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1. Retrieval Practice and Test-Potentiated Learning: A Comparison of High and Low Prior Topic Knowledge Students in Terms of Procedural Fluency and Conceptual Understanding

Author: Bruce M. May
Abstract: A cohort of pre-service mathematics students was exposed to a teaching strategy based on retrieval practice and test-potentiated learning. The aim of the study was to determine how high and low prior topic knowledge study participants compare in terms of their procedural fluency and conceptual understanding after exposure to the teaching strategy. A pre-test and post-test repeated measures design was employed in the study to compare within groups. A revised taxonomy table based on Bloom's taxonomy was utilised to categorise test items. Findings indicate significant differences between pre-test and post-test scores within groups. Results from the independent samples t-test show a significant difference between the two groups. Outcomes confirm that the benefits of retrieval practice are greatest for unfamiliar content. Findings indicate that for low prior topic knowledge students, procedural fluency is enhanced and retained more than conceptual understanding whereas for the high prior topic knowledge students it was the reverse. The strategy was not as effective for improving conceptual understanding.
Published: 2024

2. Mindfulness in a Digital Math Learning Game: Insights from Two Randomized Controlled Trials

Author: Eniko Orsolya Bereczki, Zsofia K. Takacs, J. Elizabeth Richey, Huy A. Nguyen, Michael Mogessie, and Bruce M. McLaren
Abstract: Background: Mindfulness practices enhance executive function skills and academic achievement, spurring interest in integrating mindfulness interventions into education. Embedding mindfulness practice into a digital math game may provide a low-cost, scalable way to induce mindfulness and boost game-based learning, yet this approach remains unexplored. Objectives: We investigated the learning benefits of integrating mindfulness exercises in a digital math learning game and examined how students' trait mindfulness might moderate the outcomes. Methods: Two classroom studies were conducted with 404 5th and 6th grade students from six public schools in the U.S. (n[subscript Study 1] = 227, n[subscript Study 2] = 177). The two randomized controlled experiments assigned students to one of the three conditions: passive control (playing the digital learning game "Decimal Point"), story-enriched active control, or mindfulness-enriched condition. Trait mindfulness, learning gains, and in-game problem-solving (including problem-solving duration, error count and correctness after reminder) were assessed. Study 2 included a manipulation check to better understand the effects of the mindfulness intervention. Results: Findings showed no significant differences in learning gains, problem-solving duration or error count among the conditions. Students' trait mindfulness did not moderate these outcomes. Mindfulness reminders in the mindfulness-enriched game led to more correct answers after errors than jokes in the story-enriched game. Study 2 revealed that we failed to induce higher state mindfulness through the mindfulness inductions. Conclusions: Mindfulness prompts could be especially beneficial for students experiencing frustration during gameplay, warranting more exploration for digital game-based instruction. We highlight barriers and future directions for fostering mindfulness through computer-based instruction in classrooms.
Published: 2024
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3. On Separation Logic, Computational Independence, and Pseudorandomness (Extended Version)

Author: Lago, Ugo Dal, Davoli, Davide, and Kapron, Bruce M.
Subjects: Computer Science - Cryptography and Security
Abstract: Separation logic is a substructural logic which has proved to have numerous and fruitful applications to the verification of programs working on dynamic data structures. Recently, Barthe, Hsu and Liao have proposed a new way of giving semantics to separation logic formulas in which separating conjunction is interpreted in terms of probabilistic independence. The latter is taken in its exact form, i.e., two events are independent if and only if the joint probability is the product of the probabilities of the two events. There is indeed a literature on weaker notions of independence which are computational in nature, i.e. independence holds only against efficient adversaries and modulo a negligible probability of success. The aim of this work is to explore the nature of computational independence in a cryptographic scenario, in view of the aforementioned advances in separation logic. We show on the one hand that the semantics of separation logic can be adapted so as to account for complexity bounded adversaries, and on the other hand that the obtained logical system is useful for writing simple and compact proofs of standard cryptographic results in which the adversary remains hidden. Remarkably, this allows for a fruitful interplay between independence and pseudorandomness, itself a crucial notion in cryptography., Comment: to be published in CSF'24
Published: 2024

4. Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate

Author: Mack, Taralynn M, Raddatz, Michael A, Pershad, Yash, Nachun, Daniel C, Taylor, Kent D, Guo, Xiuqing, Shuldiner, Alan R, O’Connell, Jeffrey R, Kenny, Eimear E, Loos, Ruth JF, Redline, Susan, Cade, Brian E, Psaty, Bruce M, Bis, Joshua C, Brody, Jennifer A, Silverman, Edwin K, Yun, Jeong H, Cho, Michael H, DeMeo, Dawn L, Levy, Daniel, Johnson, Andrew D, Mathias, Rasika A, Yanek, Lisa R, Heckbert, Susan R, Smith, Nicholas L, Wiggins, Kerri L, Raffield, Laura M, Carson, April P, Rotter, Jerome I, Rich, Stephen S, Manichaikul, Ani W, Gu, C Charles, Chen, Yii-Der Ida, Lee, Wen-Jane, Shoemaker, M Benjamin, Roden, Dan M, Kooperberg, Charles, Auer, Paul L, Desai, Pinkal, Blackwell, Thomas W, Smith, Albert V, Reiner, Alexander P, Jaiswal, Siddhartha, Weinstock, Joshua S, and Bick, Alexander G
Subjects: Biomedical and Clinical Sciences, Clinical Sciences, Hematology, Genetics, Biotechnology, Aging, Human Genome, Stem Cell Research, Precision Medicine, Aetiology, 2.1 Biological and endogenous factors, Cancer, Good Health and Well Being, Clinical sciences
Abstract: Clonal hematopoiesis of indeterminate potential (CHIP), whereby somatic mutations in hematopoietic stem cells confer a selective advantage and drive clonal expansion, not only correlates with age but also confers increased risk of morbidity and mortality. Here, we leverage genetically predicted traits to identify factors that determine CHIP clonal expansion rate. We used the passenger-approximated clonal expansion rate method to quantify the clonal expansion rate for 4,370 individuals in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) cohort and calculated polygenic risk scores for DNA methylation aging, inflammation-related measures and circulating protein levels. Clonal expansion rate was significantly associated with both genetically predicted and measured epigenetic clocks. No associations were identified with inflammation-related lab values or diseases and CHIP expansion rate overall. A proteome-wide search identified predicted circulating levels of myeloid zinc finger 1 and anti-Müllerian hormone as associated with an increased CHIP clonal expansion rate and tissue inhibitor of metalloproteinase 1 and glycine N-methyltransferase as associated with decreased CHIP clonal expansion rate. Together, our findings identify epigenetic and proteomic patterns associated with the rate of hematopoietic clonal expansion.
Published: 2024

5. LXR signaling pathways link cholesterol metabolism with risk for prediabetes and diabetes

Author: Ding, Jingzhong, Nguyen, Anh Tram, Lohman, Kurt, Hensley, Michael T, Parker, Daniel, Hou, Li, Taylor, Jackson, Voora, Deepak, Sawyer, Janet K, Boudyguina, Elena, Bancks, Michael P, Bertoni, Alain, Pankow, James S, Rotter, Jerome I, Goodarzi, Mark O, Tracy, Russell P, Murdoch, David M, Duprez, Daniel, Rich, Stephen S, Psaty, Bruce M, Siscovick, David, Newgard, Christopher B, Herrington, David, Hoeschele, Ina, Shea, Steven, Stein, James H, Patel, Manesh, Post, Wendy, Jacobs, David, Parks, John S, and Liu, Yongmei
Subjects: Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Atherosclerosis, Clinical Research, Health Disparities, Obesity, Diabetes, Genetics, Nutrition, Prevention, Cardiovascular, 2.1 Biological and endogenous factors, Metabolic and endocrine, Humans, Prediabetic State, Male, Female, Diabetes Mellitus, Type 2, Middle Aged, Liver X Receptors, Cholesterol, Aged, Signal Transduction, ATP Binding Cassette Transporter, Subfamily G, Member 1, Monocytes, Risk Factors, ATP Binding Cassette Transporter 1, Aged, 80 and over, Expression profiling, Metabolism, Medical and Health Sciences, Immunology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract: BACKGROUNDPreclinical studies suggest that cholesterol accumulation leads to insulin resistance. We previously reported that alterations in a monocyte cholesterol metabolism transcriptional network (CMTN) - suggestive of cellular cholesterol accumulation - were cross-sectionally associated with obesity and type 2 diabetes (T2D). Here, we sought to determine whether the CMTN alterations independently predict incident prediabetes/T2D risk, and correlate with cellular cholesterol accumulation.METHODSMonocyte mRNA expression of 11 CMTN genes was quantified among 934 Multi-Ethnic Study of Atherosclerosis (MESA) participants free of prediabetes/T2D; cellular cholesterol was measured in a subset of 24 monocyte samples.RESULTSDuring a median 6-year follow-up, lower expression of 3 highly correlated LXR target genes - ABCG1 and ABCA1 (cholesterol efflux) and MYLIP (cholesterol uptake suppression) - and not other CMTN genes, was significantly associated with higher risk of incident prediabetes/T2D. Lower expression of the LXR target genes correlated with higher cellular cholesterol levels (e.g., 47% of variance in cellular total cholesterol explained by ABCG1 expression). Further, adding the LXR target genes to overweight/obesity and other known predictors significantly improved prediction of incident prediabetes/T2D.CONCLUSIONThese data suggest that the aberrant LXR/ABCG1-ABCA1-MYLIP pathway (LAAMP) is a major T2D risk factor and support a potential role for aberrant LAAMP and cellular cholesterol accumulation in diabetogenesis.FUNDINGThe MESA Epigenomics and Transcriptomics Studies were funded by NIH grants 1R01HL101250, 1RF1AG054474, R01HL126477, R01DK101921, and R01HL135009. This work was supported by funding from NIDDK R01DK103531 and NHLBI R01HL119962.
Published: 2024

6. Numerical approximations of a lattice Boltzmann scheme with a family of partial differential equations

Author: Boghosian, Bruce M, Dubois, François, and Lallemand, Pierre
Subjects: Mathematics - Numerical Analysis
Abstract: In this contribution, we address the numerical solutions of high-order asymptotic equivalent partial differential equations with the results of a lattice Boltzmann scheme for an inhomogeneous advection problem in one spatial dimension. We first derive a family of equivalent partial differential equations at various orders, and we compare the lattice Boltzmann experimental results with a spectral approximation of the differential equations. For an unsteady situation, we show that the initialization scheme at a sufficiently high order of the microscopic moments plays a crucial role to observe an asymptotic error consistent with the orderof approximation. For a stationary long-time limit, we observe that the measured asymptotic error converges with a reduced order of precision compared to the one suggested by asymptotic analysis.
Published: 2024

7. RAS-Mutant Follicular Thyroid Tumors: A Continuous Challenge for Pathologists

Author: Hernandez-Prera, Juan C. and Wenig, Bruce M.
Published: 2024
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8. Gaming the system mediates the relationship between gender and learning outcomes in a digital learning game

Author: Baker, Ryan S., Richey, J. Elizabeth, Zhang, Jiayi, Karumbaiah, Shamya, Andres-Bray, Juan Miguel, Nguyen, Huy Anh, Andres, Juliana Maria Alexandra L., and McLaren, Bruce M.
Published: 2024
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9. A plasma protein-based risk score to predict hip fractures

