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2. A projection method for particle resampling

Author

Adams, Mark F., Finn, Daniel S., Knepley, Matthew G., and Pusztay, Joseph V.

Subjects
Physics - Plasma Physics, Physics - Computational Physics
Abstract

Particle discretizations of partial differential equations are advantageous for high-dimensional kinetic models in phase space due to their better scalability than continuum approaches with respect to dimension. Complex processes collectively referred to as \textit{particle noise} hamper long-time simulations with particle methods. One approach to address this problem is particle mesh adaptivity or remapping, known as \textit{particle resampling}. This paper introduces a resampling method that projects particles to and from a (finite element) function space. The method is simple; using standard sparse linear algebra and finite element techniques, it can adapt to almost any set of new particle locations and preserves all moments up to the order of polynomial represented exactly by the continuum function space. This work is motivated by the Vlasov-Maxwell-Landau model of magnetized plasmas with up to six dimensions, $3X$ in physical space and $3V$ in velocity space, and is developed in the context of a $1X$ + $1V$ Vlasov-Poisson model of Landau damping with logically regular particle and continuum phase space grids. The evaluation codes are publicly available, along with the data and reproducibility artifacts, and developed in the PETSc numerical library (petsc.org).

Published
2025

3. Improving Robustness of Spectrogram Classifiers with Neural Stochastic Differential Equations

Author

Brogan, Joel, Kotevska, Olivera, Torres, Anibely, Jha, Sumit, and Adams, Mark

Subjects
Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Computer Science - Computer Vision and Pattern Recognition
Abstract

Signal analysis and classification is fraught with high levels of noise and perturbation. Computer-vision-based deep learning models applied to spectrograms have proven useful in the field of signal classification and detection; however, these methods aren't designed to handle the low signal-to-noise ratios inherent within non-vision signal processing tasks. While they are powerful, they are currently not the method of choice in the inherently noisy and dynamic critical infrastructure domain, such as smart-grid sensing, anomaly detection, and non-intrusive load monitoring.

Published
2024

4. PETSc/TAO Developments for GPU-Based Early Exascale Systems

Author

Mills, Richard Tran, Adams, Mark, Balay, Satish, Brown, Jed, Faibussowitsch, Jacob, Isaac, Toby, Knepley, Matthew, Munson, Todd, Suh, Hansol, Zampini, Stefano, Zhang, Hong, and Zhang, Junchao

Subjects
Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, 00A69
Abstract

The Portable Extensible Toolkit for Scientific Computation (PETSc) library provides scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization via the Toolkit for Advanced Optimization (TAO). PETSc is used in dozens of scientific fields and is an important building block for many simulation codes. During the U.S. Department of Energy's Exascale Computing Project, the PETSc team has made substantial efforts to enable efficient utilization of the massive fine-grain parallelism present within exascale compute nodes and to enable performance portability across exascale architectures. We recap some of the challenges that designers of numerical libraries face in such an endeavor, and then discuss the many developments we have made, which include the addition of new GPU backends, features supporting efficient on-device matrix assembly, better support for asynchronicity and GPU kernel concurrency, and new communication infrastructure. We evaluate the performance of these developments on some pre-exascale systems as well the early exascale systems Frontier and Aurora, using compute kernel, communication layer, solver, and mini-application benchmark studies, and then close with a few observations drawn from our experiences on the tension between portable performance and other goals of numerical libraries., Comment: 17 pages

Published
2024

6. Characterization of Collaborative Cross mouse founder strain CAST/EiJ as a novel model for lethal COVID-19

Author

Baker, Candice N., Duso, Debra, Kothapalli, Nagarama, Hart, Tricia, Casey, Sean, Cookenham, Tres, Kummer, Larry, Hvizdos, Janine, Lanzer, Kathleen, Vats, Purva, Shanbhag, Priya, Bell, Isaac, Tighe, Mike, Travis, Kelsey, Szaba, Frank, Harder, Jeffrey M., Bedard, Olivia, Oberding, Natalie, Ward, Jerrold M., Adams, Mark D., Lutz, Cathleen, Bradrick, Shelton S., Reiley, William W., and Rosenthal, Nadia A.

Published
2024
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11. Comparison of Information Technology Professionals' Perception of Job Satisfaction and Inclusion by Gender: Insights for Recruitment and Retention of Female Students

Author

Schultz, Leah and Adams, Mark

Abstract

This paper examines responses to questions about job satisfaction and inclusion from professionals in the information technology field. Responses from over 10,000 professionals were analyzed to determine if there were differences in response to these questions based on gender of respondent. This information, along with previous research on inclusion of women in higher education and industry, are discussed to determine similarities with previous research. Results from the study are used to suggest ways that educators can use the responses to improve recruitment and retention of females in technology majors and minors.

Published
2022

12. Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference.

Author

Meng, Xiangrui, Navoly, Georgina, Giannakopoulou, Olga, Levey, Daniel, Koller, Dora, Pathak, Gita, Koen, Nastassja, Lin, Kuang, Adams, Mark, Rentería, Miguel, Feng, Yanzhe, Gaziano, J, Stein, Dan, Zar, Heather, Campbell, Megan, van Heel, David, Trivedi, Bhavi, Finer, Sarah, McQuillin, Andrew, Bass, Nick, Chundru, V, Martin, Hilary, Huang, Qin, Valkovskaya, Maria, Chu, Chia-Yi, Kanjira, Susan, Kuo, Po-Hsiu, Chen, Hsi-Chung, Tsai, Shih-Jen, Liu, Yu-Li, Kendler, Kenneth, Peterson, Roseann, Cai, Na, Fang, Yu, Sen, Srijan, Scott, Laura, Burmeister, Margit, Loos, Ruth, Preuss, Michael, Actkins, KyEra, Davis, Lea, Uddin, Monica, Wani, Agaz, Wildman, Derek, Aiello, Allison, Ursano, Robert, Kessler, Ronald, Kanai, Masahiro, Okada, Yukinori, Sakaue, Saori, Rabinowitz, Jill, Maher, Brion, Uhl, George, Eaton, William, Cruz-Fuentes, Carlos, Martinez-Levy, Gabriela, Campos, Adrian, Millwood, Iona, Chen, Zhengming, Li, Liming, Wassertheil-Smoller, Sylvia, Jiang, Yunxuan, Tian, Chao, Martin, Nicholas, Mitchell, Brittany, Byrne, Enda, Awasthi, Swapnil, Coleman, Jonathan, Ripke, Stephan, Sofer, Tamar, Walters, Robin, McIntosh, Andrew, Polimanti, Renato, Dunn, Erin, Stein, Murray, Gelernter, Joel, Lewis, Cathryn, and Kuchenbaecker, Karoline

