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1. Comparing Recent Pulsar Timing Array Results on the Nanohertz Stochastic Gravitational-wave Background

Author

G. Agazie, J. Antoniadis, A. Anumarlapudi, A. M. Archibald, P. Arumugam, S. Arumugam, Z. Arzoumanian, J. Askew, S. Babak, M. Bagchi, M. Bailes, A.-S. Bak Nielsen, P. T. Baker, C. G. Bassa, A. Bathula, B. Bécsy, A. Berthereau, N. D. R. Bhat, L. Blecha, M. Bonetti, E. Bortolas, A. Brazier, P. R. Brook, M. Burgay, S. Burke-Spolaor, R. Burnette, R. N. Caballero, A. Cameron, R. Case, A. Chalumeau, D. J. Champion, S. Chanlaridis, M. Charisi, S. Chatterjee, K. Chatziioannou, B. D. Cheeseboro, S. Chen, Z.-C. Chen, I. Cognard, T. Cohen, W. A. Coles, J. M. Cordes, N. J. Cornish, F. Crawford, H. T. Cromartie, K. Crowter, M. Curyło, C. J. Cutler, S. Dai, S. Dandapat, D. Deb, M. E. DeCesar, D. DeGan, P. B. Demorest, H. Deng, S. Desai, G. Desvignes, L. Dey, N. Dhanda-Batra, V. Di Marco, T. Dolch, B. Drachler, C. Dwivedi, J. A. Ellis, M. Falxa, Y. Feng, R. D. Ferdman, E. C. Ferrara, W. Fiore, E. Fonseca, A. Franchini, G. E. Freedman, J. R. Gair, N. Garver-Daniels, P. A. Gentile, K. A. Gersbach, J. Glaser, D. C. Good, B. Goncharov, A. Gopakumar, E. Graikou, J.-M. Griessmeier, L. Guillemot, K. Gültekin, Y. J. Guo, Y. Gupta, K. Grunthal, J. S. Hazboun, S. Hisano, G. B. Hobbs, S. Hourihane, H. Hu, F. Iraci, K. Islo, D. Izquierdo-Villalba, J. Jang, J. Jawor, G. H. Janssen, R. J. Jennings, A. Jessner, A. D. Johnson, M. L. Jones, B. C. Joshi, A. R. Kaiser, D. L. Kaplan, A. Kapur, F. Kareem, R. Karuppusamy, E. F. Keane, M. J. Keith, L. Z. Kelley, M. Kerr, J. S. Key, D. Kharbanda, T. Kikunaga, T. C. Klein, N. Kolhe, M. Kramer, M. A. Krishnakumar, A. Kulkarni, N. Laal, K. Lackeos, M. T. Lam, W. G. Lamb, B. B. Larsen, T. J. W. Lazio, K. J. Lee, Y. Levin, N. Lewandowska, T. B. Littenberg, K. Liu, T. Liu, Y. Liu, A. Lommen, D. R. Lorimer, M. E. Lower, J. Luo, R. Luo, R. S. Lynch, A. G. Lyne, C.-P. Ma, Y. Maan, D. R. Madison, R. A. Main, R. N. Manchester, R. Mandow, M. A. Mattson, A. McEwen, J. W. McKee, M. A. McLaughlin, N. McMann, B. W. Meyers, P. M. Meyers, M. B. Mickaliger, M. Miles, C. M. F. Mingarelli, A. Mitridate, P. Natarajan, R. S. Nathan, C. Ng, D. J. Nice, I. C. Niţu, K. Nobleson, S. K. Ocker, K. D. Olum, S. Osłowski, A. K. Paladi, A. Parthasarathy, T. T. Pennucci, B. B. P. Perera, D. Perrodin, A. Petiteau, P. Petrov, N. S. Pol, N. K. Porayko, A. Possenti, T. Prabu, H. Quelquejay Leclere, H. A. Radovan, P. Rana, S. M. Ransom, P. S. Ray, D. J. Reardon, A. F. Rogers, J. D. Romano, C. J. Russell, A. Samajdar, S. A. Sanidas, S. C. Sardesai, A. Schmiedekamp, C. Schmiedekamp, K. Schmitz, L. Schult, A. Sesana, G. Shaifullah, R. M. Shannon, B. J. Shapiro-Albert, X. Siemens, J. Simon, J. Singha, M. S. Siwek, L. Speri, R. Spiewak, A. Srivastava, I. H. Stairs, B. W. Stappers, D. R. Stinebring, K. Stovall, J. P. Sun, M. Surnis, S. C. Susarla, A. Susobhanan, J. K. Swiggum, K. Takahashi, P. Tarafdar, J. Taylor, S. R. Taylor, G. Theureau, E. Thrane, N. Thyagarajan, C. Tiburzi, L. Toomey, J. E. Turner, C. Unal, M. Vallisneri, E. van der Wateren, R. van Haasteren, A. Vecchio, V. Venkatraman Krishnan, J. P. W. Verbiest, S. J. Vigeland, H. M. Wahl, S. Wang, Q. Wang, C. A. Witt, J. Wang, L. Wang, K. E. Wayt, Z. Wu, O. Young, L. Zhang, S. Zhang, X.-J. Zhu, A. Zic, and The International Pulsar Timing Array Collaboration

