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1. First Results for Solar Soft X-ray Irradiance Measurements from the Third Generation Miniature X-Ray Solar Spectrometer

Author

Woods, Thomas N., Schwab, Bennet, Sewell, Robert, Kandala, Anant Kumar Telikicherla, Mason, James Paul, Caspi, Amir, Eden, Thomas, Chandran, Amal, Chamberlin, Phillip C., Jones, Andrew R., Kohnert, Richard, Moore, Christopher S., Solomon, Stanley C., and Warren, Harry

Subjects
Astrophysics - Solar and Stellar Astrophysics, Physics - Space Physics
Abstract

Three generations of the Miniature X-ray Solar Spectrometer (MinXSS) have flown on small satellites with the goal "to explore the energy distribution of soft X-ray (SXR) emissions from the quiescent Sun, active regions, and during solar flares, and to model the impact on Earth's ionosphere and thermosphere". The primary science instrument is the Amptek X123 X-ray spectrometer that has improved with each generation of the MinXSS experiment. This third generation MinXSS-3 has higher energy resolution and larger effective area than its predecessors and is also known as the Dual-zone Aperture X-ray Solar Spectrometer (DAXSS). It was launched on the INSPIRESat-1 satellite on 2022 February 14, and INSPIRESat-1 has successfully completed its 6-month prime mission. The INSPIRESat-1 is in a dawn-dusk, Sun-Synchronous Orbit (SSO) and therefore has 24-hour coverage of the Sun during most of its mission so far. The rise of Solar Cycle 25 (SC-25) has been observed by DAXSS. This paper introduces the INSPIRESat-1 DAXSS solar SXR observations, and we focus the science results here on a solar occultation experiment and multiple flares on 2022 April 24. One key flare result is that the reduction of elemental abundances is greatest during the flare impulsive phase and thus highlighting the important role of chromospheric evaporation during flares to inject warmer plasma into the coronal loops. Furthermore, these results are suggestive that the amount of chromospheric evaporation is related to flare temperature and intensity., Comment: 44 pages including 19-page Appendix A, 8 figures, 7 tables

Published
2023
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2. Small Platforms, High Return: The Need to Enhance Investment in Small Satellites for Focused Science, Career Development, and Improved Equity

Author

Mason, James Paul, Begbie, Robert G., Bowen, Maitland, Caspi, Amir, Chamberlin, Phillip C., Chandran, Amal, Cohen, Ian, DeLuca, Edward E., de Wijn, Alfred G., Dissauer, Karin, Eparvier, Francis, Filwett, Rachael, Gibson, Sarah, Gilly, Chris R., Herde, Vicki, Ho, George, Hospodarsky, George, Jaynes, Allison, Jones, Andrew R., Kasper, Justin C., Kohnert, Rick, Lee, Zoe, Mason, E. I., Merkel, Aimee, Mesquita, Rafael, Moore, Christopher S., Nikoukar, Romina, Pesnell, W. Dean, Regoli, Leonardo, Savage, Sabrina, Seaton, Daniel B., Spence, Harlan, Thiemann, Ed, Vievering, Juliana T., Wilder, Frederick, and Woods, Thomas N.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics, Astrophysics - Solar and Stellar Astrophysics, Physics - Space Physics
Abstract

In the next decade, there is an opportunity for very high return on investment of relatively small budgets by elevating the priority of smallsat funding in heliophysics. We've learned in the past decade that these missions perform exceptionally well by traditional metrics, e.g., papers/year/\$M (Spence et al. 2022 -- arXiv:2206.02968). It is also well established that there is a "leaky pipeline" resulting in too little diversity in leadership positions (see the National Academies Report at https://www.nationalacademies.org/our-work/increasing-diversity-in-the-leadership-of-competed-space-missions). Prioritizing smallsat funding would significantly increase the number of opportunities for new leaders to learn -- a crucial patch for the pipeline and an essential phase of career development. At present, however, there are far more proposers than the available funding can support, leading to selection ratios that can be as low as 6% -- in the bottom 0.5th percentile of selection ratios across the history of ROSES. Prioritizing SmallSat funding and substantially increasing that selection ratio are the fundamental recommendations being made by this white paper., Comment: White paper submitted to the Decadal Survey for Solar and Space Physics (Heliophysics) 2024-2033; 6 pages, 1 figure

Published
2023
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3. Simultaneous High Dynamic Range Algorithm, Testing, and Instrument Simulation

Author

Mason, James Paul, Seaton, Daniel B., Jones, Andrew R., Jin, Meng, Chamberlin, Phillip C., Sims, Alan, and Woods, Thomas N.

