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2. Stanley-Reisner Ideals with Pure Resolutions

Author

Carey, David and Katzman, Mordechai

Subjects
Mathematics - Commutative Algebra
Abstract

This paper investgates Stanley-Reisner ideals with pure resolutions. We first describe two infinite families of such ideals associated to highly symmetric complexes. We then prove a partial analogue to the first Boij-S\"oderberg Conjecture for Stanley-Reisner ideals, by detailing an algorithm for constructing Stanley-Reisner ideals with pure Betti diagrams of any given shape, save for an initial shift., Comment: 55 pages

Published
2024

4. Genome-wide association analysis provides insights into the molecular etiology of dilated cardiomyopathy

Author

Zheng, Sean L., Henry, Albert, Cannie, Douglas, Lee, Michael, Miller, David, McGurk, Kathryn A., Bond, Isabelle, Xu, Xiao, Issa, Hanane, Francis, Catherine, De Marvao, Antonio, Theotokis, Pantazis I., Buchan, Rachel J., Speed, Doug, Abner, Erik, Adams, Lance, Aragam, Krishna G., Ärnlöv, Johan, Raja, Anna Axelsson, Backman, Joshua D., Baksi, John, Barton, Paul J. R., Biddinger, Kiran J., Boersma, Eric, Brandimarto, Jeffrey, Brunak, Søren, Bundgaard, Henning, Carey, David J., Charron, Philippe, Cook, James P., Cook, Stuart A., Denaxas, Spiros, Deleuze, Jean-François, Doney, Alexander S., Elliott, Perry, Erikstrup, Christian, Esko, Tõnu, Farber-Eger, Eric H., Finan, Chris, Garnier, Sophie, Ghouse, Jonas, Giedraitis, Vilmantas, Guðbjartsson, Daniel F., Haggerty, Christopher M., Halliday, Brian P., Helgadottir, Anna, Hemingway, Harry, Hillege, Hans L., Kardys, Isabella, Lind, Lars, Lindgren, Cecilia M., Lowery, Brandon D., Manisty, Charlotte, Margulies, Kenneth B., Moon, James C., Mordi, Ify R., Morley, Michael P., Morris, Andrew D., Morris, Andrew P., Morton, Lori, Noursadeghi, Mahdad, Ostrowski, Sisse R., Owens, Anjali T., Palmer, Colin N. A., Pantazis, Antonis, Pedersen, Ole B. V., Prasad, Sanjay K., Shekhar, Akshay, Smelser, Diane T., Srinivasan, Sundararajan, Stefansson, Kari, Sveinbjörnsson, Garðar, Syrris, Petros, Tammesoo, Mari-Liis, Tayal, Upasana, Teder-Laving, Maris, Thorgeirsson, Guðmundur, Thorsteinsdottir, Unnur, Tragante, Vinicius, Trégouët, David-Alexandre, Treibel, Thomas A., Ullum, Henrik, Valdes, Ana M., van Setten, Jessica, van Vugt, Marion, Veluchamy, Abirami, Verschuren, W. M. Monique, Villard, Eric, Yang, Yifan, Asselbergs, Folkert W., Cappola, Thomas P., Dube, Marie-Pierre, Dunn, Michael E., Ellinor, Patrick T., Hingorani, Aroon D., Lang, Chim C., Samani, Nilesh J., Shah, Svati H., Smith, J. Gustav, Vasan, Ramachandran S., O’Regan, Declan P., Holm, Hilma, Noseda, Michela, Wells, Quinn, Ware, James S., and Lumbers, R. Thomas

Published
2024
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6. Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes

Author

Huerta-Chagoya, Alicia, Schroeder, Philip, Mandla, Ravi, Li, Jiang, Morris, Lowri, Vora, Maheak, Alkanaq, Ahmed, Nagy, Dorka, Szczerbinski, Lukasz, Madsen, Jesper G. S., Bonàs-Guarch, Silvia, Mollandin, Fanny, Cole, Joanne B., Porneala, Bianca, Westerman, Kenneth, Li, Josephine H., Pollin, Toni I., Florez, Jose C., Gloyn, Anna L., Carey, David J., Cebola, Inês, Mirshahi, Uyenlinh L., Manning, Alisa K., Leong, Aaron, Udler, Miriam, and Mercader, Josep M.

Published
2024
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8. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis.

