait hosted a more diverse and variable prey base than sites within the Bay of Fundy, and that sandpipers were selective when foraging there, appearing to prefer bivalves. Juveniles may occupy a broader dietary niche than adults along the Northumberland Strait, though appear to gain weight as efficiently. Sandpipers sampled along the Northumberland Strait had higher plasma triglyceride concentrations than those within the Bay of Fundy, which may suggest differences in fattening rate or dietary fat intake. Sandpipers that had lower triglyceride concentrations on the Northumberland Strait were more likely to move into the Bay of Fundy, while sandpipers with high triglyceride values tended to remain on the Strait. These data suggest that sandpipers made movement decisions within the region depending on their physiological state. Our results suggest adult and juvenile Semipalmated Sandpipers successfully use a variety of staging habitats in Atlantic Canada. This is an encouraging finding for sandpiper conservation in the region, but also indicates that maintaining access to a broad variety of staging habitats is critical, supporting calls for stronger conservation measures throughout the region.
Published: 2022
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5. A Randomized, Controlled, Prospective Study of the Effectiveness and Safety of an Intracanalicular Dexamethasone Ophthalmic Insert (0.4 Mg) for the Treatment of Post-Operative Inflammation in Patients Undergoing Refractive Lens Exchange (RLE)

Author: Larsen J, Whitt T, Parker B, and Swan R
Subjects: punctal plug, steroid, visual acuity, cystoid macular edema, patient preference, Ophthalmology, RE1-994
Abstract: Jacob Larsen,1 Travis Whitt,2 Briana Parker,1 Russell Swan3,4 1Clinical Research, Vance Thompson Vision, Bozeman, MT, USA; 2Department of Optometry, Vance Thompson Vision, Bozeman, MT, USA; 3Department of Ophthalmology, Vance Thompson Vision, Bozeman, MT, USA; 4Ophthalmology Moran Eye Center, University of Utah, Salt Lake City, UT, USACorrespondence: Jacob LarsenClinical Research, Vance Thompson Vision, Bozeman, MT, USATel +1 406-544-2140Fax +1 406-624-6560Email Jacob.larsen2020@outlook.comPurpose: To determine patient preference and treatment outcomes with an intracanalicular dexamethasone (0.4 mg) insert compared to standard steroid drop regimen in the contralateral eye following bilateral RLE surgery.Methods: This is a prospective, open-label, interventional, randomized, controlled study in 20 subjects who underwent bilateral RLE. Each patient served as their own control with one eye randomized to the intracanalicular insert (Group A) placed at the time of surgery and the contralateral randomized to topical corticosteroid drops (Group B). All eyes received intracameral moxifloxacin at the time of surgery, and post-operatively, topical moxifloxacin QID for one week and topical NSAID daily for four weeks. Post-operative evaluations were performed on Day 1, Week 1, and Week 4– 8.Results: Twenty patients participated. At 4– 8 weeks post-operation, 90% of patients evaluated with the COMTOL questionnaire preferred the intracanalicular insert while 10% preferred the topical steroid. Comparative analysis using the visual analog scale showed no difference in pain between the study and control group. No statistical difference was shown in post-operative corneal staining, anterior chamber cell count, anterior chamber flare or intraocular pressure. Mean LogMAR UCVA at 4– 8 weeks post-operation was 0.06 (± 0.230) in the study group and 0.065 (± 0.241) in the control group, which was not statistically or clinically different (p > 0.05).Conclusion: Patients undergoing bilateral RLE expressed a strong preference towards the use of an intracanalicular insert over a topical steroid for post-operative steroid treatment. There was no clinically or statistically significant difference in outcomes, including rate of cystoid macular edema, visual acuity and elevation of intraocular pressure.National Clinical Trial Number: 04549935.Keywords: punctal plug, steroid, visual acuity, cystoid macular edema, patient preference
Published: 2021

6. The Belle II Detector Upgrades Framework Conceptual Design Report

Author: Aihara, H., Aloisio, A., Auguste, D. P., Aversano, M., Babeluk, M., Bahinipati, S., Banerjee, Sw., Barbero, M., Baudot, J., Beaubien, A., Becherer, F., Bergauer, T., Bernlochner., F. U., Bertacchi, V., Bertolone, G., Bespin, C., Bessner, M., Bettarini, S., Bevan, A. J., Bhuyan, B., Bona, M., Bonis, J. F., Borah, J., Bosi, F., Boudagga, R., Bozek, A., Bračko, M., Branchini, P., Breugnon, P., Browder, T. E., Buch, Y., Budano, A., Campajola, M., Casarosa, G., Cecchi, C., Chen, C., Choudhury, S., Corona, L., de Marino, G., De Nardo, G., De Pietro, G., de Sangro, R., Dey, S., Dingfelder, J. C., Dong, T. V., Dorokhov, A., Dujany, G., Epifanov, D., Federici, L., Ferber, T., Fillinger, T., Finck, Ch., Finocchiaro, G., Forti, F., Frey, A., Friedl, M., Gabrielli, A., Gaioni, L., Gao, Y., Gaudino, G., Gaur, V., Gaz, A., Giordano, R., Giroletti, S., Gobbo, B., Godang, R., Haide, I., Han, Y., Hara, K., Hayasaka, K., Hearty, C., Heidelbach, A., Higuchi, T., Himmi, A., Hoferichter, M., Howgill, D. A., Hu-Guo, C., Iijima, T., Inami, K., Irmler, C., Ishikawa, A., Itoh, R., Iyer, D., Jacobs, W. W., Jaffe, D. E., Jin, Y., Junginger, T., Kandra, J., Kojima, K., Koga, T., Korobov, A. A., Korpar, S., Križan, P., Krüger, H., Kuhr, T., Kumar, A., Kumar, R ., Kuzmin, A., Kwon, Y. -J., Lacaprara, S., Lacasta, C., Lai, Y. -T., Lalwani, K., Lam, T., Lanceri, L., Lee, M. J., Leonidopoulos, C., Levit, D., Lewis, P. M., Libby, J. F., Liu, Q. Y., Liu, Z. Y., Liventsev, D., Longo, S., Mancinelli, G., Manghisoni, M., Manoni, E., Marinas, C., Martellini, C., Martens, A., Massa, M., Massaccesi, L., Mawas, F., Mazorra, J., Merola, M., Miller, C., Minuti, M., Mizuk, R., Modak, A., Moggi, A., Mohanty, G. B., Moneta, S., Muller, Th., Na, I., Nakamura, K. R., Nakao, M., Natochii, A., Niebuhr, C., Nishida, S., Novosel, A., Pangaud, P., Parker, B., Passeri, A., Pedlar, T. K., Peinaud, Y., Peng, Y., Peschke, R., Pestotnik, R., Pham, T. H., Piccolo, M., Piilonen, L. E., Prell, S., Purohit, M. V., Ratti, L., Re, V., Reuter, L., Riceputi, E., Ripp-Baudot, I., Rizzo, G., Roney, J. M., Russo, A., Sandilya, S., Santelj, L., Savinov, V., Scavino, B., Schall, L., Schnell, G., Schwanda, C., Schwartz, A. J., Schwenker, B., Schwickardi, M., Seljak, A., Serrano, J., Shiu, J. -G., Shwartz, B., Simon, F., Soffer, A., Song, W. M., Starič, M., Stavroulakis, P., Stefkova, S., Stroili, R., Tanaka, S., Taniguchi, N., Teotia, V., Tessema, N., Thalmeier, R., Torassa, E., Trabelsi, K., Trantou, F. F., Traversi, G., Urquijo, P., Vahsen, S. E., Valin, I., Varner, G. S., Varvell, K. E., Vitale, L., Vobbilisetti, V., Wang, X. L., Wessel, C., Wienands, H. U., Won, E., Xu, D., Yamada, S., Yin, J. H., Yoshihara, K., Yuan, C. Z., Zani, L., Zong, Z., and Zou, S.
Subjects: High Energy Physics - Experiment, Physics - Instrumentation and Detectors
Abstract: We describe the planned near-term and potential longer-term upgrades of the Belle II detector at the SuperKEKB electron-positron collider operating at the KEK laboratory in Tsukuba, Japan. These upgrades will allow increasingly sensitive searches for possible new physics beyond the Standard Model in flavor, tau, electroweak and dark sector physics that are both complementary to and competitive with the LHC and other experiments., Comment: Editor: F. Forti 170 pages
Published: 2024

7. In-person versus virtual administration of the American College of Rheumatology gold standard cognitive battery in systemic lupus erythematosus: Are they interchangeable?

Author: Barraclough, ML, Diaz-Martinez, JP, Knight, A, Bingham, K, Su, J, Kakvan, M, Grajales, C Muñoz, Tartaglia, MC, Ruttan, L, Wither, J, Choi, MY, Bonilla, D, Anderson, N, Appenzeller, S, Parker, B, Katz, P, Beaton, D, Green, R, Bruce, IN, and Touma, Z
Subjects: Biomedical and Clinical Sciences, Clinical Sciences, Lupus, Autoimmune Disease, Behavioral and Social Science, Clinical Research, Mental Health, Mental health, Humans, United States, Lupus Erythematosus, Systemic, Rheumatology, Retrospective Studies, Longitudinal Studies, Pandemics, COVID-19, Cognition, systemic lupus erythematosus, neuropsychiatric lupus, cognitive impairment, Arthritis & Rheumatology, Clinical sciences
Abstract: ObjectiveDuring the COVID-19 pandemic, many research studies were adapted, including our longitudinal study examining cognitive impairment (CI) in systemic lupus erythematosus (SLE). Cognitive testing was switched from in-person to virtual. This analysis aimed to determine if the administration method (in-person vs. virtual) of the ACR-neuropsychological battery (ACR-NB) affected participant cognitive performance and classification.MethodsData from our multi-visit, SLE CI study included demographic, clinical, and psychiatric characteristics, and the modified ACR-NB. Three analyses were undertaken for cognitive performance: (1) all visits, (2) non-CI group visits only and (3) intra-individual comparisons. A retrospective preferences questionnaire was given to participants who completed the ACR-NB both in-person and virtually.ResultsWe analysed 328 SLE participants who had 801 visits (696 in-person and 105 virtual). Demographic, clinical, and psychiatric characteristics were comparable except for ethnicity, anxiety and disease-related damage. Across all three comparisons, six tests were consistently statistically significantly different. CI classification changed in 11/71 (15%) participants. 45% of participants preferred the virtual administration method and 33% preferred in-person.ConclusionsOf the 19 tests in the ACR-NB, we identified one or more problems with eight (42%) tests when moving from in-person to virtual administration. As the use of virtual cognitive testing will likely increase, these issues need to be addressed - potentially by validating a virtual version of the ACR-NB. Until then, caution must be taken when directly comparing virtual to in-person test results. If future studies use a mixed administration approach, this should be accounted for during analysis.
Published: 2023

8. Olfactomedin-1 activity identifies a cell invasion checkpoint during epithelial-mesenchymal transition in the chick embryonic heart