Author: Austin, Thomas R., Nethander, Maria, Fink, Howard A., Törnqvist, Anna E., Jalal, Diana I., Buzkova, Petra, Barzilay, Joshua I., Carbone, Laura, Gabrielsen, Maiken E., Grahnemo, Louise, Lu, Tianyuan, Hveem, Kristian, Jonasson, Christian, Kizer, Jorge R., Langhammer, Arnulf, Mukamal, Kenneth J., Gerszten, Robert E., Psaty, Bruce M., Robbins, John A., Sun, Yan V., Skogholt, Anne Heidi, Kanis, John A., Johansson, Helena, Åsvold, Bjørn Olav, Valderrabano, Rodrigo J., Zheng, Jie, Richards, J. Brent, Coward, Eivind, and Ohlsson, Claes
Published: 2024
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10. Epigenetic and proteomic signatures associate with clonal hematopoiesis expansion rate

Author: Mack, Taralynn M., Raddatz, Michael A., Pershad, Yash, Nachun, Daniel C., Taylor, Kent D., Guo, Xiuqing, Shuldiner, Alan R., O’Connell, Jeffrey R., Kenny, Eimear E., Loos, Ruth J. F., Redline, Susan, Cade, Brian E., Psaty, Bruce M., Bis, Joshua C., Brody, Jennifer A., Silverman, Edwin K., Yun, Jeong H., Cho, Michael H., DeMeo, Dawn L., Levy, Daniel, Johnson, Andrew D., Mathias, Rasika A., Yanek, Lisa R., Heckbert, Susan R., Smith, Nicholas L., Wiggins, Kerri L., Raffield, Laura M., Carson, April P., Rotter, Jerome I., Rich, Stephen S., Manichaikul, Ani W., Gu, C. Charles, Chen, Yii-Der Ida, Lee, Wen-Jane, Shoemaker, M. Benjamin, Roden, Dan M., Kooperberg, Charles, Auer, Paul L., Desai, Pinkal, Blackwell, Thomas W., Smith, Albert V., Reiner, Alexander P., Jaiswal, Siddhartha, Weinstock, Joshua S., and Bick, Alexander G.
Published: 2024
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11. Declassification Policy for Program Complexity Analysis

Author: Hainry, Emmanuel, Kapron, Bruce M., Marion, Jean-Yves, and Péchoux, Romain
Subjects: Computer Science - Logic in Computer Science
Abstract: In automated complexity analysis, noninterference-based type systems statically guarantee, via soundness, the property that well-typed programs compute functions of a given complexity class, e.g., the class FP of functions computable in polynomial time. These characterizations are also extensionally complete -- they capture all functions -- but are not intensionally complete as some polytime algorithms are rejected. This impact on expressive power is an unavoidable cost of achieving a tractable characterization. To overcome this issue, an avenue arising from security applications is to find a relaxation of noninterference based on a declassification mechanism that allows critical data to be released in a safe and controlled manner. Following this path, we present a new and intuitive declassification policy preserving FP-soundness and capturing strictly more programs than existing noninterference-based systems. We show the versatility of the approach: it also provides a new characterization of the class BFF of second-order polynomial time computable functions in a second-order imperative language, with first-order procedure calls. Type inference is tractable: it can be done in polynomial time.
Published: 2024

12. Geographic Location and Corporate Ownership of Hospitals in Relation to Unfilled Positions in the 2023 Emergency Medicine Match

Author: Jarou, Zachary J., Cai, Angela G., Adelman, Leon, Carlberg, David J., Dimeo, Sara P., Fisher, Jonathan, Guth, Todd, Lo, Bruce M., Oh, Laura, Puttagunta, Rahul, and Schmitz, Gillian R.
Subjects: Emergency Medicine, residency match, match, corporate medicine, Private Equity
Abstract: Introduction: In the 2023 National Resident Matching Program (NRMP) match, there were 554 unﬁlled emergency medicine (EM) positions before the Supplemental Offer and Acceptance Program (SOAP). We sought to describe features of EM programs that participated in the match and the association between select program characteristics and unﬁlled positions. Methods: The primary outcome measures included the proportion of positions ﬁlled in relation to state and population density, hospital ownership type, and physician employment model. Secondary outcome measures included comparing program-speciﬁc attributes between ﬁlled and unﬁlled programs, including original accreditation type, year of original accreditation, the total number of approved training positions, length of training, urban-rural designation, hospital size by number of beds, resident-to-bed ratio, and the percentage of disproportionate share patients seen. Results: The NRMP Match had 276 unique participating EM programs with 554 unﬁlled positions. Six states offered 52% of the total NRMP positions available. Five states were associated with two-thirds of the unﬁlled positions. Public hospitals had a statistically signiﬁcant higher match rate (88%) when compared to non-proﬁt and for-proﬁt hospitals, which had match rates of 80% and 75%, respectively (P < 0.001). Programs with faculty employed by a health system had the highest match rate of 87%, followed by clinician partnerships at 79% and private equity groups at 68% (P < 0.001 overall and between all subgroups). Conclusion: The 2023 match in EM saw increased rates in the number of residency positions and programs that did not ﬁll before the SOAP. Public hospitals had higher match rates than for-proﬁt or non-proﬁt hospitals. Residency programs that employed academic faculty through the hospital or health system were associated with higher match rates.
Published: 2024

13. Opportunities to Enhance Diagnostic Testing and Antimicrobial Stewardship: A Qualitative Multinational Survey of Healthcare Professionals

Author: Jinks, Timothy, Subramaniam, Sumithra, Bassetti, Matteo, Gales, Ana C., Kullar, Ravina, Metersky, Mark L., Poojary, Aruna, Seifert, Harald, Warrier, Anup, Flayhart, Diane, Kelly, Timothy, Yu, Kalvin, Altevogt, Bruce M., Townsend, Andy, Marsh, Charlotte, and Willis, Clare
Published: 2024
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14. Heart-specific NFAT5 knockout suppresses type I interferon signaling and aggravates coxsackievirus-induced myocarditis

Author: Zhao, Guangze, Zhang, Huifang M., Nasseri, Ali Reza, Yip, Fione, Telkar, Nikita, Chen, Yankuan T., Aghakeshmiri, Sana, Küper, Christoph, Lam, Wan, Yang, Wenli, Zhao, James, Luo, Honglin, McManus, Bruce M., and Yang, Decheng
Published: 2024
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15. Genome-wide analysis in over 1 million individuals of European ancestry yields improved polygenic risk scores for blood pressure traits

Author: Keaton, Jacob M., Kamali, Zoha, Xie, Tian, Vaez, Ahmad, Williams, Ariel, Goleva, Slavina B., Ani, Alireza, Evangelou, Evangelos, Hellwege, Jacklyn N., Yengo, Loic, Young, William J., Traylor, Matthew, Giri, Ayush, Zheng, Zhili, Zeng, Jian, Chasman, Daniel I., Morris, Andrew P., Caulfield, Mark J., Hwang, Shih-Jen, Kooner, Jaspal S., Conen, David, Attia, John R., Morrison, Alanna C., Loos, Ruth J. F., Kristiansson, Kati, Schmidt, Reinhold, Hicks, Andrew A., Pramstaller, Peter P., Nelson, Christopher P., Samani, Nilesh J., Risch, Lorenz, Gyllensten, Ulf, Melander, Olle, Riese, Harriette, Wilson, James F., Campbell, Harry, Rich, Stephen S., Psaty, Bruce M., Lu, Yingchang, Rotter, Jerome I., Guo, Xiuqing, Rice, Kenneth M., Vollenweider, Peter, Sundström, Johan, Langenberg, Claudia, Tobin, Martin D., Giedraitis, Vilmantas, Luan, Jian’an, Tuomilehto, Jaakko, Kutalik, Zoltan, Ripatti, Samuli, Salomaa, Veikko, Girotto, Giorgia, Trompet, Stella, Jukema, J. Wouter, van der Harst, Pim, Ridker, Paul M., Giulianini, Franco, Vitart, Veronique, Goel, Anuj, Watkins, Hugh, Harris, Sarah E., Deary, Ian J., van der Most, Peter J., Oldehinkel, Albertine J., Keavney, Bernard D., Hayward, Caroline, Campbell, Archie, Boehnke, Michael, Scott, Laura J., Boutin, Thibaud, Mamasoula, Chrysovalanto, Järvelin, Marjo-Riitta, Peters, Annette, Gieger, Christian, Lakatta, Edward G., Cucca, Francesco, Hui, Jennie, Knekt, Paul, Enroth, Stefan, De Borst, Martin H., Polašek, Ozren, Concas, Maria Pina, Catamo, Eulalia, Cocca, Massimiliano, Li-Gao, Ruifang, Hofer, Edith, Schmidt, Helena, Spedicati, Beatrice, Waldenberger, Melanie, Strachan, David P., Laan, Maris, Teumer, Alexander, Dörr, Marcus, Gudnason, Vilmundur, Cook, James P., Ruggiero, Daniela, Kolcic, Ivana, Boerwinkle, Eric, Traglia, Michela, Lehtimäki, Terho, Raitakari, Olli T., Johnson, Andrew D., Newton-Cheh, Christopher, Brown, Morris J., Dominiczak, Anna F., Sever, Peter J., Poulter, Neil, Chambers, John C., Elosua, Roberto, Siscovick, David, Esko, Tõnu, Metspalu, Andres, Strawbridge, Rona J., Laakso, Markku, Hamsten, Anders, Hottenga, Jouke-Jan, de Geus, Eco, Morris, Andrew D., Palmer, Colin N. A., Nolte, Ilja M., Milaneschi, Yuri, Marten, Jonathan, Wright, Alan, Zeggini, Eleftheria, Howson, Joanna M. M., O’Donnell, Christopher J., Spector, Tim, Nalls, Mike A., Simonsick, Eleanor M., Liu, Yongmei, van Duijn, Cornelia M., Butterworth, Adam S., Danesh, John N., Menni, Cristina, Wareham, Nicholas J., Khaw, Kay-Tee, Sun, Yan V., Wilson, Peter W. F., Cho, Kelly, Visscher, Peter M., Denny, Joshua C., Levy, Daniel, Edwards, Todd L., Munroe, Patricia B., Snieder, Harold, and Warren, Helen R.
Published: 2024
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16. Bounding the approach to oligarchy in a variant of the yard-sale model

Author: Cohen, David W. and Boghosian, Bruce M.
Subjects: Condensed Matter - Statistical Mechanics, Quantitative Finance - Mathematical Finance
Abstract: We present analytical results for the Gini coefficient of economic inequality under the dynamics of a modified Yard-Sale Model of kinetic asset exchange. A variant of the Yard-Sale Model is introduced by modifying the underlying binary transaction of the classical system. It is shown that the Gini coefficient is monotone under the resulting dynamics but the approach to oligarchy, as measured by the Gini index, can be bounded by a first-order differential inequality used in conjunction with the differential Gronwall inequality. This result is in the spirit of entropy -- entropy production inequalities for diffusive PDE. The asymptotics of the modified system, with a redistributive tax, are derived and shown to agree with the original, taxed Yard-Sale Model, which implies the modified system is as suitable for matching real wealth distributions. The Gini -- Gini production inequality is shown to hold for a broader class of models.
Published: 2023

17. Cheap Trumpet

Author: Tindall, Bruce M
Abstract: The collected poems of Bruce McGarrity Tindall.
Published: 2023

18. Whole-genome sequencing in 333,100 individuals reveals rare non-coding single variant and aggregate associations with height