Subjects
Humans, Genome-Wide Association Study, Genetic Predisposition to Disease, Depressive Disorder, Major, Depression, Chromosome Mapping, Polymorphism, Single Nucleotide
Abstract

Most genome-wide association studies (GWAS) of major depression (MD) have been conducted in samples of European ancestry. Here we report a multi-ancestry GWAS of MD, adding data from 21 cohorts with 88,316 MD cases and 902,757 controls to previously reported data. This analysis used a range of measures to define MD and included samples of African (36% of effective sample size), East Asian (26%) and South Asian (6%) ancestry and Hispanic/Latin American participants (32%). The multi-ancestry GWAS identified 53 significantly associated novel loci. For loci from GWAS in European ancestry samples, fewer than expected were transferable to other ancestry groups. Fine mapping benefited from additional sample diversity. A transcriptome-wide association study identified 205 significantly associated novel genes. These findings suggest that, for MD, increasing ancestral and global diversity in genetic studies may be particularly important to ensure discovery of core genes and inform about transferability of findings.

Published
2024

15. Safe, Seamless, And Scalable Integration Of Asynchronous GPU Streams In PETSc

Author

Faibussowitsch, Jacob, Adams, Mark F., Mills, Richard Tran, Zampini, Stefano, and Zhang, Junchao

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Computer Science - Performance, Computer Science - Software Engineering
Abstract

Leveraging Graphics Processing Units (GPUs) to accelerate scientific software has proven to be highly successful, but in order to extract more performance, GPU programmers must overcome the high latency costs associated with their use. One method of reducing or hiding this latency cost is to use asynchronous streams to issue commands to the GPU. While performant, the streams model is an invasive abstraction, and has therefore proven difficult to integrate into general-purpose libraries. In this work, we enumerate the difficulties specific to library authors in adopting streams, and present recent work on addressing them. Finally, we present a unified asynchronous programming model for use in the Portable, Extensible, Toolkit for Scientific Computation (PETSc) to overcome these challenges. The new model shows broad performance benefits while remaining ergonomic to the user.

Published
2023

16. The Landau Collision Integral in the Particle Basis in the PETSc Library

Author

Pusztay, Joseph, Zonta, Filippo, Knepley, Matt, and Adams, Mark

Subjects
Physics - Plasma Physics
Abstract

The Landau collision integral is often considered the gold standard in the context of kinetic plasma simulation due to its conservative properties, despite challenges involved in its discretization. The primary challenge when implementing an efficient computation of this operator is conserving physical properties of the continuum equation when the system is discretized. Recent work has achieved continuum discretizations using the method of Finite Elements which maintain conservation of mass, momentum, and energy, but which lacks monotonic entropy production. More recently, a particle discretization has been introduced which conserves mass, momentum, and energy, but maintains the benefit of monotonic entropy production necessary for the metriplecticity of the system. We present here an implementation of the particle basis Landau collision integral in the Portable Extensible Toolkit for Scientific Computing in 2 and 3V for the construction of a full geometry solver with a novel approach to computation of the entropy functional gradients. Verification of the operator is achieved with thermal equilibration and isotropization tests. All examples are available, open source, in the PETSc repository for reproduction.

Published
2023

17. GWAS Meta-Analysis of Suicide Attempt: Identification of 12 Genome-Wide Significant Loci and Implication of Genetic Risks for Specific Health Factors.

Author

Docherty, Anna, Mullins, Niamh, Ashley-Koch, Allison, Qin, Xuejun, Coleman, Jonathan, Shabalin, Andrey, Kang, JooEun, Murnyak, Balasz, Wendt, Frank, Adams, Mark, Campos, Adrian, DiBlasi, Emily, Fullerton, Janice, Kranzler, Henry, Bakian, Amanda, Monson, Eric, Rentería, Miguel, Walss-Bass, Consuelo, Andreassen, Ole, Behera, Chittaranjan, Bulik, Cynthia, Edenberg, Howard, Kessler, Ronald, Mann, J, Nurnberger, John, Pistis, Giorgio, Streit, Fabian, Ursano, Robert, Polimanti, Renato, Dennis, Michelle, Garrett, Melanie, Hair, Lauren, Harvey, Philip, Hauser, Elizabeth, Hauser, Michael, Huffman, Jennifer, Jacobson, Daniel, Madduri, Ravi, McMahon, Benjamin, Oslin, David, Trafton, Jodie, Awasthi, Swapnil, Berrettini, Wade, Bohus, Martin, Chang, Xiao, Chen, Hsi-Chung, Chen, Wei, Christensen, Erik, Crow, Scott, Duriez, Philibert, Edwards, Alexis, Fernández-Aranda, Fernando, Galfalvy, Hanga, Gandal, Michael, Gorwood, Philip, Guo, Yiran, Hafferty, Jonathan, Hakonarson, Hakon, Halmi, Katherine, Hishimoto, Akitoyo, Jain, Sonia, Jamain, Stéphane, Jiménez-Murcia, Susana, Johnson, Craig, Kaplan, Allan, Kaye, Walter, Keel, Pamela, Kennedy, James, Kim, Minsoo, Klump, Kelly, Levey, Daniel, Li, Dong, Liao, Shih-Cheng, Lieb, Klaus, Lilenfeld, Lisa, Marshall, Christian, Mitchell, James, Okazaki, Satoshi, Otsuka, Ikuo, Pinto, Dalila, Powers, Abigail, Ramoz, Nicolas, Ripke, Stephan, Roepke, Stefan, Rozanov, Vsevolod, Scherer, Stephen, Schmahl, Christian, Sokolowski, Marcus, Starnawska, Anna, Strober, Michael, Su, Mei-Hsin, Thornton, Laura, Treasure, Janet, Ware, Erin, Watson, Hunna, Witt, Stephanie, Woodside, D, Yilmaz, Zeynep, Zillich, Lea, and Adolfsson, Rolf

