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1. Quark: Real-time, High-resolution, and General Neural View Synthesis

Author

Flynn, John, Broxton, Michael, Murmann, Lukas, Chai, Lucy, DuVall, Matthew, Godard, Clément, Heal, Kathryn, Kaza, Srinivas, Lombardi, Stephen, Luo, Xuan, Achar, Supreeth, Prabhu, Kira, Sun, Tiancheng, Tsai, Lynn, and Overbeck, Ryan

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

We present a novel neural algorithm for performing high-quality, high-resolution, real-time novel view synthesis. From a sparse set of input RGB images or videos streams, our network both reconstructs the 3D scene and renders novel views at 1080p resolution at 30fps on an NVIDIA A100. Our feed-forward network generalizes across a wide variety of datasets and scenes and produces state-of-the-art quality for a real-time method. Our quality approaches, and in some cases surpasses, the quality of some of the top offline methods. In order to achieve these results we use a novel combination of several key concepts, and tie them together into a cohesive and effective algorithm. We build on previous works that represent the scene using semi-transparent layers and use an iterative learned render-and-refine approach to improve those layers. Instead of flat layers, our method reconstructs layered depth maps (LDMs) that efficiently represent scenes with complex depth and occlusions. The iterative update steps are embedded in a multi-scale, UNet-style architecture to perform as much compute as possible at reduced resolution. Within each update step, to better aggregate the information from multiple input views, we use a specialized Transformer-based network component. This allows the majority of the per-input image processing to be performed in the input image space, as opposed to layer space, further increasing efficiency. Finally, due to the real-time nature of our reconstruction and rendering, we dynamically create and discard the internal 3D geometry for each frame, generating the LDM for each view. Taken together, this produces a novel and effective algorithm for view synthesis. Through extensive evaluation, we demonstrate that we achieve state-of-the-art quality at real-time rates. Project page: https://quark-3d.github.io/, Comment: SIGGRAPH Asia 2024 camera ready version; project page https://quark-3d.github.io/

Published
2024

2. White paper on light sterile neutrino searches and related phenomenology

Author

Acero, MA, Argüelles, CA, Hostert, M, Kalra, D, Karagiorgi, G, Kelly, KJ, Littlejohn, BR, Machado, P, Pettus, W, Toups, M, Ross-Lonergan, M, Sousa, A, Surukuchi, PT, Wong, YYY, Abdallah, W, Abdullahi, AM, Akutsu, R, Alvarez-Ruso, L, Alves, DSM, Aurisano, A, Balantekin, AB, Berryman, JM, Bertólez-Martínez, T, Brunner, J, Blennow, M, Bolognesi, S, Borusinski, M, Chen, TY, Cianci, D, Collin, G, Conrad, JM, Crow, B, Denton, PB, Duvall, M, Fernández-Martinez, E, Fong, CS, Foppiani, N, Forero, DV, Friend, M, García-Soto, A, Giganti, C, Giunti, C, Gandhi, R, Ghosh, M, Hardin, J, Heeger, KM, Ishitsuka, M, Izmaylov, A, Jones, BJP, Jordan, JR, Kamp, NW, Katori, T, Kim, SB, Koerner, LW, Lamoureux, M, Lasserre, T, Leach, KG, Learned, J, Li, YF, Link, JM, Louis, WC, Mahn, K, Meyers, PD, Maricic, J, Markoff, D, Maruyama, T, Mertens, S, Minakata, H, Mocioiu, I, Mooney, M, Moulai, MH, Nunokawa, H, Ochoa-Ricoux, JP, Oh, YM, Ohlsson, T, Päs, H, Pershey, D, Robertson, RGH, Rosauro-Alcaraz, S, Rott, C, Roy, S, Salvado, J, Scott, M, Seo, SH, Shaevitz, MH, Smiley, M, Spitz, J, Stachurska, J, Tammaro, M, Thakore, T, Ternes, CA, Thompson, A, Tseng, S, Vogelaar, B, Weiss, T, Wendell, RA, Wilson, RJ, Wright, T, Xin, Z, and Yang, BS

