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3. Software Citation in HEP: Current State and Recommendations for the Future

Author

Feickert, Matthew, Katz, Daniel S., Neubauer, Mark S., Sexton-Kennedy, Elizabeth, and Stewart, Graeme A.

Subjects
High Energy Physics - Experiment, High Energy Physics - Phenomenology
Abstract

In November 2022, the HEP Software Foundation and the Institute for Research and Innovation for Software in High-Energy Physics organized a workshop on the topic of Software Citation and Recognition in HEP. The goal of the workshop was to bring together different types of stakeholders whose roles relate to software citation, and the associated credit it provides, in order to engage the community in a discussion on: the ways HEP experiments handle citation of software, recognition for software efforts that enable physics results disseminated to the public, and how the scholarly publishing ecosystem supports these activities. Reports were given from the publication board leadership of the ATLAS, CMS, and LHCb experiments and HEP open source software community organizations (ROOT, Scikit-HEP, MCnet), and perspectives were given from publishers (Elsevier, JOSS) and related tool providers (INSPIRE, Zenodo). This paper summarizes key findings and recommendations from the workshop as presented at the 26th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2023)., Comment: 7 pages, 2 listings. Contribution to the Proceedings of the 26th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2023)

Published
2023

6. Second Analysis Ecosystem Workshop Report

Author

Aly, Mohamed, Burzynski, Jackson, Cardwell, Bryan, Craik, Daniel C., van Daalen, Tal, Dado, Tomas, Das, Ayanabha, Peris, Antonio Delgado, Doglioni, Caterina, Elmer, Peter, Eren, Engin, Eriksen, Martin B., Eschle, Jonas, Eulisse, Giulio, Fitzpatrick, Conor, Molina, José Flix, Forti, Alessandra, Galewsky, Ben, Gasiorowski, Sean, Goel, Aman, Gouskos, Loukas, Guiraud, Enrico, Gupta, Kanhaiya, Hageboeck, Stephan, Hall, Allison Reinsvold, Heinrich, Lukas, Held, Alexander, Hernández, José M., Villanueva, Michel Hernández, Hrivnac, Julius, Jouvin, Michel, Khoo, Teng Jian, Kreczko, Luke, Krumnack, Nils, Kuhr, Thomas, Kundu, Baidyanath, Lancon, Eric, Lange, Johannes, Laycock, Paul, Lieret, Kilian, Manganelli, Nicholas J., Villa, Pere Mato, Novak, Andrzej, Yzquierdo, Antonio Perez-Calero, Pivarski, Jim, Proffitt, Mason, Rembser, Jonas, Rodrigues, Eduardo, Rybkin, Grigori, Schaarschmidt, Jana, Schreiner, Henry F., Schulz, Markus, Sciabà, Andrea, Sekmen, Sezen, Sexton-Kennedy, Elizabeth, Shadura, Oksana, Simko, Tibor, Simpson, Nathan, Singh, Jaydip, Skidmore, Nicola, Smith, Nicholas, Sokoloff, Michael, Stewart, Graeme A., Strong, Giles C., Unel, Gokhan, Vassilev, Vassil, Waterlaat, Mark, Watts, Gordon, and Yazgan, Efe

Subjects
High Energy Physics - Experiment
Abstract

The second workshop on the HEP Analysis Ecosystem took place 23-25 May 2022 at IJCLab in Orsay, to look at progress and continuing challenges in scaling up HEP analysis to meet the needs of HL-LHC and DUNE, as well as the very pressing needs of LHC Run 3 analysis. The workshop was themed around six particular topics, which were felt to capture key questions, opportunities and challenges. Each topic arranged a plenary session introduction, often with speakers summarising the state-of-the art and the next steps for analysis. This was then followed by parallel sessions, which were much more discussion focused, and where attendees could grapple with the challenges and propose solutions that could be tried. Where there was significant overlap between topics, a joint discussion between them was arranged. In the weeks following the workshop the session conveners wrote this document, which is a summary of the main discussions, the key points raised and the conclusions and outcomes. The document was circulated amongst the participants for comments before being finalised here.

Published
2022
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7. The HEP Software Foundation Community

Author

Stewart, Graeme A, Elmer, Peter, and Sexton-Kennedy, Elizabeth

Subjects
Physics - Computational Physics, Computer Science - Software Engineering
Abstract

The HEP Software Foundation was founded in 2014 to tackle common problems of software development and sustainability for high-energy physics. In this paper we outline the motivation for the founding of the organisation and give a brief history of its development. We describe how the organisation functions today and what challenges remain to be faced in the future.

Published
2022

8. Software and Computing for Small HEP Experiments

Author

Casper, Dave, Monzani, Maria Elena, Nachman, Benjamin, Andreopoulos, Costas, Bailey, Stephen, Bard, Deborah, Bhimji, Wahid, Cerati, Giuseppe, Chachamis, Grigorios, Daughhetee, Jacob, Diamond, Miriam, Elvira, V. Daniel, Fan, Alden, Genser, Krzysztof, Girotti, Paolo, Kravitz, Scott, Kutschke, Robert, Pascuzzi, Vincent R., Perdue, Gabriel N., Snider, Erica, Sexton-Kennedy, Elizabeth, Stewart, Graeme Andrew, Szydagis, Matthew, Torrence, Eric, and Tunnell, Christopher

Subjects
High Energy Physics - Experiment, Physics - Computational Physics
Abstract

This white paper briefly summarized key conclusions of the recent US Community Study on the Future of Particle Physics (Snowmass 2021) workshop on Software and Computing for Small High Energy Physics Experiments., Comment: Contribution to Snowmass 2021

Published
2022

9. HL-LHC Computing Review Stage-2, Common Software Projects: Event Generators

Author

WG, The HSF Physics Event Generator, Yazgan, Efe, McFayden, Josh, Valassi, Andrea, Amoroso, Simone, Bothmann, Enrico, Buckley, Andy, Campbell, John, Chahal, Gurpreet Singh, Childers, Taylor, Corti, Gloria, Frederix, Rikkert, Frixione, Stefano, Giuli, Francesco, Grohsjean, Alexander, Hoeche, Stefan, Ilten, Phil, Krauss, Frank, Kreps, Michal, Lange, David, Lonnblad, Leif, Marshall, Zach, Mattelaer, Olivier, Mrenna, Stephen, Nason, Paolo, Plaetzer, Simon, Preuss, Christian, Re, Emanuele, Roiser, Stefan, Schoenherr, Marek, Schumann, Steffen, Seidel, Markus, Sexton-Kennedy, Elizabeth, Siegert, Frank, Siodmok, Andrzej, Stewart, Graeme A., Sugunan, Aravind Thachayath, and Was, Zbigniew

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Experiment, Physics - Computational Physics
Abstract