Author

Ghouse, Jonas, Sveinbjörnsson, Gardar, Vujkovic, Marijana, Seidelin, Anne-Sofie, Gellert-Kristensen, Helene, Ahlberg, Gustav, Tragante, Vinicius, Rand, Søren, Brancale, Joseph, Vilarinho, Silvia, Lundegaard, Pia, Sørensen, Erik, Erikstrup, Christian, Bruun, Mie, Jensen, Bitten, Brunak, Søren, Banasik, Karina, Ullum, Henrik, Verweij, Niek, Lotta, Luca, Baras, Aris, Mirshahi, Tooraj, Carey, David, Kaplan, David, Lynch, Julie, Morgan, Timothy, Schwantes-An, Tae-Hwi, Dochtermann, Daniel, Pyarajan, Saiju, Tsao, Philip, Laisk, Triin, Mägi, Reedik, Kozlitina, Julia, Tybjærg-Hansen, Anne, Jones, David, Knowlton, Kirk, Nadauld, Lincoln, Ferkingstad, Egil, Björnsson, Einar, Ulfarsson, Magnus, Sturluson, Árni, Sulem, Patrick, Pedersen, Ole, Ostrowski, Sisse, Gudbjartsson, Daniel, Stefansson, Kari, Olesen, Morten, Chang, Kyong-Mi, Holm, Hilma, Bundgaard, Henning, and Stender, Stefan

Subjects
Humans, Liver Cirrhosis, Genome-Wide Association Study, Genetic Predisposition to Disease, Liver Neoplasms, Carcinoma, Hepatocellular, Alanine Transaminase, Polymorphism, Single Nucleotide, Male, Lipase, Female, gamma-Glutamyltransferase, Membrane Proteins, Cohort Studies, Case-Control Studies, Multifactorial Inheritance, Risk Factors, Genetic Variation
Abstract

We report a multi-ancestry genome-wide association study on liver cirrhosis and its associated endophenotypes, alanine aminotransferase (ALT) and γ-glutamyl transferase. Using data from 12 cohorts, including 18,265 cases with cirrhosis, 1,782,047 controls, up to 1 million individuals with liver function tests and a validation cohort of 21,689 cases and 617,729 controls, we identify and validate 14 risk associations for cirrhosis. Many variants are located near genes involved in hepatic lipid metabolism. One of these, PNPLA3 p.Ile148Met, interacts with alcohol intake, obesity and diabetes on the risk of cirrhosis and hepatocellular carcinoma (HCC). We develop a polygenic risk score that associates with the progression from cirrhosis to HCC. By focusing on prioritized genes from common variant analyses, we find that rare coding variants in GPAM associate with lower ALT, supporting GPAM as a potential target for therapeutic inhibition. In conclusion, this study provides insights into the genetic underpinnings of cirrhosis.

Published
2024

9. Genetic risk factors for COVID-19 and influenza are largely distinct

Author

Kosmicki, Jack A., Marcketta, Anthony, Sharma, Deepika, Di Gioia, Silvio Alessandro, Batista, Samantha, Yang, Xiao-Man, Tzoneva, Gannie, Martinez, Hector, Sidore, Carlo, Kessler, Michael D., Horowitz, Julie E., Roberts, Genevieve H. L., Justice, Anne E., Banerjee, Nilanjana, Coignet, Marie V., Leader, Joseph B., Park, Danny S., Lanche, Rouel, Maxwell, Evan, Knight, Spencer C., Bai, Xiaodong, Guturu, Harendra, Baltzell, Asher, Girshick, Ahna R., McCurdy, Shannon R., Partha, Raghavendran, Mansfield, Adam J., Turissini, David A., Zhang, Miao, Mbatchou, Joelle, Watanabe, Kyoko, Verma, Anurag, Sirugo, Giorgio, Ritchie, Marylyn D., Salerno, William J., Shuldiner, Alan R., Rader, Daniel J., Mirshahi, Tooraj, Marchini, Jonathan, Overton, John D., Carey, David J., Habegger, Lukas, Reid, Jeffrey G., Economides, Aris, Kyratsous, Christos, Karalis, Katia, Baum, Alina, Cantor, Michael N., Rand, Kristin A., Hong, Eurie L., Ball, Catherine A., Siminovitch, Katherine, Baras, Aris, Abecasis, Goncalo R., and Ferreira, Manuel A. R.