Subjects
Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Within an imaging instrument's field of view, there may be many observational targets of interest. Similarly, within a spectrograph's bandpass, there may be many emission lines of interest. The brightness of these targets and lines can be orders of magnitude different, which poses a challenge to instrument and mission design. A single exposure can saturate the bright emission and/or have a low signal to noise ratio (SNR) for faint emission. Traditional high dynamic range (HDR) techniques solve this problem by either combining multiple sequential exposures of varied duration or splitting the light to different sensors. These methods, however, can result in the loss of science capability, reduced observational efficiency, or increased complexity and cost. The simultaneous HDR method described in this paper avoids these issues by utilizing a special type of detector whose rows can be read independently to define zones that are then composited, resulting in areas with short or long exposure measured simultaneously. We demonstrate this technique for the sun, which is bright on disk and faint off disk. We emulated these conditions in the lab to validate the method. We built an instrument simulator to demonstrate the method for a realistic solar imager and input. We then calculated SNRs, finding a value of 45 for a faint coronal mass ejection (CME) and 200 for a bright CME, both at 3.5 $R_{\odot}$ -- meeting or far exceeding the international standard for digital photography that defines a SNR of 10 as acceptable and 40 as excellent. Future missions should consider this type of hardware and technique in their trade studies for instrument design., Comment: 9 pages, 5 figures, accepted to ApJ

Published
2022
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5. SunCET: A compact EUV instrument to fill a critical observational gap

Author

Mason, James Paul, Chamberlin, Phillip C., Seaton, Daniel, Burkepile, Joan, Colaninno, Robin, Dissauer, Karin, Eparvier, Francis G., Fan, Yuhong, Gibson, Sarah, Jones, Andrew R., Kay, Christina, Kirk, Michael, Kohnert, Richard, Pesnell, W. Dean, Thompson, Barbara J., Veronig, Astrid M., West, Matthew J., Windt, David, and Woods, Thomas N.

Subjects
Astrophysics - Solar and Stellar Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

The Sun Coronal Ejection Tracker (SunCET) is an extreme ultraviolet imager and spectrograph instrument concept for tracking coronal mass ejections through the region where they experience the majority of their acceleration: the difficult-to-observe middle corona. It contains a wide field of view (0-4~\Rs) imager and a 1~\AA\ spectral-resolution-irradiance spectrograph spanning 170-340~\AA. It leverages new detector technology to read out different areas of the detector with different integration times, resulting in what we call "simultaneous high dynamic range", as opposed to the traditional high dynamic range camera technique of subsequent full-frame images that are then combined in post-processing. This allows us to image the bright solar disk with short integration time, the middle corona with a long integration time, and the spectra with their own, independent integration time. Thus, SunCET does not require the use of an opaque or filtered occulter. SunCET is also compact -- $\sim$15 $\times$ 15 $\times$ 10~cm in volume -- making it an ideal instrument for a CubeSat or a small, complementary addition to a larger mission. Indeed, SunCET is presently in a NASA-funded, competitive Phase A as a CubeSat and has also been proposed to NASA as an instrument onboard a 184 kg Mission of Opportunity., Comment: 22 pages, 12 figures, 5 tables, in press at Journal of Space Weather and Space Climate special issue called "Space Weather Instrumentation"

Published
2021

6. Characterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential.

Author

Meyer, Bjoern, Chiaravalli, Jeanne, Gellenoncourt, Stacy, Brownridge, Philip, Bryne, Dominic P, Daly, Leonard A, Grauslys, Arturas, Walter, Marius, Agou, Fabrice, Chakrabarti, Lisa A, Craik, Charles S, Eyers, Claire E, Eyers, Patrick A, Gambin, Yann, Jones, Andrew R, Sierecki, Emma, Verdin, Eric, Vignuzzi, Marco, and Emmott, Edward

Subjects
Cell Line, Animals, Humans, Myosin-Light-Chain Kinase, src-Family Kinases, Dipeptides, Viral Proteins, RNA, Small Interfering, Protease Inhibitors, Antiviral Agents, Proteomics, Virus Replication, Mutation, Virus Internalization, Proteolysis, COVID-19, SARS-CoV-2, Viral Proteases, Vaccine Related, Infectious Diseases, Biodefense, Pneumonia, Emerging Infectious Diseases, Immunization, Biotechnology, Lung, Prevention, 2.2 Factors relating to the physical environment, Infection
Abstract

SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigens S and N: the main targets for vaccine and antibody testing efforts. We discover significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases. We show that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, show a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.