Author: Gareth Hawkes, Robin N. Beaumont, Zilin Li, Ravi Mandla, Xihao Li, Christine M. Albert, Donna K. Arnett, Allison E. Ashley-Koch, Aneel A. Ashrani, Kathleen C. Barnes, Eric Boerwinkle, Jennifer A. Brody, April P. Carson, Nathalie Chami, Yii-Der Ida Chen, Mina K. Chung, Joanne E. Curran, Dawood Darbar, Patrick T. Ellinor, Myrian Fornage, Victor R. Gordeuk, Xiuqing Guo, Jiang He, Chii-Min Hwu, Rita R. Kalyani, Robert Kaplan, Sharon L. R. Kardia, Charles Kooperberg, Ruth J. F. Loos, Steven A. Lubitz, Ryan L. Minster, Take Naseri, Satupa’itea Viali, Braxton D. Mitchell, Joanne M. Murabito, Nicholette D. Palmer, Bruce M. Psaty, Susan Redline, M. Benjamin Shoemaker, Edwin K. Silverman, Marilyn J. Telen, Scott T. Weiss, Lisa R. Yanek, Hufeng Zhou, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Ching-Ti Liu, Kari E. North, Anne E. Justice, Jonathan M. Locke, Nick Owens, Anna Murray, Kashyap Patel, Timothy M. Frayling, Caroline F. Wright, Andrew R. Wood, Xihong Lin, Alisa Manning, and Michael N. Weedon
Subjects: Science
Abstract: Abstract The role of rare non-coding variation in complex human phenotypes is still largely unknown. To elucidate the impact of rare variants in regulatory elements, we performed a whole-genome sequencing association analysis for height using 333,100 individuals from three datasets: UK Biobank (N = 200,003), TOPMed (N = 87,652) and All of Us (N = 45,445). We performed rare (
Published: 2024
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19. Young People's Voices on Emotions: A Narrative Inquiry

Author: Roberto McLeay, Darren Powell, and Bruce M. Z. Cohen
Abstract: This article presents an innovative narrative inquiry study carried out in a primary school in Aotearoa New Zealand with three young people who provide insights into how they perceive, construct, give meaning to, and make sense of their own emotions. The analysis from this primary research draws on Foucauldian scholarship to examine how the narratives that young people construct about their feelings are shaped by dominant psy-discourses on emotions. We argue that through these discourses, certain voices of authority, knowledge, and ways of seeing are privileged in schools--while others are silenced--in order to label young people as emotionally or mentally "unwell" and in need of expert assistance. In doing so, we suggest that critical interdisciplinary work by health, psychology, counselling, and education professionals in schools can create spaces to explore inter-professional dialogue and reflexivity, as well as to challenge orthodox approaches to young people's emotional lives.
Published: 2024
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20. Understanding Latino/a/x Students' Academic Success at a Hispanic-Serving Institution: The Significance of Personal Dispositions

Author: Kerstin Hamann, Bruce M. Wilson, and Maura A. E. Pilotti
Abstract: This study examines whether racial/ethnic differences in personal dispositions, such as self-efficacy, cultural orientation, habitual explanations for good or poor academic outcomes, and age (as an index of life experience) exist among students enrolled in a general education course at a Hispanic-serving institution (HSI). Furthermore, the study examines the extent to which such dispositions may contribute differently to the academic success of students at such an institution depending on their race/ethnicity. Although the study uncovered only minor racial/ethnic differences in student dispositions, dissimilar patterns of contributions to course-specific performance and cumulative performance (as measured by grade point average) were observed for Latino/a/x/Hispanic and White students. Taken together, these findings suggest the importance of assessing the contribution of variables to academic success above and beyond the mere measurement of group differences. Applications of our findings to students at minority-serving institutions are discussed.
Published: 2024
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21. Why Surgery?

Author: Wolfe, Bruce M., primary
Published: 2024
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22. Evaluating ChatGPT's Decimal Skills and Feedback Generation in a Digital Learning Game

Author: Nguyen, Huy A., Stec, Hayden, Hou, Xinying, Di, Sarah, and McLaren, Bruce M.
Subjects: Computer Science - Human-Computer Interaction, Computer Science - Artificial Intelligence, Computer Science - Computers and Society
Abstract: While open-ended self-explanations have been shown to promote robust learning in multiple studies, they pose significant challenges to automated grading and feedback in technology-enhanced learning, due to the unconstrained nature of the students' input. Our work investigates whether recent advances in Large Language Models, and in particular ChatGPT, can address this issue. Using decimal exercises and student data from a prior study of the learning game Decimal Point, with more than 5,000 open-ended self-explanation responses, we investigate ChatGPT's capability in (1) solving the in-game exercises, (2) determining the correctness of students' answers, and (3) providing meaningful feedback to incorrect answers. Our results showed that ChatGPT can respond well to conceptual questions, but struggled with decimal place values and number line problems. In addition, it was able to accurately assess the correctness of 75% of the students' answers and generated generally high-quality feedback, similar to human instructors. We conclude with a discussion of ChatGPT's strengths and weaknesses and suggest several venues for extending its use cases in digital teaching and learning., Comment: Be accepted as a Research Paper in 18th European Conference on Technology Enhanced Learning
Published: 2023

23. The Computational Complexity of Equilibria with Strategic Constraints

Author: Kapron, Bruce M. and Samieefar, Koosha
Subjects: Computer Science - Computational Complexity, Computer Science - Computer Science and Game Theory, 68Q17, F.2
Abstract: Computational aspects of solution notions such as Nash equilibrium have been extensively studied, including settings where the ultimate goal is to find an equilibrium that possesses some additional properties. Furthermore, in order to address issues of tractability, attention has been given to approximate versions of these problems. Our work extends this direction by considering games with constraints in which players are subject to some form of restrictions on their strategic choices. We also consider the relationship between Nash equilibria and so-called constrained or social equilibria in this context, with particular attention to how they are related with respect to totality and complexity. Our results demonstrate that the computational complexity of finding an equilibrium varies significantly between games with slightly different strategic constraints. In addition to examining the computational aspects of such strategic constraints, we also demonstrate that these constraints are useful for modeling problems involving strategic resource allocation and also are of interest from the perspective of behavioral game theory.
Published: 2023

24. Association Between Whole Blood–Derived Mitochondrial DNA Copy Number, Low‐Density Lipoprotein Cholesterol, and Cardiovascular Disease Risk

Author: Liu, Xue, Sun, Xianbang, Zhang, Yuankai, Jiang, Wenqing, Lai, Meng, Wiggins, Kerri L, Raffield, Laura M, Bielak, Lawrence F, Zhao, Wei, Pitsillides, Achilleas, Haessler, Jeffrey, Zheng, Yinan, Blackwell, Thomas W, Yao, Jie, Guo, Xiuqing, Qian, Yong, Thyagarajan, Bharat, Pankratz, Nathan, Rich, Stephen S, Taylor, Kent D, Peyser, Patricia A, Heckbert, Susan R, Seshadri, Sudha, Boerwinkle, Eric, Grove, Megan L, Larson, Nicholas B, Smith, Jennifer A, Vasan, Ramachandran S, Fitzpatrick, Annette L, Fornage, Myriam, Ding, Jun, Carson, April P, Abecasis, Goncalo, Dupuis, Josée, Reiner, Alexander, Kooperberg, Charles, Hou, Lifang, Psaty, Bruce M, Wilson, James G, Levy, Daniel, Rotter, Jerome I, Bis, Joshua C, Consortium, TOPMed mtDNA Working Group in NHLBI Trans‐Omics for Precision Medicine, Satizabal, Claudia L, Arking, Dan E, and Liu, Chunyu
Subjects: Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Obesity, Prevention, Heart Disease, Atherosclerosis, Heart Disease - Coronary Heart Disease, Aging, Cardiovascular, Genetics, 2.1 Biological and endogenous factors, Aetiology, Good Health and Well Being, Humans, DNA, Mitochondrial, Risk Factors, Cardiovascular Diseases, Cholesterol, LDL, DNA Copy Number Variations, Cross-Sectional Studies, Coronary Disease, Cholesterol, HDL, Diabetes Mellitus, Hypertension, cardiometabolic risk factors, cardiovascular disease, low-density lipoprotein cholesterol, Mendelian randomization, mitochondrial DNA copy number, vascular atherosclerosis, TOPMed mtDNA Working Group in NHLBI Trans‐Omics for Precision Medicine (TOPMed) Consortium, low‐density lipoprotein cholesterol, Cardiorespiratory Medicine and Haematology, Cardiovascular medicine and haematology
Abstract: Background The relationship between mitochondrial DNA copy number (mtDNA CN) and cardiovascular disease remains elusive. Methods and Results We performed cross-sectional and prospective association analyses of blood-derived mtDNA CN and cardiovascular disease outcomes in 27 316 participants in 8 cohorts of multiple racial and ethnic groups with whole-genome sequencing. We also performed Mendelian randomization to explore causal relationships of mtDNA CN with coronary heart disease (CHD) and cardiometabolic risk factors (obesity, diabetes, hypertension, and hyperlipidemia). P
Published: 2023

25. Multi-ancestry genome-wide study identifies effector genes and druggable pathways for coronary artery calcification

Author: Kavousi, Maryam, Bos, Maxime M, Barnes, Hanna J, Lino Cardenas, Christian L, Wong, Doris, Lu, Haojie, Hodonsky, Chani J, Landsmeer, Lennart PL, Turner, Adam W, Kho, Minjung, Hasbani, Natalie R, de Vries, Paul S, Bowden, Donald W, Chopade, Sandesh, Deelen, Joris, Benavente, Ernest Diez, Guo, Xiuqing, Hofer, Edith, Hwang, Shih-Jen, Lutz, Sharon M, Lyytikäinen, Leo-Pekka, Slenders, Lotte, Smith, Albert V, Stanislawski, Maggie A, van Setten, Jessica, Wong, Quenna, Yanek, Lisa R, Becker, Diane M, Beekman, Marian, Budoff, Matthew J, Feitosa, Mary F, Finan, Chris, Hilliard, Austin T, Kardia, Sharon LR, Kovacic, Jason C, Kral, Brian G, Langefeld, Carl D, Launer, Lenore J, Malik, Shaista, Hoesein, Firdaus AA Mohamed, Mokry, Michal, Schmidt, Reinhold, Smith, Jennifer A, Taylor, Kent D, Terry, James G, van der Grond, Jeroen, van Meurs, Joyce, Vliegenthart, Rozemarijn, Xu, Jianzhao, Young, Kendra A, Zilhão, Nuno R, Zweiker, Robert, Assimes, Themistocles L, Becker, Lewis C, Bos, Daniel, Carr, J Jeffrey, Cupples, L Adrienne, de Kleijn, Dominique PV, de Winther, Menno, den Ruijter, Hester M, Fornage, Myriam, Freedman, Barry I, Gudnason, Vilmundur, Hingorani, Aroon D, Hokanson, John E, Ikram, M Arfan, Išgum, Ivana, Jacobs, David R, Kähönen, Mika, Lange, Leslie A, Lehtimäki, Terho, Pasterkamp, Gerard, Raitakari, Olli T, Schmidt, Helena, Slagboom, P Eline, Uitterlinden, André G, Vernooij, Meike W, Bis, Joshua C, Franceschini, Nora, Psaty, Bruce M, Post, Wendy S, Rotter, Jerome I, Björkegren, Johan LM, O’Donnell, Christopher J, Bielak, Lawrence F, Peyser, Patricia A, Malhotra, Rajeev, van der Laan, Sander W, and Miller, Clint L
Subjects: Biological Sciences, Genetics, Heart Disease - Coronary Heart Disease, Human Genome, Cardiovascular, Prevention, Heart Disease, Atherosclerosis, 2.1 Biological and endogenous factors, Aetiology, Humans, Black People, Coronary Artery Disease, Genome-Wide Association Study, Risk Factors, European People, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract: Coronary artery calcification (CAC), a measure of subclinical atherosclerosis, predicts future symptomatic coronary artery disease (CAD). Identifying genetic risk factors for CAC may point to new therapeutic avenues for prevention. Currently, there are only four known risk loci for CAC identified from genome-wide association studies (GWAS) in the general population. Here we conducted the largest multi-ancestry GWAS meta-analysis of CAC to date, which comprised 26,909 individuals of European ancestry and 8,867 individuals of African ancestry. We identified 11 independent risk loci, of which eight were new for CAC and five had not been reported for CAD. These new CAC loci are related to bone mineralization, phosphate catabolism and hormone metabolic pathways. Several new loci harbor candidate causal genes supported by multiple lines of functional evidence and are regulators of smooth muscle cell-mediated calcification ex vivo and in vitro. Together, these findings help refine the genetic architecture of CAC and extend our understanding of the biological and potential druggable pathways underlying CAC.
Published: 2023