Author: Alejandro Lencinas, Danny C. Chhun, Kelvin P. Dan, Kristen D. Ross, Elizabeth A. Hoover, Parker B. Antin, and Raymond B. Runyan
Subjects: Medicine, Pathology, RB1-214
Abstract: SUMMARY Endothelia in the atrioventricular (AV) canal of the developing heart undergo a prototypical epithelial mesenchymal transition (EMT) to begin heart valve formation. Using an in vitro invasion assay, an extracellular matrix protein, Olfactomedin-1 (OLFM1), was found to increase mesenchymal cell numbers in AV canals from embryonic chick hearts. Treatment with both anti-OLFM1 antibody and siRNA targeting OLFM1 inhibits mesenchymal cell formation. OLFM1 does not alter cell proliferation, migration or apoptosis. Dispersion, but lack of invasion in the presence of inhibiting antibody, identifies a specific role for OLFM1 in cell invasion during EMT. This role is conserved in other epithelia, as OLFM1 similarly enhances invasion by MDCK epithelial cells in a transwell assay. Synergy is observed when TGFβ2 and OLFM1 are added to MDCK cell cultures, indicating that OLFM-1 activity is cooperative with TGFβ. Inhibition of both OLFM1 and TGFβ in heart invasion assays shows a similar cooperative role during development. To explore OLFM1 activity during EMT, representative EMT markers were examined. Effects of OLFM1 protein and anti-OLFM1 on transcripts of cell-cell adhesion molecules and the transcription factors Snail-1, Snail-2, Twist1 and Sox-9 argue that OLFM1 does not initiate EMT. Rather, regulation of transcripts of Zeb1 and Zeb2, secreted proteases and mesenchymal cell markers by both OLFM1 and anti-OLFM1 is consistent with regulation of the cell invasion step of EMT. We conclude that OLFM1 is present and necessary during EMT in the embryonic chick heart. Its role in cell invasion and mesenchymal cell gene regulation suggests an invasion checkpoint in EMT where OLFM1 acts to promote cell invasion into the three-dimensional matrix.
Published: 2013
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9. Gastrulation EMT Is Independent of P-Cadherin Downregulation.

Author: Pricila K Moly, James R Cooley, Sebastian L Zeltzer, Tatiana A Yatskievych, and Parker B Antin
Subjects: Medicine, Science
Abstract: Epithelial-mesenchymal transition (EMT) is an evolutionarily conserved process during which cells lose epithelial characteristics and gain a migratory phenotype. Although downregulation of epithelial cadherins by Snail and other transcriptional repressors is generally considered a prerequisite for EMT, recent studies have challenged this view. Here we investigate the relationship between E-cadherin and P-cadherin expression and localization, Snail function and EMT during gastrulation in chicken embryos. Expression analyses show that while E-cadherin transcripts are detected in the epiblast but not in the primitive streak or mesoderm, P-cadherin mRNA and protein are present in the epiblast, primitive and mesoderm. Antibodies that specifically recognize E-cadherin are not presently available. During EMT, P-cadherin relocalizes from the lateral surfaces of epithelial epiblast cells to a circumferential distribution in emerging mesodermal cells. Cells electroporated with an E-cadherin expression construct undergo EMT and migrate into the mesoderm. An examination of Snail function showed that reduction of Slug (SNAI2) protein levels using a morpholino fails to inhibit EMT, and expression of human or chicken Snail in epiblast cells fails to induce EMT. In contrast, cells expressing the Rho inhibitor peptide C3 rapidly exit the epiblast without activating Slug or the mesoderm marker N-cadherin. Together, these experiments show that epiblast cells undergo EMT while retaining P-cadherin, and raise questions about the mechanisms of EMT regulation during avian gastrulation.
Published: 2016
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10. Output Mode Switching for Parallel Five-bar Manipulators Using a Graph-based Path Planner

Author: Edwards, Parker B., Baskar, Aravind, Hills, Caroline, Plecnik, Mark, and Hauenstein, Jonathan D.
Subjects: Computer Science - Robotics, Computer Science - Computational Geometry
Abstract: The configuration manifolds of parallel manipulators exhibit more nonlinearity than serial manipulators. Qualitatively, they can be seen to possess extra folds. By projecting such manifolds onto spaces of engineering relevance, such as an output workspace or an input actuator space, these folds cast edges that exhibit nonsmooth behavior. For example, inside the global workspace bounds of a five-bar linkage appear several local workspace bounds that only constrain certain output modes of the mechanism. The presence of such boundaries, which manifest in both input and output projections, serve as a source of confusion when these projections are studied exclusively instead of the configuration manifold itself. Particularly, the design of nonsymmetric parallel manipulators has been confounded by the presence of exotic projections in their input and output spaces. In this paper, we represent the configuration space with a radius graph, then weight each edge by solving an optimization problem using homotopy continuation to quantify transmission quality. We then employ a graph path planner to approximate geodesics between configuration points that avoid regions of low transmission quality. Our methodology automatically generates paths capable of transitioning between non-neighboring output modes, a motion which involves osculating multiple workspace boundaries (local, global, or both). We apply our technique to two nonsymmetric five-bar examples that demonstrate how transmission properties and other characteristics of the workspace can be selected by switching output modes., Comment: 7 pages, 6 figures
Published: 2022

11. Computing geometric feature sizes for algebraic manifolds

Author: Di Rocco, Sandra, Edwards, Parker B., Eklund, David, Gäfvert, Oliver, and Hauenstein, Jonathan D.
Subjects: Mathematics - Algebraic Geometry, Computer Science - Computational Geometry
Abstract: We introduce numerical algebraic geometry methods for computing lower bounds on the reach, local feature size, and the weak feature size of the real part of an equidimensional and smooth algebraic variety using the variety's defining polynomials as input. For the weak feature size, we also show that non-quadratic complete intersections generically have finitely many geometric bottlenecks, and describe how to compute the weak feature size directly rather than a lower bound in this case. In all other cases, we describe additional computations that can be used to determine feature size values rather than lower bounds. We also present homology inference experiments that combine persistent homology computations with implemented versions of our feature size algorithms, both with globally dense samples and samples that are adaptively dense with respect to the local feature size.
Published: 2022

12. Citizen Science Astronomy with a Network of Small Telescope: The Launch and Deployment of JWST

Author: Lambert, R. A., Marchis, F., Asencio, J., Blaclard, G., Sgro, L. A., Giorgini, J. D., Plavchan, P., White, T., Verveen, A., Goto, T., Kuossari, P., Sethu, N., Loose, M. A., Will, S., Sibbernsen, K., Pickering, J. W., Randolph, J., Fukui, K., Huet, P., Guillet, B., Clerget, O., Stahl, S., Yoblonsky, N., Lauvernier, M., Matsumura, T., Yamato, M., Laugier, J. M., Brodt-Vilain, O., Espudo, A., Kukita, R., Iida, S., Kardel, S., Green, D., Tikkanen, P., Douvas, A., Billiani, M., Knight, G., Ryno, M., Simard, G., Knight, R., Primm, M., Wildhagen, B., Poncet, J., Frachon, T., Shimizu, M., Jackson, A., Parker, B., Redfern, G., Nikiforov, P., Friday, E., Lincoln, K., Sweitzer, J., Mitsuoka, R., Cabral, K., Katterfeld, A., and Fairfax, M.
Subjects: Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Earth and Planetary Astrophysics
Abstract: We present a coordinated campaign of observations to monitor the brightness of the James Webb Space Telescope (JWST) as it travels toward the second Earth-Sun Lagrange point and unfolds using the network ofUnistellar digital telescopes. Those observations collected by citizen astronomers across the world allowed us to detect specific phases such as the separation from the booster, glare due to a change of orientation after a maneuver, the unfurling of the sunshield, and deployment of the primary mirror. After deployment of the sunshield on January 6 2022, the 6-h lightcurve has a significant amplitude and shows small variations due to the artificial rotation of the space telescope during commissionning. These variations could be due to the deployment of the primary mirror or some changes in orientation of the space telescope. This work illustrates the power of a worldwide array of small telescopes, operated by citizen astronomers, to conduct large scientific campaigns over a long timeframe. In the future, our network and others will continue to monitor JWST to detect potential degradations to the space environment by comparing the evolution of the lightcurve., Comment: 15 pages, 13 figures and 2 tables, SPIE Ground-based and Airborne Telescopes IX, AS22 SPIE Astronomical Telescopes + Instrumentation, 12182-144
Published: 2022

13. Snowmass 2021 White Paper on Upgrading SuperKEKB with a Polarized Electron Beam: Discovery Potential and Proposed Implementation

Author: Accardi, A., Asner, D. M., Atmacan, H., Baartman, R., Banerjee, Sw., Beaubien, A., Bennett, J. V., Bertemes, M., Bessner, M., Biswas, D., Bonvicini, G., Brenny, N., Briere, R. A., Browder, T. E., Chen, C., Choudhury, S., Cinabro, D., Cochran, J., Cremaldi, L. M., Deconinck, W., Di Canto, A., Dubey, S., Flood, K., Fulsom, B. G., Gaur, V., Gericke, M., Godang, R., Gu, T., Guan, Y., Guilliams, J., Hadjivasiliou, C., Hartbrich, O., Hearty, C., Hoferichter, M., Jacobs, W. W., Jaffe, D. E., Junginger, T., Kang, S., Kapitánová, L., Ketter, C., Khatri, A., Kinoshita, K., Kohani, S., Koop, I. A., Korandla, H., Sari, I. Koseoglu, Kroeger, R., Kumar, J., Kumara, K. J., Kuriki, M., Lam, T., Laycock, P. J., Diberder, F. R. Le, Li, L., Liptak, Z., Liventsev, D., Mammei, J., Martens, A., Meier, F., Miller, C., Mitra, S., Moorthy, K., Natochii, A., Nellikunnummel, N., Nishimura, K. A., Otboev, A. V., Oxford, E. R., Panta, A., Parham, K., Parker, B., Pedlar, T. K., Peng, Y., Peschke, R., Piilonen, L. E., Planche, T., Pokharel, S., Prell, S., Purwar, H., Herrmann, D. E. Ricalde, Roney, J. M., Rosenfeld, C., Sahoo, D., Sanders, D. A., Sangal, A., Savinov, V., Schneider, S., Schueler, J., Schwartz, A. J., Shatunov, Yu. M., Shebalin, V., Sibidanov, A., Signori, A., Stottler, Z. S., Strube, J., Trabelsi, K., Tripathi, S., Vahsen, S. E., Varner, G. S., Vossen, A., Wang, D., Wang, E., Wienands, U., Wood, L., Yelton, J., Zhai, Y., Zhang, B., Zhou, D., and Zomer, F.
Subjects: Physics - Accelerator Physics, High Energy Physics - Experiment
Abstract: Upgrading the SuperKEKB electron-positron collider with polarized electron beams opens a new program of precision physics at a center-of-mass energy of 10.58 GeV. This white paper describes the physics potential of this `Chiral Belle' program. It includes projections for precision measurements of $\sin^2\theta_W$ that can be obtained from independent left-right asymmetry measurements of $e^+e^-$ transitions to pairs of electrons, muons, taus, charm and b-quarks. The $\sin^2\theta_W$ precision obtainable at SuperKEKB will match that of the LEP/SLC world average, but at the centre-of-mass energy of 10.58 GeV. Measurements of the couplings for muons, charm, and $b$-quarks will be substantially improved and the existing $3\sigma$ discrepancy between the SLC $A_{LR}$ and LEP $A_{FB}^b$ measurements will be addressed. Precision measurements of neutral current universality will be more than an order of magnitude more precise than currently available. As the energy scale is well away from the $Z^0$-pole, the precision measurements will have sensitivity to the presence of a parity-violating dark sector gauge boson, $Z_{\rm dark}$. The program also enables the measurement of the anomalous magnetic moment $g-2$ form factor of the $\tau$ to be made at an unprecedented level of precision. A precision of $10^{-5}$ level is accessible with 40~ab$^{-1}$ and with more data it would start to approach the $10^{-6}$ level. This technique would provide the most precise information from the third generation about potential new physics explanations of the muon $g-2$ $4\sigma$ anomaly. Additional $\tau$ and QCD physics programs enabled or enhanced with having polarized electron beams are also discussed in this White Paper. This paper includes a summary of the path forward in R&D and next steps required to implement this upgrade and access its exciting discovery potential., Comment: 74 pages, 56 figures, contribution to Snowmass 2021
Published: 2022