Published
2024
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10. Betti Cones of Stanley-Reisner Ideals

Author

Carey, David

Subjects
Mathematics - Commutative Algebra
Abstract

The aim of this thesis is to investigate the Betti diagrams of squarefree monomial ideals in polynomial rings. We use two key tools to help us study these diagrams. The first is the Stanley-Reisner Correspondence, which assigns a unique simplicial complex to every squarefree monomial ideal, and thus allows us to compute the Betti diagrams of these ideals from combinatorial properties of their corresponding complexes. As such, most of our work is combinatorial in nature. The second tool is Boij-Soderberg Theory, which views Betti diagrams as vectors in a rational vector space, and investigates them by considering the convex cone they generate. This thesis applies the theory to the cones generated by diagrams of squarefree monomial ideals. We begin by introducing all of these concepts, along with some preliminary results in both algebra and combinatorics. Chapter 3 then presents the dimensions of our cones, along with the vector spaces they span. Chapters 4 and 5 are devoted to the pure Betti diagrams in these cones, and the combinatorial properties of their associated complexes. Finally, Chapter 6 builds on these results to prove a partial analogue of the first Boij-Soderberg conjecture for squarefree monomial ideals, by detailing an algorithm for generating pure Betti diagrams of squarefree monomial ideals of any degree type., Comment: 169 Pages, PhD Thesis

Published
2024

11. Index

Author

Carey, David, Jr.

Published
2013

12. Notes

Author

Carey, David, Jr.

Published
2013

13. Glossary

Author

Carey, David, Jr.

Published
2013

14. Appendices

Author

Carey, David, Jr.

Published
2013

23. Cover

Author

Carey, David, Jr.

Published
2013

27. Foreword

Author

Carey, David, Jr.

Published
2013

29. Increased frequency of CHEK2 germline pathogenic variants among individuals with dermatofibrosarcoma protuberans.

Author

Sargen, Michael, Kim, Jung, Haley, Jeremy, Barker, Hayley, Mundra, Piyushkumar, Ballinger, Mandy, Thomas, David, Carey, David, Goldstein, Allen, and Stewart, Douglas

Subjects
CHEK2, Cancer predisposition, Dermatofibrosarcoma protuberans, Sarcoma, Skin cancer
Abstract

PURPOSE: To identify candidate susceptibility genes for dermatofibrosarcoma protuberans (DFSP). METHODS: All individuals with DFSP from the International Sarcoma Kindred Study (n = 3767 individuals with sarcoma diagnoses from Australia, Europe, New Zealand, and United States) and cohorts that were not ascertained based on sarcoma status or other phenotypes (Geisinger MyCode, n = 170,503 individuals, United States; UK Biobank, n = 469,789 individuals, United Kingdom) were evaluated for germline pathogenic or likely pathogenic (P/LP) variants in 156 cancer genes. RESULTS: There were 92 unrelated individuals with DFSP across the 3 cohorts. The mean age at diagnosis (standard deviation) in the International Sarcoma Kindred Study, Geisinger, and UK Biobank was 40.8 (14.5), 50.3 (9.4), and 49.4 (13.2) years, respectively. Germline P/LP variants were most common in the CHEK2 gene (4/92 [4.3%]). CHEK2-related cases were often associated with early onset disease (age at diagnosis: 30-39 years) and were observed in all 3 cohorts. Among 640,292 individuals in Geisinger and UK Biobank who were not ascertained based on phenotype, there was a significantly increased frequency of CHEK2 P/LP variants among individuals with DFSP (n = 3/65 [4.6%]) compared to those without (n = 6388/640,227 [1.0%]) (Fisher exact, P = .03). Additional genes with P/LP variation (1 case for each gene) included ACD, ERCC5, ERCC1, DOCK8, GBA1, ATM, MUTYH, TP53, RECQL4, and COL7A1. CONCLUSION: This study of multiple cohorts identifies CHEK2 as a candidate susceptibility gene for DFSP. Additional epidemiologic and functional studies are needed to further characterize this potential gene-tumor relationship.

Published
2024

32. Publisher Correction: Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes

Author

Huerta-Chagoya, Alicia, Schroeder, Philip, Mandla, Ravi, Li, Jiang, Morris, Lowri, Vora, Maheak, Alkanaq, Ahmed, Nagy, Dorka, Szczerbinski, Lukasz, Madsen, Jesper G. S., Bonàs-Guarch, Silvia, Mollandin, Fanny, Cole, Joanne B., Porneala, Bianca, Westerman, Kenneth, Li, Josephine H., Pollin, Toni I., Florez, Jose C., Gloyn, Anna L., Carey, David J., Cebola, Inês, Mirshahi, Uyenlinh L., Manning, Alisa K., Leong, Aaron, Udler, Miriam, and Mercader, Josep M.