This paper has been prepared by the HEP Software Foundation (HSF) Physics Event Generator Working Group (WG), as an input to the second phase of the LHCC review of High-Luminosity LHC (HL-LHC) computing, which is due to take place in November 2021. It complements previous documents prepared by the WG in the context of the first phase of the LHCC review in 2020, including in particular the WG paper on the specific challenges in Monte Carlo event generator software for HL-LHC, which has since been updated and published, and which we are also submitting to the November 2021 review as an integral part of our contribution., Comment: 34 pages; editors Efe Yazgan, Josh McFayden and Andrea Valassi

Published
2021

13. Software Sustainability & High Energy Physics

Author

Katz, Daniel S., Malik, Sudhir, Neubauer, Mark S., Stewart, Graeme A., Assamagan, Kétévi A., Becker, Erin A., Hong, Neil P. Chue, Cosden, Ian A., Meehan, Samuel, Moyse, Edward J. W., Price-Whelan, Adrian M., Sexton-Kennedy, Elizabeth, Evans, Meirin Oan, Feickert, Matthew, Lange, Clemens, Lieret, Kilian, Quick, Rob, Pineda, Arturo Sánchez, and Tunnell, Christopher

Subjects
High Energy Physics - Experiment, Computer Science - Software Engineering
Abstract

New facilities of the 2020s, such as the High Luminosity Large Hadron Collider (HL-LHC), will be relevant through at least the 2030s. This means that their software efforts and those that are used to analyze their data need to consider sustainability to enable their adaptability to new challenges, longevity, and efficiency, over at least this period. This will help ensure that this software will be easier to develop and maintain, that it remains available in the future on new platforms, that it meets new needs, and that it is as reusable as possible. This report discusses a virtual half-day workshop on "Software Sustainability and High Energy Physics" that aimed 1) to bring together experts from HEP as well as those from outside to share their experiences and practices, and 2) to articulate a vision that helps the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) to create a work plan to implement elements of software sustainability. Software sustainability practices could lead to new collaborations, including elements of HEP software being directly used outside the field, and, as has happened more frequently in recent years, to HEP developers contributing to software developed outside the field rather than reinventing it. A focus on and skills related to sustainable software will give HEP software developers an important skill that is essential to careers in the realm of software, inside or outside HEP. The report closes with recommendations to improve software sustainability in HEP, aimed at the HEP community via IRIS-HEP and the HEP Software Foundation (HSF)., Comment: A report from the "Sustainable Software in HEP" IRIS-HEP blueprint workshop: https://indico.cern.ch/event/930127/

Published
2020
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14. HL-LHC Computing Review: Common Tools and Community Software

Author

Foundation, HEP Software, Aarrestad, Thea, Amoroso, Simone, Atkinson, Markus Julian, Bendavid, Joshua, Boccali, Tommaso, Bocci, Andrea, Buckley, Andy, Cacciari, Matteo, Calafiura, Paolo, Canal, Philippe, Carminati, Federico, Childers, Taylor, Ciulli, Vitaliano, Corti, Gloria, Costanzo, Davide, Dezoort, Justin Gage, Doglioni, Caterina, Duarte, Javier Mauricio, Dziurda, Agnieszka, Elmer, Peter, Elsing, Markus, Elvira, V. Daniel, Eulisse, Giulio, Menendez, Javier Fernandez, Fitzpatrick, Conor, Frederix, Rikkert, Frixione, Stefano, Genser, Krzysztof L, Gheata, Andrei, Giuli, Francesco, Gligorov, Vladimir V., Grasland, Hadrien Benjamin, Gray, Heather, Gray, Lindsey, Grohsjean, Alexander, Gütschow, Christian, Hageboeck, Stephan, Harris, Philip Coleman, Hegner, Benedikt, Heinrich, Lukas, Holzman, Burt, Hopkins, Walter, Hsu, Shih-Chieh, Höche, Stefan, Ilten, Philip James, Ivantchenko, Vladimir, Jones, Chris, Jouvin, Michel, Khoo, Teng Jian, Kisel, Ivan, Knoepfel, Kyle, Konstantinov, Dmitri, Krasznahorkay, Attila, Krauss, Frank, Krikler, Benjamin Edward, Lange, David, Laycock, Paul, Li, Qiang, Lieret, Kilian, Liu, Miaoyuan, Loncar, Vladimir, Lönnblad, Leif, Maltoni, Fabio, Mangano, Michelangelo, Marshall, Zachary Louis, Mato, Pere, Mattelaer, Olivier, McFayden, Joshua Angus, Meehan, Samuel, Mete, Alaettin Serhan, Morgan, Ben, Mrenna, Stephen, Muralidharan, Servesh, Nachman, Ben, Neubauer, Mark S., Neumann, Tobias, Ngadiuba, Jennifer, Ojalvo, Isobel, Pedro, Kevin, Perini, Maurizio, Piparo, Danilo, Pivarski, Jim, Plätzer, Simon, Pokorski, Witold, Pol, Adrian Alan, Prestel, Stefan, Ribon, Alberto, Ritter, Martin, Rizzi, Andrea, Rodrigues, Eduardo, Roiser, Stefan, Schulz, Holger, Schulz, Markus, Schönherr, Marek, Sexton-Kennedy, Elizabeth, Siegert, Frank, Siódmok, Andrzej, Stewart, Graeme A, Sudhir, Malik, Summers, Sioni Paris, Thais, Savannah Jennifer, Tran, Nhan Viet, Valassi, Andrea, Verderi, Marc, Bruch, Dorothea Vom, Watts, Gordon T., Wenaus, Torre, and Yazgan, Efe

Subjects
Physics - Computational Physics, High Energy Physics - Experiment
Abstract

Common and community software packages, such as ROOT, Geant4 and event generators have been a key part of the LHC's success so far and continued development and optimisation will be critical in the future. The challenges are driven by an ambitious physics programme, notably the LHC accelerator upgrade to high-luminosity, HL-LHC, and the corresponding detector upgrades of ATLAS and CMS. In this document we address the issues for software that is used in multiple experiments (usually even more widely than ATLAS and CMS) and maintained by teams of developers who are either not linked to a particular experiment or who contribute to common software within the context of their experiment activity. We also give space to general considerations for future software and projects that tackle upcoming challenges, no matter who writes it, which is an area where community convergence on best practice is extremely useful., Comment: 40 pages contribution to Snowmass 2021

Published
2020
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15. Challenges in Monte Carlo event generator software for High-Luminosity LHC

Author

WG, The HSF Physics Event Generator, Valassi, Andrea, Yazgan, Efe, McFayden, Josh, Amoroso, Simone, Bendavid, Joshua, Buckley, Andy, Cacciari, Matteo, Childers, Taylor, Ciulli, Vitaliano, Frederix, Rikkert, Frixione, Stefano, Giuli, Francesco, Grohsjean, Alexander, Gütschow, Christian, Höche, Stefan, Hopkins, Walter, Ilten, Philip, Konstantinov, Dmitri, Krauss, Frank, Li, Qiang, Lönnblad, Leif, Maltoni, Fabio, Mangano, Michelangelo, Marshall, Zach, Mattelaer, Olivier, Menendez, Javier Fernandez, Mrenna, Stephen, Muralidharan, Servesh, Neumann, Tobias, Plätzer, Simon, Prestel, Stefan, Roiser, Stefan, Schönherr, Marek, Schulz, Holger, Schulz, Markus, Sexton-Kennedy, Elizabeth, Siegert, Frank, Siódmok, Andrzej, and Stewart, Graeme A.