Subjects
Gravitational waves, Pulsars, Astrophysics, QB460-466
Abstract

The Australian, Chinese, European, Indian, and North American pulsar timing array (PTA) collaborations recently reported, at varying levels, evidence for the presence of a nanohertz gravitational-wave background (GWB). Given that each PTA made different choices in modeling their data, we perform a comparison of the GWB and individual pulsar noise parameters across the results reported from the PTAs that constitute the International Pulsar Timing Array (IPTA). We show that despite making different modeling choices, there is no significant difference in the GWB parameters that are measured by the different PTAs, agreeing within 1 σ . The pulsar noise parameters are also consistent between different PTAs for the majority of the pulsars included in these analyses. We bridge the differences in modeling choices by adopting a standardized noise model for all pulsars and PTAs, finding that under this model there is a reduction in the tension in the pulsar noise parameters. As part of this reanalysis, we “extended” each PTA’s data set by adding extra pulsars that were not timed by that PTA. Under these extensions, we find better constraints on the GWB amplitude and a higher signal-to-noise ratio for the Hellings–Downs correlations. These extensions serve as a prelude to the benefits offered by a full combination of data across all pulsars in the IPTA, i.e., the IPTA’s Data Release 3, which will involve not just adding in additional pulsars but also including data from all three PTAs where any given pulsar is timed by more than a single PTA.

Published
2024
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2. The NANOGrav 12.5 yr Data Set: Polarimetry and Faraday Rotation Measures from Observations of Millisecond Pulsars with the Green Bank Telescope

Author

H. M. Wahl, M. A. McLaughlin, P. A. Gentile, M. L. Jones, R. Spiewak, Z. Arzoumanian, K. Crowter, P. B. Demorest, M. E. DeCesar, T. Dolch, J. A. Ellis, R. D. Ferdman, E. C. Ferrara, E. Fonseca, N. Garver-Daniels, G. Jones, M. T. Lam, L. Levin, N. Lewandowska, D. R. Lorimer, R. S. Lynch, D. R. Madison, C. Ng, D. J. Nice, T. T. Pennucci, S. M. Ransom, P. Ray, I. H. Stairs, K. Stovall, J. K. Swiggum, and W. W. Zhu

Subjects
Pulsars, Interstellar medium, Astronomical techniques, Astrophysics, QB460-466
Abstract

In this work, we present polarization profiles for 23 millisecond pulsars observed at 820 and 1500 MHz with the Green Bank Telescope as part of the NANOGrav pulsar timing array. We calibrate the data using Mueller matrix solutions calculated from observations of PSRs B1929+10 and J1022+1001. We discuss the polarization profiles, which can be used to constrain pulsar emission geometry, and present both the first published radio polarization profiles for nine pulsars and the discovery of very low-intensity average profile components (“microcomponents”) in four pulsars. We obtain the Faraday rotation measures for each pulsar and use them to calculate the Galactic magnetic field parallel to the line of sight for different lines of sight through the interstellar medium. We fit for linear and sinusoidal trends in time in the dispersion measure and Galactic magnetic field and detect magnetic field variations with a period of 1 yr in some pulsars, but overall find that the variations in these parameters are more consistent with a stochastic origin.

