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2. Continuous football player tracking from discrete broadcast data

Author

Penn, Matthew J., Donnelly, Christl A., and Bhatt, Samir

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Multiagent Systems
Abstract

Player tracking data remains out of reach for many professional football teams as their video feeds are not sufficiently high quality for computer vision technologies to be used. To help bridge this gap, we present a method that can estimate continuous full-pitch tracking data from discrete data made from broadcast footage. Such data could be collected by clubs or players at a similar cost to event data, which is widely available down to semi-professional level. We test our method using open-source tracking data, and include a version that can be applied to a large set of over 200 games with such discrete data., Comment: 12 pages, 3 figures

Published
2023

3. Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees

Author

Penn, Matthew J, Scheidwasser, Neil, Penn, Joseph, Donnelly, Christl A, Duchêne, David A, and Bhatt, Samir

Subjects
Quantitative Biology - Populations and Evolution, Computer Science - Machine Learning
Abstract

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimisation is possible via automatic differentiation and our method presents an effective way forwards for exploring the most difficult, data-deficient phylogenetic questions., Comment: 26 pages, 3 figures, 2 tables, 20 supplementary pages, 3 supplementary figures

Published
2023
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4. Phylo2Vec: a vector representation for binary trees

Author

Penn, Matthew J, Scheidwasser, Neil, Khurana, Mark P, Duchêne, David A, Donnelly, Christl A, and Bhatt, Samir

Subjects
Quantitative Biology - Populations and Evolution, Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods
Abstract

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art methods rely on carefully designed heuristics for tree search, using different data structures for easy manipulation (e.g., classes in object-oriented programming languages) and readable representation of trees (e.g., Newick-format strings). Here, we present Phylo2Vec, a parsimonious encoding for phylogenetic trees that serves as a unified approach for both manipulating and representing phylogenetic trees. Phylo2Vec maps any binary tree with $n$ leaves to a unique integer vector of length $n-1$. The advantages of Phylo2Vec are fourfold: i) fast tree sampling, (ii) compressed tree representation compared to a Newick string, iii) quick and unambiguous verification if two binary trees are identical topologically, and iv) systematic ability to traverse tree space in very large or small jumps. As a proof of concept, we use Phylo2Vec for maximum likelihood inference on five real-world datasets and show that a simple hill-climbing-based optimisation scheme can efficiently traverse the vastness of tree space from a random to an optimal tree., Comment: 38 pages, 9 figures, 1 table, 2 supplementary figures

Published
2023
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5. Intrinsic Randomness in Epidemic Modelling Beyond Statistical Uncertainty

Author

Penn, Matthew J., Laydon, Daniel J., Penn, Joseph, Whittaker, Charles, Morgenstern, Christian, Ratmann, Oliver, Mishra, Swapnil, Pakkanen, Mikko S., Donnelly, Christl A., and Bhatt, Samir

Subjects
Quantitative Biology - Populations and Evolution, Mathematics - Probability, Mathematics - Statistics Theory, Statistics - Applications
Abstract

Uncertainty can be classified as either aleatoric (intrinsic randomness) or epistemic (imperfect knowledge of parameters). The majority of frameworks assessing infectious disease risk consider only epistemic uncertainty. We only ever observe a single epidemic, and therefore cannot empirically determine aleatoric uncertainty. Here, we characterise both epistemic and aleatoric uncertainty using a time-varying general branching process. Our framework explicitly decomposes aleatoric variance into mechanistic components, quantifying the contribution to uncertainty produced by each factor in the epidemic process, and how these contributions vary over time. The aleatoric variance of an outbreak is itself a renewal equation where past variance affects future variance. We find that, superspreading is not necessary for substantial uncertainty, and profound variation in outbreak size can occur even without overdispersion in the offspring distribution (i.e. the distribution of the number of secondary infections an infected person produces). Aleatoric forecasting uncertainty grows dynamically and rapidly, and so forecasting using only epistemic uncertainty is a significant underestimate. Therefore, failure to account for aleatoric uncertainty will ensure that policymakers are misled about the substantially higher true extent of potential risk. We demonstrate our method, and the extent to which potential risk is underestimated, using two historical examples.

Published
2022

6. Optimal loading of hydrogel-based drug-delivery systems

Author

Penn, Matthew J. and Hennessy, Matthew G.

Subjects
Mathematics - Optimization and Control, Condensed Matter - Other Condensed Matter
Abstract

Drug-loaded hydrogels provide a means to deliver pharmaceutical agents to specific sites within the body at a controlled rate. The aim of this paper is to understand how controlled drug release can be achieved by tuning the initial distribution of drug molecules in a hydrogel. A mathematical model is presented for a spherical drug-loaded hydrogel. The model captures the nonlinear elasticity of the polymer network and thermodynamics of swelling. By assuming that the drug molecules are dilute, the equations for hydrogel swelling and drug transport partially decouple. A fast optimisation method is developed to accurately compute the optimal initial drug concentration by minimising the error between the numerical drug-release profile and a target profile. By taking the target drug efflux to be piecewise constant, the optimal initial configuration consists of a central drug-loaded core with isolated drug packets near the free boundary of the hydrogel. The optimal initial drug concentration is highly effective at mitigating the burst effect, where a large amount of drug is rapidly released into the environment. The hydrogel stiffness can be used to further tune the rate of drug release. Although stiffer gels lead to less swelling and hence reduce the drug diffusivity, the drug-release kinetics are faster than for soft gels due to the decreased distance that drug molecules must travel to reach the free surface.