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Experiment, Physics - Computational Physics
Abstract

We review the main software and computing challenges for the Monte Carlo physics event generators used by the LHC experiments, in view of the High-Luminosity LHC (HL-LHC) physics programme. This paper has been prepared by the HEP Software Foundation (HSF) Physics Event Generator Working Group as an input to the LHCC review of HL-LHC computing, which has started in May 2020., Comment: 20 pages; editors Andrea Valassi, Efe Yazgan and Josh McFayden; addressed additional comments by journal reviewers

Published
2020
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16. Reinterpretation of LHC Results for New Physics: Status and Recommendations after Run 2

Author

Abdallah, Waleed, AbdusSalam, Shehu, Ahmadov, Azar, Ahriche, Amine, Alguero, Gaël, Allanach, Benjamin C., Araz, Jack Y., Arbey, Alexandre, Arina, Chiara, Athron, Peter, Bagnaschi, Emanuele, Bai, Yang, Baker, Michael J., Balazs, Csaba, Barducci, Daniele, Bechtle, Philip, Bharucha, Aoife, Buckley, Andy, Butterworth, Jonathan, Cai, Haiying, Campagnari, Claudio, Cesarotti, Cari, Chrzaszcz, Marcin, Coccaro, Andrea, Conte, Eric, Cornell, Jonathan M., Corpe, Louie Dartmoor, Danninger, Matthias, Darmé, Luc, Deandrea, Aldo, Desai, Nishita, Dillon, Barry, Doglioni, Caterina, Dutta, Juhi, Ellis, John R., Ellis, Sebastian, Fassi, Farida, Feickert, Matthew, Fernandez, Nicolas, Fichet, Sylvain, Kamenik, Jernej F., Flacke, Thomas, Fuks, Benjamin, Geiser, Achim, Genest, Marie-Hélène, Ghalsasi, Akshay, Gonzalo, Tomas, Goodsell, Mark, Gori, Stefania, Gras, Philippe, Greljo, Admir, Guadagnoli, Diego, Heinemeyer, Sven, Heinrich, Lukas A., Heisig, Jan, Hong, Deog Ki, Hryn'ova, Tetiana, Huitu, Katri, Ilten, Philip, Ismail, Ahmed, Jueid, Adil, Kahlhoefer, Felix, Kalinowski, Jan, Kar, Deepak, Kats, Yevgeny, Khosa, Charanjit K., Khoze, Valeri, Klingl, Tobias, Ko, Pyungwon, Kong, Kyoungchul, Kotlarski, Wojciech, Krämer, Michael, Kraml, Sabine, Kulkarni, Suchita, Kvellestad, Anders, Lange, Clemens, Lassila-Perini, Kati, Lee, Seung J., Lessa, Andre, Liu, Zhen, Iglesias, Lara Lloret, Lorenz, Jeanette M., MacDonell, Danika, Mahmoudi, Farvah, Mamuzic, Judita, Marini, Andrea C., Markowitz, Pete, del Arbol, Pablo Martinez Ruiz, Miller, David, Mitsou, Vasiliki, Moretti, Stefano, Nardecchia, Marco, Neshatpour, Siavash, Nhung, Dao Thi, Osland, Per, Owen, Patrick H., Panella, Orlando, Pankov, Alexander, Park, Myeonghun, Porod, Werner, Price, Darren, Prosper, Harrison, Raklev, Are, Reuter, Jürgen, Reyes-González, Humberto, Rizzo, Thomas, Robens, Tania, Rojo, Juan, Rosiek, Janusz A., Ruchayskiy, Oleg, Sanz, Veronica, Schmidt-Hoberg, Kai, Scott, Pat, Sekmen, Sezen, Sengupta, Dipan, Sexton-Kennedy, Elizabeth, Shao, Hua-Sheng, Shin, Seodong, Silvestrini, Luca, Singh, Ritesh, Sinha, Sukanya, Sonneveld, Jory, Soreq, Yotam, Stark, Giordon H., Stefaniak, Tim, Thaler, Jesse, Torre, Riccardo, Torrente-Lujan, Emilio, Unel, Gokhan, Vignaroli, Natascia, Waltenberger, Wolfgang, Wardle, Nicholas, Watt, Graeme, Weiglein, Georg, White, Martin J., Williamson, Sophie L., Wittbrodt, Jonas, Wu, Lei, Wunsch, Stefan, You, Tevong, Zhang, Yang, and Zurita, José

Subjects
High Energy Physics - Phenomenology, High Energy Physics - Experiment
Abstract

We report on the status of efforts to improve the reinterpretation of searches and measurements at the LHC in terms of models for new physics, in the context of the LHC Reinterpretation Forum. We detail current experimental offerings in direct searches for new particles, measurements, technical implementations and Open Data, and provide a set of recommendations for further improving the presentation of LHC results in order to better enable reinterpretation in the future. We also provide a brief description of existing software reinterpretation frameworks and recent global analyses of new physics that make use of the current data., Comment: 58 pages, minor revision following comments from SciPost referees

Published
2020
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20. HEP Software Foundation Community White Paper Working Group - Data Processing Frameworks

Author

Calafiura, Paolo, Clemencic, Marco, Grasland, Hadrien, Green, Chris, Hegner, Benedikt, Jones, Chris, Jouvin, Michel, Knoepfel, Kyle, Kuhr, Thomas, Kowalkowski, Jim, Leggett, Charles, Lyon, Adam, Malon, David, Paterno, Marc, Patton, Simon, Sexton-Kennedy, Elizabeth, Stewart, Graeme A, and Tsulaia, Vakho

Subjects
Physics - Computational Physics, High Energy Physics - Experiment
Abstract

Data processing frameworks are an essential part of HEP experiments' software stacks. Frameworks provide a means by which code developers can undertake the essential tasks of physics data processing, accessing relevant inputs and storing their outputs, in a coherent way without needing to know the details of other domains. Frameworks provide essential core services for developers and help deliver a configurable working application to the experiments' production systems. Modern HEP processing frameworks are in the process of adapting to a new computing landscape dominated by parallel processing and heterogeneity, which pose many questions regarding enhanced functionality and scaling that must be faced without compromising the maintainability of the code. In this paper we identify a program of work that can help further clarify the key concepts of frameworks for HEP and then spawn R&D activities that can focus the community's efforts in the most efficient manner to address the challenges of the upcoming experimental program.