14. Chlorinated ethenes characterization using high-resolution rock core analysis in a weathered crystalline rock aquifer in São Paulo, Brazil

Author: Lojkasek-Lima, P., Bertolo, R., Pino, D. S., Fregona, L., Hirata, R., Aravena, R., and Parker, B. L.
Published: 2024
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15. White Paper on Leading-Edge technology And Feasibility-directed (LEAF) Program aimed at readiness demonstration for Energy Frontier Circular Colliders by the next decade

Author: Ambrosio, G., Apollinari, G., Baldini, M., Carcagno, R., Boffo, C., Claypool, B., Feher, S., Hays, S., Hoang, D., Kashikhin, V., Kashikhin, V. V., Krave, S., Kufer, M., Lee, J., Lombardo, V., Marinozzi, V., Nobrega, F., Peng, X., Piekarz, H., Shiltsev, V., Stoynev, S., Strauss, T., Tran, N., Velev, G., Xu, X., Zlobin, A., Amm, K., Anerella, M., Yahia, A. Ben, Gupta, R., Joshi, P., Parker, B., Schmalzle, J., Ferracin, P., Pong, I., Prestemon, S., Wang, X., Sabbi, G., Shen, T., Cooley, L., Rochester, J., and Sumption, M. D.
Subjects: Physics - Accelerator Physics
Abstract: In this White Paper for the Snowmass 2021 Process, we propose the establishment of a magnet Leading-Edge technology And Feasibility-directed Program (LEAF Program) to achieve readiness for a future collider decision on the timescale of the next decade. The LEAF Program would rely on, and be synergetic with, generic R&D efforts presently covered - in the US - by the Magnet Development Program (MDP), the Conductor Procurement and R&D (CPRD) Program and other activities in the Office of HEP supported by Early Career Awards (ECA) or Lab Directed R&D (LDRD) funds. Where possible, ties to synergetic efforts in other Offices of DOE or NSF are highlighted and suggested as wider Collaborative efforts on the National scale. International efforts are also mentioned as potential partners in the LEAF Program. We envision the LEAF Program to concentrate on demonstrating the feasibility of magnets for muon colliders as well as next generation high energy hadron colliders, pursuing, where necessary and warranted by the nature of the application, the transition from R&D models to long models/prototypes. The LEAF Program will naturally drive accelerator-quality and experiment-interface design considerations. LEAF will also concentrate, where necessary, on cost reduction and/or industrialization steps., Comment: Contribution to Snowmass 2021, 19 pages, 5 figures. Corresponding Author: G. Apollinari apollina@fnal.gov
Published: 2022

16. Defining the Sequence Elements and Candidate Genes for the Coloboma Mutation

Author: Elizabeth A. Robb, Parker B. Antin, and Mary E. Delany
Subjects: Medicine, Science
Abstract: The chicken coloboma mutation exhibits features similar to human congenital developmental malformations such as ocular coloboma, cleft-palate, dwarfism, and polydactyly. The coloboma-associated region and encoded genes were investigated using advanced genomic, genetic, and gene expression technologies. Initially, the mutation was linked to a 990 kb region encoding 11 genes; the application of the genetic and genomic tools led to a reduction of the linked region to 176 kb and the elimination of 7 genes. Furthermore, bioinformatics analyses of capture array-next generation sequence data identified genetic elements including SNPs, insertions, deletions, gaps, chromosomal rearrangements, and miRNA binding sites within the introgressed causative region relative to the reference genome sequence. Coloboma-specific variants within exons, UTRs, and splice sites were studied for their contribution to the mutant phenotype. Our compiled results suggest three genes for future studies. The three candidate genes, SLC30A5 (a zinc transporter), CENPH (a centromere protein), and CDK7 (a cyclin-dependent kinase), are differentially expressed (compared to normal embryos) at stages and in tissues affected by the coloboma mutation. Of these genes, two (SLC30A5 and CENPH) are considered high-priority candidate based upon studies in other vertebrate model systems.
Published: 2013

17. Defining the Sequence Elements and Candidate Genes for the Mutation.

Author: Elizabeth A. Robb, Parker B. Antin, and Mary E. Delany
Subjects: Medicine, Science
Abstract: The chicken mutation exhibits features similar to human congenital developmental malformations such as ocular coloboma, cleft-palate, dwarfism, and polydactyly. The -associated region and encoded genes were investigated using advanced genomic, genetic, and gene expression technologies. Initially, the mutation was linked to a 990 kb region encoding 11 genes; the application of the genetic and genomic tools led to a reduction of the linked region to 176 kb and the elimination of 7 genes. Furthermore, bioinformatics analyses of capture array-next generation sequence data identified genetic elements including SNPs, insertions, deletions, gaps, chromosomal rearrangements, and miRNA binding sites within the introgressed causative region relative to the reference genome sequence. -specific variants within exons, UTRs, and splice sites were studied for their contribution to the mutant phenotype. Our compiled results suggest three genes for future studies. The three candidate genes, (a zinc transporter), (a centromere protein), and (a cyclin-dependent kinase), are differentially expressed (compared to normal embryos) at stages and in tissues affected by the mutation. Of these genes, two ( and ) are considered high-priority candidate based upon studies in other vertebrate model systems.
Published: 2013
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18. Search for Highly-Ionizing Particles in pp Collisions at the LHC's Run-1 Using the Prototype MoEDAL Detector

Author: Acharya, B., Alexandre, J., Benes, P., Bergmann, B., Bertolucci, S., Bevan, A., Bhattacharya, R., Branzas, H., Burian, P., Campbell, M., Cecchini, S., Cho, Y. M., de Montigny, M., De Roeck, A., Ellis, J. R., Sawy, M. El, Fairbairn, M., Felea, D., Frank, M., Hays, J., Hirt, A. M., Hung, P. Q., Janecek, J., Kalliokoski, M., Korzenev, A., Lacarrère, D. H., Leroy, C., Levi, G., Lionti, A., Margiotta, A., Maselek, R., Maulik, A., Mauri, N., Mavromatos, N. E., Mermod, P., Mieskolainen, M., Millward, L., Mitsou, V. A., Orava, R., Ostrovskiy, I., Ouimet, P. -P., Papavassiliou, J., Parker, B., Patrizii, L., Pavalas, G. E., Pinfold, J. L., Popa, L. A., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Sakurai, K., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Staelens, M., Suk, M., Tenti, M., Togo, V., Tuszynski, J. A., Upreti, A., Vento, V., and Vives, O.
Subjects: High Energy Physics - Experiment
Abstract: A search for highly electrically charged objects (HECOs) and magnetic monopoles is presented using 2.2 fb-1 of p - p collision data taken at a centre of mass energy (ECM) of 8 TeV by the MoEDAL detector during LHC's Run-1. The data were collected using MoEDAL's prototype Nuclear Track Detector array and the Trapping Detector array. The results are interpreted in terms of Drell-Yan pair production of stable HECO and monopole pairs with three spin hypotheses (0, 1/2 and 1). The search provides constraints on the direct production of magnetic monopoles carrying one to four Dirac magnetic charges (4gD) and with mass limits ranging from 590 GeV/c^2 to 1 TeV/c^2. Additionally, mass limits are placed on HECOs with charge in the range 10e to 180e, where e is the charge of an electron, for masses between 30 GeV/c^2 and 1 TeV/c^2.
Published: 2021
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19. Micro-RNA-195 and -451 regulate the LKB1/AMPK signaling axis by targeting MO25.

Author: Hao Chen, Gustavo M Untiveros, Laurel A K McKee, Jessica Perez, Jing Li, Parker B Antin, and John P Konhilas
Subjects: Medicine, Science
Abstract: BACKGROUND:Recently, MicroRNAs (miR) and AMP-kinase (AMPK) have emerged as prominent players in the development of cardiac hypertrophy and heart failure. We hypothesized that components of the adenosine monophosphate-activated kinase (AMPK) pathway are targeted by miRs and alter AMPK signaling during pathological cardiac stress. METHODOLOGY/PRINCIPAL FINDINGS:Using a mouse model of hypertrophic cardiomyopathy (HCM), we demonstrated early elevation of miR-195 and miR-451 in HCM hearts, which targets MO25, a central component of the MO25/STRAD/LKB1 complex that acts as an upstream kinase for AMPK. We show functional targeting of MO25 by miR-195 and -451. Further in vitro interrogation of MO25 as a functional target validated this hypothesis where over-expression of miR-195 in C2C12 cells knocked down MO25 expression levels and downstream AMPK signaling (phosphorylation of Acetyl CoA carboxylase [ACC] and AMPK activity assay), similar to MO25 knockdown in C2C12 cells by siRNA. Parallel changes were measured in 60 day R403Q HCM male hearts that were rescued by short-term administration of AICAR, an AMPK agonist. CONCLUSIONS/SIGNIFICANCE:Elevated miR-195 targets the LKB1/AMPK signaling axis in HCM progression and implicates a functional role in HCM disease progression. MiR-195 may serve as potential therapeutics or therapeutic targets for heart disease.
Published: 2012
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20. First experimental search for production of magnetic monopoles via the Schwinger mechanism