Published
2022

7. Unifying incidence and prevalence under a time-varying general branching process

Author

Pakkanen, Mikko S., Miscouridou, Xenia, Penn, Matthew J., Whittaker, Charles, Berah, Tresnia, Mishra, Swapnil, Mellan, Thomas A., and Bhatt, Samir

Subjects
Quantitative Biology - Populations and Evolution, Mathematics - Probability, Quantitative Biology - Quantitative Methods, Statistics - Applications, 92D30, 60J80
Abstract

Renewal equations are a popular approach used in modelling the number of new infections, i.e., incidence, in an outbreak. We develop a stochastic model of an outbreak based on a time-varying variant of the Crump-Mode-Jagers branching process. This model accommodates a time-varying reproduction number and a time-varying distribution for the generation interval. We then derive renewal-like integral equations for incidence, cumulative incidence and prevalence under this model. We show that the equations for incidence and prevalence are consistent with the so-called back-calculation relationship. We analyse two particular cases of these integral equations, one that arises from a Bellman-Harris process and one that arises from an inhomogeneous Poisson process model of transmission. We also show that the incidence integral equations that arise from both of these specific models agree with the renewal equation used ubiquitously in infectious disease modelling. We present a numerical discretisation scheme to solve these equations, and use this scheme to estimate rates of transmission from serological prevalence of SARS-CoV-2 in the UK and historical incidence data on Influenza, Measles, SARS and Smallpox., Comment: 35 pages, 4 figures, v4: major revision, including a new argument for the equivalence of incidence equations

Published
2021

12. Vector magnetic field measurements along a cooled stereo-imaged coronal loop

Author

Schad, Thomas A., Penn, Matthew J., Lin, Haosheng, and Judge, Philip G.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

The variation of the vector magnetic field along structures in the solar corona remains unmeasured. Using a unique combination of spectropolarimetry and stereoscopy, we infer and compare the vector magnetic field structure and three-dimensional morphology of an individuated coronal loop structure undergoing a thermal instability. We analyze spectropolarimetric data of the He I 10830 {\AA} triplet ($1s2s{\ }^{3}S_{1} - 1s2p{\ }^{3}P_{2,1,0}$) obtained at the Dunn Solar Telescope with the Facility Infrared Spectropolarimeter on 19 September 2011. Cool coronal loops are identified by their prominent drainage signatures in the He I data (redshifts up to 185 km sec$^{-1}$). Extinction of EUV background radiation along these loops is observed by both the Atmospheric Imaging Assembly onboard the Solar Dynamics Observatory and the Extreme Ultraviolet Imager onboard spacecraft A of the Solar Terrestrial Relations Observatory, and is used to stereoscopically triangulate the loop geometry up to heights of 70 Mm ($0.1$ $R_{sun}$) above the solar surface. The He I polarized spectra along this loop exhibit signatures indicative of atomic-level polarization as well as magnetic signatures through the Hanle and Zeeman effects. Spectropolarimetric inversions indicate that the magnetic field is generally oriented along the coronal loop axis, and provide the height dependence of the magnetic field intensity. The technique we demonstrate is a powerful one that may help better understand the thermodynamics of coronal fine structure magnetism., Comment: 16 pages, 10 figures, Accepted for publication in ApJ

Published
2016
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13. Cross-Calibrating Sunspot Magnetic Field Strength Measurements from the McMath-Pierce Solar Telescope and the Dunn Solar Telescope

Author

Watson, Fraser T., Beck, Christian, Penn, Matthew J., Tritschler, Alexandra, Pillet, Valentin Martinez, and Livingston, William C.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

In this article we describe a recent effort to cross-calibrate data from an infrared detector at the McMath-Pierce Solar Telescope and the Facility InfraRed Spectropolarimeter (FIRS) at the Dunn Solar Telescope. A synoptic observation program at the McMath-Pierce has measured umbral magnetic field strengths since 1998, and this data set has recently been compared with umbral magnetic field observations from SOHO MDI and SDO HMI. To further improve on the data from McMath-Pierce, we compared the data with measurements taken at the Dunn Solar Telescope with far greater spectral resolution than has been possible with space instrumentation. To minimise potential disruption to the study, concurrent umbral measurements were made so that the relationship between the two datasets can be most accurately characterised. We find that there is a strong agreement between the umbral magnetic field strengths recorded by each instrument, and we reduced the FIRS data in two different ways to successfully test this correlation further., Comment: 11 pages in Online first, Solar Physics 2015

Published
2015
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14. A Multi-Instrument Analysis of Sunspot Umbrae

Author

Watson, Fraser T., Penn, Matthew J., and Livingston, William C.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