Published
2021

7. Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Author

Leitner, Alexander, Bonvin, Alexandre M. J. J., Borchers, Christoph H., Chalkley, Robert J., Chamot-Rooke, Julia, Combe, Colin W., Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C., Heck, Albert J. R., Hoopmann, Michael R., Huang, Lan, Ishihama, Yasushi, Jones, Andrew R., Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L., Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A., Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaino, Juan A., Wilkins, Marc R., and Rappsilber, Juri

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative., Comment: 26 pages, 1 figure

Published
2020

12. The Instruments and Capabilities of the Miniature X-ray Solar Spectrometer (MinXSS) CubeSats

Author

Moore, Christopher S., Caspi, Amir, Woods, Thomas N., Chamberlin, Phillip C., Dennis, Brian R., Jones, Andrew R., Mason, James P., Schwartz, Richard A., and Tolbert, Anne K.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

The Miniature X-ray Solar Spectrometer (MinXSS) CubeSat is the first solar science oriented CubeSat mission flown for the NASA Science Mission Directorate, with the main objective of measuring the solar soft X-ray (SXR) flux and a science goal of determining its influence on Earth's ionosphere and thermosphere. These observations can also be used to investigate solar quiescent, active region, and flare properties. The MinXSS X-ray instruments consist of a spectrometer, called X123, with a nominal 0.15 keV full-width-half-maximum (FWHM) resolution at 5.9 keV and a broadband X-ray photometer, called XP. Both instruments are designed to obtain measurements from 0.5 - 30 keV at a nominal time cadence of 10 seconds. A description of the MinXSS instruments, performance capabilities, and relation to the Geostationary Operational Environmental Satellite (GOES) 0.1 - 0.8 nm flux are discussed in this article. Early MinXSS results demonstrate the capability to measure variations of the solar spectral SXR flux between 0.8 - 12 keV from at least GOES A5 - M5 (5 $\times$ 10$^{-8}$ - 5 $\times$ 10$^{-5}$ W m$^{-2}$) levels and infer physical properties (temperature and emission measure) from the MinXSS data alone. Moreover, coronal elemental abundances can be inferred, specifically Fe, Ca, Si, Mg, S, Ar, and Ni, when there is sufficiently high count rate at each elemental spectral feature. Additionally, temperature response curves and emission measure loci demonstrate the MinXSS sensitivity to plasma emission at different temperatures. MinXSS observations coupled with those from other solar observatories can help address some of the most compelling questions in solar coronal physics. Finally, simultaneous observations by MinXSS and Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI) can provide the most spectrally complete soft X-ray solar flare photon flux measurements to date., Comment: 45 pages, 16 figures, accepted for publication in Solar Physics

Published
2018
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15. Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome

Author

Ramsbottom, Kerry A., primary, Prakash, Ananth, additional, Perez-Riverol, Yasset, additional, Camacho, Oscar Martin, additional, Sun, Zhi, additional, Kundu, Deepti J., additional, Bowler-Barnett, Emily, additional, Martin, Maria, additional, Fan, Jun, additional, Chebotarov, Dmytro, additional, McNally, Kenneth L., additional, Deutsch, Eric W., additional, Vizcaíno, Juan Antonio, additional, and Jones, Andrew R., additional

Published
2024
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19. The mzIdentML Data Standard Version 1.2, Supporting Advances in Proteome Informatics*

Author

Vizcaíno, Juan Antonio, Mayer, Gerhard, Perkins, Simon, Barsnes, Harald, Vaudel, Marc, Perez-Riverol, Yasset, Ternent, Tobias, Uszkoreit, Julian, Eisenacher, Martin, Fischer, Lutz, Rappsilber, Juri, Netz, Eugen, Walzer, Mathias, Kohlbacher, Oliver, Leitner, Alexander, Chalkley, Robert J, Ghali, Fawaz, Martínez-Bartolomé, Salvador, Deutsch, Eric W, and Jones, Andrew R

Subjects
Biotechnology, Networking and Information Technology R&D (NITRD), Bioengineering, Generic health relevance, Computational Biology, Databases, Protein, Proteomics, Software, Biochemistry & Molecular Biology
Abstract

The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012-capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well-supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (1) scores associated with localization of modifications on peptides; (2) statistics performed at the level of peptides; (3) identification of cross-linked peptides; and (4) support for proteogenomics approaches. In addition, there is now improved support for the encoding of de novo sequencing of peptides, spectral library searches, and protein inference. As a key point, the underlying XML schema has only undergone very minor modifications to simplify as much as possible the transition from version 1.1 to version 1.2 for implementers, but there have been several notable updates to the format specification, implementation guidelines, controlled vocabularies and validation software. mzIdentML 1.2 can be described as backwards compatible, in that reading software designed for mzIdentML 1.1 should function in most cases without adaptation. We anticipate that these developments will provide a continued stable base for software teams working to implement the standard. All the related documentation is accessible at http://www.psidev.info/mzidentml.

Published
2017

20. Emirates Mars Mission Characterization of Mars Atmosphere Dynamics and Processes

Author

Almatroushi, Hessa, AlMazmi, Hoor, AlMheiri, Noora, AlShamsi, Mariam, AlTunaiji, Eman, Badri, Khalid, Lillis, Robert J., Lootah, Fatma, Yousuf, Maryam, Amiri, Sarah, Brain, David A., Chaffin, Michael, Deighan, Justin, Edwards, Christopher S., Forget, Francois, Smith, Michael D., Wolff, Michael J., Christensen, Philip R., England, Scott, Fillingim, Matthew, Holsclaw, Gregory M., Jain, Sonal, Jones, Andrew R., Osterloo, Mikki, Jakosky, Bruce M., Luhmann, Janet G., and Young, Roland M. B.