Author: Acharya, B., Alexandre, J., Benes, P., Bergmann, B., Bertolucci, S., Bevan, A., Branzas, H., Burian, P., Campbell, M., Cho, Y. M., de Montigny, M., De Roeck, A., Ellis, J. R., Sawy, M. El, Fairbairn, M., Felea, D., Frank, M., Gould, O., Hays, J., Hirt, A. M., Ho, D. L. J., Hung, P. Q., Janecek, J., Kalliokoski, M., Korzenev, A., Lacarrère, D. H., Leroy, C., Levi, G., Lionti, A., Maulik, A., Margiotta, A., Mauri, N., Mavromatos, N. E., Mermod, P., Millward, L., Mitsou, V. A., Ostrovskiy, I., Ouimet, P. -P., Papavassiliou, J., Parker, B., Patrizii, L., Păvălaş, G. E., Pinfold, J. L., Popa, L. A., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Staelens, M., Suk, M., Tenti, M., Togo, V., Tuszyński, J. A., Upreti, A., Vento, V., and Vives, O.
Subjects: High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract: Schwinger showed that electrically-charged particles can be produced in a strong electric field by quantum tunnelling through the Coulomb barrier. By electromagnetic duality, if magnetic monopoles (MMs) exist, they would be produced by the same mechanism in a sufficiently strong magnetic field. Unique advantages of the Schwinger mechanism are that its rate can be calculated using semiclassical techniques without relying on perturbation theory, and the finite MM size and strong MM-photon coupling are expected to enhance their production. Pb-Pb heavy-ion collisions at the LHC produce the strongest known magnetic fields in the current Universe, and this article presents the first search for MM production by the Schwinger mechanism. It was conducted by the MoEDAL experiment during the 5.02 TeV/nucleon heavy-ion run at the LHC in November 2018, during which the MoEDAL trapping detectors (MMTs) were exposed to 0.235 nb$^{-1}$ of Pb-Pb collisions. The MMTs were scanned for the presence of magnetic charge using a SQUID magnetometer. MMs with Dirac charges 1$g_D$ $\leq$ $g$ $\leq$ 3$g_D$ and masses up to 75 GeV/c$^2$ were excluded by the analysis. This provides the first lower mass limit for finite-size MMs from a collider search and significantly extends previous mass bounds., Comment: Minor fixes to the authorship list found during production
Published: 2021
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21. Design concept for the second interaction region for Electron-Ion Collider

Author: Gamage, B. R., Aschenauer, E. -C., Berg, J. S., Burkert, V., Ent, R., Furletova, Y., Higinbotham, D., Hutton, A., Hyde, C., Jentsch, A., Kiselev, A., Lin, F., Michalski, T., Montag, C., Morozov, V. S., Nadel-Turonski, P., Palmer, R., Parker, B., Ptitsyn, V., Rajput-Ghoshal, R., Romanov, D., Satogata, T., Seryi, A., Sy, A., Weiss, C., Willeke, F., Wiseman, M., Witte, H., Wittmer, W., and Zhang, Y.
Subjects: Physics - Accelerator Physics
Abstract: The possibility of two interaction regions (IRs) is a design requirement for the Electron Ion Collider (the EIC). There is also a significant interest from the nuclear physics community in a 2nd IR with measurements capabilities complementary to those of the first IR. While the 2nd IR will be in operation over the entire energy range of ~20GeV to ~140GeV center of mass (CM). The 2nd IR can also provide an acceptance coverage complementary to that of the first. We present a brief overview and the current progress of the 2nd IR design in terms of the parameters, magnet layout, and beam dynamics., Comment: To be published in the proceedings of IPAC'21
Published: 2021

22. Output Mode Switching for Parallel Five-bar Manipulators Using a Graph-based Path Planner.

Author: Parker B. Edwards, Aravind Baskar, Caroline Hills, Mark M. Plecnik, and Jonathan D. Hauenstein
Published: 2023
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23. Immunomodulatory therapy in children with paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS, MIS-C; RECOVERY): a randomised, controlled, open-label, platform trial

Author: Faust, Saul N, Haynes, Richard, Jones, Christine E, Staplin, Natalie, Whittaker, Elizabeth, Jaki, Thomas, Juszczak, Ed, Spata, Enti, Wan, Mandy, Bamford, Alasdair, Dimitri, Paul, Finn, Adam, Furness, John, Ramanan, Athimalaipet V, Gale, Christopher, Cathie, Katrina, Drysdale, Simon, Bernatoniene, Jolanta, Murray, Clare, Roehr, Charles C, Fleming, Paul, Riordan, Andrew, Bandi, Srini, Jyothish, Deepthi, Evans, Jennifer, Emonts, Marieke, Kelly, Dominic, Pathan, Nazima, Davies, Patrick, Hague, Rosie, Pollock, Louisa, Semple, Malcolm G, Peto, Leon, Baillie, J Kenneth, Buch, Maya, Jeffery, Katie, Knight, Marian, Lim, Wei Shen, Montgomery, Alan, Mukherjee, Aparna, Mumford, Andrew, Rowan, Kathryn, Thwaites, Guy, Mafham, Marion, Emberson, Jonathan, Landray, Martin J, Horby, Peter W, Chappell, Lucy, Day, Jeremy, Dung, DV, Quang, NN, Binh, Prof, Burhan, E, Alisjahbana, B, Koirala, J, Basnet, S, Kestelyn, E, Basnyat, B, Gyanwali, P, Hamers, RL, Sandercock, P, Darbyshire, J, DeMets, D, Fowler, R, Lalloo, D, Munavvar, M, Roberts, I, Warris, A, Wittes, J, Craddock-Bamford, A, Barton, J, Basoglu, A, Brown, R, Brudlo, W, Denis, E, Fletcher, L, Howard, S, Musini, S, Taylor, K, Cui, G, Goodenough, B, King, A, Lay, M, Murray, D, Stevens, W, Wallendszus, K, Welsh, R, Crichton, C, Davies, J, Goldacre, R, Harper, C, Knight, F, Nunn, M, Salih, H, Welch, J, Campbell, M, Pessoa-Amorim, G, Zayed, M, Wiles, J, Bagley, G, Cameron, S, Chamberlain, S, Farrell, B, Freeman, H, Kennedy, A, Whitehouse, A, Wilkinson, S, Wood, C, Reith, C, Davies, K, Halls, H, Holland, L, Truell, R, Wilson, K, Lingwood, Emma, Howie, L, Lunn, M, Rodgers, Penelope, Amuasi, J, Baird, K, Bao, T, Bittaye, M, Bonney, J, D'Alessandro, U, Dhimal, M, Huyen, T, Jagne, A, Karkey, A, Maiga, O, Matey, E, Nadjm, B, Nel, J, Pant, S, Puspatriani, K, Rahardjani, M, Raijal, S, Rees, H, Rimainar, A, Roberts, C, Rocca, A, Shrestha, S, Usuf, E, Vidaillic, C, Wulandari, F, Alexander, A, Amezaga, M, Armah, C, Asghar, A, Aubrey, P, Barker-Williams, K, Barnard, A, Bartholomew, J, Beaumont-Jewell, D, Beddows, S, Beety, J, Birch, C, Boyle, P, Brend, M, Brookes, M, Callens, C, Campbell, D, Campbell, H, Cate, H, Chambers, E, Chapman, K, Coe, A, Collins, J, Crawshaw, S, Das, S, De Soyza, A, Denton, E, Dicks, P, Dolman, M, Donaldson, K, Dowden, L, Dowling, S, Drake, C, Duckles-Leech, H, Duffy, H, Gerdes, L, Gibbons, K, Gill, L, Gilmour, K, Goodwin, J, Graham, J, Green, C, Hall, C, Hall, A, Hampshire, K, Hanson, J, Harman, T, Harper, H, Harrison, S, Hicks, J, Hodgson, H, Hough, M, Jackson, S, Johnson, G, Kirk, J, Lemoine, N, Levett, C, Lock, S, Lockett, T, Logan, M, Lomme, K, Luo, J, McMillan, N, Membrey, H, Mguni, N, Minton, J, Monaghan, H, Murphy, S, Muzengi, N, Naz, M, Nickson, I, Odam, M, Ohia, U, Okell, E, Oliver, A, Pearson, K, Pine, K, Pleass, R, Porter, D, Porter, L, Potter, A, Poustie, V, Pratt, S, Price, A, Priest, A, Rodgers, A, Rook, C, Ryan, P, Sam, S, Sharratt, P, Sheffield, J, Shenton, J, Shirley, K, Skinner, T, Slade, H, Sutu, M, Taylor, J, Thomas, E, Tinkler, H, Unsworth, A, Usher, R, van't Hoff, W, Walker, S, Walters, J, Walton, E, Warmington, J, Wayman, E, Williams, P, Williamson, J, Williamson, D, Yelnoorkar, F, Knight, M, Hodson, K, Pavord, S, Williamson, C, Bowman, L, Chen, F, Clarke, R, Goonasekara, M, Herrington, W, Judge, P, Ng, S, Preiss, D, Sammons, E, Zhu, D, Arkley, C, Bowker, P, Bruce, J, Byrne-Watts, V, Chapman, G, Coleman, G, Denwood, T, Gray, J, Harrison, D, Mather, N, Pinches, H, Rees, A, Rees, S, Turner, G, Abani, O, Abbas, A, Abbas, F, Abbas, J, Abbas, K, Abbas, M, Abbasi, S, Abbass, H, Abbott, A, Abdallah, N, Abdelaziz, A, Abdelfattah, M, Abdelqader, B, Abdul, A, Abdul, B, Abdul, S, Abdul Rasheed, A, Abdulakeem, A, Abdul-Kadir, R, Abdullah, A, Abdulmumeen, A, Abdul-Raheem, R, Abdulshukkoor, N, Abdusamad, K, Abed El Khaleq, Y, Abedalla, M, Abeer Ul Amna, A, Abel, L, Abernethy, K, Abeywickrema, M, Abhinaya, C, Aboaba, A, Aboagye-Odei, A, Aboelela, H, Abo-Leyah, H, Abouelela, K, Abou-Haggar, A, Abouibrahim, M, Abousamra, A, Abouzaid, M, Abraham, M, Abraham, T, Abraheem, A, Abrams, J, Abrams, R, Abu, H, Abu-Arafeh, A, Abubacker, S, Abung, A, Abusamra, Y, Aceampong, Y, Achara, A, Acharya, D, Acheampong, S, Acheampong, P, Acheson, J, Achieng, S, Acosta, A, Acquah, R, Acton, C, Adabie-Ankrah, J, Adair, P, Adam, F, Adam, M, Adamali, H, Adamczyk, M, Adams, C, Adams, D, Adams, K, Adams, L, Adams, N, Adams, R, Adams, T, Adamu-Ikeme, L, Adati, K, Adcock, K, Addo, A, Adeagbo, O, Adebiyi, A, Adedeji, O, Adegeye, Y, Adegoke, K, Adell, V, Adenwalla, S, Adeoye, F, Adesemoye, O, Adewunmi, E, Adeyanju, A, Adeyemi, J, Adeyemo, T, Adhikary, R, Aditya, A, Adkins, G, Adnan, A, Aeron-Thomas, J, Affleck, D, Afnan, C, Afridi, M, Aftab, Z, Agarwal, M, Agbeko, R, Agbo, C, Aggarwal, S, Aghababaie, A, Aguilar Jimenez, L, Ahamed Sadiq, S, Ahammed Nazeer, M, Ahmed, A, Ahmed, B, Ahmed, F, Ahmed, H, Ahmed, I, Ahmed, K, Ahmed, L, Ahmad, M, Ahmed, N, Ahmed, O, Ahmed, R, Ahmad, S, Ahmed, S H, Ahmed Ali, R, Ahmed Mohamud, B, Ahmer, S, Ahonia, A, Aiken, C, Ail, D, Ainsworth, M, Aissa, M, Aitken, L, Ajay, B, Ajibode, A, Ajmi, A, Akhtar, N, Akili, S, Akinbiyi, B, Akindolie, O, Akinfenwa, Y, Akinkugbe, O, Akinpelu, I, Akram, M, Aktinade, O, Akudi, U, Al Aaraj, A, Al Balushi, A, Al Dakhola, M, Al Swaifi, A, Al-Abadi, E, Alabi, A, Aladangady, N, Alafifi, M, Alam, A, Alam, S, Al-Asadi, A, Alatzoglou, K, Albert, P, Albon, L, Alcala, A, Alcorn, G, Alcorn, S, Aldana, A, Alderdice, D, Aldesouki, A, Aldouri, R, Aldridge, J, Aldridge, N, Alegria, A, Alexander, C, Alexander, J, Alexander, P, Al-Fori, J, Alghazawi, L, Alhabsha, O, Al-Hakim, B, Alhameed, R, Al-Hayali, M, Al-Hity, S, Ali, A, Ali, F, Ali, J, Ali, M, Ali, N, Ali, O, Ali, R, Ali, S, Aliberti, E, Alin, J, Alina, A, Alipustain, A, Aliyuda, F, Alizaedeh, K, Al-Jibury, M, Al-Juboori, S, Al-Khalil, M, Alkhudhayri, A, Alkhusheh, M, Allan, F, Allan, N, Allanson, A, Allcock, R, Allen, E, Allen, J, Allen, K, Allen, L, Allen, P, Allen, R, Allen, S, Allen, T, Alli, A, Allison, K, Allman, B, Allsup, D, Allsop, H, Allsop, L, Almahroos, A, Al-Moasseb, H, Al-Obaidi, M, Alomari, L, Al-Rabahi, A, Al-Ramadhani, B, Al-Saadi, Z, Al-Sammarraie, R, Alshaer, I, Al-Shahi Salman, R, Al-Shamkhani, W, Alsheikh, F, Al-Sheklly, B, Altaf, S, Alty, A, Alvarez, M, Alvarez Corral, M, Alveyn, E, Alzetani, M, Amamou, S, Amar, N, Ambalavanan, S, Ambrogetti, R, Ambrose, C, Ameen, A, Ames, K, Amin, A, Amin, K, Amin, S, Amin, T, Amit, B, Amjad, A, Amjad, N, Amosun, V, Amsal, M, Amsha, K, Amutio Martin, N, Amy, P, Anada, A, Anand, A, Anandappa, S, Anantapatnaikuni, S, Anderson, E, Anderson, J, Anderson, L, Anderson, M, Anderson, N, Anderson, R, Anderson, S, Anderson, W, Andreou, P, Andrews, A, Andrews, J, Aneke, K, Ang, A, Ang, W, Angel, T, Angela, A, Angelini, P, Anguvaa, L, Anichtchik, O, Anim-Somuah, M, Aniruddhan, K, Annett, J, Anning, L, Anstey, P, Anstey, R, Anthony, A, Anthony-Pillai, A, Antill, P, Antonnia, Z, Anu, V, 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Zulaikha, R, Zulfikar, S, Zullo, C, and Zuriaga-Alvaro, A
Published: 2024
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24. Certified evaluations of H\'older continuous functions at roots of polynomials