Published
2018

21. HEP Software Foundation Community White Paper Working Group -- Data Organization, Management and Access (DOMA)

Author

Berzano, Dario, Bianchi, Riccardo Maria, Bird, Ian, Bockelman, Brian, Campana, Simone, De, Kaushik, Duellmann, Dirk, Elmer, Peter, Gardner, Robert, Garonne, Vincent, Grandi, Claudio, Gutsche, Oliver, Hanushevsky, Andrew, Holzman, Burt, Jayatilaka, Bodhitha, Jimenez, Ivo, Jouvin, Michel, Keeble, Oliver, Klimentov, Alexei, Kuznetsov, Valentin, Lancon, Eric, Lassnig, Mario, Livny, Miron, Maltzahn, Carlos, McKee, Shawn, Menasce, Dario, Norman, Andrew, Pivarski, Jim, Riedel, Benedikt, Schulz, Markus, Severini, Horst, Sevilla, Michael, Sexton-Kennedy, Elizabeth, Vaandering, Eric, Vukotic, Ilija, Watkins, Noah, Wenaus, Torre, and Wuerthwein, Frank

Subjects
Physics - Computational Physics
Abstract

Without significant changes to data organization, management, and access (DOMA), HEP experiments will find scientific output limited by how fast data can be accessed and digested by computational resources. In this white paper we discuss challenges in DOMA that HEP experiments, such as the HL-LHC, will face as well as potential ways to address them. A research and development timeline to assess these changes is also proposed., Comment: arXiv admin note: text overlap with arXiv:1712.06592

Published
2018

22. HEP Software Foundation Community White Paper Working Group - Data Analysis and Interpretation

Author

Bauerdick, Lothar, Bianchi, Riccardo Maria, Bockelman, Brian, Castro, Nuno, Cranmer, Kyle, Elmer, Peter, Gardner, Robert, Girone, Maria, Gutsche, Oliver, Hegner, Benedikt, Hernández, José M., Jayatilaka, Bodhitha, Lange, David, Neubauer, Mark S., Katz, Daniel S., Kreczko, Lukasz, Letts, James, McKee, Shawn, Paus, Christoph, Pedro, Kevin, Pivarski, Jim, Ritter, Martin, Rodrigues, Eduardo, Sakuma, Tai, Sexton-Kennedy, Elizabeth, Sokoloff, Michael D., Vuosalo, Carl, Würthwein, Frank, and Watts, Gordon

Subjects
Physics - Computational Physics, High Energy Physics - Experiment
Abstract

At the heart of experimental high energy physics (HEP) is the development of facilities and instrumentation that provide sensitivity to new phenomena. Our understanding of nature at its most fundamental level is advanced through the analysis and interpretation of data from sophisticated detectors in HEP experiments. The goal of data analysis systems is to realize the maximum possible scientific potential of the data within the constraints of computing and human resources in the least time. To achieve this goal, future analysis systems should empower physicists to access the data with a high level of interactivity, reproducibility and throughput capability. As part of the HEP Software Foundation Community White Paper process, a working group on Data Analysis and Interpretation was formed to assess the challenges and opportunities in HEP data analysis and develop a roadmap for activities in this area over the next decade. In this report, the key findings and recommendations of the Data Analysis and Interpretation Working Group are presented., Comment: arXiv admin note: text overlap with arXiv:1712.06592

Published
2018

23. The DeepMIP contribution to PMIP4: methodologies for selection, compilation and analysis of latest Paleocene and early Eocene climate proxy data, incorporating version 0.1 of the DeepMIP database

Author

Hollis, Christopher J, Jones, Tom Dunkley, Anagnostou, Eleni, Bijl, Peter K, Cramwinckel, Margot J, Cui, Ying, Dickens, Gerald R, Edgar, Kirsty M, Eley, Yvette, Evans, David, Foster, Gavin L, Frieling, Joost, Inglis, Gordon N, Kennedy, Elizabeth M, Kozdon, Reinhard, Lauretano, Vittoria, Lear, Caroline H, Littler, Kate, Lourens, Lucas, Meckler, A Nele, Naafs, B David A, Paelike, Heiko, Pancost, Richard D, Pearson, Paul N, Roehl, Ursula, Royer, Dana L, Salzmann, Ulrich, Schubert, Brian A, Seebeck, Hannu, Sluijs, Appy, Speijer, Robert P, Stassen, Peter, Tierney, Jessica, Tripati, Aradhna, Wade, Bridget, Westerhold, Thomas, Witkowski, Caitlyn, Zachos, James C, Zhang, Yi Ge, Huber, Matthew, and Lunt, Daniel J

Subjects
Earth Sciences
Abstract

Abstract. The early Eocene (56 to 48 million years ago) is inferred to havebeen the most recent time that Earth's atmospheric CO2 concentrationsexceeded 1000 ppm. Global mean temperatures were also substantially warmerthan those of the present day. As such, the study of early Eocene climate provides insightinto how a super-warm Earth system behaves and offers an opportunity toevaluate climate models under conditions of high greenhouse gas forcing. TheDeep Time Model Intercomparison Project (DeepMIP) is a systematicmodel–model and model–data intercomparison of three early Paleogene timeslices: latest Paleocene, Paleocene–Eocene thermal maximum (PETM) and earlyEocene climatic optimum (EECO). A previous article outlined the modelexperimental design for climate model simulations. In this article, weoutline the methodologies to be used for the compilation and analysis ofclimate proxy data, primarily proxies for temperature and CO2. Thispaper establishes the protocols for a concerted and coordinated effort tocompile the climate proxy records across a wide geographic range. Theresulting climate “atlas” will be used to constrain and evaluate climatemodels for the three selected time intervals and provide insights into themechanisms that control these warm climate states. We provide version 0.1 ofthis database, in anticipation that this will be expanded in subsequentpublications.

Published
2019

25. Bacterial community assembly of specific pathogen-free neonatal mice.

Author

Kennedy, Elizabeth A., Weagley, James S., Kim, Andrew H., Antia, Avan, DeVeaux, Anna L., and Baldridge, Megan T.