26. Plasma Trimethylamine‐N ‐Oxide and Incident Ischemic Stroke: The Cardiovascular Health Study and the Multi‐Ethnic Study of Atherosclerosis

Author: Lemaitre, Rozenn N, Jensen, Paul N, Wang, Zeneng, Fretts, Amanda M, Sitlani, Colleen M, Nemet, Ina, Sotoodehnia, Nona, de Oliveira Otto, Marcia C, Zhu, Weifei, Budoff, Matt, Longstreth, WT, Psaty, Bruce M, Siscovick, David S, Hazen, Stanley L, and Mozaffarian, Dariush
Subjects: Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Neurosciences, Brain Disorders, Cardiovascular, Atherosclerosis, Stroke, Aging, Cerebrovascular, Women's Health, Good Health and Well Being, Aged, Female, Humans, Ischemic Stroke, Methylamines, Oxides, Prospective Studies, Risk Factors, United States, TMAO, epidemiology, risk factors, stroke, Cardiorespiratory Medicine and Haematology, Cardiovascular medicine and haematology
Abstract: Background The association of circulating trimethylamine-N-oxide (TMAO) with stroke has received limited attention. To address this gap, we examined the associations of serial measures of plasma TMAO with incident ischemic stroke. Methods and Results We used a prospective cohort design with data pooled from 2 cohorts. The settings were the CHS (Cardiovascular Health Study), a cohort of older adults, and the MESA (Multi-Ethnic Study of Atherosclerosis), both in the United States. We measured plasma concentrations of TMAO at baseline and again during the follow-up using high-performance liquid chromatography and mass spectrometry. We assessed the association of plasma TMAO with incident ischemic stroke using proportional hazards regression adjusted for risk factors. The combined cohorts included 11 785 participants without a history of stroke, on average 73 (CHS) and 62 (MESA) years old at baseline, including 60% (CHS) and 53% (MESA) women. We identified 1031 total incident ischemic strokes during a median 15-year follow-up in the combined cohorts. In multivariable analyses, TMAO was significantly associated with incident ischemic stroke risk (hazard ratios comparing a doubling of TMAO: 1.11 [1.03-1.18], P=0.004). The association was linear over the range of TMAO concentrations and appeared restricted to those without diagnosed coronary heart disease. An association with hemorrhagic stroke was not found. Conclusions Plasma TMAO levels are associated with incident ischemic stroke in a diverse population. Registration URL: https://www.clinicaltrials.gov. Unique identifier: NCT00005133.
Published: 2023

27. Whole-genome sequencing in 333,100 individuals reveals rare non-coding single variant and aggregate associations with height

Author: Hawkes, Gareth, Beaumont, Robin N., Li, Zilin, Mandla, Ravi, Li, Xihao, Albert, Christine M., Arnett, Donna K., Ashley-Koch, Allison E., Ashrani, Aneel A., Barnes, Kathleen C., Boerwinkle, Eric, Brody, Jennifer A., Carson, April P., Chami, Nathalie, Chen, Yii-Der Ida, Chung, Mina K., Curran, Joanne E., Darbar, Dawood, Ellinor, Patrick T., Fornage, Myrian, Gordeuk, Victor R., Guo, Xiuqing, He, Jiang, Hwu, Chii-Min, Kalyani, Rita R., Kaplan, Robert, Kardia, Sharon L. R., Kooperberg, Charles, Loos, Ruth J. F., Lubitz, Steven A., Minster, Ryan L., Naseri, Take, Viali, Satupa’itea, Mitchell, Braxton D., Murabito, Joanne M., Palmer, Nicholette D., Psaty, Bruce M., Redline, Susan, Shoemaker, M. Benjamin, Silverman, Edwin K., Telen, Marilyn J., Weiss, Scott T., Yanek, Lisa R., Zhou, Hufeng, Liu, Ching-Ti, North, Kari E., Justice, Anne E., Locke, Jonathan M., Owens, Nick, Murray, Anna, Patel, Kashyap, Frayling, Timothy M., Wright, Caroline F., Wood, Andrew R., Lin, Xihong, Manning, Alisa, and Weedon, Michael N.
Published: 2024
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28. Machine learning models for predicting blood pressure phenotypes by combining multiple polygenic risk scores

Author: Hrytsenko, Yana, Shea, Benjamin, Elgart, Michael, Kurniansyah, Nuzulul, Lyons, Genevieve, Morrison, Alanna C., Carson, April P., Haring, Bernhard, Mitchell, Braxton D., Psaty, Bruce M., Jaeger, Byron C., Gu, C. Charles, Kooperberg, Charles, Levy, Daniel, Lloyd-Jones, Donald, Choi, Eunhee, Brody, Jennifer A., Smith, Jennifer A., Rotter, Jerome I., Moll, Matthew, Fornage, Myriam, Simon, Noah, Castaldi, Peter, Casanova, Ramon, Chung, Ren-Hua, Kaplan, Robert, Loos, Ruth J. F., Kardia, Sharon L. R., Rich, Stephen S., Redline, Susan, Kelly, Tanika, O’Connor, Timothy, Zhao, Wei, Kim, Wonji, Guo, Xiuqing, Ida Chen, Yii-Der, and Sofer, Tamar
Published: 2024
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29. Determinants of mosaic chromosomal alteration fitness

Author: Pershad, Yash, Mack, Taralynn, Poisner, Hannah, Jakubek, Yasminka A., Stilp, Adrienne M., Mitchell, Braxton D., Lewis, Joshua P., Boerwinkle, Eric, Loos, Ruth J. F., Chami, Nathalie, Wang, Zhe, Barnes, Kathleen, Pankratz, Nathan, Fornage, Myriam, Redline, Susan, Psaty, Bruce M., Bis, Joshua C., Shojaie, Ali, Silverman, Edwin K., Cho, Michael H., Yun, Jeong H., DeMeo, Dawn, Levy, Daniel, Johnson, Andrew D., Mathias, Rasika A., Taub, Margaret A., Arnett, Donna, North, Kari E., Raffield, Laura M., Carson, April P., Doyle, Margaret F., Rich, Stephen S., Rotter, Jerome I., Guo, Xiuqing, Cox, Nancy J., Roden, Dan M., Franceschini, Nora, Desai, Pinkal, Reiner, Alex P., Auer, Paul L., Scheet, Paul A., Jaiswal, Siddhartha, Weinstock, Joshua S., and Bick, Alexander G.
Published: 2024
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30. Utility of UV Signature Mutations in the Diagnostic Assessment of Metastatic Head and Neck Carcinomas of Unknown Primary

Author: Furlan, Karina Colossi, Saeed-Vafa, Daryoush, Mathew, Tiffani M., Saller, James J., Tabbara, Sana O., Boyle, Theresa A., Wenig, Bruce M., and Hernandez-Prera, Juan C.
Published: 2024
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31. Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications

Author: Sterenborg, Rosalie B. T. M., Steinbrenner, Inga, Li, Yong, Bujnis, Melissa N., Naito, Tatsuhiko, Marouli, Eirini, Galesloot, Tessel E., Babajide, Oladapo, Andreasen, Laura, Astrup, Arne, Åsvold, Bjørn Olav, Bandinelli, Stefania, Beekman, Marian, Beilby, John P., Bork-Jensen, Jette, Boutin, Thibaud, Brody, Jennifer A., Brown, Suzanne J., Brumpton, Ben, Campbell, Purdey J., Cappola, Anne R., Ceresini, Graziano, Chaker, Layal, Chasman, Daniel I., Concas, Maria Pina, Coutinho de Almeida, Rodrigo, Cross, Simone M., Cucca, Francesco, Deary, Ian J., Kjaergaard, Alisa Devedzic, Echouffo Tcheugui, Justin B., Ellervik, Christina, Eriksson, Johan G., Ferrucci, Luigi, Freudenberg, Jan, Fuchsberger, Christian, Gieger, Christian, Giulianini, Franco, Gögele, Martin, Graham, Sarah E., Grarup, Niels, Gunjača, Ivana, Hansen, Torben, Harding, Barbara N., Harris, Sarah E., Haunsø, Stig, Hayward, Caroline, Hui, Jennie, Ittermann, Till, Jukema, J. Wouter, Kajantie, Eero, Kanters, Jørgen K., Kårhus, Line L., Kiemeney, Lambertus A. L. M., Kloppenburg, Margreet, Kühnel, Brigitte, Lahti, Jari, Langenberg, Claudia, Lapauw, Bruno, Leese, Graham, Li, Shuo, Liewald, David C. M., Linneberg, Allan, Lominchar, Jesus V. T., Luan, Jian’an, Martin, Nicholas G., Matana, Antonela, Meima, Marcel E., Meitinger, Thomas, Meulenbelt, Ingrid, Mitchell, Braxton D., Møllehave, Line T., Mora, Samia, Naitza, Silvia, Nauck, Matthias, Netea-Maier, Romana T., Noordam, Raymond, Nursyifa, Casia, Okada, Yukinori, Onano, Stefano, Papadopoulou, Areti, Palmer, Colin N. A., Pattaro, Cristian, Pedersen, Oluf, Peters, Annette, Pietzner, Maik, Polašek, Ozren, Pramstaller, Peter P., Psaty, Bruce M., Punda, Ante, Ray, Debashree, Redmond, Paul, Richards, J. Brent, Ridker, Paul M., Russ, Tom C., Ryan, Kathleen A., Olesen, Morten Salling, Schultheiss, Ulla T., Selvin, Elizabeth, Siddiqui, Moneeza K., Sidore, Carlo, Slagboom, P. Eline, Sørensen, Thorkild I. A., Soto-Pedre, Enrique, Spector, Tim D., Spedicati, Beatrice, Srinivasan, Sundararajan, Starr, John M., Stott, David J., Tanaka, Toshiko, Torlak, Vesela, Trompet, Stella, Tuhkanen, Johanna, Uitterlinden, André G., van den Akker, Erik B., van den Eynde, Tibbert, van der Klauw, Melanie M., van Heemst, Diana, Verroken, Charlotte, Visser, W. Edward, Vojinovic, Dina, Völzke, Henry, Waldenberger, Melanie, Walsh, John P., Wareham, Nicholas J., Weiss, Stefan, Willer, Cristen J., Wilson, Scott G., Wolffenbuttel, Bruce H. R., Wouters, Hanneke J. C. M., Wright, Margaret J., Yang, Qiong, Zemunik, Tatijana, Zhou, Wei, Zhu, Gu, Zöllner, Sebastian, Smit, Johannes W. A., Peeters, Robin P., Köttgen, Anna, Teumer, Alexander, and Medici, Marco
Published: 2024
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32. Proteomics for heart failure risk stratification: a systematic review