Author: Edwards, Parker B., Hauenstein, Jonathan D., and Smyth, Clifford D.
Subjects: Computer Science - Symbolic Computation, Mathematics - Numerical Analysis, 65H14 (Primary) 65H04, 14-04 (Secondary), I.1.2
Abstract: Various methods can obtain certified estimates for roots of polynomials. Many applications in science and engineering additionally utilize the value of functions evaluated at roots. For example, critical values are obtained by evaluating an objective function at critical points. For analytic evaluation functions, Newton's method naturally applies to yield certified estimates. These estimates no longer apply, however, for H\"older continuous functions, which are a generalization of Lipschitz continuous functions where continuous derivatives need not exist. This work develops and analyzes an alternative approach for certified estimates of evaluating locally H\"older continuous functions at roots of polynomials. An implementation of the method in Maple demonstrates efficacy and efficiency., Comment: 15 pages, 1 figure, associated software package at https://github.com/P-Edwards/EvalCertification
Published: 2021

25. 3D Mechanical Analysis of a Compact Nb3Sn IR Quadrupole for EIC

Author: Vallone, G, Anerella, M, Parker, B, Cozzolino, J, Michalski, T, Plate, S, Prestemon, S, Sabbi, G, and Schmalzle, J
Subjects: Electron ion collider, Nb3Sn magnet, mechanical performance, Bioengineering, General Physics, Condensed Matter Physics, Electrical and Electronic Engineering, Materials Engineering
Abstract: The Electron Ion Collider (EIC) will require large aperture quadrupole magnets for the Hadron beam in the insertion region. Key requirements include high field, compact size, and tight control of the fringe fields. A 120 mm aperture, 308.4 mm outer diameter actively shielded Nb3Sn quadrupole model is under development to support these goals. This work is being carried out by a collaboration of BNL, JLAB and LBNL. A compact shell-based structure preloaded with a bladder and key system was developed for this project. In this paper, the effect of the compact structure on the mechanical behavior was investigated. In particular, the impact of the assembly tolerances and coil size variations on the actual coil stresses and bladder pressures was computed and compared with results from larger bladder and key structures developed for the LHC IR. The longitudinal preload is provided by stainless steel rods. Differently from other bladder and key magnets, the rods are first preloaded axially before coil axial load is applied. This new design aims to increase the overall stiffness of the system and reduce the longitudinal coil displacement during powering. Based on the results of a 3D mechanical analysis, the preliminary pre-load targets for the EIC quadrupole assembly will be reviewed and discussed.
Published: 2021

26. The Large Hadron-Electron Collider at the HL-LHC

Author: Agostini, P., Aksakal, H., Alekhin, S., Allport, P. P., Andari, N., Andre, K. D. J., Angal-Kalinin, D., Antusch, S., Bella, L. Aperio, Apolinario, L., Apsimon, R., Apyan, A., Arduini, G., Ari, V., Armbruster, A., Armesto, N., Auchmann, B., Aulenbacher, K., Azuelos, G., Backovic, S., Bailey, I., Bailey, S., Balli, F., Behera, S., Behnke, O., Ben-Zvi, I., Benedikt, M., Bernauer, J., Bertolucci, S., Biswal, S. S., Blümlein, J., Bogacz, A., Bonvini, M., Boonekamp, M., Bordry, F., Boroun, G. R., Bottura, L., Bousson, S., Bouzas, A. O., Bracco, C., Bracinik, J., Britzger, D., Brodsky, S. J., Bruni, C., Brüning, O., Burkhardt, H., Cakir, O., Calaga, R., Caldwell, A., Calıskan, A., Camarda, S., Catalan-Lasheras, N. C., Cassou, K., Cepila, J., Cetinkaya, V., Chetvertkova, V., Cole, B., Coleppa, B., Cooper-Sarkar, A., Cormier, E., Cornell, A. S., Corsini, R., Cruz-Alaniz, E., Currie, J., Curtin, D., D'Onofrio, M., Dainton, J., Daly, E., Das, A., Das, S. P., Dassa, L., de Blas, J., Rose, L. Delle, Denizli, H., Deshpande, K. S., Douglas, D., Duarte, L., Dupraz, K., Dutta, S., Efremov, A. V., Eichhorn, R., Eskola, K. J., Ferreiro, E. G., Fischer, O., Flores-Sánchez, O., Forte, S., Gaddi, A., Gao, J., Gehrmann, T., Ridder, A. Gehrmann-De, Gerigk, F., Gilbert, A., Giuli, F., Glazov, A., Glover, N., Godbole, R. M., Goddard, B., Gonçalves, V., Gonzalez-Sprinberg, G. A., Goyal, A., Grames, J., Granados, E., Grassellino, A., Gunaydin, Y. O., Guo, Y. C., Guzey, V., Gwenlan, C., Hammad, A., Han, C. C., Harland-Lang, L., Haug, F., Hautmann, F., Hayden, D., Hessler, J., Helenius, I., Henry, J., Hernandez-Sanchez, J., Hesari, H., Hobbs, T. J., Hod, N., Hoffstaetter, G. H., Holzer, B., Honorato, C. G., Hounsell, B., Hu, N., Hug, F., Huss, A., Hutton, A., Islam, R., Iwamoto, S., Jana, S., Jansova, M., Jensen, E., Jones, T., Jowett, J. M., Kaabi, W., Kado, M., Kalinin, D. A., Karadeniz, H., Kawaguchi, S., Kaya, U., Khalek, R. A., Khanpour, H., Kilic, A., Klein, M., Klein, U., Kluth, S., Köksal, M., Kocak, F., Korostelev, M., Kostka, P., Krelina, M., Kretzschmar, J., Kuday, S., Kulipanov, G., Kumar, M., Kuze, M., Lappi, T., Larios, F., Latina, A., Laycock, P., Lei, G., Levitchev, E., Levonian, S., Levy, A., Li, R., Li, X., Liang, H., Litvinenko, V., Liu, M., Liu, T., Liu, W., Liu, Y., Liuti, S., Lobodzinska, E., Longuevergne, D., Luo, X., Ma, W., Machado, M., Mandal, S., Mäntysaari, H., Marhauser, F., Marquet, C., Martens, A., Martin, R., Marzani, S., McFayden, J., Mcintosh, P., Mellado, B., Meot, F., Milanese, A., Milhano, J. G., Militsyn, B., Mitra, M., Moch, S., Najafabadi, M. Mohammadi, Mondal, S., Moretti, S., Morgan, T., Morreale, A., Nadolsky, P., Navarra, F., Nergiz, Z., Newman, P., Niehues, J., Nissen, E. A., Nowakowski, M., Okada, N., Olivier, G., Olness, F., Olry, G., Osborne, J. A., Ozansoy, A., Pan, R., Parker, B., Patra, M., Paukkunen, H., Peinaud, Y., Pellegrini, D., Perez-Segurana, G., Perini, D., Perrot, L., Pietralla, N., Pilicer, E., Pire, B., Pires, J., Placakyte, R., Poelker, M., Polifka, R., Polini, A., Poulose, P., Pownall, G., Pupkov, Y. A., Queiroz, F. S., Rabbertz, K., Radescu, V., Rahaman, R., Rai, S. K., Raicevic, N., Ratoff, P., Rashed, A., Raut, D., Raychaudhuri, S., Repond, J., Rezaeian, A. H., Rimmer, R., Rinolfi, L., Rojo, J., Rosado, A., Ruan, X., Russenschuck, S., Sahin, M., Salgado, C. A., Sampayo, O. A., Satendra, K., Satyanarayan, N., Schenke, B., Schirm, K., Schopper, H., Schott, M., Schulte, D., Schwanenberger, C., Sekine, T., Senol, A., Seryi, A., Setiniyaz, S., Shang, L., Shen, X., Shipman, N., Sinha, N., Slominski, W., Smith, S., Solans, C., Song, M., Spiesberger, H., Stanyard, J., Starostenko, A., Stasto, A., Stocchi, A., Strikman, M., Stuart, M. J., Sultansoy, S., Sun, H., Sutton, M., Szymanowski, L., Tapan, I., Tapia-Takaki, D., Tanaka, M., Tang, Y., Tasci, A. T., Ten-Kate, A. T., Thonet, P., Tomas-Garcia, R., Tommasini, D., Trbojevic, D., Trott, M., Tsurin, I., Tudora, A., Cakir, I. Turk, Tywoniuk, K., Vallerand, C., Valloni, A., Verney, D., Vilella, E., Walker, D., Wallon, S., Wang, B., Wang, K., Wang, X., Wang, Z. S., Wei, H., Welsch, C., Willering, G., Williams, P. H., Wollmann, D., Xiaohao, C., Xu, T., Yaguna, C. E., Yamaguchi, Y., Yamazaki, Y., Yang, H., Yilmaz, A., Yock, P., Yue, C. X., Zadeh, S. G., Zenaiev, O., Zhang, C., Zhang, J., Zhang, R., Zhang, Z., Zhu, G., Zhu, S., Zimmermann, F., Zomer, F., Zurita, J., and Zurita, P.
Subjects: High Energy Physics - Experiment, High Energy Physics - Phenomenology, Nuclear Experiment, Nuclear Theory
Abstract: The Large Hadron electron Collider (LHeC) is designed to move the field of deep inelastic scattering (DIS) to the energy and intensity frontier of particle physics. Exploiting energy recovery technology, it collides a novel, intense electron beam with a proton or ion beam from the High Luminosity--Large Hadron Collider (HL-LHC). The accelerator and interaction region are designed for concurrent electron-proton and proton-proton operation. This report represents an update of the Conceptual Design Report (CDR) of the LHeC, published in 2012. It comprises new results on parton structure of the proton and heavier nuclei, QCD dynamics, electroweak and top-quark physics. It is shown how the LHeC will open a new chapter of nuclear particle physics in extending the accessible kinematic range in lepton-nucleus scattering by several orders of magnitude. Due to enhanced luminosity, large energy and the cleanliness of the hadronic final states, the LHeC has a strong Higgs physics programme and its own discovery potential for new physics. Building on the 2012 CDR, the report represents a detailed updated design of the energy recovery electron linac (ERL) including new lattice, magnet, superconducting radio frequency technology and further components. Challenges of energy recovery are described and the lower energy, high current, 3-turn ERL facility, PERLE at Orsay, is presented which uses the LHeC characteristics serving as a development facility for the design and operation of the LHeC. An updated detector design is presented corresponding to the acceptance, resolution and calibration goals which arise from the Higgs and parton density function physics programmes. The paper also presents novel results on the Future Circular Collider in electron-hadron mode, FCC-eh, which utilises the same ERL technology to further extend the reach of DIS to even higher centre-of-mass energies., Comment: 373 pages, many figures, to be published by J. Phys. G
Published: 2020
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27. First search for dyons with the full MoEDAL trapping detector in 13 TeV pp collisions