Published
2021
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22. Guidelines for reporting the use of gel electrophoresis in proteomics

Author

Gibson, Frank, Anderson, Leigh, Babnigg, Gyorgy, Baker, Mark, Berth, Matthias, Binz, Pierre-Alain, Borthwick, Andy, Cash, Phil, Day, Billy W, Friedman, David B, Garland, Donita, Gutstein, Howard B, Hoogland, Christine, Jones, Neil A, Khan, Alamgir, Klose, Joachim, Lamond, Angus I, Lemkin, Peter F, Lilley, Kathryn S, Minden, Jonathan, Morris, Nicholas J, Paton, Norman W, Pisano, Michael R, Prime, John E, Rabilloud, Thierry, Stead, David A, Taylor, Chris F, Voshol, Hans, Wipat, Anil, and Jones, Andrew R

Subjects
Quantitative Biology - Genomics
Abstract

the MIAPE Gel Electrophoresis (MIAPE-GE) guidelines specify the minimum information that should be provided when reporting the use of n-dimensional gel electrophoresis in a proteomics experiment. Developed through a joint effort between the gel-based analysis working group of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO-PSI; http://www.psidev.info/) and the wider proteomics community, they constitute one part of the overall Minimum Information about a Proteomics Experiment (MIAPE) documentation system published last August in Nature Biotechnology

Published
2009
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26. A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome

Author

Ramsbottom, Kerry A, primary, Prakash, Ananth, additional, Riverol, Yasset Perez, additional, Camacho, Oscar Martin, additional, Sun, Zhi, additional, Kundu, Deepti J., additional, Bowler-Barnett, Emily, additional, Martin, Maria, additional, Fan, Jun, additional, Chebotarov, Dmytro, additional, McNally, Kenneth L, additional, Deutsch, Eric W, additional, Vizcaíno, Juan Antonio, additional, and Jones, Andrew R, additional

Published
2023
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30. First Results for Solar Soft X-Ray Irradiance Measurements from the Third-generation Miniature X-Ray Solar Spectrometer

Author

Woods, Thomas N., primary, Schwab, Bennet, additional, Sewell, Robert, additional, Telikicherla Kandala, Anant Kumar, additional, Mason, James Paul, additional, Caspi, Amir, additional, Eden, Thomas, additional, Chandran, Amal, additional, Chamberlin, Phillip C., additional, Jones, Andrew R., additional, Kohnert, Richard, additional, Moore, Christopher S., additional, Solomon, Stanley C., additional, and Warren, Harry, additional

Published
2023
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33. A systems approach reveals species differences in hepatic stress response capacity

Author

Russomanno, Giusy, primary, Sison-Young, Rowena, additional, Livoti, Lucia A, additional, Coghlan, Hannah, additional, Jenkins, Rosalind E, additional, Kunnen, Steven J, additional, Fisher, Ciarán P, additional, Reddyhoff, Dennis, additional, Gardner, Iain, additional, Rehman, Adeeb H, additional, Fenwick, Stephen W, additional, Jones, Andrew R, additional, Vermeil De Conchard, Guy, additional, Simonin, Gilles, additional, Bertheux, Helene, additional, Weaver, Richard J, additional, Johnson, Robert L, additional, Liguori, Michael J, additional, Clausznitzer, Diana, additional, Stevens, James L, additional, Goldring, Christopher E, additional, and Copple, Ian M, additional

Published
2023
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34. Small Platforms, High Return: The Need to Enhance Investment in Small Satellites for Focused Science, Career Development, and Improved Equity

Author

Mason, James Paul, primary, Begbie, Robert G., additional, Bowen, Maitland, additional, Caspi, Amir, additional, Chamberlin, Phillip C., additional, Chandran, Amal, additional, Cohen, Ian, additional, DeLuca, Edward E., additional, Wijn, Alfred G. de, additional, Dissauer, Karin, additional, Eparvier, Francis, additional, Filwett, Rachael, additional, Gibson, Sarah, additional, Gilly, Chris R., additional, Herde, Vicki, additional, Ho, George, additional, Hospodarsky, George, additional, Jaynes, Allison, additional, Jones, Andrew R., additional, Kasper, Justin C., additional, Kohnert, Rick, additional, Lee, Zoe, additional, Mason, Emily I., additional, Merkel, Aimee, additional, Mesquita, Rafael, additional, Moore, Christopher S., additional, Nikoukar, Romina, additional, Pesnell, W. Dean, additional, Regoli, Leonardo, additional, Savage, Sabrina, additional, Seaton, Daniel B., additional, Spence, Harlan, additional, Thiemann, Edward E., additional, Vievering, Juliana T., additional, Wilder, Frederick, additional, and Woods, Thomas N., additional