Author: Kuku, Kayode O., Oyetoro, Rebecca, Hashemian, Maryam, Livinski, Alicia A., Shearer, Joseph J., Joo, Jungnam, Psaty, Bruce M., Levy, Daniel, Ganz, Peter, and Roger, Véronique L.
Published: 2024
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33. Multi-omics and pathway analyses of genome-wide associations implicate regulation and immunity in verbal declarative memory performance

Author: Mei, Hao, Simino, Jeannette, Li, Lianna, Jiang, Fan, Bis, Joshua C., Davies, Gail, Hill, W David, Xia, Charley, Gudnason, Vilmundur, Yang, Qiong, Lahti, Jari, Smith, Jennifer A., Kirin, Mirna, De Jager, Philip, Armstrong, Nicola J., Ghanbari, Mohsen, Kolcic, Ivana, Moran, Christopher, Teumer, Alexander, Sargurupremraj, Murali, Mahmud, Shamsed, Fornage, Myriam, Zhao, Wei, Satizabal, Claudia L., Polasek, Ozren, Räikkönen, Katri, Liewald, David C., Homuth, Georg, Callisaya, Michele, Mather, Karen A., Windham, B. Gwen, Zemunik, Tatijana, Palotie, Aarno, Pattie, Alison, van der Auwera, Sandra, Thalamuthu, Anbupalam, Knopman, David S., Rudan, Igor, Starr, John M., Wittfeld, Katharina, Kochan, Nicole A., Griswold, Michael E., Vitart, Veronique, Brodaty, Henry, Gottesman, Rebecca, Cox, Simon R., Psaty, Bruce M., Boerwinkle, Eric, Chasman, Daniel I., Grodstein, Francine, Sachdev, Perminder S., Srikanth, Velandai, Hayward, Caroline, Wilson, James F., Eriksson, Johan G., Kardia, Sharon L. R., Grabe, Hans J., Bennett, David A., Ikram, M. Arfan, Deary, Ian J., van Duijn, Cornelia M., Launer, Lenore, Fitzpatrick, Annette L., Seshadri, Sudha, Bressler, Jan, Debette, Stephanie, and Mosley, Jr, Thomas H.
Published: 2024
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34. X-chromosome and kidney function: evidence from a multi-trait genetic analysis of 908,697 individuals reveals sex-specific and sex-differential findings in genes regulated by androgen response elements

Author: Scholz, Markus, Horn, Katrin, Pott, Janne, Wuttke, Matthias, Kühnapfel, Andreas, Nasr, M. Kamal, Kirsten, Holger, Li, Yong, Hoppmann, Anselm, Gorski, Mathias, Ghasemi, Sahar, Li, Man, Tin, Adrienne, Chai, Jin-Fang, Cocca, Massimiliano, Wang, Judy, Nutile, Teresa, Akiyama, Masato, Åsvold, Bjørn Olav, Bansal, Nisha, Biggs, Mary L., Boutin, Thibaud, Brenner, Hermann, Brumpton, Ben, Burkhardt, Ralph, Cai, Jianwen, Campbell, Archie, Campbell, Harry, Chalmers, John, Chasman, Daniel I., Chee, Miao Ling, Chee, Miao Li, Chen, Xu, Cheng, Ching-Yu, Cifkova, Renata, Daviglus, Martha, Delgado, Graciela, Dittrich, Katalin, Edwards, Todd L., Endlich, Karlhans, Michael Gaziano, J., Giri, Ayush, Giulianini, Franco, Gordon, Scott D., Gudbjartsson, Daniel F., Hallan, Stein, Hamet, Pavel, Hartman, Catharina A., Hayward, Caroline, Heid, Iris M., Hellwege, Jacklyn N., Holleczek, Bernd, Holm, Hilma, Hutri-Kähönen, Nina, Hveem, Kristian, Isermann, Berend, Jonas, Jost B., Joshi, Peter K., Kamatani, Yoichiro, Kanai, Masahiro, Kastarinen, Mika, Khor, Chiea Chuen, Kiess, Wieland, Kleber, Marcus E., Körner, Antje, Kovacs, Peter, Krajcoviechova, Alena, Kramer, Holly, Krämer, Bernhard K., Kuokkanen, Mikko, Kähönen, Mika, Lange, Leslie A., Lash, James P., Lehtimäki, Terho, Li, Hengtong, Lin, Bridget M., Liu, Jianjun, Loeffler, Markus, Lyytikäinen, Leo-Pekka, Magnusson, Patrik K. E., Martin, Nicholas G., Matsuda, Koichi, Milaneschi, Yuri, Mishra, Pashupati P., Mononen, Nina, Montgomery, Grant W., Mook-Kanamori, Dennis O., Mychaleckyj, Josyf C., März, Winfried, Nauck, Matthias, Nikus, Kjell, Nolte, Ilja M., Noordam, Raymond, Okada, Yukinori, Olafsson, Isleifur, Oldehinkel, Albertine J., Penninx, Brenda W. J. H., Perola, Markus, Pirastu, Nicola, Polasek, Ozren, Porteous, David J., Poulain, Tanja, Psaty, Bruce M., Rabelink, Ton J., Raffield, Laura M., Raitakari, Olli T., Rasheed, Humaira, Reilly, Dermot F., Rice, Kenneth M., Richmond, Anne, Ridker, Paul M., Rotter, Jerome I., Rudan, Igor, Sabanayagam, Charumathi, Salomaa, Veikko, Schneiderman, Neil, Schöttker, Ben, Sims, Mario, Snieder, Harold, Stark, Klaus J., Stefansson, Kari, Stocker, Hannah, Stumvoll, Michael, Sulem, Patrick, Sveinbjornsson, Gardar, Svensson, Per O., Tai, E-Shyong, Taylor, Kent D., Tayo, Bamidele O., Teren, Andrej, Tham, Yih-Chung, Thiery, Joachim, Thio, Chris H. L., Thomas, Laurent F., Tremblay, Johanne, Tönjes, Anke, van der Most, Peter J., Vitart, Veronique, Völker, Uwe, Wang, Ya Xing, Wang, Chaolong, Wei, Wen Bin, Whitfield, John B., Wild, Sarah H., Wilson, James F., Winkler, Thomas W., Wong, Tien-Yin, Woodward, Mark, Sim, Xueling, Chu, Audrey Y., Feitosa, Mary F., Thorsteinsdottir, Unnur, Hung, Adriana M., Teumer, Alexander, Franceschini, Nora, Parsa, Afshin, Köttgen, Anna, Schlosser, Pascal, and Pattaro, Cristian
Published: 2024
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35. Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

Author: Suzuki, Ken, Hatzikotoulas, Konstantinos, Southam, Lorraine, Taylor, Henry J., Yin, Xianyong, Lorenz, Kim M., Mandla, Ravi, Huerta-Chagoya, Alicia, Melloni, Giorgio E. M., Kanoni, Stavroula, Rayner, Nigel W., Bocher, Ozvan, Arruda, Ana Luiza, Sonehara, Kyuto, Namba, Shinichi, Lee, Simon S. K., Preuss, Michael H., Petty, Lauren E., Schroeder, Philip, Vanderwerff, Brett, Kals, Mart, Bragg, Fiona, Lin, Kuang, Guo, Xiuqing, Zhang, Weihua, Yao, Jie, Kim, Young Jin, Graff, Mariaelisa, Takeuchi, Fumihiko, Nano, Jana, Lamri, Amel, Nakatochi, Masahiro, Moon, Sanghoon, Scott, Robert A., Cook, James P., Lee, Jung-Jin, Pan, Ian, Taliun, Daniel, Parra, Esteban J., Chai, Jin-Fang, Bielak, Lawrence F., Tabara, Yasuharu, Hai, Yang, Thorleifsson, Gudmar, Grarup, Niels, Sofer, Tamar, Wuttke, Matthias, Sarnowski, Chloé, Gieger, Christian, Nousome, Darryl, Trompet, Stella, Kwak, Soo-Heon, Long, Jirong, Sun, Meng, Tong, Lin, Chen, Wei-Min, Nongmaithem, Suraj S., Noordam, Raymond, Lim, Victor J. Y., Tam, Claudia H. T., Joo, Yoonjung Yoonie, Chen, Chien-Hsiun, Raffield, Laura M., Prins, Bram Peter, Nicolas, Aude, Yanek, Lisa R., Chen, Guanjie, Brody, Jennifer A., Kabagambe, Edmond, An, Ping, Xiang, Anny H., Choi, Hyeok Sun, Cade, Brian E., Tan, Jingyi, Broadaway, K. Alaine, Williamson, Alice, Kamali, Zoha, Cui, Jinrui, Thangam, Manonanthini, Adair, Linda S., Adeyemo, Adebowale, Aguilar-Salinas, Carlos A., Ahluwalia, Tarunveer S., Anand, Sonia S., Bertoni, Alain, Bork-Jensen, Jette, Brandslund, Ivan, Buchanan, Thomas A., Burant, Charles F., Butterworth, Adam S., Canouil, Mickaël, Chan, Juliana C. N., Chang, Li-Ching, Chee, Miao-Li, Chen, Ji, Chen, Shyh-Huei, Chen, Yuan-Tsong, Chen, Zhengming, Chuang, Lee-Ming, Cushman, Mary, Danesh, John, Das, Swapan K., de Silva, H. Janaka, Dedoussis, George, Dimitrov, Latchezar, Doumatey, Ayo P., Du, Shufa, Duan, Qing, Eckardt, Kai-Uwe, Emery, Leslie S., Evans, Daniel S., Evans, Michele K., Fischer, Krista, Floyd, James S., Ford, Ian, Franco, Oscar H., Frayling, Timothy M., Freedman, Barry I., Genter, Pauline, Gerstein, Hertzel C., Giedraitis, Vilmantas, González-Villalpando, Clicerio, González-Villalpando, Maria Elena, Gordon-Larsen, Penny, Gross, Myron, Guare, Lindsay A., Hackinger, Sophie, Hakaste, Liisa, Han, Sohee, Hattersley, Andrew T., Herder, Christian, Horikoshi, Momoko, Howard, Annie-Green, Hsueh, Willa, Huang, Mengna, Huang, Wei, Hung, Yi-Jen, Hwang, Mi Yeong, Hwu, Chii-Min, Ichihara, Sahoko, Ikram, Mohammad Arfan, Ingelsson, Martin, Islam, Md. Tariqul, Isono, Masato, Jang, Hye-Mi, Jasmine, Farzana, Jiang, Guozhi, Jonas, Jost B., Jørgensen, Torben, Kamanu, Frederick K., Kandeel, Fouad R., Kasturiratne, Anuradhani, Katsuya, Tomohiro, Kaur, Varinderpal, Kawaguchi, Takahisa, Keaton, Jacob M., Kho, Abel N., Khor, Chiea-Chuen, Kibriya, Muhammad G., Kim, Duk-Hwan, Kronenberg, Florian, Kuusisto, Johanna, Läll, Kristi, Lange, Leslie A., Lee, Kyung Min, Lee, Myung-Shik, Lee, Nanette R., Leong, Aaron, Li, Liming, Li, Yun, Li-Gao, Ruifang, Ligthart, Symen, Lindgren, Cecilia M., Linneberg, Allan, Liu, Ching-Ti, Liu, Jianjun, Locke, Adam E., Louie, Tin, Luan, Jian’an, Luk, Andrea O., Luo, Xi, Lv, Jun, Lynch, Julie A., Lyssenko, Valeriya, Maeda, Shiro, Mamakou, Vasiliki, Mansuri, Sohail Rafik, Matsuda, Koichi, Meitinger, Thomas, Melander, Olle, Metspalu, Andres, Mo, Huan, Morris, Andrew D., Moura, Filipe A., Nadler, Jerry L., Nalls, Michael A., Nayak, Uma, Ntalla, Ioanna, Okada, Yukinori, Orozco, Lorena, Patel, Sanjay R., Patil, Snehal, Pei, Pei, Pereira, Mark A., Peters, Annette, Pirie, Fraser J., Polikowsky, Hannah G., Porneala, Bianca, Prasad, Gauri, Rasmussen-Torvik, Laura J., Reiner, Alexander P., Roden, Michael, Rohde, Rebecca, Roll, Katheryn, Sabanayagam, Charumathi, Sandow, Kevin, Sankareswaran, Alagu, Sattar, Naveed, Schönherr, Sebastian, Shahriar, Mohammad, Shen, Botong, Shi, Jinxiu, Shin, Dong Mun, Shojima, Nobuhiro, Smith, Jennifer A., So, Wing Yee, Stančáková, Alena, Steinthorsdottir, Valgerdur, Stilp, Adrienne M., Strauch, Konstantin, Taylor, Kent D., Thorand, Barbara, Thorsteinsdottir, Unnur, Tomlinson, Brian, Tran, Tam C., Tsai, Fuu-Jen, Tuomilehto, Jaakko, Tusie-Luna, Teresa, Udler, Miriam S., Valladares-Salgado, Adan, van Dam, Rob M., van Klinken, Jan B., Varma, Rohit, Wacher-Rodarte, Niels, Wheeler, Eleanor, Wickremasinghe, Ananda R., van Dijk, Ko Willems, Witte, Daniel R., Yajnik, Chittaranjan S., Yamamoto, Ken, Yamamoto, Kenichi, Yoon, Kyungheon, Yu, Canqing, Yuan, Jian-Min, Yusuf, Salim, Zawistowski, Matthew, Zhang, Liang, Zheng, Wei, Raffel, Leslie J., Igase, Michiya, Ipp, Eli, Redline, Susan, Cho, Yoon Shin, Lind, Lars, Province, Michael A., Fornage, Myriam, Hanis, Craig L., Ingelsson, Erik, Zonderman, Alan B., Psaty, Bruce M., Wang, Ya-Xing, Rotimi, Charles N., Becker, Diane M., Matsuda, Fumihiko, Liu, Yongmei, Yokota, Mitsuhiro, Kardia, Sharon L. R., Peyser, Patricia A., Pankow, James S., Engert, James C., Bonnefond, Amélie, Froguel, Philippe, Wilson, James G., Sheu, Wayne H. H., Wu, Jer-Yuarn, Hayes, M. Geoffrey, Ma, Ronald C. W., Wong, Tien-Yin, Mook-Kanamori, Dennis O., Tuomi, Tiinamaija, Chandak, Giriraj R., Collins, Francis S., Bharadwaj, Dwaipayan, Paré, Guillaume, Sale, Michèle M., Ahsan, Habibul, Motala, Ayesha A., Shu, Xiao-Ou, Park, Kyong-Soo, Jukema, J. Wouter, Cruz, Miguel, Chen, Yii-Der Ida, Rich, Stephen S., McKean-Cowdin, Roberta, Grallert, Harald, Cheng, Ching-Yu, Ghanbari, Mohsen, Tai, E-Shyong, Dupuis, Josee, Kato, Norihiro, Laakso, Markku, Köttgen, Anna, Koh, Woon-Puay, Bowden, Donald W., Palmer, Colin N. A., Kooner, Jaspal S., Kooperberg, Charles, Liu, Simin, North, Kari E., Saleheen, Danish, Hansen, Torben, Pedersen, Oluf, Wareham, Nicholas J., Lee, Juyoung, Kim, Bong-Jo, Millwood, Iona Y., Walters, Robin G., Stefansson, Kari, Ahlqvist, Emma, Goodarzi, Mark O., Mohlke, Karen L., Langenberg, Claudia, Haiman, Christopher A., Loos, Ruth J. F., Florez, Jose C., Rader, Daniel J., Ritchie, Marylyn D., Zöllner, Sebastian, Mägi, Reedik, Marston, Nicholas A., Ruff, Christian T., van Heel, David A., Finer, Sarah, Denny, Joshua C., Yamauchi, Toshimasa, Kadowaki, Takashi, Chambers, John C., Ng, Maggie C. Y., Sim, Xueling, Below, Jennifer E., Tsao, Philip S., Chang, Kyong-Mi, McCarthy, Mark I., Meigs, James B., Mahajan, Anubha, Spracklen, Cassandra N., Mercader, Josep M., Boehnke, Michael, Rotter, Jerome I., Vujkovic, Marijana, Voight, Benjamin F., Morris, Andrew P., and Zeggini, Eleftheria
Published: 2024
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36. Clonal hematopoiesis of indeterminate potential is associated with acute kidney injury