Author: Acharya, B., Alexandre, J., Benes, P., Bergmann, B., Bernabeu, J., Bevan, A., Branzas, H., Burian, P., Campbell, M., Cecchini, S., Cho, Y. M., de Montigny, M., De Roeck, A., Ellis, J. R., Sawy, M. El, Fairbairn, M., Felea, D., Frank, M., Hays, J., Hirt, A. M., Janecek, J., Kalliokoski, M., Korzenev, A., Lacarrere, D. H., Leroy, C., Levi, G., Lionti, A., Mamuzic, J., Maulik, A., Margiotta, A., Mauri, N., Mavromatos, N. E., Mermod, P., Mieskolainen, M., Millward, L., Mitsou, V. A., Orava, R., Ostrovskiy, I., Ouimet, P. -P., Papavassiliou, J., Parker, B., Patrizii, L., Pavalas, G. E., Pinfold, J. L., Popa, L. A., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Staelens, M., Suk, M., Tenti, M., Togo, V., Tuszynski, J. A., Upreti, A., Vento, V., Vives, O., and Wall, A.
Subjects: High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract: The MoEDAL trapping detector, consists of approximately 800 kg of aluminium volumes. It was exposed during Run-2 of the LHC program to 6.46 fb^-1 of 13 TeV proton-proton collisions at the LHCb interaction point. Evidence for dyons (particles with electric and magnetic charge) captured in the trapping detector was sought by passing the aluminium volumes comprising the detector through a SQUID magnetometer. The presence of a trapped dyon would be signalled by a persistent current induced in the SQUID magnetometer. On the basis of a Drell-Yan production model, we exclude dyons with a magnetic charge ranging up to 5 Dirac charges, and an electric charge up to 200 times the fundamental electric charge for mass limits in the range 790 - 3130 GeV., Comment: arXiv admin note: text overlap with arXiv:1903.08491
Published: 2020
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28. Empagliflozin in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial

Author: Abani, O, Abbas, A, Abbas, F, Abbas, J, Abbas, K, Abbas, M, Abbasi, S, Abbass, H, Abbott, A, Abdallah, N, Abdelaziz, A, Abdelfattah, M, Abdelqader, B, Abdul, A, Abdul, B, Abdul, S, Abdul Rasheed, A, Abdulakeem, A, Abdul-Kadir, R, Abdullah, A, Abdulmumeen, A, Abdul-Raheem, R, Abdulshukkoor, N, Abdusamad, K, Abed El Khaleq, Y, Abedalla, M, Abeer Ul Amna, A, Abel, L, Abernethy, K, Abeywickrema, M, Abhinaya, C, Abidin, A, Aboaba, A, Aboagye-Odei, A, Aboah, C, Aboelela, H, Abo-Leyah, H, Abouelela, K, Abou-Haggar, A, Abouibrahim, M, Abousamra, A, Abouzaid, M, Abraham, M, Abraham, T, Abraheem, A, Abrams, J, Abrams, R, Abu, HJ, Abu-Arafeh, A, Abubacker, SM, Abung, A, Abusamra, Y, Aceampong, Y, Achara, A, Acharya, D, Acheampong, F, Acheampong, P, Acheampong, S, Acheson, J, Achieng, S, Acosta, A, Acquah, R, Acton, C, Adabie-Ankrah, J, Adair, P, Adam, AS, Adam, F, Adam, M, Adamali, H, Adamczyk, M, Adams, C, Adams, D, Adams, K, Adams, L, Adams, N, Adams, R, Adams, T, Adamu-Ikeme, L, Adatia, K, Adcock, K, Addai-Boampong, L, Addo, A, Adeagbo, O, Adebiyi, A, Adedeji, O, Adegeye, Y, Adegoke, K, Adell, V, Adenwalla, S, Adeoye, FW, Adesemoye, OA, Adewunmi, EO, Adeyanju, A, Adeyemi, J, Adeyemo, T, Adhikari, B, Adhikari, SA, Adhikary, R, Aditya, A, Adjepong, P, Adkins, G, Adnan, A, Adriaanse, M, Aeron-Thomas, J, Affleck, D, Afnan, C, Afridi, M, Afrim, P, Afriyie, FA, Aftab, ZA, Afum-Adjei Awuah, A, Agarwal, M, Agasiya, PN, Agbeko, R, Agbo, C, Aggarwal, S, Aghababaie, A, Aguilar Jimenez, L, Agyekum, JA, Agyen, K, Ahadome, EK, Ahamed Sadiq, S, Ahammed Nazeer, MH, Ahmad, M, Ahmad, S, Ahmed, A, Ahmed, BAR, Ahmed, B, Ahmed, F, Ahmed, H, Ahmed, I, Ahmed, K, Ahmed, L, Ahmed, M, Ahmed, MC, Ahmed, MS, Ahmed, N, Ahmed, O, Ahmed, RA, Ahmed, R, Ahmed, S, Ahmed, SG, Ahmed, SH, Ahmed Ali, R, Ahmed Mohamud, B, Ahmer, S, Ahonia, A, Aidoo, C, Aiken, C, Ail, D, Ainsworth, M, Aissa, M, Aitken, L, Ajay, B, Ajibode, A, Ajmi, A, Akhtar, N, Akili, S, Akinbiyi, B, Akindolie, O, Akinfenwa, Y, Akinkugbe, O, Akinpelu, I, Akram, M, Aktinade, O, Akudi, U, Al Aaraj, ASAR, Al Balushi, A, Al Dakhola, M, Al Swaifi, A, Al-Abadi, E, Alabi, A, Aladangady, N, Alafifi, M, Alam, A, Alam, S, Al-Asadi, A, Alatzoglou, K, Albert, P, Albertus, A, Albon, L, Alcala, A, Alcorn, G, Alcorn, S, Aldana, A, Alderdice, D, Aldesouki, A, Aldouri, R, Aldridge, J, Aldridge, N, Ale, RM, Alegria, A, Alexander, A, Alexander, C, Alexander, J, Alexander, PDG, Al-fori, J, Alghazawi, L, Alhabsha, O, Al-Hakim, B, Alhameed, R, Al-Hayali, M, Al-Hity, S, Ali, A, Ali, FR, Ali, J, Ali, M, Ali, MS, Ali, N, Ali, O, Ali, R, Ali, S, Aliberti, E, Alin, J, Alina, A, Alipustain, A, Alisjahbana, B, Aliyuda, F, Alizadeh, K, Al-Jibury, M, Al-Juboori, S, Al-Khalil, M, Alkhudhayri, A, Alkhusheh, M, Allan, F, Allan, N, Allanson, A, Allcock, R, Allen, E, Allen, J, Allen, K, Allen, L, Allen, P, Allen, R, Allen, S, Allen, T, Alli, A, Allison, K, Allman, B, Allsop, HK, Allsop, L, Allsup, D, Almahroos, AFT, Al-Moasseb, H, Al-Obaidi, M, 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Wong, MY, Wong, N, Wong, S, Wong, T, Wongkyezeng, AA, Wood, A, Wood, C, Wood, D, Wood, F, Wood, G, Wood, H, Wood, J, Wood, L, Wood, M, Wood, S, Wood, T, Woodall, K, Woodfield, R, Woodford, C, Woodford, E, Woodford, J, Woodhead, L, Woodhead, T, Woodland, P, Woodman, M, Woodmansey, S, Woods, C, Woods, J, Woods, K, Woods, S, Woodward, Z, Woolcock, M, Wooldridge, G, Woolf, R, Woollard, C, Woollen, L, Woolley, E, Woolley, J, Woosey, D, Wootton, D, Wootton, J, Worley, D, Worton, S, Wraight, J, Wray, M, Wren, K, Wren, L, Wrey Brown, C, Wright, C, Wright, D, Wright, F, Wright, H, Wright, I, Wright, L, Wright, R, Wright, S, Wright, T, Wroe, C, Wroe, H, Wu, H, Wu, P, Wubetu, J, Wulandari, F, Wulandari, R, Wurie, S, Wyatt, C, Wyn-Griffiths, F, Wynter, I, Xavier, B, Xhikola, A, Xia, BE, Xia, Z, Yacoba, E, Yadav, S, Yakubi, M, Yan, M, Yanagisawa, Y, Yang, F, Yang, Y, Yanney, M, Yap, WL, Yaqoob, N, Yasmin, S, Yates, B, Yates, D, Yates, E, Yates, H, Yates, T, Yates, M, Ye, J, Yearwood Martin, C, Yein, K, Yelnoorkar, F, Yen, LM, Yeoh, A, Yeung, CY, Yew, P, Yewatkar, D, Ylquimiche Melly, L, Ynter, I, Yong, H, Yorke, J, Youens, J, Younes Ibrahim, A, Young, E, Young, G, Young, L, Yousafzar, A, Youssouf, S, Yousuf, A, Yovita, H, Yu, C, Yuan, JSJ, Yufaniaputri, N, Yung, B, Yusef, D, Yusef, S, Yusuf, I, Zafar, A-S, Zagalo, S, Zaher, S, Zahoor, A, Zainab, M, Zak, T, Zaki, K, Zakir, N, Zalewska, K, Zamalloa, A, Zaman, M, Zaman, S, Zamikula, J, Zammit, L, Zammit-Mangion, M, Zawadzka, M, Zayed, M, Zebracki, E, Zehnder, D, Zeidan, L, Zeinali, D, Zhang, J, Zhao, X, Zheng, D, Zhu, D, Zia, M, Zibdeh, O, Zill-E-Huma, R, Zin, ET, Zincone, E, Zindoga, G, Zinkin, E, Zinyemba, V, Zipitis, C, Zitter, L, Zmierczak, A, Zubikarai, G, Zubir, A, Zuhra, N, Zulaikha, R, Zulfikar, S, Zullo, C, and Zuriaga-Alvaro, A
Published: 2023
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29. Computing Geometric Feature Sizes for Algebraic Manifolds.