The recent solar minimum and rise phase of solar cycle 24 have been unlike any period since the early 1900s. This article examines some of the properties of sunspot umbrae over the last 17 years with three different instruments on the ground and in space: MDI, HMI and BABO. The distribution of magnetic fields and their evolution over time is shown and reveals that the field distribution in cycle 24 is fundamentally different from that in cycle 23. The annual average umbral magnetic field is then examined for the 17 year observation period and shows a small decrease of 375 Gauss in sunspot magnetic fields over the period 1996 to 2013, but the mean intensity of sunspot umbrae does not vary significantly over this time. A possible issue with sample sizes in a previous study is then explored to explain disagreements in data from two of the source instruments. All three instruments show that the relationship between umbral magnetic fields and umbral intensity agrees with past studies in that the umbral intensity decreases as the field strength increases. This apparent contradiction can be explained by the range of magnetic field values measured for a given umbral intensity being larger than the measured 375 G change in umbral field strength over time., Comment: 9 pages, accepted to the Astrophysical journal

Published
2015
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16. Acceleration of Coronal Mass Ejection Plasma in the Low Corona as Measured by the Citizen CATE Experiment

Author

Eric Weitzel & Team, Penn, Matthew J, Baer, Robert, Walter, Donald, Pierce, Michael, Gelderman, Richard, Ursache, Andrei, Elmore, David, Mitchell, Adrianna, Kovac, Sarah, Hare, Honor, McKay, Myles, Jensen, Logan, Watson, Zachary, Conley, Mike, Powers, Lynn, Lazarova, Marianna, Wright, Joseph, Young, David, Isberner, Fred, Hart, C. Alexandra, Sheeley, N. R., Penn, Debbie, Allen-Penn, Kate, Alder, Bruce, Alder, Ryan, Hall-Conley, Geri, Gerdes, David, Weber, Katherine, Johnson, Jeffrey, Matzek, Gerald, Somes, Steven, Sobnosky, Rob, McGowen, Robert, Meo, Michael, Proctor, Damani, Wessinger, Charlie, Schilling, Jeannine, Kerr, Jay, Beltzer-Sweeney, Alexander, Falatoun, Alex, Higgins, David, Boyce, Grady, Hettick, Jared, Blanco, Philip, Dixon, Scott, Ardebilianfard, Sepehr, Boyce, Pat, Lighthill, Richard, Lighthill, Denese, Anderson, David, Anderson, Mine, Schad, Thomas, Smith, Sonna, Jensen, Declan, Allen, Anthony, Smith, Donavan, Brandon, Gage, Earp, Joe, Earp, Jane, Blair, Bob, Claver, Chuck F., Claver, Jennifer A., Claver, Ryan H., Hoops, Danielle, Rivera, Esteban, Gibson, Llanee, Hiner, Martin, Lann, Rein, Miller, Shaedyn, Briggs, Burton, Davis, Karan, Jackson, Brian, Kautzsch, Kaleb, Sandidge, Wesley, Lucas, Russell, Gregg, Duane, Kamenetzky, Julia, Rivera, Tiffany, Shaw, Joe, Scherrer, Bryan, Sandbak, Dylan, McFate, Richard, Harris, Wilson, Brasier, Zachery, McNeil, Stephen, Jensen, Jack, Jensen, Makai, Moore, Mason, Temple, Alexandria, Vanderhorst, Thomas, Kautz, Richard, Bellorado, Orion, Jenkins, LaVor R, Pantuso, Corey, Carey, Marley, Byrnes, Josh, Scholtens, Kyle, Web, Julian, Baker, Brain, Barngrover, Katie, Hathaway, Drew, Smith, Kallen, Chandler, Kellyn, Hinkle, Lydia, Chandler, Ione, Gisler, Galen, Benner, Jack, Mas, Madison, Rogers, Maya, Moore, Prescott, Pelofske, Elijah, Gulley, Stephen, Short, Beth, Crooker, Isabel, Hammock, Jennifer, Cardenas, Katsina, Cardenas, Kateri, Wellman, Jennifer, Roy, Mark, Meyer, Joe, Brough, Jalynne, Brough, Kameron, Nelson, Tim, Nelson, Zack, Russell, Caleb, Bautz, Theresa, Wistisen, Michele, Aagard, Shae, Whipps, Zachary, Neuroth, Logan, Poste, Dawson, Worthen, Connor, Gosain, Sanjay, Steward, Mark, Gosain, Vanshita, Gosain, Ruchi, Jorgensen, Janet, Doucette, Eleanor, Doucette, Reba, Iwen, Elliott, Cochran, Alexus, Stith, James, Scribner, Doug, Kenney, Austen, Pisciotti, Kolby, Pease, Irene, Cynamon, Samuel, Cynamon, Charles, Cynamon, Dawn, Tolbert, Bart, Dupree, Jean A., Weremeichik, Jeremy, Pindell, Nathan, Stives, Kristen, Simacek, Thomas K, Simacek, Yolanta G, Simacek, Anne L., Boeck, Wayne, Boeck, Andreea, Ryan, Austin, Wierzorec, Gabriel, Klebe, Dimitri, Costanza, Bryan, Cerny, Arnie, Schmale, Trevor, Hoffman, Tessa, Streeter, Sam, Erickson, Jack, McClellan, Michele, Erickson, Ella, Brettell, Brynn, Shoffner, Savannah, McClellan, Emilie, VanVoorhis, Julie, Bramhall, Cole, Stelly, Daniel, Bee, Bentley, Acevedo, Bruno, Kroeger, Madison, Trumpenski, Ben, Sump, Nolan, Brook, Liam, Ernzen, Jagert, Lewis, Jessica, Maderak, Ryan, Kennedy, Charles, Dembinski, David, Wright, Rita, Foster, Michael, Ahmadbasir, Mohammad, Laycox, Monty, Foster, James, Orr, Ethan, Staab, Ashley, Speck, Angela, Baldridge, Sean, Kegley, Lucy, Bavlnka, Jordan, Ballew, Thomas, Callen, Bruce, Ojakangas, Gregory, Bremer, Mark, Angliongto, Maryanne, Redecker, Mark, Bremer, Chris, Hill, Peggy, Rodgers, Michael, Duncan, Jordan, Fincher, Sam, Nielsen, Ben, Hasler, Samantha, Shivelbine, Taylor, Howard, Tyler, Midden, Chris, Patrick, Sean, Glenn, Kerry, Mandrell, Chris, Dawson, Kyle, Cortez, Margaret, Levsky, Alyssa, Gallaba, Dinuka, Perrone, Mason, Taylor, Jasmyn, Yanamandra-Fisher, Padma A., Harper, Howard, Adams, Lindsay, Springer, Michaela, Menard, BillyJoe, Boggs, Dylan, Lynch, Caitlin, Watson, Jacob, York, Andi, Matthews, David, Brown, Kiley, Garrison, Dylan, Mangin, Jonathan, Mangin, Isaac, Birriel, Jennifer, Birriel, Ignacio, Yess, Capp, Anderson, Jesse, Caudill, Ethan, Smith, Allyn, Buckner, Spencer, Longhurst, Russ, Fagan, Ben, Nations, Christian, DiMatties, Jeffrey, Thompson, Patricia, Garrison, David, Garrison, Thomas, Garrison, William, Kidd, Mary, Baker, Maria, Ledford, Mary-Beth, Winebarger, Amy, Freed, Michael, Church, Morgyn, Dickens, Jim, Anderson, Bob, Smith, Ned, Dorsey, Lynne, Justice, Doug, Zavala, Daniel, Stockbridge, Zach, Brittain, Sean, Jensen, Stanley, Leiendecker, Harrison, Thompson, Erin, Deady, Michelle, Quinn-Hughes, Kelly, Slimmer, David, Granger, Valerie, LaRoche, Michael, LaRoche, Serena Hill, Manspeaker, Rachel, Nguyen, Peter, Smith, Daniel, Payne, Jim, Zissett, Jerry, Roberts, Arianna M., Roberts, Gabrielle W., Roberts, Harrison, Riddle, Amy, Ursache, Corina, and Ursache, Elena