Published
2022
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17. Co-design Center for Exascale Machine Learning Technologies (ExaLearn).

Author

Francis J. Alexander, James A. Ang, Jenna A. Bilbrey, Jan Balewski, Tiernan Casey, Ryan Chard, Jong Choi 0001, Sutanay Choudhury, Bert J. Debusschere, Anthony M. DeGennaro, Nikoli Dryden, J. Austin Ellis, Ian T. Foster, Cristina Garcia-Cardona, Sayan Ghosh, Peter Harrington, Yunzhi Huang, Shantenu Jha, Travis Johnston, Ai Kagawa, Ramakrishnan Kannan, Neeraj Kumar, Zhengchun Liu, Naoya Maruyama, Satoshi Matsuoka, Erin McCarthy, Jamaludin Mohd-Yusof, Peter Nugent, Yosuke Oyama, Thomas Proffen, David Pugmire, Sivasankaran Rajamanickam, Vinay Ramakrishnaiah, Malachi Schram, Sudip K. Seal, Ganesh Sivaraman, Christine Sweeney, Li Tan, Rajeev Thakur, Brian Van Essen, Logan T. Ward, Paul M. Welch, Michael Wolf, Sotiris S. Xantheas, Kevin G. Yager, Shinjae Yoo, and Byung-Jun Yoon

Published
2021
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26. The AACN Essentials journey

Author

Roxie Barnes, Jen Remick, Marsha Hughes-Gay, Angela Opsahl, Carolyn Townsend, Rebecca Lash, and Rebecca J. Bartlett Ellis

Subjects
General Nursing
Published
2023
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27. Minimizing Honey Bee Exposure to Pesticides

Author

Amy T. Vu, J. D. Ellis, J. Klopchin, E. Buss, L. Diepenbrock, F. M. Fishel, W. H. Kern, C. Mannion, E. McAvoy, L. S. Osborne, M. Rogers, M. Sanford, H. Smith, B. S. Stanford, P. Stansly, L. Stelinski, and S. Webb

Subjects
Agriculture (General), S1-972, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

To safely solve a pest problem, growers and pesticide applicators must be aware of the potential impacts of some pest-control strategies on bees, other pollinators, and beneficial arthropods. This 14-page fact sheet written by J. D. Ellis, J. Klopchin, E. Buss, and others and published by the UF/IFAS Entomology and Nematology Department explains the issue and provides strategies to protect honey bees and other beneficial insects from pesticides. https://edis.ifas.ufl.edu/in1027

Published
2021

33. Discovery and Optimization of Potent, Selective, and Brain-Penetrant 1-Heteroaryl-1H-Indazole LRRK2 Kinase Inhibitors for the Treatment of Parkinson’s Disease

Author

David A. Candito, Vladimir Simov, Anmol Gulati, Solomon Kattar, Ryan W. Chau, Blair T. Lapointe, Joey L. Methot, Duane E. DeMong, Thomas H. Graham, Ravi Kurukulasuriya, Mitchell H. Keylor, Ling Tong, Gregori J. Morriello, John J. Acton, Barbara Pio, Weiguo Liu, Jack D. Scott, Michael J. Ardolino, Theodore A. Martinot, Matthew L. Maddess, Xin Yan, Hakan Gunaydin, Rachel L. Palte, Spencer E. McMinn, Lisa Nogle, Hongshi Yu, Ellen C. Minnihan, Charles A. Lesburg, Ping Liu, Jing Su, Laxminarayan G. Hegde, Lily Y. Moy, Janice D. Woodhouse, Robert Faltus, Tina Xiong, Paul Ciaccio, Jennifer A. Piesvaux, Karin M. Otte, Matthew E. Kennedy, David Jonathan Bennett, Erin F. DiMauro, Matthew J. Fell, Santhosh Neelamkavil, Harold B. Wood, Peter H. Fuller, and J. Michael Ellis