Subjects
Biological Markers, Depressive Disorders, Genetics, Schizophrenia Spectrum and Other Psychotic Disorders, Self-Harm, Suicide, Humans, Genome-Wide Association Study, Suicide, Attempted, Depressive Disorder, Major, Risk Factors, Suicidal Ideation, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease, Genetic Loci
Abstract

OBJECTIVE: Suicidal behavior is heritable and is a major cause of death worldwide. Two large-scale genome-wide association studies (GWASs) recently discovered and cross-validated genome-wide significant (GWS) loci for suicide attempt (SA). The present study leveraged the genetic cohorts from both studies to conduct the largest GWAS meta-analysis of SA to date. Multi-ancestry and admixture-specific meta-analyses were conducted within groups of significant African, East Asian, and European ancestry admixtures. METHODS: This study comprised 22 cohorts, including 43,871 SA cases and 915,025 ancestry-matched controls. Analytical methods across multi-ancestry and individual ancestry admixtures included inverse variance-weighted fixed-effects meta-analyses, followed by gene, gene-set, tissue-set, and drug-target enrichment, as well as summary-data-based Mendelian randomization with brain expression quantitative trait loci data, phenome-wide genetic correlation, and genetic causal proportion analyses. RESULTS: Multi-ancestry and European ancestry admixture GWAS meta-analyses identified 12 risk loci at p values

Published
2023

18. A Numerical Study of Landau Damping with PETSc-PIC

Author

Finn, Daniel S., Knepley, Matthew G., Pusztay, Joseph V., and Adams, Mark F.

Subjects
Physics - Plasma Physics, Computer Science - Computational Engineering, Finance, and Science
Abstract

We present a study of the standard plasma physics test, Landau damping, using the Particle-In-Cell (PIC) algorithm. The Landau damping phenomenon consists of the damping of small oscillations in plasmas without collisions. In the PIC method, a hybrid discretization is constructed with a grid of finitely supported basis functions to represent the electric, magnetic and/or gravitational fields, and a distribution of delta functions to represent the particle field. Approximations to the dispersion relation are found to be inadequate in accurately calculating values for the electric field frequency and damping rate when parameters of the physical system, such as the plasma frequency or thermal velocity, are varied. We present a full derivation and numerical solution for the dispersion relation, and verify the PETSC-PIC numerical solutions to the Vlasov-Poisson for a large range of wave numbers and charge densities., Comment: 14 pages, 7 figures

Published
2023

20. A bespoke multigrid approach for magnetohydrodynamics models of magnetized plasmas in PETSc

Author

Adams, Mark F. and Knepley, Matthew K.

Subjects
Physics - Plasma Physics, Physics - Computational Physics
Abstract

Fully realizing the potential of multigrid solvers often requires custom algorithms for a given application model, discretizations and even regimes of interest, despite considerable effort from the applied math community to develop fully algebraic multigrid (AMG) methods for almost 40 years. Classic geometric multigrid (GMG) has been effectively applied to challenging, non-elliptic problems in engineering and scientifically relevant codes, but application specific algorithms are generally required that do not lend themselves to deployment in numerical libraries. However, tools in libraries that support discretizations, distributed mesh management and high performance computing (HPC) can be used to develop such solvers. This report develops a magnetohydrodynamics (MHD) code in PETSc (Portable Extensible Toolkit for Scientific computing) with a fully integrated GMG solver that is designed to demonstrate the potential of our approach to providing fast and robust solvers for production applications. These applications must, however, be able to provide, in addition to the Jacobian matrix and residual of a pure AMG solver, a hierarchy of meshes and knowledge of the application's equations and discretization. An example of a 2D, two field reduced resistive MHD model, using existing tools in PETSc that is verified with a ``tilt" instability problem that is well documented in the literature is presented and is an example in the PETSc repository (\path{src/ts/tutorials/ex48.c}). Preliminary CPU-only performance data demonstrates that the solver can be robust and scalable for the model problem that is pushed into a regime with highly localized current sheets, which generates strong, localized non-linearity, that is a challenge for iterative solvers.

Published
2023

21. Inhibition of Aurora B kinase (AURKB) enhances the effectiveness of 5-fluorouracil chemotherapy against colorectal cancer cells

Author

Shah, Esha T., Molloy, Christopher, Gough, Madeline, Kryza, Thomas, Samuel, Selwin G., Tucker, Amos, Bhatia, Maneet, Ferguson, Genevieve, Heyman, Rebecca, Vora, Shivam, Monkman, James, Bolderson, Emma, Kulasinghe, Arutha, He, Yaowu, Gabrielli, Brian, Hooper, John D., Richard, Derek J., O’Byrne, Kenneth J., and Adams, Mark N.

Published
2024
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23. A performance portable, fully implicit Landau collision operator with batched linear solvers

Author

Adams, Mark F., Wang, Peng, Merson, Jacob, Huck, Kevin, and Knepley, Matthew G.

Subjects
Physics - Plasma Physics
Abstract

Modern accelerators use hierarchical parallel programming models that enable massive multithreading within a processing element (PE), with multiple PEs per device driven by traditional processes. Batching is a technique for exposing PE-level parallelism in algorithms that have traditionally run on MPI processes or multiple threads within a single process. Opportunities for batching arise in, for example, kinetic discretizations of magnetized plasmas where collisions are advanced in velocity space at each spatial point independently. This paper builds on previous work on a high-performance, fully nonlinear, Landau collision operator by batching the linear solver, as well as batching the spatial point problems and adding new support for multiple grids for multiscale, multi-species problems. An anisotropic relaxation verification test that agrees well with previous published results and analytical models is presented. The performance results from NVIDIA A100 and AMD MI250X nodes are presented with hardware utilization analysis for each architecture. The entire implicit Landau operator time advance is implemented in Kokkos for performance portability, running entirely on the device and is available in the PETSc numerical library.