Published
2020

17. The limits of the constant-rate birth-death prior for phylogenetic tree topology inference

Author

Khurana, Mark P, Scheidwasser-Clow, Neil, Penn, Matthew J, Bhatt, Samir, Duchêne, David A, Khurana, Mark P, Scheidwasser-Clow, Neil, Penn, Matthew J, Bhatt, Samir, and Duchêne, David A

Abstract

Birth-death models are stochastic processes describing speciation and extinction through time and across taxa, and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios, but also highlights that empirically observed phylogenetic imbalance is highly

Published
2024

20. Leaping through Tree Space:Continuous Phylogenetic Inference for Rooted and Unrooted Trees

Author

Penn, Matthew J., Scheidwasser, Neil Alexandre, Penn, Joseph, Donnelly, Christl A., Duchene, David, Bhatt, Samir, Penn, Matthew J., Scheidwasser, Neil Alexandre, Penn, Joseph, Donnelly, Christl A., Duchene, David, and Bhatt, Samir

Abstract

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimization is possible via automatic differentiation and our method presents an effective way forward for exploring the most difficult, data-deficient phylogenetic questions.

Published
2023

21. Sherlock—A flexible, low‐resource tool for processing camera‐trapping images.

Author

Penn, Matthew J., Miles, Verity, Astley, Kelly L., Ham, Cally, Woodroffe, Rosie, Rowcliffe, Marcus, and Donnelly, Christl A.

Subjects
PITFALL traps, BIG data, OLD World badger, ANIMAL traps, IMAGE recognition (Computer vision), ARTIFICIAL intelligence
Abstract

The use of camera traps to study wildlife has increased markedly in the last two decades. Camera surveys typically produce large data sets which require processing to isolate images containing the species of interest. This is time consuming and costly, particularly if there are many empty images that can result from false triggers. Computer vision technology can assist with data processing, but existing artificial intelligence algorithms are limited by the requirement of a training data set, which itself can be challenging to acquire. Furthermore, deep‐learning methods often require powerful hardware and proficient coding skills.We present Sherlock, a novel algorithm that can reduce the time required to process camera trap data by removing a large number of unwanted images. The code is adaptable, simple to use and requires minimal processing power.We tested Sherlock on 240,596 camera trap images collected from 46 cameras placed in a range of habitats on farms in Cornwall, United Kingdom, and set the parameters to find European badgers (Meles meles). The algorithm correctly classified 91.9% of badger images and removed 49.3% of the unwanted 'empty' images. When testing model parameters, we found that faster processing times were achieved by reducing both the number of sampled pixels and 'bouncing' attempts (the number of paths explored to identify a disturbance), with minimal implications for model sensitivity and specificity. When Sherlock was tested on two sites which contained no livestock in their images, its performance greatly improved and it removed 92.3% of the empty images.Although further refinements may improve its performance, Sherlock is currently an accessible, simple and useful tool for processing camera trap data. [ABSTRACT FROM AUTHOR]