Subjects
Drug Discovery, Molecular Medicine
Published
2022
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36. Modeling the Uncertainties of Solar System Ephemerides for Robust Gravitational-wave Searches with Pular-timing Arrays

Author

M Vallisneri, S R Taylor, J Simon, W M Folkner, R S Park, C Cutler, J A Ellis, T J W Lazio, S J Vigeland, K Aggarwal, Z Arzoumanian, P T Baker, A Brazier, P R Brook, S Burke-Spolaor, S Chatterjee, J M Cordes, N J Cornish, F Crawford, H T Cromartie, K Crowter, M DeCesar, P B Demorest, T Dolch, R D Ferdman, E C Ferrara, E Fonseca, N Garver-Daniels, P Gentile, D Good, J S Hazboun, A M Holgado, E A Huerta, K Islo, R Jennings, G Jones, M L Jones, D L Kaplan, L Z Kelley, J S Key, M T Lam, L Levin, D R Lorimer, J Luo, R S Lynch, D R Madison, M A McLaughlin, S T McWilliams, C M F Mingarelli, C Ng, D J Nice, T T Pennucci, N S Pol, S M Ransom, P S Ray, X Siemens, R Spiewak, I H Stairs, D R Stinebring, K Stovall, J K Swiggum, R van Haasteren, C A Witt, and W W Zhu

Subjects
Astrophysics
Abstract

The regularity of pulsar emissions becomes apparent once we reference the pulses’ times of arrivals to the inertial rest frame of the solar system. It follows that errors in the determination of Earthʼs position with respect to the solar system barycenter can appear as a time-correlated bias in pulsar-timing residual time series, affecting the searches for low-frequency gravitational waves performed with pulsar-timing arrays. Indeed, recent array data sets yield different gravitational-wave background upper limits and detection statistics when analyzed with different solar system ephemerides. Crucially, the ephemerides do not generally provide usable error representations. In this article, we describe the motivation, construction, and application of a physical model of solar system ephemeris uncertainties, which focuses on the degrees of freedom (Jupiterʼs orbital elements) most relevant to gravitational-wave searches with pulsar-timing arrays. This model, BAYESEPHEM, was used to derive ephemeris-robust results in NANOGravʼs 11 yr stochastic-background search, and it provides a foundation for future searches by NANOGrav and other consortia. The analysis and simulations reported here suggest that ephemeris modeling reduces the gravitational-wave sensitivity of the 11 yr data set and that this degeneracy will vanish with improved ephemerides and with pulsar-timing data sets that extend well beyond a single Jovian orbital period.

Published
2020
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37. The NANOGrav 11 yr Data Set: Contraints on Planetary Masses Around 45 Millisecond Pulsars

Author

E A Behrens, S M Ransom, D R Madison, Z Arzoumanian, K Crowter, M E DeCesar, P B Demorest, T Dolch, J A Ellis, R D Ferdman, E C Ferrara, E Fonseca, P A Gentile, G Jones, M L Jones, M T Lam, L Levin, D R Lorimer, R S Lynch, M A McLaughlin, C Ng, D J Nice, T T Pennucci, B B P Perera, P S Ray, R Spiewak, I H Stairs, K Stovall, J K Swiggum, and W W Zhu

Subjects
Astronomy
Abstract

We search for extrasolar planets around millisecond pulsars using pulsar timing data and seek to determine the minimum detectable planetary masses as a function of orbital period. Using the 11 yr data set from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav), we look for variations from our models of pulse arrival times due to the presence of exoplanets. No planets are detected around the millisecond pulsars in the NANOGrav 11 yr data set, but taking into consideration the noise levels of each pulsar and the sampling rate of our observations, we develop limits that show we are sensitive to planetary masses as low as that of the moon. We analyzed potential planet periods, P, in the range 7 days < P < 2000 days, with somewhat smaller ranges for some binary pulsars. The planetary-mass limit for our median-sensitivity pulsar within this period range is 1 Mmoon (P 100 days)-2/3.