Author: Vlasschaert, Caitlyn, Robinson-Cohen, Cassianne, Chen, Jianchun, Akwo, Elvis, Parker, Alyssa C., Silver, Samuel A., Bhatraju, Pavan K., Poisner, Hannah, Cao, Shirong, Jiang, Ming, Wang, Yinqiu, Niu, Aolei, Siew, Edward, Van Amburg, Joseph C., Kramer, Holly J., Kottgen, Anna, Franceschini, Nora, Psaty, Bruce M., Tracy, Russell P., Alonso, Alvaro, Arking, Dan E., Coresh, Josef, Ballantyne, Christie M., Boerwinkle, Eric, Grams, Morgan, Zhang, Ming-Zhi, Kestenbaum, Bryan, Lanktree, Matthew B., Rauh, Michael J., Harris, Jr, Raymond C., and Bick, Alexander G.
Published: 2024
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37. Dalbavancin Sequential Therapy for Gram-Positive Bloodstream Infection: A Multicenter Observational Study

Author: Rebold, Nicholas, Alosaimy, Sara, Pearson, Jeffrey C., Dionne, Brandon, Taqi, Ahmad, Lagnf, Abdalhamid, Lucas, Kristen, Biagi, Mark, Lombardo, Nicholas, Eudy, Joshua, Anderson, Daniel T., Mahoney, Monica V., Kufel, Wesley D., D’Antonio, Joseph A., Jones, Bruce M., Frens, Jeremy J., Baumeister, Tyler, Geriak, Matthew, Sakoulas, George, Farmakiotis, Dimitrios, Delaportas, Dino, Larew, Jeremy, Veve, Michael P., and Rybak, Michael J.
Published: 2024
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38. Freshwater mussel glochidia infesting anadromous Gaspereau below a hydroelectric generating station: implications for mussel conservation

Author: Dobbs, K. D. R., Lynn, T. J., Bruce, M. R., Reyes-Prieto, A., Samways, K. M., Curry, R. A., and Duffy, M. S.
Published: 2024
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39. General fourth order Chapman-Enskog expansion of lattice Boltzmann schemes

Author: Dubois, François, Boghosian, Bruce M, and Lallemand, Pierre
Subjects: Mathematics - Numerical Analysis
Abstract: In order to derive the equivalent partial differential equations of a lattice Boltzmann scheme,the Chapman Enskog expansion is very popular in the lattive Boltzmann community. A maindrawback of this approach is the fact that multiscale expansions are used without any clearmathematical signification of the various variables and operators. Independently of thisframework, the Taylor expansion method allows to obtain formally the equivalent partialdifferential equations. In this contribution, we prove that both approaches give identicalresults with acoustic scaling for a very general family of lattice Boltzmann schemes and upto fourth order accuracy. Examples with a single scalar conservation illustrate our purpose.
Published: 2023

40. Opportunities to Enhance Diagnostic Testing and Antimicrobial Stewardship: A Qualitative Multinational Survey of Healthcare Professionals

Author: Timothy Jinks, Sumithra Subramaniam, Matteo Bassetti, Ana C. Gales, Ravina Kullar, Mark L. Metersky, Aruna Poojary, Harald Seifert, Anup Warrier, Diane Flayhart, Timothy Kelly, Kalvin Yu, Bruce M. Altevogt, Andy Townsend, Charlotte Marsh, and Clare Willis
Subjects: Antimicrobial resistance, Antimicrobial stewardship, Bacteria and bacterial infections, Diagnostic technologies, Healthcare professional survey, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Introduction Antimicrobial resistance (AMR) is a global public health challenge. Global efforts to decrease AMR through antimicrobial stewardship (AMS) initiatives include education and optimising the use of diagnostic technologies and antibiotics. Despite this, economic and societal challenges hinder AMS efforts. The objective of this study was to obtain insights from healthcare professionals (HCPs) on current challenges and identify opportunities for optimising diagnostic test utilisation and AMS efforts. Methods Three hundred HCPs from six countries (representing varied gross national incomes per capita, healthcare system structure, and AMR rates) were surveyed between November 2022 through January 2023. A targeted literature review and expert interviews were conducted to inform survey development. Descriptive statistics were used to summarise survey responses. Results These findings suggest that the greatest challenges to diagnostic test utilisation were economic in nature; many HCPs reported that AMS initiatives were lacking investment (32.3%) and resourcing (40.3%). High resistance rates were considered the greatest barriers to appropriate antimicrobial use (52.0%). Most HCPs found local and national guidelines to be very useful (≥ 51.0%), but areas for improvement were noted. The importance of AMS initiatives was confirmed; diagnostic practices were acknowledged to have a positive impact on decreasing AMR (70.3%) and improving patient outcomes (81.0%). Conclusion AMS initiatives, including diagnostic technology utilisation, are pivotal to decreasing AMR rates. Interpretation of these survey results suggests that while HCPs consider diagnostic practices to be important in AMS efforts, several barriers to successful implementation still exist including patient/institutional costs, turnaround time of test results, resourcing, AMR burden, and education. While some barriers differ by country, these survey results highlight areas of opportunities in all countries for improved use of diagnostic technologies and broader AMS efforts, as perceived by HCPs. Greater investment, resourcing, education, and updated guidelines offer opportunities to further strengthen global AMS efforts.
Published: 2024
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41. Perioperative and safety outcomes following tissue-sparing posterior cervical fusion to revise a pseudarthrosis: A multicenter retrospective review of 150 cases