Subjects
Nuclear and Plasma Physics, Particle and High Energy Physics, Physical Sciences, Atomic, Molecular, Nuclear, Particle and Plasma Physics, Nuclear & Particles Physics, Nuclear and plasma physics, Particle and high energy physics
Published
2024

3. Computationally Checking if a Reaction Network is Monotone or Non-expansive

Author

Duvall, Alon

Subjects
Mathematics - Dynamical Systems, Quantitative Biology - Molecular Networks
Abstract

We describe a procedure for testing for non-expansivity and monotonicity of reaction networks. We demonstrate how this procedure can be used to generate explicit norms for which a reaction network is non-expansive, cones for which the system is monotone, or to prove no such objects exist. We demonstrate how this procedure recovers past results, generates new ones, as well as proves that certain reaction networks will not be monotone or non-expansive with respect to any cone or norm. Lastly, we also note a duality relationship for monotone reaction networks.

Published
2024

4. Polarization Measurement of Gamma-ray Bursts with Fermi-GBM: The Case of GRB 180720B

Author

Veres, P., Duvall, W., Goldstein, A., Briggs, M. S., and Grove, J. E.

Subjects
Astrophysics - High Energy Astrophysical Phenomena
Abstract

To achieve confident non-zero polarization measurements for gamma-ray bursts (GRBs) we need sensitive polarimeters and bright GRBs. Here we report on the polarimetric analysis of the bright GRB 180720B using the \Fermi Gamma-ray Burst Monitor (GBM). We rely on the detection of photons that scattered off Earth's atmosphere and into GBM from this burst. Polarized gamma-rays will exhibit a characteristic pattern when scattering off the atmosphere that differs from an unpolarized beam. We compare the measured photon counts in the GBM detectors with extensive simulations of polarized beams to derive the most probable polarization degree (PD) and angle (PA). For the entire GRB, we find PD$=72^{+24}_{-30}\% ~(1\sigma)$ and PA$=91^{+11}_{-9}$ deg ($1\sigma$, equatorial frame). Interestingly, the PA value is broadly consistent with an early optical PA measurement by the Kanata telescope, starting shortly after the end of the prompt emission. The consistency of PAs lends support for this method. The relatively high polarization degree (albeit with large uncertainties) agrees with similar past measurements suggesting that some GRBs might be highly polarized. This will be confirmed or refuted by the upcoming dedicated GRB polarimeters., Comment: 8 pages, 5 figures, submitted to AAS journals

Published
2024

6. Interplay between Contractivity and Monotonicity for Reaction Networks

Author

Duvall, Alon, Al-Radhawi, M. Ali, Jatkar, Dhruv D., and Sontag, Eduardo

Subjects
Mathematics - Dynamical Systems, Quantitative Biology - Molecular Networks
Abstract

This work studies relationships between monotonicity and contractivity, and applies the results to establish that many reaction networks are weakly contractive, and thus, under appropriate compactness conditions, globally convergent to equilibria. Verification of these properties is achieved through a novel algorithm that can be used to generate cones for monotone systems. The results given here allow a unified proof of global convergence for several classes of networks that had been previously studied in the literature.

Published
2024

7. A remark on omega limit sets for non-expansive dynamics

Author

Duvall, Alon and Sontag, Eduardo D.

Subjects
Mathematics - Dynamical Systems
Abstract

In this paper, we study systems of time-invariant ordinary differential equations whose flows are non-expansive with respect to a norm, meaning that the distance between solutions may not increase. Since non-expansiveness (and contractivity) are norm-dependent notions, the topology of $\omega$-limit sets of solutions may depend on the norm. For example, and at least for systems defined by real-analytic vector fields, the only possible $\omega$-limit sets of systems that are non-expansive with respect to polyhedral norms (such as $\ell^p$ norms with $p =1$ or $p=\infty$) are equilibria. In contrast, for non-expansive systems with respect to Euclidean ($\ell^2$) norm, other limit sets may arise (such as multi-dimensional tori): for example linear harmonic oscillators are non-expansive (and even isometric) flows, yet have periodic orbits as $\omega$-limit sets. This paper shows that the Euclidean linear case is what can be expected in general: for flows that are contractive with respect to any strictly convex norm (such as $\ell^p$ for any $p\not=1,\infty$), and if there is at least one bounded solution, then the $\omega$-limit set of every trajectory is also an omega limit set of a linear time-invariant system., Comment: 8 pages