Published
2020
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38. The NANOGrav 11 yr data set: Evolution of Gravitational-wave Background Statistics

Author

J S Hazboun, J Simon, S R Taylor, M T Lam, S J Vigeland, K Islo, J S Key, Z Arzoumanian, P T Baker, A Brazier, P R Brook, S Burke-Spolaor, S Chatterjee, J M Cordes, N J Cornish, F Crawford, K Crowter, H T Cromartie, M DeCesar, P B Demorest, T Dolch, J A Ellis, R D Ferdman, E Ferrara, E Fonseca, N Garver-Daniels, P Gentile, D Good, A M Holgado, E A Huerta, R Jennings, G Jones, M L Jones, A R Kaiser, D L Kaplan, L Z Kelley, T J W Lazio, L Levin, A N Lommen, D R Lorimer, J Luo, R S Lynch, D R Madison, M A McLaughlin, S T McWilliams, C M F Mingarelli, C Ng, D J Nice, T T Pennucci, N S Pol, S M Ransom, P S Ray, X Siemens, R Spiewak, I H Stairs, D R Stinebring, K Stovall, J K Swiggum, J E Turner, M Vallisneri, R van Haasteren, C A Witt, and W W Zhu

Subjects
Astronomy
Abstract

An ensemble of inspiraling supermassive black hole binaries should produce a stochastic background of very low frequency gravitational waves. This stochastic background is predicted to be a power law, with a gravitational-wave strain spectral index of −2/3, and it should be detectable by a network of precisely timed millisecond pulsars, widely distributed on the sky. This paper reports a new “time slicing” analysis of the 11 yr data release from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) using 34 millisecond pulsars. Methods to flag potential “false-positive” signatures are developed, including techniques to identify responsible pulsars. Mitigation strategies are then presented. We demonstrate how an incorrect noise model can lead to spurious signals, and we show how independently modeling noise across 30 Fourier components, spanning NANOGrav’s frequency range, effectively diagnoses and absorbs the excess power in gravitational-wave searches. This results in a nominal, and expected, progression of our gravitational-wave statistics. Additionally, we show that the first interstellar medium event in PSR J1713+0747 pollutes the common red-noise process with low spectral index noise, and we use a tailored noise model to remove these effects.

Published
2020
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39. The NANOGrav 11 yr data set: Limits on Gravitational Wave Memory

Author

K Aggarwal, Zaven Arzoumanian, P T Baker, A Brazier, P R Brook, S Burke-Spolaor, S Chatterjee, J M Cordes, N J Cornish, F Crawford, H T Cromartie, K Crowter, M DeCesar, P B Demorest, T Dolch, J A Ellis, R D Ferdman, E C Ferrara, E Fonseca, N Garver-Daniels, P Gentile, M L Jones, D L Kaplan, L Z Kelley, J S Key, M T Lam, T J W Lazio, L Levin, D R Lorimer, J Luo, R S Lynch, D R Madison, M A McLaughlin, S T McWilliams, C M F Mingarelli, C Ng, D J Nice, T T Pennucci, N S Pol, S M Ransom, P S Ray, X Siemens, J Simon, R Spiewak, I H Stairs, D R Stinebring, K Stovall, J K Swiggum, S R Taylor, M Vallisneri, R van Haasteren, S J Vigeland, C A Witt, and W W Zhu

Subjects
Astronomy
Abstract

The mergers of supermassive black hole binaries (SMBHBs) promise to be incredible sources of gravitational waves (GWs).While the oscillatory part of the merger gravitational waveform will be outside the frequency sensitivity range of pulsar timing arrays, the nonoscillatory GW memory effect is detectable. Further, any burst of GWs will produce GW memory, making memory a useful probe of unmodeled exotic sources and new physics. We searched the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) 11 yr data set for GW memory. This data set is sensitive to very low-frequency GWs of ∼3 to 400 nHz (periods of ∼11 yr–1 month). Finding no evidence for GWs, we placed limits on the strain amplitude of GW memory events during the observation period. We then used the strain upper limits to place limits on the rate of GW memory causing events. At a strain of 2.5 × 10−14, corresponding to the median upper limit as a function of source sky position, we set a limit on the rate of GW memory events at <0.4 yr−1. That strain corresponds to an SMBHB merger with reduced mass of ηM ~2 × 1010Mmoonand inclination of ι = π/3 at a distance of 1 Gpc. As a test of our analysis, we analyzed the NANOGrav 9 yr data set as well. This analysis found an anomolous signal, which does not appear in the 11 yr data set. This signal is not a GW, and its origin remains unknown.