Published
2022

24. Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies

Author

Adams, Mark J., Streit, Fabian, Meng, Xiangrui, Awasthi, Swapnil, Adey, Brett N., Choi, Karmel W., Chundru, V. Kartik, Coleman, Jonathan R.I., Ferwerda, Bart, Foo, Jerome C., Gerring, Zachary F., Giannakopoulou, Olga, Gupta, Priya, Hall, Alisha S.M., Harder, Arvid, Howard, David M., Hübel, Christopher, Kwong, Alex S.F., Levey, Daniel F., Mitchell, Brittany L., Ni, Guiyan, Ota, Vanessa K., Pain, Oliver, Pathak, Gita A., Schulte, Eva C., Shen, Xueyi, Thorp, Jackson G., Walker, Alicia, Yao, Shuyang, Zeng, Jian, Zvrskovec, Johan, Aarsland, Dag, Actkins, Ky'Era V., Adli, Mazda, Agerbo, Esben, Aichholzer, Mareike, Aiello, Allison, Air, Tracy M., Als, Thomas D., Andersson, Evelyn, Andlauer, Till F.M., Arolt, Volker, Ask, Helga, Bäckman, Julia, Badola, Sunita, Ballard, Clive, Banasik, Karina, Bass, Nicholas J., Beekman, Aartjan T.F., Belangero, Sintia, Bigdeli, Tim B., Binder, Elisabeth B., Bjerkeset, Ottar, Bjornsdottir, Gyda, Børte, Sigrid, Bränn, Emma, Braun, Alice, Brodersen, Thorsten, Brückl, Tanja M., Brunak, Søren, Bruun, Mie T., Burmeister, Margit, Buspavanich, Pichit, Bybjerg-Grauholm, Jonas, Byrne, Enda M., Cai, Jianwen, Campbell, Archie, Campbell, Megan L., Campos, Adrian I., Castelao, Enrique, Cervilla, Jorge, Chaumette, Boris, Chen, Chia-Yen, Chen, Hsi-Chung, Chen, Zhengming, Cichon, Sven, Colodro-Conde, Lucía, Corbett, Anne, Corfield, Elizabeth C., Couvy-Duchesne, Baptiste, Craddock, Nick, Dannlowski, Udo, Davies, Gail, de Geus, E.J.C., Deary, Ian J., Degenhardt, Franziska, Dehghan, Abbas, DePaulo, J. Raymond, Deuschle, Michael, Didriksen, Maria, Dinh, Khoa Manh, Direk, Nese, Djurovic, Srdjan, Docherty, Anna R., Domschke, Katharina, Dowsett, Joseph, Drange, Ole Kristian, Dunn, Erin C., Eaton, William, Einarsson, Gudmundur, Eley, Thalia C., Elsheikh, Samar S.M., Engelmann, Jan, Benros, Michael E., Erikstrup, Christian, Escott-Price, Valentina, Fabbri, Chiara, Fang, Yu, Finer, Sarah, Frank, Josef, Free, Robert C., Gallo, Linda, Gao, He, Gill, Michael, Gilles, Maria, Goes, Fernando S., Gordon, Scott Douglas, Grove, Jakob, Gudbjartsson, Daniel F., Gutierrez, Blanca, Hahn, Tim, Hall, Lynsey S., Hansen, Thomas F., Haraldsson, Magnus, Hartman, Catharina A., Havdahl, Alexandra, Hayward, Caroline, Heilmann-Heimbach, Stefanie, Herms, Stefan, Hickie, Ian B., Hjalgrim, Henrik, Hjerling-Leffler, Jens, Hoffmann, Per, Homuth, Georg, Horn, Carsten, Hottenga, Jouke-Jan, Hougaard, David M., Hovatta, Iiris, Huang, Qin Qin, Hucks, Donald, Huider, Floris, Hunt, Karen A., Ialongo, Nicholas S., Ising, Marcus, Isometsä, Erkki, Jansen, Rick, Jiang, Yunxuan, Jones, Ian, Jones, Lisa A., Jonsson, Lina, Kanai, Masahiro, Karlsson, Robert, Kasper, Siegfried, Kendler, Kenneth S., Kessler, Ronald C., Kloiber, Stefan, Knowles, James A., Koen, Nastassja, Kraft, Julia, Kranzler, Henry R., Krebs, Kristi, Kallak, Theodora Kunovac, Kutalik, Zoltán, Lahtela, Elisa, Lake, Marilyn, Larsen, Margit Hørup, Lenze, Eric J., Lewins, Melissa, Lewis, Glyn, Li, Liming, Lin, Bochao Danae, Lin, Kuang, Lind, Penelope A., Liu, Yu-Li, MacIntyre, Donald J., MacKinnon, Dean F., Maher, Brion S., Maier, Wolfgang, Marshe, Victoria S., Martinez-Levy, Gabriela A., Matsuda, Koichi, Mbarek, Hamdi, McGuffin, Peter, Medland, Sarah E., Meinert, Susanne, Mikkelsen, Christina, Mikkelsen, Susan, Milaneschi, Yuri, Millwood, Iona Y., Molina, Esther, Mondimore, Francis M., Mortensen, Preben Bo, Mulsant, Benoit H., Naamanka, Joonas, Najman, Jake M., Nauck, Matthias, Nenadić, Igor, Nielsen, Kasper R., Nolt, Ilja M., Nordentoft, Merete, Nöthen, Markus M., Nyegaard, Mette, O'Donovan, Michael C., Oddsson, Asmundur, Oliveira, Adrielle M., Olsen, Catherine M., Oskarsson, Hogni, Ostrowski, Sisse Rye, Owen, Michael J., Packer, Richard, Palviainen, Teemu, Pan, Pedro M., Pato, Carlos N., Pato, Michele T., Pedersen, Nancy L., Pedersen, Ole Birger, Peyrot, Wouter J., Potash, James B., Preisig, Martin, Preuss, Michael H., Quiroz, Jorge A., Renteria, Miguel E., Reynolds III, Charles F., Rice, John P., Sakaue, Saori, Santoro, Marcos L., Schoevers, Robert A., Schork, Andrew, Schulze, Thomas G., Send, Tabea S., Shi, Jianxin, Sigurdsson, Engilbert, Singh, Kritika, Sinnamon, Grant C.B., Sirignano, Lea, Smeland, Olav B., Smith, Daniel J., Sofer, Tamar, Sørensen, Erik, Srinivasan, Sundararajan, Stefansson, Hreinn, Stefansson, Kari, Straub, Peter, Su, Mei-Hsin, Tadic, André, Teismann, Henning, Teumer, Alexander, Thapar, Anita, Thomson, Pippa A., Thørner, Lise Wegner, Topaloudi, Apostolia, Tsai, Shih-Jen, Tzoulaki, Ioanna, Uhl, George, Uitterlinden, André G., Ullum, Henrik, Umbricht, Daniel, Ursano, Robert J., Van der Auwera, Sandra, van Hemert, Albert M., Veluchamy, Abirami, Viktorin, Alexander, Völzke, Henry, Walters, G. Bragi, Wang, Xiaotong, Wani, Agaz, Weissman, Myrna M., Wellmann, Jürgen, Whiteman, David C., Wildman, Derek, Willemsen, Gonneke, Williams, Alexander T., Winsvold, Bendik S., Witt, Stephanie H., Xiong, Ying, Zillich, Lea, Zwart, John-Anker, Twenty-Three and Me Research Team, China Kadoorie Biobank Collaborative Group, Estonian Biobank Research Team, Genes & Health Research Team, HUNT All-In Psychiatry, The BioBank Japan Project, VA Million Veteran Program, Andreassen, Ole A., Baune, Bernhard T., Berger, Klaus, Boomsma, Dorret I., Børglum, Anders D., Breen, Gerome, Cai, Na, Coon, Hilary, Copeland, William E., Creese, Byron, Cruz-Fuentes, Carlos S., Czamara, Darina, Davis, Lea K., Derks, Eske M., Domenici, Enrico, Elliott, Paul, Forstner, Andreas J., Gawlik, Micha, Gelernter, Joel, Grabe, Hans J., Hamilton, Steven P., Hveem, Kristian, John, Catherine, Kaprio, Jaakko, Kircher, Tilo, Krebs, Marie-Odile, Kuo, Po-Hsiu, Landén, Mikael, Lehto, Kelli, Levinson, Douglas F., Li, Qingqin S., Lieb, Klaus, Loos, Ruth J.F., Lu, Yi, Lucae, Susanne, Luykx, Jurjen J., Maes, Hermine H.M., Magnusson, Patrik K., Martin, Hilary C., Martin, Nicholas G., McQuillin, Andrew, Middeldorp, Christel M., Milani, Lili, Mors, Ole, Müller, Daniel J., Müller-Myhsok, Bertram, Okada, Yukinori, Oldehinkel, Albertine J., Paciga, Sara A., Palmer, Colin N.A., Paschou, Peristera, Penninx, Brenda W.J.H., Perlis, Roy H., Peterson, Roseann E., Pistis, Giorgio, Polimanti, Renato, Porteous, David J., Posthuma, Danielle, Rabinowitz, Jill A., Reichborn-Kjennerud, Ted, Reif, Andreas, Rice, Frances, Ricken, Roland, Rietschel, Marcella, Rivera, Margarita, Rück, Christian, Salum, Giovanni A., Schaefer, Catherine, Sen, Srijan, Serretti, Alessandro, Skalkidou, Alkistis, Smoller, Jordan W., Stein, Dan J., Stein, Frederike, Stein, Murray B., Sullivan, Patrick F., Tesli, Martin, Thorgeirsson, Thorgeir E., Tiemeier, Henning, Timpson, Nicholas J., Uddin, Monica, Uher, Rudolf, van Heel, David A., Verweij, Karin J.H., Walters, Robin G., Wassertheil-Smoller, Sylvia, Wendland, Jens R., Werge, Thomas, Zwinderman, Aeilko H., Kuchenbaecker, Karoline, Wray, Naomi R., Ripke, Stephan, Lewis, Cathryn M., and McIntosh, Andrew M.