Published
2024

8. Competition for binding targets results in paradoxical effects for simultaneous activator and repressor action -- Extended Version

Author

Al-Radhawi, M. Ali, Manoj, Krishna, Jatkar, Dhruv D., Duvall, Alon, Del Vecchio, Domitilla, and Sontag, Eduardo D.

Subjects
Quantitative Biology - Molecular Networks, Quantitative Biology - Biomolecules
Abstract

In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of the element being regulated. It has been postulated that this paradoxical behavior can be explained by activating and repressing transcription factors competing for binding to other possible targets. It is very difficult to prove this hypothesis in mammalian cells, due to the large number of potential players and the complexity of endogenous intracellular regulatory networks. Instead, this paper analyzes this issue through an analogous synthetic biology construct which aims to reproduce the paradoxical behavior using standard bacterial gene expression networks. The paper first reviews the motivating cancer biology work, and then describes a proposed synthetic construct. A mathematical model is formulated, and basic properties of uniqueness of steady states and convergence to equilibria are established, as well as an identification of parameter regimes which should lead to observing such paradoxical phenomena (more activator leads to less activity at steady state). A proof is also given to show that this is a steady-state property, and for initial transients the phenomenon will not be observed. This work adds to the general line of work of resource competition in synthetic circuits., Comment: 14 pages, 7 figures

Published
2024

9. Directional Response of Several Geometries for Reactor-Neutrino Detectors

Author

Duvall, Mark J., Crow, Brian C., Dornfest, Max A. A., Learned, John G., Bergevin, Marc F., Dazeley, Steven A., and Li, Viacheslav A.

Subjects
Physics - Instrumentation and Detectors, Astrophysics - Instrumentation and Methods for Astrophysics, High Energy Physics - Experiment, Nuclear Experiment
Abstract

We report simulation studies of six low-energy electron-antineutrino detector designs, with the goal of determining their ability to resolve the direction to an antineutrino source. Such detectors with target masses on the one-ton scale are well-suited to reactor monitoring at distances of 5--25 meters from the core. They can provide accurate measurements of reactor operating power, fuel mix, and burnup, as well as unsurpassed nuclear non-proliferation information in a non-contact cooperating reactor scenario such as those used by IAEA. A number of groups around the world are working on programs to develop detectors similar to some of those in this study. Here, we examine and compare several approaches to detector geometry for their ability not only to detect the inverse beta decay (IBD) reaction, but also to determine the source direction of incident antineutrinos. The information from these detectors provides insight into reactor power and burning profile, which is especially useful in constraining the clandestine production of weapons material. In a live deployment, a non-proliferation detector must be able to isolate the subject reactor, possibly from a field of much-larger power reactors; directional sensitivity can help greatly with this task. We also discuss implications for using such detectors in longer-distance observation of reactors, from a few km to hundreds of km. We have modeled six abstracted detector designs, including two for which we have operational data for validating our computer modeling and analytical processes. We have found that the most promising options, regardless of scale and range, have angular resolutions on the order of a few degrees, which is better than any yet achieved in practice by a factor of at least two., Comment: 16 pages, 17 figures Primary Author: Mark J. Duvall

Published
2024
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10. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program