Abstract

Background: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters. Results: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14 days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species. Conclusions: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. 9CunmNp3_d6oLBRK9YAPEH Video Abstract [ABSTRACT FROM AUTHOR]

Published
2025
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26. A Roadmap for HEP Software and Computing R&D for the 2020s

Author

Albrecht, Johannes, Alves Jr, Antonio Augusto, Amadio, Guilherme, Andronico, Giuseppe, Anh-Ky, Nguyen, Aphecetche, Laurent, Apostolakis, John, Asai, Makoto, Atzori, Luca, Babik, Marian, Bagliesi, Giuseppe, Bandieramonte, Marilena, Banerjee, Sunanda, Barisits, Martin, Bauerdick, Lothar A. T., Belforte, Stefano, Benjamin, Douglas, Bernius, Catrin, Bhimji, Wahid, Bianchi, Riccardo Maria, Bird, Ian, Biscarat, Catherine, Blomer, Jakob, Bloom, Kenneth, Boccali, Tommaso, Bockelman, Brian, Bold, Tomasz, Bonacorsi, Daniele, Boveia, Antonio, Bozzi, Concezio, Bracko, Marko, Britton, David, Buckley, Andy, Buncic, Predrag, Calafiura, Paolo, Campana, Simone, Canal, Philippe, Canali, Luca, Carlino, Gianpaolo, Castro, Nuno, Cattaneo, Marco, Cerminara, Gianluca, Villanueva, Javier Cervantes, Chang, Philip, Chapman, John, Chen, Gang, Childers, Taylor, Clarke, Peter, Clemencic, Marco, Cogneras, Eric, Coles, Jeremy, Collier, Ian, Colling, David, Corti, Gloria, Cosmo, Gabriele, Costanzo, Davide, Couturier, Ben, Cranmer, Kyle, Cranshaw, Jack, Cristella, Leonardo, Crooks, David, Crépé-Renaudin, Sabine, Currie, Robert, Dallmeier-Tiessen, Sünje, De, Kaushik, De Cian, Michel, De Roeck, Albert, Peris, Antonio Delgado, Derue, Frédéric, Di Girolamo, Alessandro, Di Guida, Salvatore, Dimitrov, Gancho, Doglioni, Caterina, Dotti, Andrea, Duellmann, Dirk, Duflot, Laurent, Dykstra, Dave, Dziedziniewicz-Wojcik, Katarzyna, Dziurda, Agnieszka, Egede, Ulrik, Elmer, Peter, Elmsheuser, Johannes, Elvira, V. Daniel, Eulisse, Giulio, Farrell, Steven, Ferber, Torben, Filipcic, Andrej, Fisk, Ian, Fitzpatrick, Conor, Flix, José, Formica, Andrea, Forti, Alessandra, Franzoni, Giovanni, Frost, James, Fuess, Stu, Gaede, Frank, Ganis, Gerardo, Gardner, Robert, Garonne, Vincent, Gellrich, Andreas, Genser, Krzysztof, George, Simon, Geurts, Frank, Gheata, Andrei, Gheata, Mihaela, Giacomini, Francesco, Giagu, Stefano, Giffels, Manuel, Gingrich, Douglas, Girone, Maria, Gligorov, Vladimir V., Glushkov, Ivan, Gohn, Wesley, Lopez, Jose Benito Gonzalez, Caballero, Isidro González, Fernández, Juan R. González, Govi, Giacomo, Grandi, Claudio, Grasland, Hadrien, Gray, Heather, Grillo, Lucia, Guan, Wen, Gutsche, Oliver, Gyurjyan, Vardan, Hanushevsky, Andrew, Hariri, Farah, Hartmann, Thomas, Harvey, John, Hauth, Thomas, Hegner, Benedikt, Heinemann, Beate, Heinrich, Lukas, Heiss, Andreas, Hernández, José M., Hildreth, Michael, Hodgkinson, Mark, Hoeche, Stefan, Holzman, Burt, Hristov, Peter, Huang, Xingtao, Ivanchenko, Vladimir N., Ivanov, Todor, Iven, Jan, Jashal, Brij, Jayatilaka, Bodhitha, Jones, Roger, Jouvin, Michel, Jun, Soon Yung, Kagan, Michael, Kalderon, Charles William, Kane, Meghan, Karavakis, Edward, Katz, Daniel S., Kcira, Dorian, Keeble, Oliver, Kersevan, Borut Paul, Kirby, Michael, Klimentov, Alexei, Klute, Markus, Komarov, Ilya, Konstantinov, Dmitri, Koppenburg, Patrick, Kowalkowski, Jim, Kreczko, Luke, Kuhr, Thomas, Kutschke, Robert, Kuznetsov, Valentin, Lampl, Walter, Lancon, Eric, Lange, David, Lassnig, Mario, Laycock, Paul, Leggett, Charles, Letts, James, Lewendel, Birgit, Li, Teng, Lima, Guilherme, Linacre, Jacob, Linden, Tomas, Livny, Miron, Presti, Giuseppe Lo, Lopienski, Sebastian, Love, Peter, Lyon, Adam, Magini, Nicolò, Marshall, Zachary L., Martelli, Edoardo, Martin-Haugh, Stewart, Mato, Pere, Mazumdar, Kajari, McCauley, Thomas, McFayden, Josh, McKee, Shawn, McNab, Andrew, Mehdiyev, Rashid, Meinhard, Helge, Menasce, Dario, Lorenzo, Patricia Mendez, Mete, Alaettin Serhan, Michelotto, Michele, Mitrevski, Jovan, Moneta, Lorenzo, Morgan, Ben, Mount, Richard, Moyse, Edward, Murray, Sean, Nairz, Armin, Neubauer, Mark S., Norman, Andrew, Novaes, Sérgio, Novak, Mihaly, Oyanguren, Arantza, Ozturk, Nurcan, Pages, Andres Pacheco, Paganini, Michela, Pansanel, Jerome, Pascuzzi, Vincent R., Patrick, Glenn, Pearce, Alex, Pearson, Ben, Pedro, Kevin, Perdue, Gabriel, Yzquierdo, Antonio Perez-Calero, Perrozzi, Luca, Petersen, Troels, Petric, Marko, Petzold, Andreas, Piedra, Jónatan, Piilonen, Leo, Piparo, Danilo, Pivarski, Jim, Pokorski, Witold, Polci, Francesco, Potamianos, Karolos, Psihas, Fernanda, Navarro, Albert Puig, Quast, Günter, Raven, Gerhard, Reuter, Jürgen, Ribon, Alberto, Rinaldi, Lorenzo, Ritter, Martin, Robinson, James, Rodrigues, Eduardo, Roiser, Stefan, Rousseau, David, Roy, Gareth, Rybkine, Grigori, Sailer, Andre, Sakuma, Tai, Santana, Renato, Sartirana, Andrea, Schellman, Heidi, Schovancová, Jaroslava, Schramm, Steven, Schulz, Markus, Sciabà, Andrea, Seidel, Sally, Sekmen, Sezen, Serfon, Cedric, Severini, Horst, Sexton-Kennedy, Elizabeth, Seymour, Michael, Sgalaberna, Davide, Shapoval, Illya, Shiers, Jamie, Shiu, Jing-Ge, Short, Hannah, Siroli, Gian Piero, Skipsey, Sam, Smith, Tim, Snyder, Scott, Sokoloff, Michael D., Spentzouris, Panagiotis, Stadie, Hartmut, Stark, Giordon, Stewart, Gordon, Stewart, Graeme A., Sánchez, Arturo, Sánchez-Hernández, Alberto, Taffard, Anyes, Tamponi, Umberto, Templon, Jeff, Tenaglia, Giacomo, Tsulaia, Vakhtang, Tunnell, Christopher, Vaandering, Eric, Valassi, Andrea, Vallecorsa, Sofia, Valsan, Liviu, Van Gemmeren, Peter, Vernet, Renaud, Viren, Brett, Vlimant, Jean-Roch, Voss, Christian, Votava, Margaret, Vuosalo, Carl, Sierra, Carlos Vázquez, Wartel, Romain, Watts, Gordon T., Wenaus, Torre, Wenzel, Sandro, Williams, Mike, Winklmeier, Frank, Wissing, Christoph, Wuerthwein, Frank, Wynne, Benjamin, Xiaomei, Zhang, Yang, Wei, and Yazgan, Efe