Published
2025
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26. Conservative Projection Between Finite Element and Particle Bases

Author

Pusztay, Joseph V., Knepley, Matthew G., and Adams, Mark F.

Subjects
Physics - Plasma Physics
Abstract

Particle-in-Cell (PIC) methods employ particle representations of unknown fields, but also employ continuum fields for other parts of the problem. Thus projection between particle and continuum bases is required. Moreover, we often need to enforce conservation constraints on this projection. We derive a mechanism for enforcement based on weak equality, and implement it in the PETSc libraries. Scalability is demonstrated to more than 1B particles.

Published
2022
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28. A duty to intervene?

Author

Adams, Mark, Maj

Subjects
INTERVENTION - Study and Teaching, HUMAN RIGHTS, INTERNATIONAL LAW, SECURITY, INTERNATIONAL, ETHICS
Abstract

illus bibliog

Published
2000

29. The PETSc Community Is the Infrastructure

Author

Adams, Mark, Balay, Satish, Marin, Oana, McInnes, Lois Curfman, Mills, Richard Tran, Munson, Todd, Zhang, Hong, Zhang, Junchao, Brown, Jed, Eijkhout, Victor, Faibussowitsch, Jacob, Knepley, Matthew, Kong, Fande, Kruger, Scott, Sanan, Patrick, and Smith, Barry F.

Subjects
Computer Science - Software Engineering
Abstract

The communities who develop and support open source scientific software packages are crucial to the utility and success of such packages. Moreover, these communities form an important part of the human infrastructure that enables scientific progress. This paper discusses aspects of the PETSc (Portable Extensible Toolkit for Scientific Computation) community, its organization, and technical approaches that enable community members to help each other efficiently.

Published
2022

30. Runway incursions

Author

Adams, Mark T., Maj

Subjects
RUNWAYS - Safety Measures, AIRSTRIPS - Safety Measures, PILOTS - Safety Measures
Abstract

bibliog illus

Published
2008

34. Landau collision operator in the CUDA programming model applied to thermal quench plasmas

Author

Adams, Mark F, Brennan, Dylan P, Knepley, Matthew G, and Wang, Peng

Subjects
Information and Computing Sciences, Applied Computing, Physical Sciences
Abstract

Collisional processes are critical in the understanding of non-Maxwellian plasmas. The Landau form of the Fokker-Planck equation is the gold standard for modeling collisions in most plasmas, however mathcal{O}(N{2}) work complexity inhibits its widespread use. We show that with advanced numerical methods and GPU hardware this cost can be effectively mitigated. This paper extends previous work on a conservative, high order accurate, finite element discretization with adaptive mesh refinement of the Landau operator, with extensions to GPU hardware and implementations in both the CUDA and Kokkos programming languages. This work focuses on the Landau kernels and on NVIDIA hardware, however preliminary results on AMD and Fujitsu/ARM hardware, as well as end-to-end performance of a velocity space model of a plasma thermal quench, are also presented. Both the fully implicit Landau time integrator and the plasma thermal quench model are publicly available in PETSc (Portable, Extensible, Toolkit for Scientific computing).