Published
2024
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31. Acceleration of Coronal Mass Ejection Plasma in the Low Corona as Measured by the Citizen CATE Experiment

Author

Penn, Matthew J, primary, Baer, Robert, additional, Walter, Donald, additional, Pierce, Michael, additional, Gelderman, Richard, additional, Ursache, Andrei, additional, Elmore, David, additional, Mitchell, Adrianna, additional, Kovac, Sarah, additional, Hare, Honor, additional, McKay, Myles, additional, Jensen, Logan, additional, Watson, Zachary, additional, Conley, Mike, additional, Powers, Lynn, additional, Lazarova, Marianna, additional, Wright, Joseph, additional, Young, David, additional, Isberner, Fred, additional, Hart, C. Alexandra, additional, Sheeley, N. R., additional, Penn, Debbie, additional, Allen-Penn, Kate, additional, Alder, Bruce, additional, Alder, Ryan, additional, Hall-Conley, Geri, additional, Gerdes, David, additional, Weber, Katherine, additional, Johnson, Jeffrey, additional, Matzek, Gerald, additional, Somes, Steven, additional, Sobnosky, Rob, additional, McGowen, Robert, additional, Meo, Michael, additional, Proctor, Damani, additional, Wessinger, Charlie, additional, Schilling, Jeannine, additional, Kerr, Jay, additional, Beltzer-Sweeney, Alexander, additional, Falatoun, Alex, additional, Higgins, David, additional, Boyce, Grady, additional, Hettick, Jared, additional, Blanco, Philip, additional, Dixon, Scott, additional, Ardebilianfard, Sepehr, additional, Boyce, Pat, additional, Lighthill, Richard, additional, Lighthill, Denese, additional, Anderson, David, additional, Anderson, Mine, additional, Schad, Thomas, additional, Smith, Sonna, additional, Jensen, Declan, additional, Allen, Anthony, additional, Smith, Donavan, additional, Brandon, Gage, additional, Earp, Joe, additional, Earp, Jane, additional, Blair, Bob, additional, Claver, Chuck F., additional, Claver, Jennifer A., additional, Claver, Ryan H., additional, Hoops, Danielle, additional, Rivera, Esteban, additional, Gibson, Llanee, additional, Hiner, Martin, additional, Lann, Rein, additional, Miller, Shaedyn, additional, Briggs, Burton, additional, Davis, Karan, additional, Jackson, Brian, additional, Kautzsch, Kaleb, additional, Sandidge, Wesley, additional, Lucas, Russell, additional, Gregg, Duane, additional, Kamenetzky, Julia, additional, Rivera, Tiffany, additional, Shaw, Joe, additional, Scherrer, Bryan, additional, Sandbak, Dylan, additional, McFate, Richard, additional, Harris, Wilson, additional, Brasier, Zachery, additional, McNeil, Stephen, additional, Jensen, Jack, additional, Jensen, Makai, additional, Moore, Mason, additional, Temple, Alexandria, additional, Vanderhorst, Thomas, additional, Kautz, Richard, additional, Bellorado, Orion, additional, Jenkins, LaVor R, additional, Pantuso, Corey, additional, Carey, Marley, additional, Byrnes, Josh, additional, Scholtens, Kyle, additional, Web, Julian, additional, Baker, Brain, additional, Barngrover, Katie, additional, Hathaway, Drew, additional, Smith, Kallen, additional, Chandler, Kellyn, additional, Hinkle, Lydia, additional, Chandler, Ione, additional, Gisler, Galen, additional, Benner, Jack, additional, Mas, Madison, additional, Rogers, Maya, additional, Moore, Prescott, additional, Pelofske, Elijah, additional, Gulley, Stephen, additional, Short, Beth, additional, Crooker, Isabel, additional, Hammock, Jennifer, additional, Cardenas, Katsina, additional, Cardenas, Kateri, additional, Wellman, Jennifer, additional, Roy, Mark, additional, Meyer, Joe, additional, Brough, Jalynne, additional, Brough, Kameron, additional, Nelson, Tim, additional, Nelson, Zack, additional, Russell, Caleb, additional, Bautz, Theresa, additional, Weitzel & Team, Eric, additional, Wistisen, Michele, additional, Aagard, Shae, additional, Whipps, Zachary, additional, Neuroth, Logan, additional, Poste, Dawson, additional, Worthen, Connor, additional, Gosain, Sanjay, additional, Steward, Mark, additional, Gosain, Vanshita, additional, Gosain, Ruchi, additional, Jorgensen, Janet, additional, Doucette, Eleanor, additional, Doucette, Reba, additional, Iwen, Elliott, additional, Cochran, Alexus, additional, Stith, James, additional, Scribner, Doug, additional, Kenney, Austen, additional, Pisciotti, Kolby, additional, Pease, Irene, additional, Cynamon, Samuel, additional, Cynamon, Charles, additional, Cynamon, Dawn, additional, Tolbert, Bart, additional, Dupree, Jean A., additional, Weremeichik, Jeremy, additional, Pindell, Nathan, additional, Stives, Kristen, additional, Simacek, Thomas K, additional, Simacek, Yolanta G, additional, Simacek, Anne L., additional, Boeck, Wayne, additional, Boeck, Andreea, additional, Ryan, Austin, additional, Wierzorec, Gabriel, additional, Klebe, Dimitri, additional, Costanza, Bryan, additional, Cerny, Arnie, additional, Schmale, Trevor, additional, Hoffman, Tessa, additional, Streeter, Sam, additional, Erickson, Jack, additional, McClellan, Michele, additional, Erickson, Ella, additional, Brettell, Brynn, additional, Shoffner, Savannah, additional, McClellan, Emilie, additional, VanVoorhis, Julie, additional, Bramhall, Cole, additional, Stelly, Daniel, additional, Bee, Bentley, additional, Acevedo, Bruno, additional, Kroeger, Madison, additional, Trumpenski, Ben, additional, Sump, Nolan, additional, Brook, Liam, additional, Ernzen, Jagert, additional, Lewis, Jessica, additional, Maderak, Ryan, additional, Kennedy, Charles, additional, Dembinski, David, additional, Wright, Rita, additional, Foster, Michael, additional, Ahmadbasir, Mohammad, additional, Laycox, Monty, additional, Foster, James, additional, Orr, Ethan, additional, Staab, Ashley, additional, Speck, Angela, additional, Baldridge, Sean, additional, Kegley, Lucy, additional, Bavlnka, Jordan, additional, Ballew, Thomas, additional, Callen, Bruce, additional, Ojakangas, Gregory, additional, Bremer, Mark, additional, Angliongto, Maryanne, additional, Redecker, Mark, additional, Bremer, Chris, additional, Hill, Peggy, additional, Rodgers, Michael, additional, Duncan, Jordan, additional, Fincher, Sam, additional, Nielsen, Ben, additional, Hasler, Samantha, additional, Shivelbine, Taylor, additional, Howard, Tyler, additional, Midden, Chris, additional, Patrick, Sean, additional, Glenn, Kerry, additional, Mandrell, Chris, additional, Dawson, Kyle, additional, Cortez, Margaret, additional, Levsky, Alyssa, additional, Gallaba, Dinuka, additional, Perrone, Mason, additional, Taylor, Jasmyn, additional, Yanamandra-Fisher, Padma A., additional, Harper, Howard, additional, Adams, Lindsay, additional, Springer, Michaela, additional, Menard, BillyJoe, additional, Boggs, Dylan, additional, Lynch, Caitlin, additional, Watson, Jacob, additional, York, Andi, additional, Matthews, David, additional, Brown, Kiley, additional, Garrison, Dylan, additional, Mangin, Jonathan, additional, Mangin, Isaac, additional, Birriel, Jennifer, additional, Birriel, Ignacio, additional, Yess, Capp, additional, Anderson, Jesse, additional, Caudill, Ethan, additional, Smith, Allyn, additional, Buckner, Spencer, additional, Longhurst, Russ, additional, Fagan, Ben, additional, Nations, Christian, additional, DiMatties, Jeffrey, additional, Thompson, Patricia, additional, Garrison, David, additional, Garrison, Thomas, additional, Garrison, William, additional, Kidd, Mary, additional, Baker, Maria, additional, Ledford, Mary-Beth, additional, Winebarger, Amy, additional, Freed, Michael, additional, Church, Morgyn, additional, Dickens, Jim, additional, Anderson, Bob, additional, Smith, Ned, additional, Dorsey, Lynne, additional, Justice, Doug, additional, Zavala, Daniel, additional, Stockbridge, Zach, additional, Brittain, Sean, additional, Jensen, Stanley, additional, Leiendecker, Harrison, additional, Thompson, Erin, additional, Deady, Michelle, additional, Quinn-Hughes, Kelly, additional, Slimmer, David, additional, Granger, Valerie, additional, LaRoche, Michael, additional, LaRoche, Serena Hill, additional, Manspeaker, Rachel, additional, Nguyen, Peter, additional, Smith, Daniel, additional, Payne, Jim, additional, Zissett, Jerry, additional, Roberts, Arianna M., additional, Roberts, Gabrielle W., additional, Roberts, Harrison, additional, Riddle, Amy, additional, Ursache, Corina, additional, and Ursache, Elena, additional