Author: Sandra Di Rocco, Parker B. Edwards, David Eklund, Oliver Gäfvert, and Jonathan D. Hauenstein
Published: 2023
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30. Abstract 18984: Artificial Intelligence-Based Automated Left Ventricle Mass Quantification From Non-Contrast Cardiac CT Scans: Correlation With Contrast CT and Cardiac MRI

Author: Han, Donghee, Shanbhag, Aakash, Killekar, Aditya, Waechter, Parker B, Kwok, Nicholas, Berman, Daniel, and Slomka, Piotr J
Published: 2023
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31. Graded persistence diagrams and persistence landscapes

Author: Betthauser, Leo, Bubenik, Peter, and Edwards, Parker B.
Subjects: Mathematics - Algebraic Topology, 55N31, 06A07
Abstract: We introduce a refinement of the persistence diagram, the graded persistence diagram. It is the Mobius inversion of the graded rank function, which is obtained from the rank function using the unary numeral system. Both persistence diagrams and graded persistence diagrams are integer-valued functions on the Cartesian plane. Whereas the persistence diagram takes non-negative values, the graded persistence diagram takes values of 0, 1, or -1. The sum of the graded persistence diagrams is the persistence diagram. We show that the positive and negative points in the k-th graded persistence diagram correspond to the local maxima and minima, respectively, of the k-th persistence landscape. We prove a stability theorem for graded persistence diagrams: the 1-Wasserstein distance between k-th graded persistence diagrams is bounded by twice the 1-Wasserstein distance between the corresponding persistence diagrams, and this bound is attained. In the other direction, the 1-Wasserstein distance is a lower bound for the sum of the 1-Wasserstein distances between the k-th graded persistence diagrams. In fact, the 1-Wasserstein distance for graded persistence diagrams is more discriminative than the 1-Wasserstein distance for the corresponding persistence diagrams., Comment: accepted for publication in Discrete and Computational Geometry
Published: 2019
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32. Magnetic monopole search with the full MoEDAL trapping detector in 13 TeV $pp$ collisions interpreted in photon-fusion and Drell-Yan production

Author: MoEDAL Collaboration, Acharya, B., Alexandre, J., Baines, S., Benes, P., Bergmann, B., Bernabéu, J., Bevan, A., Branzas, H., Campbell, M., Cecchini, S., Cho, Y. M., de Montigny, M., De Roeck, A., Ellis, J. R., Sawy, M. El, Fairbairn, M., Felea, D., Frank, M., Hays, J., Hirt, A. M., Janecek, J., Kim, D. -W., Korzenev, A., Lacarrère, D. H., Lee, S. C., Leroy, C., Levi, G., Lionti, A., Mamuzic, J., Margiotta, A., Mauri, N., Mavromatos, N. E., Mermod, P., Mieskolainen, M., Millward, L., Mitsou, V. A., Orava, R., Ostrovskiy, I., Papavassiliou, J., Parker, B., Patrizii, L., Păvălaş, G. E., Pinfold, J. L., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Staelens, M., Suk, M., Tenti, M., Togo, V., Tuszyński, J. A., Vento, V., Vives, O., Vykydal, Z., Wall, A., and Zgura, I. S.
Subjects: High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract: MoEDAL is designed to identify new physics in the form of stable or pseudostable highly ionizing particles produced in high-energy Large Hadron Collider (LHC) collisions. Here we update our previous search for magnetic monopoles in Run 2 using the full trapping detector with almost four times more material and almost twice more integrated luminosity. For the first time at the LHC, the data were interpreted in terms of photon-fusion monopole direct production in addition to the Drell-Yan-like mechanism. The MoEDAL trapping detector, consisting of 794 kg of aluminum samples installed in the forward and lateral regions, was exposed to 4.0 fb$^{-1}$ of 13 TeV proton-proton collisions at the LHCb interaction point and analyzed by searching for induced persistent currents after passage through a superconducting magnetometer. Magnetic charges equal to or above the Dirac charge are excluded in all samples. Monopole spins 0, 1/2 and 1 are considered and both velocity-independent and -dependent couplings are assumed. This search provides the best current laboratory constraints for monopoles with magnetic charges ranging from two to five times the Dirac charge., Comment: 7 pages REVTeX 4, 11 figures, 1 table, matches published version in Physical Review Letters
Published: 2019
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33. Aggregating community maps.

Author: Erin W. Chambers, Moon Duchin, Ranthony A. C. Edmonds, Parker B. Edwards, JN Matthews, Anthony E. Pizzimenti, Chanel Richardson, Parker Rule, and Ari Stern
Published: 2022
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34. Understanding mechanisms of recharge through fractured sandstone using high-frequency water-level-response data

Author: Manna, F., Kennel, J., and Parker, B. L.
Published: 2022
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35. Reduction of coastal lighting decreases seabird strandings

Author: Burt, Tori V., primary, Collins, Sydney M., additional, Green, Sherry, additional, Doiron, Parker B., additional, Wilhelm, Sabina I., additional, and Montevecchi, William A., additional
Published: 2024
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36. Sampling real algebraic varieties for topological data analysis

Author: Dufresne, Emilie, Edwards, Parker B., Harrington, Heather A., and Hauenstein, Jonathan D.
Subjects: Mathematics - Algebraic Topology, Mathematics - Algebraic Geometry, Mathematics - Numerical Analysis
Abstract: Topological data analysis (TDA) provides a growing body of tools for computing geometric and topological information about spaces from a finite sample of points. We present a new adaptive algorithm for finding provably dense samples of points on real algebraic varieties given a set of defining polynomials. The algorithm utilizes methods from numerical algebraic geometry to give formal guarantees about the density of the sampling and it also employs geometric heuristics to reduce the size of the sample. As TDA methods consume significant computational resources that scale poorly in the number of sample points, our sampling minimization makes applying TDA methods more feasible. We provide a software package that implements the algorithm and also demonstrate the implementation with several examples., Comment: Updated section 5, added links to implementation software package, improved figure resolution in section 5
Published: 2018

37. Comparing Unicompartmental Knee Arthroplasty and High Tibial Osteotomy for Isolated Medial Compartment Knee Osteoarthritis

Author: Goodell, Parker B., Johansen, Phillip M., Bartels, Douglas W., Sherman, Seth L., and Amanatullah, Derek F.
Published: 2023
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38. Search for magnetic monopoles with the MoEDAL forward trapping detector in 2.11 fb$^{-1}$ of 13 TeV proton-proton collisions at the LHC

Author: MoEDAL Collaboration, Acharya, B., Alexandre, J., Baines, S., Benes, P., Bergmann, B., Bernabéu, J., Bevan, A., Branzas, H., Campbell, M., Caramete, L., Cecchini, S., de Montigny, M., De Roeck, A., Ellis, J. R., Fairbairn, M., Felea, D., Frank, M., Frekers, D., Garcia, C., Hays, J., Hirt, A. M., Janecek, J., Kim, D. -W., Kinoshita, K., Korzenev, A., Lacarrère, D. H., Lee, S. C., Leroy, C., Levi, G., Lionti, A., Mamuzic, J., Margiotta, A., Mauri, N., Mavromatos, N. E., Mermod, P., Mitsou, V. A., Orava, R., Ostrovskiy, I., Parker, B., Patrizii, L., Păvălaş, G. E., Pinfold, J. L., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Srivastava, Y. N., Suk, M., Swain, J., Tenti, M., Togo, V., Tuszyński, J. A., Vento, V., Vives, O., Vykydal, Z., Widom, A., Willems, G., Yoon, J. H., and Zgura, I. S.
Subjects: High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract: We update our previous search for trapped magnetic monopoles in LHC Run 2 using nearly six times more integrated luminosity and including additional models for the interpretation of the data. The MoEDAL forward trapping detector, comprising 222~kg of aluminium samples, was exposed to 2.11~fb$^{-1}$ of 13 TeV proton-proton collisions near the LHCb interaction point and analysed by searching for induced persistent currents after passage through a superconducting magnetometer. Magnetic charges equal to the Dirac charge or above are excluded in all samples. The results are interpreted in Drell-Yan production models for monopoles with spins 0, 1/2 and 1: in addition to standard point-like couplings, we also consider couplings with momentum-dependent form factors. The search provides the best current laboratory constraints for monopoles with magnetic charges ranging from two to five times the Dirac charge., Comment: 8 pages, 5 figures, 1 table, accepted for publication in Phys. Lett. B
Published: 2017
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39. A robotically extruded sugar waste composite for a circular biomateriality in architecture

Author: Meng, J., primary, Alnaeb, D., additional, Salmane, A. K., additional, Devadass, P., additional, Cruz, M., additional, and Parker, B., additional
Published: 2022
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40. Predictive Modeling for Geriatric Hip Fracture Patients: Early Surgery and Delirium Have the Largest Influence on Length of Stay.