Published
2023
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35. COMPLETE: a flagship mission for complete understanding of 3D coronal magnetic energy release

Author

Caspi, Amir, primary, Casini, Roberto, additional, Downs, Cooper, additional, Gibson, Sarah, additional, Gilbert, Holly, additional, Glesener, Lindsay, additional, Guidoni, Silvina, additional, Hughes, J. Marcus, additional, McKenzie, David, additional, Plowman, Joseph, additional, Seaton, Daniel, additional, Reeves, Katharine, additional, Saint-Hilaire, Pascal, additional, Shih, Albert Y., additional, West, Matthew, additional, Alaoui, Meriem, additional, Alexander, David, additional, Allred, Joel C., additional, Ashfield, William, additional, Bradshaw, Stephen J., additional, Bröse, Malte, additional, Buitrago-Casas, Juan Camilo, additional, Chamberlin, Phillip, additional, Chandra, Ramesh, additional, Che, Haihong, additional, Chen, Thomas Y., additional, Chen, Bin, additional, Cheng, Xin, additional, Christe, Steven, additional, Dahlin, Joel, additional, Nolfo, Georgia de, additional, Dickson, Ewan C. M., additional, Dudík, Jaroslav, additional, Emslie, Gordon, additional, Erdelyi, Robertus, additional, Gallagher, Peter T., additional, Gan, Weiqun, additional, Gary, Dale, additional, Guo, Fan, additional, Hayes, Laura A., additional, Hudson, Hugh, additional, Ji, Hantao, additional, Jones, Andrew R., additional, Kerr, Graham S., additional, Keshav, Aggarwal, additional, Knuth, Trevor, additional, Kooi, Jason, additional, Kumari, Anshu, additional, Li, Ying, additional, Limousin, Olivier, additional, Longo, Francesco, additional, Maharana, Anwesha, additional, Mandrini, Cristina H., additional, Oliveros, Juan Carlos Martinez, additional, Massone, Anna Maria, additional, McAteer, R. T. James, additional, McConnell, Mark, additional, McTiernan, James, additional, Meuris, Aline, additional, Mitchell, J. Grant, additional, Motorina, Galina, additional, Mrozek, Tomasz, additional, Musset, Sophie, additional, Narukage, Noriyuki, additional, Nayak, Sushree S., additional, Newmark, Jeffrey, additional, Nitta, Nariaki, additional, Panesar, Navdeep, additional, Pariat, Etienne, additional, Piana, Michele, additional, Qiu, Jiong, additional, Raouafi, Nour E., additional, Reale, Fabio, additional, Rozelot, Jean Pierre, additional, Samaiyah, Farid, additional, Sarkar, Ranadeep, additional, Shaik, Shaheda Begum, additional, Skokic, Ivica, additional, Stores, Morgan, additional, Struminsky, Alexei, additional, Su, Yang, additional, Takahashi, Tadayuki, additional, Tiwari, Sanjiv, additional, Tsiklauri, David, additional, Vievering, Juliana T., additional, Warmuth, Alexander, additional, White, Stephen, additional, Zhang, Jie, additional, and Zimovets, Ivan V., additional

Published
2023
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36. Uninterrupted Tracking of Coronal Mass Ejections

Author

Mason, James Paul, primary, Chamberlin, Phillip C., additional, Dissauer, Karin, additional, Eparvier, Francis, additional, Gibson, Sarah, additional, Gilly, Chris R., additional, Jin, Meng, additional, Jones, Andrew R., additional, Pesnell, W. Dean, additional, Seaton, Daniel B., additional, Veronig, Astrid M., additional, West, Matthew J., additional, and Woods, Thomas N., additional

Published
2023
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37. Improving Multi-Dimensional Data Formats, Access, and Assimilation Tools for the Twenty-First Century

Author

Seaton, Daniel, primary, Caspi, Amir, additional, Casini, Roberto, additional, Downs, Cooper, additional, Gibson, Sarah, additional, Gilbert, Holly, additional, Glesener, Lindsay, additional, Guidoni, Silvina, additional, Hughes, J. Marcus, additional, McKenzie, David, additional, Plowman, Joseph, additional, Reeves, Katharine, additional, Saint-Hilaire, Pascal, additional, Shih, Albert Y., additional, West, Matthew, additional, Alaoui, Meriem, additional, Alzate, Nathalia, additional, Ashfield, William, additional, Bradshaw, Stephen J., additional, Buitrago-Casas, Juan Camilo, additional, Che, Haiong, additional, Chen, Thomas Y., additional, Christe, Steven, additional, Erdelyi, Robertus, additional, Farid, Samaiyah, additional, Gallagher, Peter T., additional, Gary, Dale, additional, Gilly, Chris, additional, Guo, Fan, additional, Hayes, Laura A., additional, Hudson, Hugh, additional, Ji, Hantao, additional, Jones, Andrew R., additional, Keshav, Aggarwal, additional, Kirk, Michael S., additional, Knuth, Trevor, additional, Kobelski, Adam, additional, Kooi, Jason, additional, Kumari, Anshu, additional, Li, Ying, additional, Li, Jing, additional, Lowder, Chris, additional, Mandrini, Cristina H., additional, Oliveros, Juan Carlos Martinez, additional, Mason, James Paul, additional, Mason, E. I., additional, Massone, Anna Maria, additional, McAteer, R. T. James, additional, McTiernan, James, additional, Motorina, Galina, additional, Nayak, Sushree S., additional, Nitta, Nariaki, additional, Panesar, Navdeep, additional, Pariat, Etienne, additional, Piana, Michele, additional, Reale, Fabio, additional, Reardon, Kevin, additional, Rivera, Yeimy, additional, Sarkar, Ranadeep, additional, Shaikh, Zubair, additional, Stores, Morgan, additional, Tiwari, Sanjiv, additional, Warmuth, Alexander, additional, and White, Stephen, additional