Published
2020
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41. Tests of gravitational symmetries with pulsar binary J1713+0747

Author

W W Zhu, G Desvignes, N Wex, R N Caballero, D J Champion, P B Demorest, J A Ellis, G H Janssen, M Kramer, A Krieger, L Lentati, D J Nice, S M Ransom, I H Stairs, B W Stappers, J P W Verbiest, Z Arzoumanian, C G Bassa, M Burgay, I Cognard, K Crowter, T Dolch, R D Ferdman, E Fonseca, M E Gonzalez, E Graikou, L Guillemot, J W T Hessels, A Jessner, G Jones, M L Jones, C Jordan, R Karuppusamy, M T Lam, K Lazaridis, P Lazarus, K J Lee, L Levin, K Liu, A G Lyne, J W McKee, M A McLaughlin, S Osłowski, T Pennucci, D Perrodin, A Possenti, S Sanidas, G Shaifullah, R Smits, K Stovall, J Swiggum, G Theureau, and C Tiburzi

Published
2018
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42. High-Performance Single-Photon Sources at Telecom Wavelength Based on Broadband Hybrid Circular Bragg Gratings

Author

Andrea Barbiero, Jan Huwer, Joanna Skiba-Szymanska, David J. P. Ellis, R. Mark Stevenson, Tina Müller, Ginny Shooter, Lucy E. Goff, David A. Ritchie, and Andrew J. Shields

Subjects
Quantum Physics, Physics::Optics, FOS: Physical sciences, Electrical and Electronic Engineering, Quantum Physics (quant-ph), Atomic and Molecular Physics, and Optics, Physics - Optics, Optics (physics.optics), Biotechnology, Electronic, Optical and Magnetic Materials
Abstract

Semiconductor quantum dots embedded in hybrid circular Bragg gratings are a promising platform for the efficient generation of nonclassical light. The scalable fabrication of multiple devices with similar performance is highly desirable for their practical use as sources of single and entangled photons, while the ability to operate at telecom wavelength is essential for their integration with the existing fiber infrastructure. In this work we combine the promising properties of broadband hybrid circular Bragg gratings with a membrane-transfer process performed on 3" wafer scale. We develop and study single-photon sources based on InAs/GaAs quantum dots emitting in the telecom O-band, demonstrating bright single-photon emission with Purcell factor > 5 and count rates up to 10 MHz. Furthermore, we address the question of reproducibility by benchmarking the performance of 10 devices covering a wide spectral range of 50 nm within the O-band.

Published
2022
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43. Using Nucs in Beekeeping Operations

Author

J. D. Ellis

Subjects
Honey bees, beekeeping, nucleus hives, hives, beekeeping practices, Agriculture (General), S1-972, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

This revised 9-page illustrated fact sheet by James D. Ellis discusses the merits of using nucleus colonies, or nucs, which are smaller versions of full-sized Langstroth hives. The publication explains how to create and manage nucs and how to use them to control swarming, strengthen production colonies, re-queen hives, hive swarms, produce queens to sell to other beekeepers, and in general strengthen and expand a beekeeping operation. Published by the UF Department of Entomology and Nematology. http://edis.ifas.ufl.edu/in869 Original Publication: Ellis, James, and Catherine Nalen. 2010. “The Advantages of Using Nucs in Beekeeping Operations”. EDIS 2010 (7). https://journals.flvc.org/edis/article/view/118804.