Author: Alexander C. Lemons, Michael M. Haglund, Bruce M. McCormack, Daniel M. Williams, Adam D. Bohr, and Erik M. Summerside
Subjects: complications, facet fixation, nonunion, posterior cervical fusion, pseudarthrosis, revision, tissue sparing, Diseases of the musculoskeletal system, RC925-935
Abstract: Background: Posterior cervical fusion (PCF) with lateral mass screws is a favorable treatment option to revise a symptomatic pseudarthrosis due to reliable rates of arthrodesis; however, this technique introduces elevated risk for wound infection and hospital readmission. A tissue-sparing PCF approach involving facet fixation instrumentation reduces the rates of postoperative complications while stabilizing the symptomatic level to achieve arthrodesis; however, these outcomes have been limited to small study cohorts from individual surgeons commonly with mixed indications for treatment. Materials and Methods: One hundred and fifty cases were identified from a retrospective chart review performed by seven surgeons across six sites in the United States. All cases involved PCF revision for a pseudarthrosis at one or more levels from C3 to C7 following anterior cervical discectomy and fusion (ACDF). PCF was performed using a tissue-sparing technique with facet instrumentation. Cases involving additional supplemental fixation such as lateral mass screws, rods, wires, or other hardware were excluded. Demographics, operative notes, postoperative complications, hospital readmission, and subsequent surgical interventions were summarized as an entire cohort and according to the following risk factors: age, sex, number of levels revised, body mass index (BMI), and history of nicotine use. Results: The average age of patients at the time of PCF revision was 55 ± 11 years and 63% were female. The average BMI was 29 ± 6 kg/m2 and 19% reported a history of nicotine use. Postoperative follow-up visits were available with a median of 68 days (interquartile range = 41–209 days) from revision PCF. There were 91 1-level, 49 2-level, 8 3-level, and 2 4±-level PCF revision cases. The mean operative duration was 52 ± 3 min with an estimated blood loss of 14 ± 1.5cc. Participants were discharged an average of 1 ± 0.05 days following surgery. Multilevel treatment resulted in longer procedure times (single = 45 min, multi = 59 min, P = 0.01) but did not impact estimated blood loss (P = 0.94). Total nights in the hospital increased by 0.2 nights with multilevel treatment (P = 0.01). Sex, age, nicotine history, and BMI had no effect on recorded perioperative outcomes. There was one instance of rehospitalization due to deep-vein thrombosis, one instance of persistent pseudarthrosis at the revised level treated with ACDF, and four instances of adjacent segment disease. In patients initially treated with multilevel ACDF, revisions occurred most commonly on the caudal level (48% of revised levels), followed by the cranial (43%), and least often in the middle level (9%). Conclusions: This chart review of perioperative and safety outcomes provides evidence in support of tissue-sparing PCF with facet instrumentation as a treatment for symptomatic pseudarthrosis after ACDF. The most common locations requiring revision were the caudal and cranial levels. Operative duration and estimated blood loss were favorable when compared to open alternatives. There were no instances of postoperative wound infection, and the majority of patients were discharged the day following surgery.
Published: 2024
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42. Machine learning models for predicting blood pressure phenotypes by combining multiple polygenic risk scores

Author: Yana Hrytsenko, Benjamin Shea, Michael Elgart, Nuzulul Kurniansyah, Genevieve Lyons, Alanna C. Morrison, April P. Carson, Bernhard Haring, Braxton D. Mitchell, Bruce M. Psaty, Byron C. Jaeger, C. Charles Gu, Charles Kooperberg, Daniel Levy, Donald Lloyd-Jones, Eunhee Choi, Jennifer A. Brody, Jennifer A. Smith, Jerome I. Rotter, Matthew Moll, Myriam Fornage, Noah Simon, Peter Castaldi, Ramon Casanova, Ren-Hua Chung, Robert Kaplan, Ruth J. F. Loos, Sharon L. R. Kardia, Stephen S. Rich, Susan Redline, Tanika Kelly, Timothy O’Connor, Wei Zhao, Wonji Kim, Xiuqing Guo, Yii-Der Ida Chen, The Trans-Omics in Precision Medicine Consortium, and Tamar Sofer
Subjects: Medicine, Science
Abstract: Abstract We construct non-linear machine learning (ML) prediction models for systolic and diastolic blood pressure (SBP, DBP) using demographic and clinical variables and polygenic risk scores (PRSs). We developed a two-model ensemble, consisting of a baseline model, where prediction is based on demographic and clinical variables only, and a genetic model, where we also include PRSs. We evaluate the use of a linear versus a non-linear model at both the baseline and the genetic model levels and assess the improvement in performance when incorporating multiple PRSs. We report the ensemble model’s performance as percentage variance explained (PVE) on a held-out test dataset. A non-linear baseline model improved the PVEs from 28.1 to 30.1% (SBP) and 14.3% to 17.4% (DBP) compared with a linear baseline model. Including seven PRSs in the genetic model computed based on the largest available GWAS of SBP/DBP improved the genetic model PVE from 4.8 to 5.1% (SBP) and 4.7 to 5% (DBP) compared to using a single PRS. Adding additional 14 PRSs computed based on two independent GWASs further increased the genetic model PVE to 6.3% (SBP) and 5.7% (DBP). PVE differed across self-reported race/ethnicity groups, with primarily all non-White groups benefitting from the inclusion of additional PRSs. In summary, non-linear ML models improves BP prediction in models incorporating diverse populations.
Published: 2024
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43. Determinants of mosaic chromosomal alteration fitness

Author: Yash Pershad, Taralynn Mack, Hannah Poisner, Yasminka A. Jakubek, Adrienne M. Stilp, Braxton D. Mitchell, Joshua P. Lewis, Eric Boerwinkle, Ruth J. F. Loos, Nathalie Chami, Zhe Wang, Kathleen Barnes, Nathan Pankratz, Myriam Fornage, Susan Redline, Bruce M. Psaty, Joshua C. Bis, Ali Shojaie, Edwin K. Silverman, Michael H. Cho, Jeong H. Yun, Dawn DeMeo, Daniel Levy, Andrew D. Johnson, Rasika A. Mathias, Margaret A. Taub, Donna Arnett, Kari E. North, Laura M. Raffield, April P. Carson, Margaret F. Doyle, Stephen S. Rich, Jerome I. Rotter, Xiuqing Guo, Nancy J. Cox, Dan M. Roden, Nora Franceschini, Pinkal Desai, Alex P. Reiner, Paul L. Auer, Paul A. Scheet, Siddhartha Jaiswal, Joshua S. Weinstock, and Alexander G. Bick
Subjects: Science
Abstract: Abstract Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.
Published: 2024
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44. Towards a Tutoring System to Support Robotics Activities in Classrooms -- Two Wizard-of-Oz Studies

Author: Schulz, Sandra, McLaren, Bruce M., and Pinkwart, Niels
Abstract: This paper develops a method for the construction and evaluation of cognitive models to support students in their problem-solving skills during robotics in school, aiming to build a basis for an implementation of a tutoring system in the future. Two Wizard-of-Oz studies were conducted, one in the classroom and one in the lab. Based on the cognitive model, the human wizards gave support to 20 students working in pairs. The studies were video recorded and a qualitative analysis was conducted. This qualitative research approach is described in detail. The evaluation of the studies showed that students reacted mostly positively to the wizards. We also uncovered ways in which students' problem-solving skills could be improved. Based on the evaluation and observations of the Wizard-of-Oz studies, the paper proposes a design for a future robotics skills tutoring system.
Published: 2023
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45. Increased risk of kidney failure in patients with genetic kidney disorders

Author: Elliott, Mark D., Vena, Natalie, Marasa, Maddalena, Cocchi, Enrico, Bheda, Shiraz, Bogyo, Kelsie, Shang, Ning, Zanoni, Francesca, Verbitsky, Miguel, Wang, Chen, Kolupaeva, Victoria, Jin, Gina, Sofer, Maayan, Pena, Rafael Gras, Canetta, Pietro A., Bomback, Andrew S., Guay-Woodford, Lisa M., Hou, Jean, Gillespie, Brenda W., Robinson, Bruce M., Klein, Jon B., Rheault, Michelle N., Smoyer, William E., Greenbaum, Larry A., Holzman, Larry B., Falk, Ronald J., Parsa, Afshin, Sanna-Cherchi, Simone, Mariani, Laura H., Kretzler, Matthias, Kiryluk, Krzysztof, and Gharavi, Ali G.
Subjects: Physiological aspects, Complications and side effects, Risk factors, Medical research, Genetic disorders -- Physiological aspects -- Complications and side effects, Chronic kidney failure -- Risk factors -- Physiological aspects, Medicine, Experimental
Abstract: Introduction Chronic kidney disease (CKD) is a heterogeneous group of conditions affecting over 10% of the population, causing substantial morbidity and mortality (1-3). Genetic kidney disorders are well-recognized causes of [...], BACKGROUND. It is unknown whether the risk of kidney disease progression and failure differs between patients with and without genetic kidney disorders. METHODS. Three cohorts were evaluated: the prospective Cure Glomerulonephropathy Network (CureGN) and 2 retrospective cohorts from Columbia University, including 5,727 adults and children with kidney disease from any etiology who underwent whole-genome or exome sequencing. The effects of monogenic kidney disorders and APOL1 kidney-risk genotypes on the risk of kidney failure, estimated glomerular filtration rate (eGFR) decline, and disease remission rates were evaluated along with diagnostic yields and the impact of American College of Medical Genetics secondary findings (ACMG SFs). RESULTS. Monogenic kidney disorders were identified in 371 patients (6.5%), high-risk APOL1 genotypes in 318 (5.5%), and ACMG SFs in 100 (5.2%). Family history of kidney disease was the strongest predictor of monogenic disorders. After adjustment for traditional risk factors, monogenic kidney disorders were associated with an increased risk of kidney failure (hazard ratio [HR] = 1.72), higher rate of eGFR decline (-3.06 vs. 0.25 mL/min/1.73 [m.sup.2]/year), and lower risk of complete remission ([odds ratio.sub.Not achieving CR] = 5.25). High-risk APOL1 genotypes were associated with an increased risk of kidney failure (HR = 1.67) and faster eGFR decline (-2.28 vs. 0.25 mL/min/1.73 [m.sup.2]), replicating prior findings. ACMG SFs were not associated with personal or family history of associated diseases, but were predicted to impact care in 70% of cases. CONCLUSIONS. Monogenic kidney disorders were associated with an increased risk of kidney failure, faster eGFR decline, and lower rates of complete remission, suggesting opportunities for early identification and intervention based on molecular diagnosis. TRIAL REGISTRATION. NA. FUNDING. National Institute of Diabetes and Digestive and Kidney Diseases grants U24DK100845 (formerly UM1DK100845), U01DK100846 (formerly UM1DK100846), U01DK100876 (formerly UM1DK100876), U01DK100866 (formerly UM1DK100866), U01DK100867 (formerly UM1DK100867), U24DK100845, DK081943, RC2DK116690, 2U01DK100876, 1R01DK136765, 5R01DK082753, and RC2-DK122397; NephCure Kidney International; Department of Defense Research Awards PR201425, W81XWH-16-1-0451, and W81XWH-22-1-0966; National Center for Advancing Translational Sciences grant UL1TR001873; National Library of Medicine grant R01LM013061; National Human Genome Research Institute grant 2U01HG008680.
Published: 2024
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46. Corrigendum

Author: Ding, Jingzhong, Nguyen, Anh Tram, Lohman, Kurt, Hensley, Michael T., Parker, Daniel, Hou, Li, Taylor, Jackson, Voora, Deepak, Sawyer, Janet K., Boudyguina, Elena, Bancks, Michael P., Bertoni, Alain, Pankow, James S., Rotter, Jerome I., Goodarzi, Mark O., Tracy, Russell P., Murdoch, David M., Duprez, Daniel, Rich, Stephen S., Psaty, Bruce M., Siscovick, David, Newgard, Christopher B., Herrington, David, Hoeschele, Ina, Shea, Steven, Stein, James H., Patel, Manesh, Post, Wendy, Jacobs, David, Jr., Parks, John S., and Liu, Yongmei
Abstract: Original citation: J Clin Invest. 2024; 134(10):e173278. https://doi.org/10.1172/JCI173278. Citation for this corrigendum: J Clin Invest. 2024;134(16):e185290. https://doi.org/10.1172/JCI185290 During the preparation of this manuscript, Daniel Duprez's information was inadvertently omitted from [...]
Published: 2024
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47. Association of Mitochondrial DNA Copy Number With Brain MRI Markers and Cognitive Function