Published
2023
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38. Magnetic Energy Powers the Corona: How We Can Understand its 3D Storage & Release

Author

Caspi, Amir, primary, Seaton, Daniel, additional, Casini, Roberto, additional, Downs, Cooper, additional, Gibson, Sarah, additional, Gilbert, Holly, additional, Glesener, Lindsay, additional, Guidoni, Silvina, additional, Hughes, J. Marcus, additional, McKenzie, David, additional, Plowman, Joseph, additional, Reeves, Katharine, additional, Saint-Hilaire, Pascal, additional, Shih, Albert Y., additional, West, Matthew, additional, Alaoui, Meriem, additional, Alexander, David, additional, Allred, Joel C., additional, Antiochos, Spiro, additional, Ashfield, William, additional, Ballai, Istvan, additional, Barata, Teresa, additional, Barta, Miroslav, additional, Benz, Arnold O., additional, Berlicki, Arkadiusz, additional, Bradshaw, Stephen J., additional, Bröse, Malte, additional, Buitrago-Casas, Juan Camilo, additional, Cassak, Paul, additional, Chamberlin, Phillip, additional, Che, Haihong, additional, Chen, Thomas Y., additional, Chen, Bin, additional, Cheng, Xin, additional, Christe, Steven, additional, Comisso, Luca, additional, Dahlin, Joel, additional, Nolfo, Georgia de, additional, Dennis, Brian, additional, Dickson, Ewan C. M., additional, Drake, James, additional, Dudík, Jaroslav, additional, Dzifcakova, Elena, additional, Emslie, Gordon, additional, Erdelyi, Robertus, additional, Farid, Samaiyah, additional, Fleishman, Gregory, additional, French, Ryan, additional, Gallagher, Peter T., additional, Gan, Weiqun, additional, Gary, Dale, additional, Guo, Fan, additional, Hayes, Laura A., additional, Hudson, Hugh, additional, Ji, Hantao, additional, Jones, Andrew R., additional, Kansabanik, Devojyoti, additional, Kawate, Tomoko, additional, Kerr, Graham S., additional, Keshav, Aggarwal, additional, Knuth, Trevor, additional, Kobelski, Adam, additional, Kooi, Jason, additional, Kumari, Anshu, additional, Lee, Jeongwoo, additional, Li, Ying, additional, Longo, Francesco, additional, Maharana, Anwesha, additional, Mandrini, Cristina H., additional, Oliveros, Juan Carlos Martinez, additional, Mason, James Paul, additional, Mason, E. I., additional, Massone, Anna Maria, additional, McAteer, R. T. James, additional, McConnell, Mark, additional, McTiernan, James, additional, Mitchell, J. Grant, additional, Mohan, Atul, additional, Motorina, Galina, additional, Mrozek, Tomasz, additional, Musset, Sophie, additional, Narukage, Noriyuki, additional, Nayak, Sushree S., additional, Nitta, Nariaki, additional, Panesar, Navdeep, additional, Pariat, Etienne, additional, Piana, Michele, additional, Pohjolainen, Silja, additional, Qiu, Jiong, additional, Reale, Fabio, additional, Rivera, Yeimy, additional, Rozelot, Jean Pierre, additional, Sarkar, Ranadeep, additional, Setterberg, William, additional, Shaik, Shaheda Begum, additional, Shaikh, Zubair, additional, Sharma, Rohit, additional, Skokic, Ivica, additional, Stores, Morgan, additional, Struminsky, Alexei, additional, Sylwester, Janusz, additional, Takahashi, Tadayuki, additional, Tiwari, Sanjiv, additional, Tsiklauri, David, additional, Vievering, Juliana T., additional, Warmuth, Alexander, additional, White, Stephen, additional, and Zimovets, Ivan V., additional

Published
2023
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41. Proteomics Standards Initiative (PSI) proposed peak annotation format (mzPAF) and spectral library format (mzSpecLib) standards