Subjects
Physics - Computational Physics, High Energy Physics - Experiment
Abstract

Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R&D activities required to prepare for this software upgrade.

Published
2017
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28. Software Citation in HEP: Current State and Recommendations for the Future

Author

Feickert Matthew, Katz Daniel S., Neubauer Mark S., Sexton-Kennedy Elizabeth, and Stewart Graeme A.

Subjects
Physics, QC1-999
Abstract

In November 2022, the HEP Software Foundation and the Institute for Research and Innovation for Software in High-Energy Physics organized a workshop on the topic of Software Citation and Recognition in HEP. The goal of the workshop was to bring together different types of stakeholders whose roles relate to software citation, and the associated credit it provides, in order to engage the community in a discussion on: the ways HEP experiments handle citation of software, recognition for software efforts that enable physics results disseminated to the public, and how the scholarly publishing ecosystem supports these activities. Reports were given from the publication board leadership of the ATLAS, CMS, and LHCb experiments and HEP open source software community organizations (ROOT, Scikit-HEP, MCnet), and perspectives were given from publishers (Elsevier, JOSS) and related tool providers (INSPIRE, Zenodo). This paper summarizes key findings and recommendations from the workshop as presented at the 26th International Conference on Computing in High Energy and Nuclear Physics (CHEP 2023).

Published
2024
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32. Cognitive Functioning Influences Mortality Risk Among Older Adults with COPD.

Author

Banerjee, Srikanta, Khubchandani, Jagdish, England-Kennedy, Elizabeth, McIntyre, Rhonda, Kopera-Frye, Karen, and Batra, Kavita

Subjects
MORTALITY risk factors, BODY mass index, DESCRIPTIVE statistics, CHI-squared test, KAPLAN-Meier estimator, RACE, COGNITION disorders, OBSTRUCTIVE lung diseases, AGING, SOCIODEMOGRAPHIC factors, DATA analysis software, OLD age
Abstract

Background/Objeectives: Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of mortality in the United States (U.S.), with rates varying by disease severity, comorbidities, and sociodemographic factors. Cognitive impairment has been independently associated with increased mortality, but has not been well studied in relation to COPD despite being a frequently overlooked comorbidity in COPD patients. The purpose of this nationwide study was to assess the relationship between low cognitive performance and the risk of mortality among older adults with COPD while adjusting for major sociodemographic and health-related characteristics. Methods: This study utilized the 1999–2002 National Health and Nutrition Examination Survey (NHANES) and the respiratory mortality data of noninstitutionalized US adults aged over 65 years. Survival curves showing the combined effect of cognitive decline and COPD using the Kaplan–Meier product-limit method to estimate the percent survival of the subject at each point in time were used. Results: The final sample included 2013 older adults, with 39.1% showing low cognitive performance and 12.7% having COPD. Those with low cognitive performance were older, less educated, had lower income, were more likely to be racial/ethnic minorities, and had a history of cardiovascular diseases (CVD); they were also more likely to have COPD or chronic kidney disease (CKD). The adjusted hazard ratio for respiratory-related mortality risk was highest for individuals with both COPD and low cognitive performance (hazards ratio = 8.53), people with COPD alone also had a higher respiratory-related mortality risk (hazards ratio = 4.92), but low cognitive performance alone did not significantly increase respiratory-related mortality risk. Conclusions: These findings provide clearer insights into how cognitive impairment affects mortality risk in older adults with COPD and we discuss potential strategies to address this dual chronic health challenge effectively. [ABSTRACT FROM AUTHOR]

Published
2024
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33. Working together with people with intellectual disability to make a difference: a protocol for a mixed-method co-production study to address inequities in cervical screening participation

Author

Bateson, Deborah, primary, Ussher, Jane, additional, Strnadová, Iva, additional, Loblinzk, Julie, additional, David, Michael, additional, Chang, Ee-Lin, additional, Carter, Allison, additional, Sweeney, Sally, additional, Winkler, Lauren, additional, Power, Rosalie, additional, Basckin, Caroline, additional, Kennedy, Elizabeth, additional, and Jolly, Heather, additional

Published
2024
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34. An epigenetic clock for gestational age at birth based on blood methylation data

Author

Knight, Anna K, Craig, Jeffrey M, Theda, Christiane, Bækvad-Hansen, Marie, Bybjerg-Grauholm, Jonas, Hansen, Christine S, Hollegaard, Mads V, Hougaard, David M, Mortensen, Preben B, Weinsheimer, Shantel M, Werge, Thomas M, Brennan, Patricia A, Cubells, Joseph F, Newport, D Jeffrey, Stowe, Zachary N, Cheong, Jeanie LY, Dalach, Philippa, Doyle, Lex W, Loke, Yuk J, Baccarelli, Andrea A, Just, Allan C, Wright, Robert O, Téllez-Rojo, Mara M, Svensson, Katherine, Trevisi, Letizia, Kennedy, Elizabeth M, Binder, Elisabeth B, Iurato, Stella, Czamara, Darina, Räikkönen, Katri, Lahti, Jari MT, Pesonen, Anu-Katriina, Kajantie, Eero, Villa, Pia M, Laivuori, Hannele, Hämäläinen, Esa, Park, Hea Jin, Bailey, Lynn B, Parets, Sasha E, Kilaru, Varun, Menon, Ramkumar, Horvath, Steve, Bush, Nicole R, LeWinn, Kaja Z, Tylavsky, Frances A, Conneely, Karen N, and Smith, Alicia K