Published
2019
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32. Investigating the formation of the helium spectrum with coordinated SOHO/Kitt Peak/Sacramento Peak observations

Author

Andretta, Vincenzo, Jordan, Stuart D, Jones, Harrison P, and Penn, Matthew J

Subjects
Solar Physics
Abstract

The results of the investigations on the mechanism responsible for the formation of helium lines in the quiescent solar atmosphere are discussed. The observations were performed on 16 and 17 January 1997 by the coronal diagnostic spectrometer (CDS) and the solar ultraviolet measurement of emitted radiation (SUMER) onboard the Solar and Heliospheric Observatory (SOHO). The statistical properties of the helium spectrum and the constraints that such observations bring up are discussed.

Published
1997

33. H-alpha spectra of dynamic chromospheric processes in five well-observed X-ray flares

Author

Canfield, Richard C, Penn, Matthew J, Wulser, Jean-Pierre, and Kiplinger, Alan L

Subjects
Solar Physics
Abstract

Simultaneous H-alpha and hard X-ray (HXR) spectra were obtained for five solar flares to determine the relationship of H-alpha profiles and the nonthermal part of the flare represented by the hard X-ray burst. All five flares exhibited impulsive-phase redshifted H-alpha in emission, which was temporarily and spatially associated with intense HXR emission and broad impulsive-phase H-alpha wings. A few small regions within two flares showed a blueshifted H-alpha emission which appeared only early in the impulsive phase and was temporally correlated with the HXR emission but not with broad H-alpha wings. Finally, there were both redshifted and blueshifted absorption spectra with properties fully consistent with those known for erupting and untwisting filaments.