Published
2024
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42. Student-Athletes’, Coaches’, and Administrators’ Perspectives of Sexual Violence Prevention on Three Campuses with National Collegiate Athletic Association Division I and II Athletic Programs

Author

Carey, David Stoddard, Sumstine, Stephanie, Amabile, Claire, Helvink, Heather, Sorin, Cierra Raine, Swendeman, Dallas, Park, Eunhee, and Wagman, Jennifer A

Subjects
Sociology, Human Society, Clinical Research, Physical Injury - Accidents and Adverse Effects, Prevention, Peace, Justice and Strong Institutions, Athletes, Humans, Sex Offenses, Sports, Students, Universities, reporting, disclosure, support seeking, sexual harassment, prevention, sports, college athlete, sport, satudent resources, reporting/disclosure, Criminology, Social Work, Psychology, Social work, Clinical and health psychology
Abstract

Research has found associations between intercollegiate athletics and risk for sexual violence, and that sexual violence is more pervasive at colleges and universities with National Collegiate Athletic Association (NCAA) Division I athletic programs, relative to NCAA Division II, NCAA Division III and no athletic programs. Simultaneously, sports involvement is linked with prosocial values and there are documented developmental benefits of sports participation. College athletic programs hold promise for fostering sexual violence prevention but there is limited knowledge about how student-athletes conceptualize sexual violence and how athletes, coaches, and administrators perceive available prevention and response programs. We conducted seven Focus Group Discussions (FGDs) and 21 In-Depth Interviews (IDIs) with student-athletes, athletic directors, and coaches from public university Division I (n = 2) and Division II (n = 1) campuses. We assessed perceptions of sexual violence, knowledge and opinions of available prevention and response programs, and sought input on how to bridge gaps in campus sexual violence policies. Student-athletes associated sexual violence with alcohol in their relationships with peers and asymmetrical power dynamics in relationships with coaches and faculty. Athletes felt strong connections with teammates and sports programs but isolated from the larger campus. This created barriers to students' use of services and the likelihood of reporting sexual violence. Athletes felt the mandatory sexual violence prevention training, including additional NCAA components, were ineffective and offered to protect the university and its athletic programs from legal complications or cultural ridicule. Athletic staff were aware of policies and programs for reporting and referring sexual violence cases but their knowledge on how these served students was limited. Student-athletes were uncomfortable disclosing information regarding relationships and sexual violence to coaches and preferred peer-led prevention approaches.

Published
2022

43. Enhancing Trajectory Prediction using Sparse Outputs: Application to Team Sports

Author

Victor, Brandon, Nibali, Aiden, He, Zhen, and Carey, David L.

Subjects
Computer Science - Machine Learning, Statistics - Machine Learning, I.2.6
Abstract

Sophisticated trajectory prediction models that effectively mimic team dynamics have many potential uses for sports coaches, broadcasters and spectators. However, through experiments on soccer data we found that it can be surprisingly challenging to train a deep learning model for player trajectory prediction which outperforms linear extrapolation on average distance between predicted and true future trajectories. We propose and test a novel method for improving training by predicting a sparse trajectory and interpolating using constant acceleration, which improves performance for several models. This interpolation can also be used on models that aren't trained with sparse outputs, and we find that this consistently improves performance for all tested models. Additionally, we find that the accuracy of predicted trajectories for a subset of players can be improved by conditioning on the full trajectories of the other players, and that this is further improved when combined with sparse predictions. We also propose a novel architecture using graph networks and multi-head attention (GraN-MA) which achieves better performance than other tested state-of-the-art models on our dataset and is trivially adapted for both sparse trajectories and full-trajectory conditioned trajectory prediction., Comment: 10 pages (not including references), 7 figures. Published in Neural Computing and Applications on 20 March 2021

Published
2021
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45. Dimensions of Betti Cones on Edge Ideals

Author

Carey, David

Subjects
Mathematics - Commutative Algebra, 13A02 (Primary) 13D02, 05C25 (Secondary)
Abstract

Boij-S\"{o}derberg Theory views the Betti diagrams of graded modules over polynomial rings as vectors in a rational vector space, and studies the cone that these vectors generate (called a 'Betti Cone'). The objects of study in this paper are the Betti cones generated by edge ideals; in particular this paper will present and prove a formula for the dimensions of these cones, and for the subcones generated by edge ideals of specific heights., Comment: 23 pages, 0 figures, 1 table (Replacement article, after small-scale edits)

Published
2021

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