Published
2022

35. Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Author

Trubetskoy, Vassily, Pardiñas, Antonio F, Qi, Ting, Panagiotaropoulou, Georgia, Awasthi, Swapnil, Bigdeli, Tim B, Bryois, Julien, Chen, Chia-Yen, Dennison, Charlotte A, Hall, Lynsey S, Lam, Max, Watanabe, Kyoko, Frei, Oleksandr, Ge, Tian, Harwood, Janet C, Koopmans, Frank, Magnusson, Sigurdur, Richards, Alexander L, Sidorenko, Julia, Wu, Yang, Zeng, Jian, Grove, Jakob, Kim, Minsoo, Li, Zhiqiang, Voloudakis, Georgios, Zhang, Wen, Adams, Mark, Agartz, Ingrid, Atkinson, Elizabeth G, Agerbo, Esben, Al Eissa, Mariam, Albus, Margot, Alexander, Madeline, Alizadeh, Behrooz Z, Alptekin, Köksal, Als, Thomas D, Amin, Farooq, Arolt, Volker, Arrojo, Manuel, Athanasiu, Lavinia, Azevedo, Maria Helena, Bacanu, Silviu A, Bass, Nicholas J, Begemann, Martin, Belliveau, Richard A, Bene, Judit, Benyamin, Beben, Bergen, Sarah E, Blasi, Giuseppe, Bobes, Julio, Bonassi, Stefano, Braun, Alice, Bressan, Rodrigo Affonseca, Bromet, Evelyn J, Bruggeman, Richard, Buckley, Peter F, Buckner, Randy L, Bybjerg-Grauholm, Jonas, Cahn, Wiepke, Cairns, Murray J, Calkins, Monica E, Carr, Vaughan J, Castle, David, Catts, Stanley V, Chambert, Kimberley D, Chan, Raymond CK, Chaumette, Boris, Cheng, Wei, Cheung, Eric FC, Chong, Siow Ann, Cohen, David, Consoli, Angèle, Cordeiro, Quirino, Costas, Javier, Curtis, Charles, Davidson, Michael, Davis, Kenneth L, de Haan, Lieuwe, Degenhardt, Franziska, DeLisi, Lynn E, Demontis, Ditte, Dickerson, Faith, Dikeos, Dimitris, Dinan, Timothy, Djurovic, Srdjan, Duan, Jubao, Ducci, Giuseppe, Dudbridge, Frank, Eriksson, Johan G, Fañanás, Lourdes, Faraone, Stephen V, Fiorentino, Alessia, Forstner, Andreas, Frank, Josef, Freimer, Nelson B, Fromer, Menachem, Frustaci, Alessandra, Gadelha, Ary, Genovese, Giulio, and Gershon, Elliot S

Subjects
Brain Disorders, Human Genome, Mental Health, Schizophrenia, Serious Mental Illness, Biotechnology, Neurosciences, Genetics, Aetiology, 2.1 Biological and endogenous factors, Alleles, Genetic Predisposition to Disease, Genome-Wide Association Study, Genomics, Humans, Polymorphism, Single Nucleotide, Indonesia Schizophrenia Consortium, PsychENCODE, Psychosis Endophenotypes International Consortium, SynGO Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, General Science & Technology
Abstract

Schizophrenia has a heritability of 60-80%1, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies.

Published
2022

36. Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors.

Author

Mullins, Niamh, Kang, JooEun, Campos, Adrian I, Coleman, Jonathan RI, Edwards, Alexis C, Galfalvy, Hanga, Levey, Daniel F, Lori, Adriana, Shabalin, Andrey, Starnawska, Anna, Su, Mei-Hsin, Watson, Hunna J, Adams, Mark, Awasthi, Swapnil, Gandal, Michael, Hafferty, Jonathan D, Hishimoto, Akitoyo, Kim, Minsoo, Okazaki, Satoshi, Otsuka, Ikuo, Ripke, Stephan, Ware, Erin B, Bergen, Andrew W, Berrettini, Wade H, Bohus, Martin, Brandt, Harry, Chang, Xiao, Chen, Wei J, Chen, Hsi-Chung, Crawford, Steven, Crow, Scott, DiBlasi, Emily, Duriez, Philibert, Fernández-Aranda, Fernando, Fichter, Manfred M, Gallinger, Steven, Glatt, Stephen J, Gorwood, Philip, Guo, Yiran, Hakonarson, Hakon, Halmi, Katherine A, Hwu, Hai-Gwo, Jain, Sonia, Jamain, Stéphane, Jiménez-Murcia, Susana, Johnson, Craig, Kaplan, Allan S, Kaye, Walter H, Keel, Pamela K, Kennedy, James L, Klump, Kelly L, Li, Dong, Liao, Shih-Cheng, Lieb, Klaus, Lilenfeld, Lisa, Liu, Chih-Min, Magistretti, Pierre J, Marshall, Christian R, Mitchell, James E, Monson, Eric T, Myers, Richard M, Pinto, Dalila, Powers, Abigail, Ramoz, Nicolas, Roepke, Stefan, Rozanov, Vsevolod, Scherer, Stephen W, Schmahl, Christian, Sokolowski, Marcus, Strober, Michael, Thornton, Laura M, Treasure, Janet, Tsuang, Ming T, Witt, Stephanie H, Woodside, D Blake, Yilmaz, Zeynep, Zillich, Lea, Adolfsson, Rolf, Agartz, Ingrid, Air, Tracy M, Alda, Martin, Alfredsson, Lars, Andreassen, Ole A, Anjorin, Adebayo, Appadurai, Vivek, Soler Artigas, María, Van der Auwera, Sandra, Azevedo, M Helena, Bass, Nicholas, Bau, Claiton HD, Baune, Bernhard T, Bellivier, Frank, Berger, Klaus, Biernacka, Joanna M, Bigdeli, Tim B, Binder, Elisabeth B, Boehnke, Michael, Boks, Marco P, Bosch, Rosa, and Braff, David L

Subjects
Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Eating Disorders Working Group of the Psychiatric Genomics Consortium, German Borderline Genomics Consortium, MVP Suicide Exemplar Workgroup, VA Million Veteran Program, Humans, Risk Factors, Suicide, Attempted, Mental Disorders, Depressive Disorder, Major, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic correlation, Genome-wide association study, Pleiotropy, Polygenicity, Suicide, Suicide attempt, Human Genome, Behavioral and Social Science, Mental Health, Prevention, Genetics, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

BackgroundSuicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders.MethodsWe conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors.ResultsTwo loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged.ConclusionsOur results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders.