Author: Hecht, Garin, Slee, Christina A, Goodell, Parker B, Taylor, Sandra L, and Wolinsky, Philip R
Subjects: Physical Injury - Accidents and Adverse Effects, Mental Health, Aging, Patient Safety, Clinical Research, Aged, Delirium, Female, Geriatric Assessment, Hip Fractures, Humans, Injury Severity Score, Length of Stay, Linear Models, Male, Models, Statistical, Multivariate Analysis, Orthopedic Procedures, Retrospective Studies, Time Factors, Clinical Sciences, Orthopedics
Abstract: BackgroundAveraging length of stay (LOS) ignores patient complexity and is a poor metric for quality control in geriatric hip fracture programs. We developed a predictive model of LOS that compares patient complexity to the logistic effects of our institution's hip fracture care pathway.MethodsA retrospective analysis was performed on patients enrolled into a hip fracture co-management pathway at an academic level I trauma center from 2014 to 2015. Patient complexity was approximated using the Charlson Comorbidity Index and ASA score. A predictive model of LOS was developed from patient-specific and system-specific variables using a multivariate linear regression analysis; it was tested against a sample of patients from 2016.ResultsLOS averaged 5.95 days. Avoidance of delirium and reduced time to surgery were found to be notable predictors of reduced LOS. The Charlson Comorbidity Index was not a strong predictor of LOS, but the ASA score was. Our predictive LOS model worked well for 63% of patients from the 2016 group; for those it did not work well for, 80% had postoperative complications.DiscussionPredictive LOS modeling accounting for patient complexity was effective for identifying (1) reasons for outliers to the expected LOS and (2) effective measures to target for improving our hip fracture program.Level of evidenceIII.
Published: 2019

41. CT-measurement predicts shortening of stable intertrochanteric hip fractures

Author: Hecht, Garin, Shelton, Trevor J, Saiz, Augustine M, Goodell, Parker B, and Wolinsky, Philip
Subjects: Biomedical and Clinical Sciences, Clinical Sciences, Physical Injury - Accidents and Adverse Effects, Biomedical Imaging, Injuries and accidents, Hip fracture, Computed tomography, Cephalomedullary nail, Sliding hip screw, Other Medical and Health Sciences, Clinical sciences
Abstract: PurposeIntertrochanteric (IT) hip fractures can be treated with sliding hip screws (SHS) or cephalomedullary nails (CMN) based on the stability of the fracture. This stability is affected by the initial impaction of the fracture which can be difficult to assess. The aim of this paper is to develop specific pre-operative computed tomography (CT) measurements of IT fractures which are predictive of post-operative shortening.MethodsA retrospective review was performed of 141 patients with AO/OTA 31A1 or 31A2 fracture patterns, who had pre-operative radiographs and CT scans, and who were treated with a SHS or a CMN. Pre-operative and post-operative imaging of IT fractures were analyzed for those fractures that shortened ≥15 mm post-fixation.Results11 fractures shortened ≥15 mm with CMN being protective of shortening (6/36 SHS versus 5/105 CMN, p = 0.0268). A novel measurement made on the pre-operative CT scan called the cortical thin point (CTP) detected differences between patients with
Published: 2018

42. Graded Persistence Diagrams and Persistence Landscapes.

Author: Leo Betthauser, Peter Bubenik, and Parker B. Edwards
Published: 2022
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43. Search for magnetic monopoles produced via the Schwinger mechanism

Author: Acharya, B., Alexandre, J., Benes, P., Bergmann, B., Bertolucci, S., Bevan, A., Branzas, H., Burian, P., Campbell, M., Cho, Y. M., de Montigny, M., De Roeck, A., Ellis, J. R., Sawy, M. El, Fairbairn, M., Felea, D., Frank, M., Gould, O., Hays, J., Hirt, A. M., Ho, D. L.-J., Hung, P. Q., Janecek, J., Kalliokoski, M., Korzenev, A., Lacarrère, D. H., Leroy, C., Levi, G., Lionti, A., Maulik, A., Margiotta, A., Mauri, N., Mavromatos, N. E., Mermod, P., Millward, L., Mitsou, V. A., Ostrovskiy, I., Ouimet, P.-P., Papavassiliou, J., Parker, B., Patrizii, L., Păvălaş, G. E., Pinfold, J. L., Popa, L. A., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Staelens, M., Suk, M., Tenti, M., Togo, V., Tuszyn’ski, J. A., Upreti, A., Vento, V., and Vives, O.
Published: 2022
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44. Graded Persistence Diagrams and Persistence Landscapes

Author: Betthauser, Leo, Bubenik, Peter, and Edwards, Parker B.
Published: 2022
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45. Antidotal treatment of botulism in rats by continuous infusion with 3,4-diaminopyridine

Author: Machamer, James B., Vazquez-Cintron, Edwin J., O’Brien, Sean W., Kelly, Kyle E., Altvater, Amber C., Pagarigan, Kathleen T., Dubee, Parker B., Ondeck, Celinia A., and McNutt, Patrick M.
Published: 2022
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46. SuperKEKB beam final focus superconducting magnet system

Author: Ohuchi, N., Arimoto, Y., Akai, K., Aoki, K., Higashi, N., Kanazawa, K., Kawai, M., Kawamoto, T., Koiso, H., Kondou, Y., Masuzawa, M., Morita, A., Nakamura, S., Ohnishi, Y., Ohsawa, Y., Oide, K., Okada, N., Oki, T., Sugimoto, H., Tawada, M., Tsuchiya, K., Ueki, R., Wang, X., Yamaoka, H., Zong, Z., Parker, B., Anerella, M., Escallier, J., Ghosh, A., Hocker, H., Jain, A., Marone, A., Wanderer, P., DiMarco, J., Nogiec, J., Tartaglia, M., and Velev, G.
Published: 2022
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47. Search for magnetic monopoles with the MoEDAL forward trapping detector in 13 TeV proton-proton collisions at the LHC

Author: MoEDAL Collaboration, Acharya, B., Alexandre, J., Baines, S., Benes, P., Bergmann, B., Bernabéu, J., Branzas, H., Campbell, M., Caramete, L., Cecchini, S., de Montigny, M., De Roeck, A., Ellis, J. R., Fairbairn, M., Felea, D., Flores, J., Frank, M., Frekers, D., Garcia, C., Hirt, A. M., Janecek, J., Kalliokoski, M., Katre, A., Kim, D. -W., Kinoshita, K., Korzenev, A., Lacarrère, D. H., Lee, S. C., Leroy, C., Lionti, A., Mamuzic, J., Margiotta, A., Mauri, N., Mavromatos, N. E., Mermod, P., Mitsou, V. A., Orava, R., Parker, B., Pasqualini, L., Patrizii, L., Păvălaş, G. E., Pinfold, J. L., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., de Austri, R. Ruiz, Sahnoun, Z., Sakellariadou, M., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Srivastava, Y. N., Suk, M., Swain, J., Tenti, M., Togo, V., Tuszyński, J. A., Vento, V., Vives, O., Vykydal, Z., Whyntie, T., Widom, A., Willems, G., Yoon, J. H., and Zgura, I. S.
Subjects: High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract: MoEDAL is designed to identify new physics in the form of long-lived highly-ionising particles produced in high-energy LHC collisions. Its arrays of plastic nuclear-track detectors and aluminium trapping volumes provide two independent passive detection techniques. We present here the results of a first search for magnetic monopole production in 13 TeV proton-proton collisions using the trapping technique, extending a previous publication with 8 TeV data during LHC run-1. A total of 222 kg of MoEDAL trapping detector samples was exposed in the forward region and analysed by searching for induced persistent currents after passage through a superconducting magnetometer. Magnetic charges exceeding half the Dirac charge are excluded in all samples and limits are placed for the first time on the production of magnetic monopoles in 13 TeV $pp$ collisions. The search probes mass ranges previously inaccessible to collider experiments for up to five times the Dirac charge., Comment: 6 pages, 1 table, 2 figures, accepted for publication in Phys. Rev. Lett
Published: 2016
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48. Search for highly-ionizing particles in pp collisions at the LHC’s Run-1 using the prototype MoEDAL detector

Author: Acharya, B., Alexandre, J., Benes, P., Bergmann, B., Bertolucci, S., Bevan, A., Bhattacharyya, R., Branzas, H., Burian, P., Campbell, M., Cecchini, S., Cho, Y. M., de Montigny, M., De Roeck, A., Ellis, J. R., El Sawy, M., Fairbairn, M., Felea, D., Frank, M., Hays, J., Hirt, A. M., Hung, P. Q., Janecek, J., Kalliokoski, M., Korzenev, A., Lacarrére, D. H., Leroy, C., Levi, G., Lionti, A., Margiotta, A., Maselek, R., Maulik, A., Mauri, N., Mavromatos, N. E., Musumeci, E., Mieskolainen, M., Millward, L., Mitsou, V. A., Orava, R., Ostrovskiy, I., Ouimet, P.-P., Papavassiliou, J., Parker, B., Patrizii, L., Păvălaş, G. E., Pinfold, J. L., Popa, L. A., Popa, V., Pozzato, M., Pospisil, S., Rajantie, A., Ruiz de Austri, R., Sahnoun, Z., Sakellariadou, M., Sakurai, K., Santra, A., Sarkar, S., Semenoff, G., Shaa, A., Sirri, G., Sliwa, K., Soluk, R., Spurio, M., Staelens, M., Suk, M., Tenti, M., Togo, V., Tuszyński, J. A., Upreti, A., Vento, V., and Vives, O.
Published: 2022
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49. CyVerse: Cyberinfrastructure for open science

Author: Swetnam, Tyson L., primary, Antin, Parker B., additional, Bartelme, Ryan, additional, Bucksch, Alexander, additional, Camhy, David, additional, Chism, Greg, additional, Choi, Illyoung, additional, Cooksey, Amanda M., additional, Cosi, Michele, additional, Cowen, Cindy, additional, Culshaw-Maurer, Michael, additional, Davey, Robert, additional, Davey, Sean, additional, Devisetty, Upendra, additional, Edgin, Tony, additional, Edmonds, Andy, additional, Fedorov, Dmitry, additional, Frady, Jeremy, additional, Fonner, John, additional, Gillan, Jeffrey K., additional, Hossain, Iqbal, additional, Joyce, Blake, additional, Lang, Konrad, additional, Lee, Tina, additional, Littin, Shelley, additional, McEwen, Ian, additional, Merchant, Nirav, additional, Micklos, David, additional, Nelson, Andrew, additional, Ramsey, Ashley, additional, Roberts, Sarah, additional, Sarando, Paul, additional, Skidmore, Edwin, additional, Song, Jawon, additional, Sprinkle, Mary Margaret, additional, Srinivasan, Sriram, additional, Stanzione, Dan, additional, Strootman, Jonathan D., additional, Stryeck, Sarah, additional, Tuteja, Reetu, additional, Vaughn, Matthew, additional, Wali, Mojib, additional, Wall, Mariah, additional, Walls, Ramona, additional, Wang, Liya, additional, Wickizer, Todd, additional, Williams, Jason, additional, Wregglesworth, John, additional, and Lyons, Eric, additional
Published: 2024
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50. Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland

Author: McPhail, Gretchen M., primary, Collins, Sydney M., additional, Burt, Tori V., additional, Careen, Noah G., additional, Doiron, Parker B., additional, Avery-Gomm, Stephanie, additional, Barychka, Tatsiana, additional, English, Matthew, additional, Giacinti, Jolene A., additional, Jones, Megan E.B., additional, Provencher, Jennifer F., additional, Soos, Catherine, additional, Ward, Christopher R.E., additional, Duffy, Steven, additional, Wilhelm, Sabina I., additional, Wight, Jordan, additional, Rahman, Ishraq, additional, Hargan, Kathryn E., additional, Lang, Andrew S., additional, and Montevecchi, William A., additional
Published: 2024
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