Published
1990
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36. Spectropolarimetry of Fine Magnetized Structures in the Upper Solar Atmosphere

Author

Penn, Matthew J., Giacalone, Joe, Jokipii, J. R. Randy, Harvey, John, McMillan, Robert, Schad, Thomas Anthony, Penn, Matthew J., Giacalone, Joe, Jokipii, J. R. Randy, Harvey, John, McMillan, Robert, and Schad, Thomas Anthony

Abstract

One of the earliest indications of magnetic fields acting in the solar atmosphere came at the beginning of the 20th century when George Hale noted a "decided definiteness of structure" in photographs within the Hydrogen Balmer-alpha line core. Fine structure both in the chromosphere and in the corona result from processes that are not well understood but accepted as a consequence of the solar magnetic field. Our knowledge of this field is lacking, and until recently, the assumed relationship between fine thermal structure and the magnetic field remained untested. Here, spectropolarimetric diagnostics of fine structures in the solar chromosphere and cool corona are advanced using the infrared He I triplet at 1083 nm. Precise calibration procedures are developed for the Facility Infrared Spectropolarimeter (FIRS), recently commissioned at the Dunn Solar Telescope. Together with high-order adaptive optics, we simultaneously map fine structures while obtaining a polarimetric sensitivity of up to 2 x 10 ⁻⁴ of the incoming intensity. These instrument improvements result in the first maps of the He I polarized signatures within an active region superpenumbra, where Hale first recognized fine-structuring. Selective absorption and emission processes due to non-equilibrium optical pumping are recognized. Our interpretation, using advanced inversions of the He I triplet, provides confirmation of Hale's initial suspicion--the fine structures of the solar chromosphere are visual markers for the magnetic field. Yet, the fine chromospheric thermal structure is not matched by an equivalently fine magnetic structure. Our ability to measure this field suggests the utility of the He I triplet as an inner boundary condition for the inner heliospheric magnetic field. In the corona itself, we infer the vector properties of a catastrophically-cooled coronal loop, uniting space-based and ground-based instrumentation. We determine how fine loops are anchored in the photosphere via a narrow