Published
2022

37. The PETSc Community as Infrastructure

Author

Adams, Mark, Balay, Satish, Marin, Oana, McInnes, Lois Curfman, Mills, Richard Tran, Munson, Todd, Zhang, Hong, Zhang, Junchao, Brown, Jed, Eijkhout, Victor, Faibussowitsch, Jacob, Knepley, Matthew, Kong, Fande, Kruger, Scott, Sanan, Patrick, and Smith, Barry F

Subjects
Information and Computing Sciences, Numerical and Computational Mathematics, Computation Theory and Mathematics, Distributed Computing, Fluids & Plasmas, Engineering, Information and computing sciences
Abstract

The communities that develop and support open-source scientific software packages are crucial to the utility and success of such packages. Moreover, they form an important part of the human infrastructure that enables scientific progress. This article discusses aspects of the Portable Extensible Toolkit for Scientific Computation community, its organization, and technical approaches that enable community members to help each other efficiently and effectively.

Published
2022

38. Speech Rhythm Auto-Recurrence is Negatively Linked to Quality of Mental-Health Counseling Interactions

Author

Kempe, Vera, Adams, Mark A., Lovell, George, McLean, Janet F, and Smith, Kate

Subjects
Psychology, Interactive behavior, Corpus studies, Dynamic Systems Modeling
Abstract

We explored use of Recurrence Quantification Analysis (RQA) of speech rhythm data from mental-health counseling sessions for prediction of quality of psychotherapy. Time-series of inter-syllable intervals (ISIs) were extracted from 239 counseling sessions conducted by 12 therapists who repeatedly interacted with 30 clients. We found a negative association between recurrence metrics and client-rated session quality and a negative link between percent of laminarity and therapist-rated session quality, after controlling for self-reported client depression and distress measures and duration of speech sound within a session. Placing value on reduced recurrence in patterns of ISIs, and especially reduced degree of a dyadic system remaining in the same speech-rhythm pattern may be indicative of a desire for variation in content and strategies of client-therapist interaction. These exploratory findings point to the possibility of RQA-based automated systems to capture the ‘footprint’ of the non-verbal dynamic that is indicative of successful mental-health counseling.

Published
2022

39. Toward performance-portable PETSc for GPU-based exascale systems

Author

Mills, Richard Tran, Adams, Mark F, Balay, Satish, Brown, Jed, Dener, Alp, Knepley, Matthew, Kruger, Scott E, Morgan, Hannah, Munson, Todd, Rupp, Karl, Smith, Barry F, Zampini, Stefano, Zhang, Hong, and Zhang, Junchao

Subjects
Information and Computing Sciences, Applied Computing, Distributed Computing, Cognitive Sciences, Distributed computing and systems software
Abstract

The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization. The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. A blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.

Published
2021

40. Characterisation of age and polarity at onset in bipolar disorder.

Author

Kalman, Janos L, Olde Loohuis, Loes M, Vreeker, Annabel, McQuillin, Andrew, Stahl, Eli A, Ruderfer, Douglas, Grigoroiu-Serbanescu, Maria, Panagiotaropoulou, Georgia, Ripke, Stephan, Bigdeli, Tim B, Stein, Frederike, Meller, Tina, Meinert, Susanne, Pelin, Helena, Streit, Fabian, Papiol, Sergi, Adams, Mark J, Adolfsson, Rolf, Adorjan, Kristina, Agartz, Ingrid, Aminoff, Sofie R, Anderson-Schmidt, Heike, Andreassen, Ole A, Ardau, Raffaella, Aubry, Jean-Michel, Balaban, Ceylan, Bass, Nicholas, Baune, Bernhard T, Bellivier, Frank, Benabarre, Antoni, Bengesser, Susanne, Berrettini, Wade H, Boks, Marco P, Bromet, Evelyn J, Brosch, Katharina, Budde, Monika, Byerley, William, Cervantes, Pablo, Chillotti, Catina, Cichon, Sven, Clark, Scott R, Comes, Ashley L, Corvin, Aiden, Coryell, William, Craddock, Nick, Craig, David W, Croarkin, Paul E, Cruceanu, Cristiana, Czerski, Piotr M, Dalkner, Nina, Dannlowski, Udo, Degenhardt, Franziska, Del Zompo, Maria, DePaulo, J Raymond, Djurovic, Srdjan, Edenberg, Howard J, Eissa, Mariam Al, Elvsåshagen, Torbjørn, Etain, Bruno, Fanous, Ayman H, Fellendorf, Frederike, Fiorentino, Alessia, Forstner, Andreas J, Frye, Mark A, Fullerton, Janice M, Gade, Katrin, Garnham, Julie, Gershon, Elliot, Gill, Michael, Goes, Fernando S, Gordon-Smith, Katherine, Grof, Paul, Guzman-Parra, Jose, Hahn, Tim, Hasler, Roland, Heilbronner, Maria, Heilbronner, Urs, Jamain, Stephane, Jimenez, Esther, Jones, Ian, Jones, Lisa, Jonsson, Lina, Kahn, Rene S, Kelsoe, John R, Kennedy, James L, Kircher, Tilo, Kirov, George, Kittel-Schneider, Sarah, Klöhn-Saghatolislam, Farah, Knowles, James A, Kranz, Thorsten M, Lagerberg, Trine Vik, Landen, Mikael, Lawson, William B, Leboyer, Marion, Li, Qingqin S, Maj, Mario, Malaspina, Dolores, Manchia, Mirko, and Mayoral, Fermin

Subjects
Psychiatric Genomics Consortium (PGC) Bipolar Disorder Working Group, International Consortium on Lithium Genetics, Colombia-US Cross Disorder Collaboration in Psychiatric Genetics, Humans, Bipolar Disorder, Depressive Disorder, Major, Age of Onset, Multifactorial Inheritance, Genome-Wide Association Study, Autism Spectrum Disorder, Bipolar disorder, GWAS, age at onset, polarity at onset, polygenic score, Genetics, Mental Health, Prevention, Brain Disorders, Serious Mental Illness, 2.1 Biological and endogenous factors, Aetiology, Mental health, Good Health and Well Being, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