Author

Verma, Anurag, Huffman, Jennifer E, Rodriguez, Alex, Conery, Mitchell, Liu, Molei, Ho, Yuk-Lam, Kim, Youngdae, Heise, David A, Guare, Lindsay, Panickan, Vidul Ayakulangara, Garcon, Helene, Linares, Franciel, Costa, Lauren, Goethert, Ian, Tipton, Ryan, Honerlaw, Jacqueline, Davies, Laura, Whitbourne, Stacey, Cohen, Jeremy, Posner, Daniel C, Sangar, Rahul, Murray, Michael, Wang, Xuan, Dochtermann, Daniel R, Devineni, Poornima, Shi, Yunling, Nandi, Tarak Nath, Assimes, Themistocles L, Brunette, Charles A, Carroll, Robert J, Clifford, Royce, Duvall, Scott, Gelernter, Joel, Hung, Adriana, Iyengar, Sudha K, Joseph, Jacob, Kember, Rachel, Kranzler, Henry, Kripke, Colleen M, Levey, Daniel, Luoh, Shiuh-Wen, Merritt, Victoria C, Overstreet, Cassie, Deak, Joseph D, Grant, Struan FA, Polimanti, Renato, Roussos, Panos, Shakt, Gabrielle, Sun, Yan V, Tsao, Noah, Venkatesh, Sanan, Voloudakis, Georgios, Justice, Amy, Begoli, Edmon, Ramoni, Rachel, Tourassi, Georgia, Pyarajan, Saiju, Tsao, Philip, O'Donnell, Christopher J, Muralidhar, Sumitra, Moser, Jennifer, Casas, Juan P, Bick, Alexander G, Zhou, Wei, Cai, Tianxi, Voight, Benjamin F, Cho, Kelly, Gaziano, J Michael, Madduri, Ravi K, Damrauer, Scott, and Liao, Katherine P

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Human Genome, 2.1 Biological and endogenous factors, Mental health, Humans, Male, Genetic Predisposition to Disease, Genetic Variation, Genome-Wide Association Study, Longitudinal Studies, Polymorphism, Single Nucleotide, Quantitative Trait Loci, United States, United States Department of Veterans Affairs, Veterans, Female, General Science & Technology
Abstract

One of the justifiable criticisms of human genetic studies is the underrepresentation of participants from diverse populations. Lack of inclusion must be addressed at-scale to identify causal disease factors and understand the genetic causes of health disparities. We present genome-wide associations for 2068 traits from 635,969 participants in the Department of Veterans Affairs Million Veteran Program, a longitudinal study of diverse United States Veterans. Systematic analysis revealed 13,672 genomic risk loci; 1608 were only significant after including non-European populations. Fine-mapping identified causal variants at 6318 signals across 613 traits. One-third (n = 2069) were identified in participants from non-European populations. This reveals a broadly similar genetic architecture across populations, highlights genetic insights gained from underrepresented groups, and presents an extensive atlas of genetic associations.

Published
2024

11. Clinical and genetic risk factors for progressive fibrosis in metabolic dysfunction-associated steatotic liver disease.

Author

Kaplan, David, Teerlink, Craig, Schwantes-An, Tae-Hwi, Norden-Krichmar, Trina, DuVall, Scott, Morgan, Timothy, Tsao, Philip, Voight, Benjamin, Lynch, Julie, Vujković, Marijana, and Chang, Kyong-Mi

Subjects
Humans, Male, Female, Liver Cirrhosis, Middle Aged, Retrospective Studies, Disease Progression, Genome-Wide Association Study, Risk Factors, Aged, Membrane Proteins, Fatty Liver, Biomarkers, Non-alcoholic Fatty Liver Disease, Acyltransferases, Phospholipases A2, Calcium-Independent
Abstract

BACKGROUND: Fibrosis-4 (FIB4) is a recommended noninvasive test to assess hepatic fibrosis among patients with metabolic dysfunction-associated steatotic liver disease (MASLD). Here, we used FIB4 trajectory over time (ie, slope of FIB4) as a surrogate marker of liver fibrosis progression and examined if FIB4 slope is associated with clinical and genetic factors among individuals with clinically defined MASLD within the Million Veteran Program Cohort. METHODS: In this retrospective cohort study, FIB4 slopes were estimated through linear regression for participants with clinically defined MASLD and FIB4