Author

Lam, Henry Hei Ning, Mak, Tytus, Klein, Joshua A., Bittremieux, Wout, Gabriels, Ralf, Perez-riverol, Yasset, Van den bossche, Tim, Jones, Andrew R., Binz, Pierre-Alain, Kawano, Shin, Mendoza, Luis, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nils, Shofstahl, Jim, Zhu, Yunping, Heche, Helge, Deutsch, Eric W., Vizcaino, Juan-Antonio, Lam, Henry Hei Ning, Mak, Tytus, Klein, Joshua A., Bittremieux, Wout, Gabriels, Ralf, Perez-riverol, Yasset, Van den bossche, Tim, Jones, Andrew R., Binz, Pierre-Alain, Kawano, Shin, Mendoza, Luis, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nils, Shofstahl, Jim, Zhu, Yunping, Heche, Helge, Deutsch, Eric W., and Vizcaino, Juan-Antonio

Published
2023

42. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

Author

Deutsch, Eric W, Vizcaíno, Juan Antonio, Jones, Andrew R., Binz, Pierre-Alain, Lam, Hei Ning, Klein, Joshua, Bittremieux, Wout, Perez-Riverol, Yasset, Tabb, David L, Walzer, Mathias, Ricard-Blum, Sylvie, Hermjakob, Henning, Neumann, Steffen, Mak, Tytus D., Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nil, Shofstahl, Jim, Zhu, Yunping, Licata, Luana, Quaglia, Federica, Tosatto, Silvio C. E., Orchard, Sandra E, Deutsch, Eric W, Vizcaíno, Juan Antonio, Jones, Andrew R., Binz, Pierre-Alain, Lam, Hei Ning, Klein, Joshua, Bittremieux, Wout, Perez-Riverol, Yasset, Tabb, David L, Walzer, Mathias, Ricard-Blum, Sylvie, Hermjakob, Henning, Neumann, Steffen, Mak, Tytus D., Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Bandeira, Nuno, Carver, Jeremy, Pullman, Benjamin, Sun, Zhi, Hoffmann, Nil, Shofstahl, Jim, Zhu, Yunping, Licata, Luana, Quaglia, Federica, Tosatto, Silvio C. E., and Orchard, Sandra E

Abstract

The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception 20 years ago. Here we describe the general operation of the PSI, including its leadership, working groups, yearly workshops, and the document process by which proposals are thoroughly and publicly reviewed in order to be ratified as PSI standards. We briefly describe the current state of the many existing PSI standards, some of which remain the same as when originally developed, some of which have undergone subsequent revisions, and some of which have become obsolete. Then the set of proposals currently being developed are described, with an open call to the community for participation in the forging of the next generation of standards. Finally, we describe some synergies and collaborations with other organizations and look to the future in how the PSI will continue to promote the open sharing of data and thus accelerate the progress of the field of proteomics. © 2023 The Authors. Published by American Chemical Society.

Published
2023

43. GET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation

Author

Wellcome Trust, Consejo Superior de Investigaciones Científicas (España), European Molecular Biology Laboratory, Contreras-Moreira, Bruno [0000-0002-5462-907X], Casas Cendoya, Ana María [0000-0003-3484-2655], Contreras-Moreira, Bruno, Saraf, Shradha, Naamati, Guy, Casas Cendoya, Ana María, Amberkar, Sandeep S., Flicek, Paul, Jones, Andrew R., Dyer, Sarah, Wellcome Trust, Consejo Superior de Investigaciones Científicas (España), European Molecular Biology Laboratory, Contreras-Moreira, Bruno [0000-0002-5462-907X], Casas Cendoya, Ana María [0000-0003-3484-2655], Contreras-Moreira, Bruno, Saraf, Shradha, Naamati, Guy, Casas Cendoya, Ana María, Amberkar, Sandeep S., Flicek, Paul, Jones, Andrew R., and Dyer, Sarah

Abstract

Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts.

Published
2023

44. The GOES-R EUVS model for EUV irradiance variability

Author

Thiemann Edward M. B., Eparvier Francis G., Woodraska Don, Chamberlin Phillip C., Machol Janet, Eden Thomas, Jones Andrew R., Meisner Randy, Mueller Steven, Snow Martin, Viereck Rodney, and Woods Thomas N.