BackgroundStudying phenotypic and genetic characteristics of age at onset (AAO) and polarity at onset (PAO) in bipolar disorder can provide new insights into disease pathology and facilitate the development of screening tools.AimsTo examine the genetic architecture of AAO and PAO and their association with bipolar disorder disease characteristics.MethodGenome-wide association studies (GWASs) and polygenic score (PGS) analyses of AAO (n = 12 977) and PAO (n = 6773) were conducted in patients with bipolar disorder from 34 cohorts and a replication sample (n = 2237). The association of onset with disease characteristics was investigated in two of these cohorts.ResultsEarlier AAO was associated with a higher probability of psychotic symptoms, suicidality, lower educational attainment, not living together and fewer episodes. Depressive onset correlated with suicidality and manic onset correlated with delusions and manic episodes. Systematic differences in AAO between cohorts and continents of origin were observed. This was also reflected in single-nucleotide variant-based heritability estimates, with higher heritabilities for stricter onset definitions. Increased PGS for autism spectrum disorder (β = -0.34 years, s.e. = 0.08), major depression (β = -0.34 years, s.e. = 0.08), schizophrenia (β = -0.39 years, s.e. = 0.08), and educational attainment (β = -0.31 years, s.e. = 0.08) were associated with an earlier AAO. The AAO GWAS identified one significant locus, but this finding did not replicate. Neither GWAS nor PGS analyses yielded significant associations with PAO.ConclusionsAAO and PAO are associated with indicators of bipolar disorder severity. Individuals with an earlier onset show an increased polygenic liability for a broad spectrum of psychiatric traits. Systematic differences in AAO across cohorts, continents and phenotype definitions introduce significant heterogeneity, affecting analyses.

Published
2021

41. Mark Adams

Author

Adams, Mark

Published
2006

42. Toward Performance-Portable PETSc for GPU-based Exascale Systems

Author

Mills, Richard Tran, Adams, Mark F., Balay, Satish, Brown, Jed, Dener, Alp, Knepley, Matthew, Kruger, Scott E., Morgan, Hannah, Munson, Todd, Rupp, Karl, Smith, Barry F., Zampini, Stefano, Zhang, Hong, and Zhang, Junchao

Subjects
Computer Science - Mathematical Software, Computer Science - Distributed, Parallel, and Cluster Computing, 65F10, 65F50, 68N99, 68W10, G.4
Abstract

The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization.The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. A blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems., Comment: 15 pages, 10 figures, 2 tables

Published
2020

50. Polygenic contributions to alcohol use and alcohol use disorders across population-based and clinically ascertained samples

Author

Johnson, Emma C, Sanchez-Roige, Sandra, Acion, Laura, Adams, Mark J, Bucholz, Kathleen K, Chan, Grace, Chao, Michael J, Chorlian, David B, Dick, Danielle M, Edenberg, Howard J, Foroud, Tatiana, Hayward, Caroline, Heron, Jon, Hesselbrock, Victor, Hickman, Matthew, Kendler, Kenneth S, Kinreich, Sivan, Kramer, John, Kuo, Sally I-Chun, Kuperman, Samuel, Lai, Dongbing, McIntosh, Andrew M, Meyers, Jacquelyn L, Plawecki, Martin H, Porjesz, Bernice, Porteous, David, Schuckit, Marc A, Su, Jinni, Zang, Yong, Palmer, Abraham A, Agrawal, Arpana, Clarke, Toni-Kim, and Edwards, Alexis C

Subjects
Biological Psychology, Biomedical and Clinical Sciences, Psychology, Human Genome, Alcoholism, Alcohol Use and Health, Prevention, Genetics, Clinical Research, Substance Misuse, Underage Drinking, Brain Disorders, Behavioral and Social Science, Pediatric, Oral and gastrointestinal, Good Health and Well Being, Alcohol Drinking, Alcoholism, Cohort Studies, Genome-Wide Association Study, Humans, Longitudinal Studies, Phenotype, Scotland, Alcohol consumption, alcohol dependence, alcohol use disorder, AUDIT, genetics, GWAS, polygenic risk score, Neurosciences, Public Health and Health Services, Psychiatry, Clinical sciences, Biological psychology, Clinical and health psychology
Abstract

BackgroundStudies suggest that alcohol consumption and alcohol use disorders have distinct genetic backgrounds.MethodsWe examined whether polygenic risk scores (PRS) for consumption and problem subscales of the Alcohol Use Disorders Identification Test (AUDIT-C, AUDIT-P) in the UK Biobank (UKB; N = 121 630) correlate with alcohol outcomes in four independent samples: an ascertained cohort, the Collaborative Study on the Genetics of Alcoholism (COGA; N = 6850), and population-based cohorts: Avon Longitudinal Study of Parents and Children (ALSPAC; N = 5911), Generation Scotland (GS; N = 17 461), and an independent subset of UKB (N = 245 947). Regression models and survival analyses tested whether the PRS were associated with the alcohol-related outcomes.ResultsIn COGA, AUDIT-P PRS was associated with alcohol dependence, AUD symptom count, maximum drinks (R2 = 0.47-0.68%, p = 2.0 × 10-8-1.0 × 10-10), and increased likelihood of onset of alcohol dependence (hazard ratio = 1.15, p = 4.7 × 10-8); AUDIT-C PRS was not an independent predictor of any phenotype. In ALSPAC, the AUDIT-C PRS was associated with alcohol dependence (R2 = 0.96%, p = 4.8 × 10-6). In GS, AUDIT-C PRS was a better predictor of weekly alcohol use (R2 = 0.27%, p = 5.5 × 10-11), while AUDIT-P PRS was more associated with problem drinking (R2 = 0.40%, p = 9.0 × 10-7). Lastly, AUDIT-P PRS was associated with ICD-based alcohol-related disorders in the UKB subset (R2 = 0.18%, p < 2.0 × 10-16).ConclusionsAUDIT-P PRS was associated with a range of alcohol-related phenotypes across population-based and ascertained cohorts, while AUDIT-C PRS showed less utility in the ascertained cohort. We show that AUDIT-P is genetically correlated with both use and misuse and demonstrate the influence of ascertainment schemes on PRS analyses.

Published
2021

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