Published
2024

12. Exploring the Interagency Collaboration between a Pediatric Oncology Health Care Setting and Community Schools

Author

Evan Rooney, Ayanna A. Johnson, Sarah Klein, Niki Jurbergs, Anne Duvall, R. Elyse Heidelberg, Brian S. Potter, Jennifer Harman, Emily K. Browne, Anna M. Jones, and Rachel T. Webster

Abstract

Globally, approximately 400,000 youth are diagnosed with pediatric cancer each year. Treatment-related side effects, psychosocial challenges, and frequent school absences may adversely impact learning and the education experience among these youth. Efforts to enhance interagency collaboration between health care settings and community schools are imperative to facilitate school reintegration. The "Standards for the Psychosocial Care of Children with Cancer and Their Families" outline specific guidelines related to the continuity of education for students impacted by pediatric cancer. In particular, the "Academic Continuity and School Reentry Support" and "Monitoring and Assessment of Neuropsychological Outcomes" standards of care highlighted within this article align with extant programmatic efforts for transitioning hospitalized school-aged children back into community schools. This article aims to describe systematic programmatic efforts within hospital-based psychosocial programs that are consistent with the "Standards for the Psychosocial Care of Children with Cancer and Their Families," as well as interagency collaboration with community schools to support student-centered education for youth impacted by pediatric cancer. Resources for school psychologists, teachers, hospital-based programs, and others involved in student-centered education for pediatric cancer patients and survivors are presented.

Published
2024
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13. Direct-Acting Oral Anticoagulants and Potential Inconsistencies with FDA-Approved Dosing for Non-Valvular Atrial Fibrillation: A Retrospective Real-World Analysis Across Nine US Healthcare Systems

Author

DeLor, Bonnie, Glover, Jon J., Hartman, Timothy J., Manzey, Laura L., Ateya, Mohammad, Kelsh, Shelby, Taylor, Katie, Zemrak, Wesley R., Gowen, Jaclynne R., Parks, Ann, Gust, Carmen, Medico, Charles, Akpoji, Ukwen C., Naylor, Shane, Chou, Carolyn W., Fakelmann, Gregory, Hart, Sara, Wiethorn, Eryne E., Trinh, Thach, Wilson, William W., Bowen, Rachel, Stanton, Jennifer, Duvall, Laura, and Davis, Lynette T.

Published
2024
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17. Structural optimization of siRNA conjugates for albumin binding achieves effective MCL1-directed cancer therapy

Author

Hoogenboezem, Ella N., Patel, Shrusti S., Lo, Justin H., Cavnar, Ashley B., Babb, Lauren M., Francini, Nora, Gbur, Eva F., Patil, Prarthana, Colazo, Juan M., Michell, Danielle L., Sanchez, Violeta M., McCune, Joshua T., Ma, Jinqi, DeJulius, Carlisle R., Lee, Linus H., Rosch, Jonah C., Allen, Ryan M., Stokes, Larry D., Hill, Jordan L., Vickers, Kasey C., Cook, Rebecca S., and Duvall, Craig L.

Published
2024
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18. Comparing venetoclax in combination with hypomethylating agents to hypomethylating agent-based therapies for treatment naive TP53-mutated acute myeloid leukemia: results from the Consortium on Myeloid Malignancies and Neoplastic Diseases (COMMAND)

Author

Badar, Talha, Nanaa, Ahmad, Atallah, Ehab, Shallis, Rory M., Guilherme, Sacchi de Camargo Correia, Goldberg, Aaron D., Saliba, Antoine N., Patel, Anand, Bewersdorf, Jan P., DuVall, Adam S., Bradshaw, Danielle, Abaza, Yasmin, Murthy, Guru Subramanian Guru, Palmisiano, Neil, Zeidan, Amer M., Kota, Vamsi, and Litzow, Mark R.