Subjects
spectral irradiance, space weather, modeling, space environment, solar activity, Meteorology. Climatology, QC851-999
Abstract

The Geostationary Operational Environmental Satellite R (GOES-R) series of four satellites are the next generation NOAA GOES satellites. Once on orbit and commissioned, they are renamed GOES 16–19, making critical terrestrial and space weather measurements through 2035. GOES 16 and 17 are currently on orbit, having been launched in 2016 and 2018, respectively. The GOES-R satellites include the Extreme Ultraviolet (EUV) and X-ray Irradiance Sensors (EXIS) instrument suite, which measures calibrated solar irradiance in eight lines or bands between 25 nm and 285 nm with the Extreme Ultraviolet Sensors (EUVS) instrument. EXIS also includes the X-Ray Sensor (XRS) instrument, which measures solar soft X-ray irradiance at the legacy GOES bands. The EUVS Measurements are used as inputs to the EUVS Model, a solar spectral irradiance model for space weather operations that predicts irradiance in twenty-two 5 nm wide intervals from 5 nm to 115 nm, and one 10 nm wide interval from 117 to 127 nm at 30 s cadence. Once fully operational, NOAA will distribute the EUVS Model irradiance with 1 min latency as a primary space weather data product, ushering in a new era of rapid dissemination and measurement continuity of EUV irradiance spectra. This paper describes the EUVS Model algorithms, data sources, calibration methods and associated uncertainties. Typical model (relative) uncertainties are less than ~5% for variability at time-scales longer than 6 h, and are ~25% for solar flare induced variability. The absolute uncertainties, originating from the instruments used to calibrate the EUVS Model, are ~10%. Examples of model results are presented at both sub-daily and multi-year timescales to demonstrate the model’s capabilities and limitations. Example solar flare irradiances are also modeled.

Published
2019
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46. SunCET: The Sun Coronal Ejection Tracker Concept

Author

Mason James Paul, Chamberlin Phillip C., Seaton Daniel, Burkepile Joan, Colaninno Robin, Dissauer Karin, Eparvier Francis G., Fan Yuhong, Gibson Sarah, Jones Andrew R., Kay Christina, Kirk Michael, Kohnert Richard, Pesnell W. Dean, Thompson Barbara J., Veronig Astrid M., West Matthew J, Windt David, and Woods Thomas N.

Subjects
euv instrument, coronal mass ejections, high dynamic range, cubesat, Meteorology. Climatology, QC851-999
Abstract

The Sun Coronal Ejection Tracker (SunCET) is an extreme ultraviolet imager and spectrograph instrument concept for tracking coronal mass ejections through the region where they experience the majority of their acceleration: the difficult-to-observe middle corona. It contains a wide field of view (0–4 R⊙) imager and a 1 Å spectral-resolution-irradiance spectrograph spanning 170–340 Å. It leverages new detector technology to read out different areas of the detector with different integration times, resulting in what we call “simultaneous high dynamic range”, as opposed to the traditional high dynamic range camera technique of subsequent full-frame images that are then combined in post-processing. This allows us to image the bright solar disk with short integration time, the middle corona with a long integration time, and the spectra with their own, independent integration time. Thus, SunCET does not require the use of an opaque or filtered occulter. SunCET is also compact – ~15 × 15 × 10 cm in volume – making it an ideal instrument for a CubeSat or a small, complementary addition to a larger mission. Indeed, SunCET is presently in a NASA-funded, competitive Phase A as a CubeSat and has also been proposed to NASA as an instrument onboard a 184 kg Mission of Opportunity.

Published
2021
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47. Allele Frequency Net Database

Author

Gonzalez-Galarza, Faviel F., primary, McCabe, Antony, additional, Melo dos Santos, Eduardo J., additional, Takeshita, Louise, additional, Ghattaoraya, Gurpreet, additional, Jones, Andrew R., additional, and Middleton, Derek, additional

Published
2018
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48. TriTrypDB: An integrated functional genomics resource for kinetoplastida

Author

Shanmugasundram, Achchuthan, primary, Starns, David, additional, Böhme, Ulrike, additional, Amos, Beatrice, additional, Wilkinson, Paul A., additional, Harb, Omar S., additional, Warrenfeltz, Susanne, additional, Kissinger, Jessica C., additional, McDowell, Mary Ann, additional, Roos, David S., additional, Crouch, Kathryn, additional, and Jones, Andrew R., additional

Published
2023
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49. Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work

Author

Deutsch, Eric W., primary, Vizcaíno, Juan Antonio, additional, Jones, Andrew R., additional, Binz, Pierre-Alain, additional, Lam, Henry, additional, Klein, Joshua, additional, Bittremieux, Wout, additional, Perez-Riverol, Yasset, additional, Tabb, David L., additional, Walzer, Mathias, additional, Ricard-Blum, Sylvie, additional, Hermjakob, Henning, additional, Neumann, Steffen, additional, Mak, Tytus D., additional, Kawano, Shin, additional, Mendoza, Luis, additional, Van Den Bossche, Tim, additional, Gabriels, Ralf, additional, Bandeira, Nuno, additional, Carver, Jeremy, additional, Pullman, Benjamin, additional, Sun, Zhi, additional, Hoffmann, Nils, additional, Shofstahl, Jim, additional, Zhu, Yunping, additional, Licata, Luana, additional, Quaglia, Federica, additional, Tosatto, Silvio C. E., additional, and Orchard, Sandra E., additional

Published
2023
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