Author: Zhang, Yuankai, Liu, Xue, Wiggins, Kerri L, Kurniansyah, Nuzulul, Guo, Xiuqing, Rodrigue, Amanda L, Zhao, Wei, Yanek, Lisa R, Ratliff, Scott M, Pitsillides, Achilleas, Aguirre Patiño, Juan Sebastian, Sofer, Tamar, Arking, Dan E, Austin, Thomas R, Beiser, Alexa S, Blangero, John, Boerwinkle, Eric, Bressler, Jan, Curran, Joanne E, Hou, Lifang, Hughes, Timothy M, Kardia, Sharon LR, Launer, Lenore J, Levy, Daniel, Mosley, Thomas H, Nasrallah, Ilya M, Rich, Stephen S, Rotter, Jerome I, Seshadri, Sudha, Tarraf, Wassim, González, Kevin A, Ramachandran, Vasan, Yaffe, Kristine, Nyquist, Paul A, Psaty, Bruce M, DeCarli, Charles S, Smith, Jennifer A, Glahn, David C, González, Hector M, Bis, Joshua C, Fornage, Myriam, Heckbert, Susan R, Fitzpatrick, Annette L, Liu, Chunyu, Satizabal, Claudia L, Aguilera, Norma, Ament, Seth, Ammous, Farah, Arnett, Donna K, Becker, Diane, Bis, Joshua, Blue, Elizabeth, Breaux, Camille, Chaar, Dima, MHI, Clarkson-Townsend, Danielle, Cooper, Brigidann, Coresh, Josef, Correa, Adolfo, DeStefano, Anita, Ding, Jingzhong, Fardo, David, Fitzpatrick, Annette, French, Jennifer, Glahn, David, Gonzalez, Hector, Granot-Hershkovitz, Einat, Hanly, Patrick, Hayden, Kathleen, Heckbert, Susan, Heemann, Scott, Horvath, Steve, Hoth, Karin, Hughes, Timothy, Jaiswal, Sidd, Jian, Xueqiu, Katsumata, Yuriko, Kho, Minjung, Kooperberg, Charles, Launer, Lenore, Lin, Honghuang, Litkowski, Elizabeth, Longstreth, Will, Martin, Alexandra, Mayeux, Richard, Mikulla, Julie, Miller, Amy, Misra, Biswapriya, Mosley, Thomas, Nyquist, Paul, O'Connell, Jeff, Olivier, Michael, Peloso, Gina, Perry, James, Psaty, Bruce, Purcell, Shaun, and Raffield, Laura
Subjects: Biomedical and Clinical Sciences, Neurosciences, Clinical Sciences, Alzheimer's Disease, Neurodegenerative, Dementia, Aging, Biomedical Imaging, Acquired Cognitive Impairment, Behavioral and Social Science, Brain Disorders, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Clinical Research, Precision Medicine, Genetics, 4.1 Discovery and preclinical testing of markers and technologies, 2.1 Biological and endogenous factors, Mental health, Neurological, Good Health and Well Being, Middle Aged, Humans, Female, Aged, Male, DNA, Mitochondrial, DNA Copy Number Variations, Prospective Studies, Cross-Sectional Studies, Alzheimer Disease, Magnetic Resonance Imaging, Cognition, Brain, NHLBI Trans-Omics for Precision Medicine (TOPMed) program, Mitochondrial and Neurocognitive Working Groups, Cognitive Sciences, Neurology & Neurosurgery, Clinical sciences
Abstract: Background and objectivesPrevious studies suggest that lower mitochondrial DNA (mtDNA) copy number (CN) is associated with neurodegenerative diseases. However, whether mtDNA CN in whole blood is related to endophenotypes of Alzheimer disease (AD) and AD-related dementia (AD/ADRD) needs further investigation. We assessed the association of mtDNA CN with cognitive function and MRI measures in community-based samples of middle-aged to older adults.MethodsWe included dementia-free participants from 9 diverse community-based cohorts with whole-genome sequencing in the Trans-Omics for Precision Medicine (TOPMed) program. Circulating mtDNA CN was estimated as twice the ratio of the average coverage of mtDNA to nuclear DNA. Brain MRI markers included total brain, hippocampal, and white matter hyperintensity volumes. General cognitive function was derived from distinct cognitive domains. We performed cohort-specific association analyses of mtDNA CN with AD/ADRD endophenotypes assessed within ±5 years (i.e., cross-sectional analyses) or 5-20 years after blood draw (i.e., prospective analyses) adjusting for potential confounders. We further explored associations stratified by sex and age (
Published: 2023

48. Investigating Gene-Diet Interactions Impacting the Association Between Macronutrient Intake and Glycemic Traits.

Author: Westerman, Kenneth E, Walker, Maura E, Gaynor, Sheila M, Wessel, Jennifer, DiCorpo, Daniel, Ma, Jiantao, Alonso, Alvaro, Aslibekyan, Stella, Baldridge, Abigail S, Bertoni, Alain G, Biggs, Mary L, Brody, Jennifer A, Chen, Yii-Der Ida, Dupuis, Joseé, Goodarzi, Mark O, Guo, Xiuqing, Hasbani, Natalie R, Heath, Adam, Hidalgo, Bertha, Irvin, Marguerite R, Johnson, W Craig, Kalyani, Rita R, Lange, Leslie, Lemaitre, Rozenn N, Liu, Ching-Ti, Liu, Simin, Moon, Jee-Young, Nassir, Rami, Pankow, James S, Pettinger, Mary, Raffield, Laura M, Rasmussen-Torvik, Laura J, Selvin, Elizabeth, Senn, Mackenzie K, Shadyab, Aladdin H, Smith, Albert V, Smith, Nicholas L, Steffen, Lyn, Talegakwar, Sameera, Taylor, Kent D, de Vries, Paul S, Wilson, James G, Wood, Alexis C, Yanek, Lisa R, Yao, Jie, Zheng, Yinan, Boerwinkle, Eric, Morrison, Alanna C, Fornage, Miriam, Russell, Tracy P, Psaty, Bruce M, Levy, Daniel, Heard-Costa, Nancy L, Ramachandran, Vasan S, Mathias, Rasika A, Arnett, Donna K, Kaplan, Robert, North, Kari E, Correa, Adolfo, Carson, April, Rotter, Jerome I, Rich, Stephen S, Manson, JoAnn E, Reiner, Alexander P, Kooperberg, Charles, Florez, Jose C, Meigs, James B, Merino, Jordi, Tobias, Deirdre K, Chen, Han, and Manning, Alisa K
Subjects: Biomedical and Clinical Sciences, Nutrition and Dietetics, Nutrition, Diabetes, Human Genome, Minority Health, Genetics, Cardiovascular, Health Disparities, Prevention, Precision Medicine, Clinical Research, Metabolic and endocrine, Good Health and Well Being, Humans, Glycated Hemoglobin, Diet, Diabetes Mellitus, Eating, Guanine Nucleotide Dissociation Inhibitors, Genome-Wide Association Study, Medical and Health Sciences, Endocrinology & Metabolism, Biomedical and clinical sciences
Abstract: Few studies have demonstrated reproducible gene-diet interactions (GDIs) impacting metabolic disease risk factors, likely due in part to measurement error in dietary intake estimation and insufficient capture of rare genetic variation. We aimed to identify GDIs across the genetic frequency spectrum impacting the macronutrient-glycemia relationship in genetically and culturally diverse cohorts. We analyzed 33,187 participants free of diabetes from 10 National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program cohorts with whole-genome sequencing, self-reported diet, and glycemic trait data. We fit cohort-specific, multivariable-adjusted linear mixed models for the effect of diet, modeled as an isocaloric substitution of carbohydrate for fat, and its interactions with common and rare variants genome-wide. In main effect meta-analyses, participants consuming more carbohydrate had modestly lower glycemic trait values (e.g., for glycated hemoglobin [HbA1c], -0.013% HbA1c/250 kcal substitution). In GDI meta-analyses, a common African ancestry-enriched variant (rs79762542) reached study-wide significance and replicated in the UK Biobank cohort, indicating a negative carbohydrate-HbA1c association among major allele homozygotes only. Simulations revealed that >150,000 samples may be necessary to identify similar macronutrient GDIs under realistic assumptions about effect size and measurement error. These results generate hypotheses for further exploration of modifiable metabolic disease risk in additional cohorts with African ancestry.Article highlightsWe aimed to identify genetic modifiers of the dietary macronutrient-glycemia relationship using whole-genome sequence data from 10 Trans-Omics for Precision Medicine program cohorts. Substitution models indicated a modest reduction in glycemia associated with an increase in dietary carbohydrate at the expense of fat. Genome-wide interaction analysis identified one African ancestry-enriched variant near the FRAS1 gene that may interact with macronutrient intake to influence hemoglobin A1c. Simulation-based power calculations accounting for measurement error suggested that substantially larger sample sizes may be necessary to discover further gene-macronutrient interactions.
Published: 2023

49. Asynchronous Posting and Reading Both Reflect Communities of Inquiry

Author: Magon, Juss Kaur and Shore, Bruce M.
Abstract: This descriptive case study explored the presence of a community of inquiry among 4492 secondary learners enrolled in four asynchronous online discussion forums over a full year. The forums (Ethics and Philosophy, Reading, Astronomy and Space, and General Debates, among others not studied) were external to the students' schools across England. The data had been archived by the sponsoring organisation. We coded 3,113 transcribed messages posted or read by students using Garrison's Community-of-Inquiry model and coding tools--addressing social, cognitive, and teaching presence within the interactions, plus 307 online questionnaire responses from a cross-section of participants about reasons for posting or not and overall participation plus representative quotes were also presented. Of the 4,492 enrollees, 1,523 (34%) posted messages, 1,748 (39%) only read or viewed posts, and 1,222 (27%) never logged in. This posting rate was almost quadruple the rate previously reported for online communities. Participation was also wider. The largest numbers of messages reflected community-of-inquiry social presence, especially following-up others' messages. Cognitive presence particularly reflected sharpening thinking skills and knowledge. Teaching presence included asking stimulating questions and providing encouragement. Students who only viewed others' messages logged in frequently, reported stimulation and strong benefits in learning skills, and only occasionally reported shyness or intimidation. Active student participation and engagement include more than posting messages; they also include reading or viewing others' posts. Community of inquiry was highly evident in the asynchronous, secondary, online setting. An asynchronous platform, with effective teaching presence, can support important qualities of a community of inquiry.
Published: 2022

50. Comparative efficacy and safety of anti-cryptosporidial agents: an in vitro study on nitazoxanide, halofuginone lactate, KDU731, and paromomycin against Cryptosporidium parvum

Author: Saffron T. G. Whitta, Bridget Lamont, Rossarin Suwanarusk, Bruce M. Russell, and Morad-Rémy Muhsin-Sharafaldine
Subjects: Cryptosporidium, anti-parasitics, cryptosporidiosis, apicomplexa pathogen, nitazoxanide, halofuginone lactate, Microbiology, QR1-502
Abstract: This study evaluated the in vitro effectiveness of anti-cryptosporidial agents nitazoxanide, halofuginone, the pyrazolopyridine analog KDU731, and paromomycin (PMC) in combating the significant zoonotic pathogen Cryptosporidium parvum. The study utilized HCT-8 host cells to culture C. parvum and fluorescent microscopy/quantitative PCR (qPCR) for detecting parasitic growth. The efficacy of the compounds was assessed by calculating their inhibitory concentrations (IC) against the total growth of C. parvum at 48 h post-infection. The study further investigated the impact of these compounds on early parasitophorous vacuole (PV) formation, merozoite egress, host cell viability, and cell growth cycle. KDU731 displayed the most promising profile, with low nanomolar (102 nM ± 2.28) activity and negligible host cell toxicity. This study offers new insights into the relative efficacy and safety of various anti-cryptosporidial compounds, highlighting their stage-specific effects on C. parvum and the consequential impacts on host cells. Identifying safe and effective anti-cryptosporidial agents contributes significantly to the One Health approach, which emphasizes the importance of integrated strategies in controlling zoonotic diseases.
Published: 2024
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