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Infant Mortality, Clinical Research, Preterm, Low Birth Weight and Health of the Newborn, Perinatal Period - Conditions Originating in Perinatal Period, Pediatric, 4.2 Evaluation of markers and technologies, Detection, screening and diagnosis, Reproductive health and childbirth, Generic health relevance, Adult, Aging, Biomarkers, Birth Weight, CpG Islands, DNA Methylation, Epigenesis, Genetic, Female, Fetal Development, Gestational Age, Humans, Infant, Newborn, Male, Pregnancy, Developmental age, Epigenetic clock, DNA methylation, Preterm birth, Cord blood, Fetus, Blood spot, Biomarker, Medicaid, Socioeconomic status, Birthweight, Environmental Sciences, Information and Computing Sciences, Bioinformatics
Abstract

BackgroundGestational age is often used as a proxy for developmental maturity by clinicians and researchers alike. DNA methylation has previously been shown to be associated with age and has been used to accurately estimate chronological age in children and adults. In the current study, we examine whether DNA methylation in cord blood can be used to estimate gestational age at birth.ResultsWe find that gestational age can be accurately estimated from DNA methylation of neonatal cord blood and blood spot samples. We calculate a DNA methylation gestational age using 148 CpG sites selected through elastic net regression in six training datasets. We evaluate predictive accuracy in nine testing datasets and find that the accuracy of the DNA methylation gestational age is consistent with that of gestational age estimates based on established methods, such as ultrasound. We also find that an increased DNA methylation gestational age relative to clinical gestational age is associated with birthweight independent of gestational age, sex, and ancestry.ConclusionsDNA methylation can be used to accurately estimate gestational age at or near birth and may provide additional information relevant to developmental stage. Further studies of this predictor are warranted to determine its utility in clinical settings and for research purposes. When clinical estimates are available this measure may increase accuracy in the testing of hypotheses related to developmental age and other early life circumstances.

Published
2016

35. The transcriptional landscape of age in human peripheral blood.

Author

Peters, Marjolein J, Joehanes, Roby, Pilling, Luke C, Schurmann, Claudia, Conneely, Karen N, Powell, Joseph, Reinmaa, Eva, Sutphin, George L, Zhernakova, Alexandra, Schramm, Katharina, Wilson, Yana A, Kobes, Sayuko, Tukiainen, Taru, NABEC/UKBEC Consortium, Ramos, Yolande F, Göring, Harald HH, Fornage, Myriam, Liu, Yongmei, Gharib, Sina A, Stranger, Barbara E, De Jager, Philip L, Aviv, Abraham, Levy, Daniel, Murabito, Joanne M, Munson, Peter J, Huan, Tianxiao, Hofman, Albert, Uitterlinden, André G, Rivadeneira, Fernando, van Rooij, Jeroen, Stolk, Lisette, Broer, Linda, Verbiest, Michael MPJ, Jhamai, Mila, Arp, Pascal, Metspalu, Andres, Tserel, Liina, Milani, Lili, Samani, Nilesh J, Peterson, Pärt, Kasela, Silva, Codd, Veryan, Peters, Annette, Ward-Caviness, Cavin K, Herder, Christian, Waldenberger, Melanie, Roden, Michael, Singmann, Paula, Zeilinger, Sonja, Illig, Thomas, Homuth, Georg, Grabe, Hans-Jörgen, Völzke, Henry, Steil, Leif, Kocher, Thomas, Murray, Anna, Melzer, David, Yaghootkar, Hanieh, Bandinelli, Stefania, Moses, Eric K, Kent, Jack W, Curran, Joanne E, Johnson, Matthew P, Williams-Blangero, Sarah, Westra, Harm-Jan, McRae, Allan F, Smith, Jennifer A, Kardia, Sharon LR, Hovatta, Iiris, Perola, Markus, Ripatti, Samuli, Salomaa, Veikko, Henders, Anjali K, Martin, Nicholas G, Smith, Alicia K, Mehta, Divya, Binder, Elisabeth B, Nylocks, K Maria, Kennedy, Elizabeth M, Klengel, Torsten, Ding, Jingzhong, Suchy-Dicey, Astrid M, Enquobahrie, Daniel A, Brody, Jennifer, Rotter, Jerome I, Chen, Yii-Der I, Houwing-Duistermaat, Jeanine, Kloppenburg, Margreet, Slagboom, P Eline, Helmer, Quinta, den Hollander, Wouter, Bean, Shannon, Raj, Towfique, Bakhshi, Noman, Wang, Qiao Ping, Oyston, Lisa J, Psaty, Bruce M, Tracy, Russell P, Montgomery, Grant W, and Turner, Stephen T

Subjects
NABEC/UKBEC Consortium, Humans, Gene Expression Profiling, DNA Methylation, Aging, European Continental Ancestry Group, Transcriptome, Biomarkers
Abstract

Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the 'transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts.

Published
2015

36. Snowmass Computing Frontier: Software Development, Staffing and Training

Author

Brown, David, Elmer, Peter, Pordes, Ruth, Asner, David, Dubois-Felsmann, Gregory, Elvira, V. Daniel, Hatcher, Robert, Jones, Chris, Kutschke, Robert, Lange, David, Sexton-Kennedy, Elizabeth, and Tull, Craig

Subjects
Physics - Computational Physics, High Energy Physics - Experiment
Abstract

Report of the Snowmass CpF-I4 subgroup on Software Development, Staffing and Training

Published
2013

38. Methylome-wide association study provides evidence of particulate matter air pollution-associated DNA methylation

Author

Gondalia, Rahul, Baldassari, Antoine, Holliday, Katelyn M., Justice, Anne E., Méndez-Giráldez, Raúl, Stewart, James D., Liao, Duanping, Yanosky, Jeff D., Brennan, Kasey J.M., Engel, Stephanie M., Jordahl, Kristina M., Kennedy, Elizabeth, Ward-Caviness, Cavin K., Wolf, Kathrin, Waldenberger, Melanie, Cyrys, Josef, Peters, Annette, Bhatti, Parveen, Horvath, Steve, Assimes, Themistocles L., Pankow, James S., Demerath, Ellen W., Guan, Weihua, Fornage, Myriam, Bressler, Jan, North, Kari E., Conneely, Karen N., Li, Yun, Hou, Lifang, Baccarelli, Andrea A., and Whitsel, Eric A.