Published
2013

40. Acceleration of Coronal Mass Ejection Plasma in the Low Corona as Measured by the Citizen CATE Experiment

Author

Penn, Matthew J, Baer, Robert, Walter, Donald, Pierce, Michael, Gelderman, Richard, Ursache, Andrei, Elmore, David, Mitchell, Adrianna, Kovac, Sarah, Hare, Honor, McKay, Myles, Jensen, Logan, Watson, Zachary, Conley, Mike, Powers, Lynn, Lazarova, Marianna, Wright, Joseph, Young, David, Isberner, Fred, Hart, C. Alexandra, Sheeley, N. R., Penn, Debbie, Allen-Penn, Kate, Alder, Bruce, Alder, Ryan, Hall-Conley, Geri, Gerdes, David, Weber, Katherine, Johnson, Jeffrey, Matzek, Gerald, Somes, Steven, Sobnosky, Rob, McGowen, Robert, Meo, Michael, Proctor, Damani, Wessinger, Charlie, Schilling, Jeannine, Kerr, Jay, Beltzer-Sweeney, Alexander, Falatoun, Alex, Higgins, David, Boyce, Grady, Hettick, Jared, Blanco, Philip, Dixon, Scott, Ardebilianfard, Sepehr, Boyce, Pat, Lighthill, Richard, Lighthill, Denese, Anderson, David, Anderson, Mine, Schad, Thomas, Smith, Sonna, Jensen, Declan, Allen, Anthony, Smith, Donavan, Brandon, Gage, Earp, Joe, Earp, Jane, Blair, Bob, Claver, Chuck F., Claver, Jennifer A., Claver, Ryan H., Hoops, Danielle, Rivera, Esteban, Gibson, Llanee, Hiner, Martin, Lann, Rein, Miller, Shaedyn, Briggs, Burton, Davis, Karan, Jackson, Brian, Kautzsch, Kaleb, Sandidge, Wesley, Lucas, Russell, Gregg, Duane, Kamenetzky, Julia, Rivera, Tiffany, Shaw, Joe, Scherrer, Bryan, Sandbak, Dylan, McFate, Richard, Harris, Wilson, Brasier, Zachery, McNeil, Stephen, Jensen, Jack, Jensen, Makai, Moore, Mason, Temple, Alexandria, Vanderhorst, Thomas, Kautz, Richard, Bellorado, Orion, Jenkins, LaVor R, Pantuso, Corey, Carey, Marley, Byrnes, Josh, Scholtens, Kyle, Web, Julian, Baker, Brain, Barngrover, Katie, Hathaway, Drew, Smith, Kallen, Chandler, Kellyn, Hinkle, Lydia, Chandler, Ione, Gisler, Galen, Benner, Jack, Mas, Madison, Rogers, Maya, Moore, Prescott, Pelofske, Elijah, Gulley, Stephen, Short, Beth, Crooker, Isabel, Hammock, Jennifer, Cardenas, Katsina, Cardenas, Kateri, Wellman, Jennifer, Roy, Mark, Meyer, Joe, Brough, Jalynne, Brough, Kameron, Nelson, Tim, Nelson, Zack, Russell, Caleb, Bautz, Theresa, Weitzel & Team, Eric, Wistisen, Michele, Aagard, Shae, Whipps, Zachary, Neuroth, Logan, Poste, Dawson, Worthen, Connor, Gosain, Sanjay, Steward, Mark, Gosain, Vanshita, Gosain, Ruchi, Jorgensen, Janet, Doucette, Eleanor, Doucette, Reba, Iwen, Elliott, Cochran, Alexus, Stith, James, Scribner, Doug, Kenney, Austen, Pisciotti, Kolby, Pease, Irene, Cynamon, Samuel, Cynamon, Charles, Cynamon, Dawn, Tolbert, Bart, Dupree, Jean A., Weremeichik, Jeremy, Pindell, Nathan, Stives, Kristen, Simacek, Thomas K, Simacek, Yolanta G, Simacek, Anne L., Boeck, Wayne, Boeck, Andreea, Ryan, Austin, Wierzorec, Gabriel, Klebe, Dimitri, Costanza, Bryan, Cerny, Arnie, Schmale, Trevor, Hoffman, Tessa, Streeter, Sam, Erickson, Jack, McClellan, Michele, Erickson, Ella, Brettell, Brynn, Shoffner, Savannah, McClellan, Emilie, VanVoorhis, Julie, Bramhall, Cole, Stelly, Daniel, Bee, Bentley, Acevedo, Bruno, Kroeger, Madison, Trumpenski, Ben, Sump, Nolan, Brook, Liam, Ernzen, Jagert, Lewis, Jessica, Maderak, Ryan, Kennedy, Charles, Dembinski, David, Wright, Rita, Foster, Michael, Ahmadbasir, Mohammad, Laycox, Monty, Foster, James, Orr, Ethan, Staab, Ashley, Speck, Angela, Baldridge, Sean, Kegley, Lucy, Bavlnka, Jordan, Ballew, Thomas, Callen, Bruce, Ojakangas, Gregory, Bremer, Mark, Angliongto, Maryanne, Redecker, Mark, Bremer, Chris, Hill, Peggy, Rodgers, Michael, Duncan, Jordan, Fincher, Sam, Nielsen, Ben, Hasler, Samantha, Shivelbine, Taylor, Howard, Tyler, Midden, Chris, Patrick, Sean, Glenn, Kerry, Mandrell, Chris, Dawson, Kyle, Cortez, Margaret, Levsky, Alyssa, Gallaba, Dinuka, Perrone, Mason, Taylor, Jasmyn, Yanamandra-Fisher, Padma A., Harper, Howard, Adams, Lindsay, Springer, Michaela, Menard, BillyJoe, Boggs, Dylan, Lynch, Caitlin, Watson, Jacob, York, Andi, Matthews, David, Brown, Kiley, Garrison, Dylan, Mangin, Jonathan, Mangin, Isaac, Birriel, Jennifer, Birriel, Ignacio, Yess, Capp, Anderson, Jesse, Caudill, Ethan, Smith, Allyn, Buckner, Spencer, Longhurst, Russ, Fagan, Ben, Nations, Christian, DiMatties, Jeffrey, Thompson, Patricia, Garrison, David, Garrison, Thomas, Garrison, William, Kidd, Mary, Baker, Maria, Ledford, Mary-Beth, Winebarger, Amy, Freed, Michael, Church, Morgyn, Dickens, Jim, Anderson, Bob, Smith, Ned, Dorsey, Lynne, Justice, Doug, Zavala, Daniel, Stockbridge, Zach, Brittain, Sean, Jensen, Stanley, Leiendecker, Harrison, Thompson, Erin, Deady, Michelle, Quinn-Hughes, Kelly, Slimmer, David, Granger, Valerie, LaRoche, Michael, LaRoche, Serena Hill, Manspeaker, Rachel, Nguyen, Peter, Smith, Daniel, Payne, Jim, Zissett, Jerry, Roberts, Arianna M., Roberts, Gabrielle W., Roberts, Harrison, Riddle, Amy, Ursache, Corina, and Ursache, Elena

Abstract

The citizen Continental-America Telescopic Eclipse (CATE) Experiment was a new type of citizen science experiment designed to capture a time sequence of white-light coronal observations during totality from 17:16 to 18:48 UT on 2017 August 21. Using identical instruments the CATE group imaged the inner corona from 1 to 2.1 RSun with 1.?43 pixels at a cadence of 2.1 s. A slow coronal mass ejection (CME) started on the SW limb of the Sun before the total eclipse began. An analysis of CATE data from 17:22 to 17:39 UT maps the spatial distribution of coronal flow velocities from about 1.2 to 2.1 RSun, and shows the CME material accelerates from about 0 to 200 km s?1across this part of the corona. This CME is observed by LASCO C2 at 3.1-13 RSun with a constant speed of 254 km s?1. The CATE and LASCO observations are not fit by either constant acceleration nor spatially uniform velocity change, and so the CME acceleration mechanism must produce variable acceleration in this region of the corona.

Published
2020
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