Published
2019

45. Autophagy receptor NDP52 alters DNA conformation to modulate RNA polymerase II transcription

Author

Ália dos Santos, Daniel E. Rollins, Yukti Hari-Gupta, Hannah McArthur, Mingxue Du, Sabrina Yong Zi Ru, Kseniia Pidlisna, Ane Stranger, Faeeza Lorgat, Danielle Lambert, Ian Brown, Kevin Howland, Jesse Aaron, Lin Wang, Peter J. I. Ellis, Teng-Leong Chew, Marisa Martin-Fernandez, Alice L. B. Pyne, and Christopher P. Toseland

Subjects
Multidisciplinary, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract

NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear functions for NDP52. Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We find that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription. Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation. Overall, here we uncover nuclear roles for NDP52 in gene expression and DNA structure regulation.

Published
2023
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46. Volcanic earthquake catalog enhancement using integrated detection, matched-filtering, and relocation tools

Author

Darren Tan, David Fee, Alicia J. Hotovec-Ellis, Jeremy D. Pesicek, Matthew M. Haney, John A. Power, and Társilo Girona

Subjects
General Earth and Planetary Sciences
Abstract

Volcanic earthquake catalogs are an essential data product used to interpret subsurface volcanic activity and forecast eruptions. Advances in detection techniques (e.g., matched-filtering, machine learning) and relative relocation tools have improved catalog completeness and refined event locations. However, most volcano observatories have yet to incorporate these techniques into their catalog-building workflows. This is due in part to complexities in operationalizing, automating, and calibrating these techniques in a satisfactory way for disparate volcano networks and their varied seismicity. In an effort to streamline the integration of catalog-enhancing tools at the Alaska Volcano Observatory (AVO), we have integrated four popular open-source tools: REDPy, EQcorrscan, HypoDD, and GrowClust. The combination of these tools offers the capability of adding seismic event detections and relocating events in a single workflow. The workflow relies on a combination of standard triggering and cross-correlation clustering (REDPy) to consolidate representative templates used in matched-filtering (EQcorrscan). The templates and their detections are then relocated using the differential time methods provided by HypoDD and/or GrowClust. Our workflow also provides codes to incorporate campaign data at appropriate junctures, and calculate magnitude and frequency index for valid events. We apply this workflow to three datasets: the 2012–2013 seismic swarm sequence at Mammoth Mountain (California), the 2009 eruption of Redoubt Volcano (Alaska), and the 2006 eruption of Augustine Volcano (Alaska); and compare our results with previous studies at each volcano. In general, our workflow provides a significant increase in the number of events and improved locations, and we relate the event clusters and temporal progressions to relevant volcanic activity. We also discuss workflow implementation best practices, particularly in applying these tools to sparse volcano seismic networks. We envision that our workflow and the datasets presented here will be useful for detailed volcano analyses in monitoring and research efforts.

Published
2023
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49. Further solutions to an isotope dilution model for partitioning phenylalanine and tyrosine between milk protein synthesis and other metabolic fates by the mammary gland of lactating dairy cows

Author

L. A. Crompton, L. A. McKnight, C. K. Reynolds, J. L. Ellis, J. Dijkstra, and J. France

Subjects
Animal Nutrition, Phenylalanine, Mammary gland, WIAS, Genetics, Tyrosine, Animal Science and Zoology, Kinetic model, Isotope dilution, Diervoeding, Agronomy and Crop Science
Abstract

Phenylalanine (PHE) and to a lesser extent TYR are two commonly used amino acid tracers for measuring protein metabolism in a variety of species and tissues. The model examined in this paper was developed to resolve trans-organ and stable isotope dilution data collected from experiments with lactating dairy cows using these tracers. Two methods of solving the model, i.e. as two four-pool submodels, one representing PHE and the other TYR, or as an integrated eight-pool model, are investigated and the alternative solutions are contrasted. Solving the model as the two four-pool submodels rather than the integrated 8-pool model is preferred as the equations are slightly simpler and their application less susceptible to any compounding of measurement errors. The data used to illustrate the model were taken from experiments conducted to investigate the effects of high and low protein diets on the partitioning of PHE and TYR between milk protein synthesis and other metabolic fates by the mammary gland.

Published
2022
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