Published
2019
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40. El Salvador in Motion: Socioeconomic Causes of Child Migration

Author

Kennedy, Elizabeth Gail

Subjects
Demography, Social research, Latin American studies, Childhood Adolescence and Family, Development, El Salvador, Human rights, Migration, Violence
Abstract

For four decades now, there has been no consensus on the number of Salvadorans living outside of El Salvador, despite El Salvador’s census bureau identifying it in 2008 as the most important factor in determining true population growth in the country. Amidst a time of increasing migrant child and family arrivals from El Salvador to the United States in the 2010s, meaning the country had among the highest rates of emigration in the world, I wanted to speak with children themselves about why they were leaving, and in so doing, speak to the policy and practice needed at different places and times according to the geography, gender and causes children provided. From January to September 2014, Karla Castillo and I conducted just short of 600 interviews with 232 girls, 417 boys and their adult relatives who were deported from Mexico, over 90 percent of whom wanted to reach the United States. In El Salvador, children and their families lived in at least 411 neighborhoods of 155 municipalities in all 14 departments of the country. From each department, we interviewed between 15 and 34 percent of the children who migrated in 2014. For this dissertation, I analyzed the combined results for five departments – Ahuachapán, Chalatenango, Cuscatlán, Morazán and Sonsonate – on two of children’s explicit reasons for migrating (poverty and health) and reasons that children and adolescents did not explicitly give that nonetheless seemed to play a role in their decisions – or would have entitled them to legal status, if they reached the United States. Beyond the interviews conducted with children and families, I sought different sources regarding reasons to migrate, in order to validate the data collected, which are presented alongside the interview data. This includes Salvadoran and US census bureau data, in addition to historical documents on the civil war when poor communities organized to demand that their rights be respected. They wanted their own land to farm, healthcare and education for themselves and their children, a dignified life and so much more. They disproportionately fought in the war and lost their lives or became displaced. Yet, they were least served by the war, and in many ways today find themselves in similar or worse situations than in the pre-war and war periods today. Silber (2011) argues that for this reason, having seen that war did not serve their revolutionary goals, migration has become the home of revolutionary imagination and hope for the poor, who disproportionately constituted the children we interviewed. From there, I inspect the contours of poverty in their lives to unpack them in light of the Capabilities Approach. I explore how their hopes to get out of poverty had even more to do with the desire to be able to become, if not fully themselves, at least more of themselves than El Salvador’s lowest class structure permits. This study is the first of its kind in several ways: it interviewed a representative sample of Salvadoran child migrants, crossed those interviews with quantitative and qualitative data sets and provides geographic and gendered insights to both children’s and families’ migration. As such, the proposed project is critical to better research on migration worldwide and creating holistic and informed policy and practice for child, adult and family migrants at local, national, regional and global levels.

Published
2022

41. Cervical screening participation and access facilitators and barriers for people with intellectual disability: a systematic review and meta-analysis.

Author

Power, Rosalie, David, Michael, Strnadová, Iva, Touyz, Lauren, Basckin, Caroline, Loblinzk, Julie, Jolly, Heather, Kennedy, Elizabeth, Ussher, Jane, Sweeney, Sally, Ee-Lin Chang, Carter, Allison, and Bateson, Deborah

Subjects
EARLY detection of cancer, PEOPLE with intellectual disabilities, INTELLECTUAL disabilities, CINAHL database, SCREEN time
Abstract

Background: The World Health Organisation's vision of eliminating cervical cancer as a public health problem is achievable, but elimination must be achieved equitably, including for people with intellectual disability. A better understanding of cervical screening within the context of the lives of people with intellectual disability is needed. This study systematically reviewed research on the rates of cervical screening participation among people with intellectual disability, and facilitators and barriers that affect participation. Method: Six electronic databases were systematically searched: MEDLINE, CINAHL, Scopus, PsycINFO, Embase and Pro-Quest Central Social Sciences Collection. Empirical studies published between 1986 and 2023, in English language peer-reviewed journals were eligible for inclusion. Further articles were identified through forward and backward citation tracking, and hand-searching the index lists of two key journals. Two authors screened the studies, extracted the data and collated study outcomes using a standardised software program. Ametaanalysis was performed using the DerSimonian and Laird method to estimate pooled effect sizes in prevalence rates and odds ratios (ORs). The socio-ecological model (SEM) was used as a framework to thematically analyse facilitators and barriers impacting participation in cervical screening. Results: Sixty-three articles met the inclusion criteria. Of these, 42 reported on rates of cervical screening participation and 24 reported on facilitators or barriers to cervical screening for people with intellectual disability. Overall, the studies reported a screening prevalence of 35% (95% CI: 26% to 45%), indicating that just over a third of people with intellectual disability have had cervical screening. The pooled odds ratio of 0.30 (95% CI: 0.23 to 0.41) indicated that people with intellectual disability are significantly less likely to have a cervical screening test compared with people without intellectual disability. Most studies examined individual and interpersonal factors impacting cervical screening. These included: (i) fear and anxiety among people with intellectual disability, (ii) misassumptions preventing screening participation, (iii) the role of support people, (iv) the need for education, (v) accessible information, and time to prepare for screening, (vi) patient-provider communication including challenges obtaining informed consent, and (vii) healthcare provider lack of confidence. Conclusion: Future research, policy and practice efforts must address barriers to cervical screening participation among people with intellectual disability and ensure these efforts are co-produced and community-led. This is critical to ensuring equity in global and local efforts to eliminate cervical cancer. [ABSTRACT FROM AUTHOR]

Published
2024
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47. Amber inclusions from New Zealand

Author

Schmidt, Alexander R., Kaulfuss, Uwe, Bannister, Jennifer M., Baranov, Viktor, Beimforde, Christina, Bleile, Natalie, Borkent, Art, Busch, Ariane, Conran, John G., Engel, Michael S., Harvey, Mark, Kennedy, Elizabeth M., Kerr, Peter H., Kettunen, Elina, Kiecksee, Anna Philie, Lengeling, Franziska, Lindqvist, Jon K., Maraun, Mark, Mildenhall, Dallas C., Perrichot, Vincent, Rikkinen, Jouko, Sadowski, Eva-Maria, Seyfullah, Leyla J., Stebner, Frauke, Szwedo, Jacek, Ulbrich, Philipp, and Lee, Daphne E.

Published
2018
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48. Commissioning the CDF Offline Software

Author

Sexton-Kennedy, Elizabeth and Murat, Pasha

Subjects
Physics - Computational Physics, Physics - Accelerator Physics
Abstract

CDF II is one of the two large collider experiments at Fermilab's Tevatron. Over the past two years we have commissioned the offline computing system. A task that has involved bringing up hundreds of computers and millions of lines of C++ software. This paper reports on this experience, concentrating on the software aspects of the project. We will highlight some of the successes as well as describe some of the work still to do., Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 2 pages, no figures PSN THJT001

Published
2003

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