Published
2024
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19. Longitudinal assessment of health-related quality of life in patients with adult congenital heart disease undergoing cardiac surgeryCentral MessagePerspective

Author

Brittany A. Potz, MD, Justin A. Robinson, MD, Jeevanantham Rajeswaran, PhD, Carla Duvall, MSN, Beata Earl, BS, John Urchek, BS, Natalie Salvatore, DNP, MBA, RN, Lars G. Svensson, MD, PhD, and Tara Karamlou, MD, MSc

Subjects
adult congenital heart disease, cardiac surgery, quality of life, social determinants of health, survey, Diseases of the circulatory (Cardiovascular) system, RC666-701, Surgery, RD1-811
Abstract

Objective: The study objective was to assess longitudinal postoperative health-related quality of life among patients with adult congenital heart disease facilitated by a novel electronic medical record–based patient-reported outcomes follow-up platform. Methods: From January 2022 to October 2023, 559 patients with adult congenital heart disease underwent cardiac surgery; 491 (88%) completed a 23-element health-related quality of life questionnaire covering 3 domains (physical, mental, and social) yielding 911 assessments. Automated questionnaires via electronic medical record were sent at 7 days preoperatively and postoperatively at 1, 3, 6, and 12 months. Nonlinear multiphase mixed effects models and boosting approach using multivariate trees were used to assess longitudinal trends and the relationship among patient characteristics, clinical variables, and health-related quality of life outcomes. Results: Mean age of patients was 53 years (range, 19-86), 238 (43%) were female, 109 (20%) were STAT category 3 or 4, postoperative mortality was 0, and stroke was 4 (0.7%). Diagnosis included hypertrophic obstructive cardiomyopathy (276, 50%), anomalous coronary artery (42, 7.5%), congenital aortic valve disease (42, 7.5%), bicuspid aortic valve (64, 12%), and aortic aneurysm (25, 4.5%). Although baseline health-related quality of life scores were below population norms, rapid postoperative increases were seen in physical, mental, and social scores, surpassing population norms between 2 and 6 months. Patients with higher baseline health-related quality of life had higher longitudinal scores. Female patients and those of Black race had higher Area Deprivation Index and lower postoperative physical health-related quality of life scores. Conclusions: Patients with adult congenital heart disease require lifelong medical surveillance and repeated interventions. Our innovative electronic medical record–embedded time-series tool assessing health-related quality of life after cardiac surgery shows improved patient-reported outcomes across mental, physical, and social domains that endure through at least the first postoperative year.

Published
2024
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21. Global exponential stability (and contraction of an unforced system) does not imply entrainment to periodic inputs

Author

Duvall, Alon and Sontag, Eduardo

Subjects
Mathematics - Optimization and Control, 93D23
Abstract

It is often of interest to know which systems will approach a periodic trajectory when given a periodic input. Results are available for certain classes of systems, such as contracting systems, showing that they always entrain to periodic inputs. In contrast to this, we demonstrate that there exist systems which are globally exponentially stable yet do not entrain to a periodic input. This could be seen as surprising, as it is known that globally exponentially stable systems are in fact contracting with respect to some Riemannian metric., Comment: 7 pages, 1 figure

Published
2023

22. Agent orange exposure and prostate cancer risk in the million veteran program

Author

Pagadala, Meghana S, Lui, Asona J, Zhong, Allison Y, Lynch, Julie A, Karunamuni, Roshan, Lee, Kyung Min, Plym, Anna, Rose, Brent S, Carter, Hannah K, Kibel, Adam S, DuVall, Scott L, Gaziano, J Michael, Panizzon, Matthew S, Hauger, Richard L, and Seibert, Tyler M

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Prostate Cancer, Cancer, Urologic Diseases, Humans, Male, Agent Orange, Prostatic Neoplasms, Veterans, Middle Aged, Aged, Vietnam Conflict, United States, Defoliants, Chemical, Risk Factors, 2, 4, 5-Trichlorophenoxyacetic Acid, 2, 4-Dichlorophenoxyacetic Acid, Polychlorinated Dibenzodioxins, prostate cancer, MVP, race/ ethnicity, health disparities, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

BackgroundThe US government considers veterans to have been exposed to Agent Orange if they served in Vietnam while the carcinogen was in use, and these veterans are often deemed at high risk of prostate cancer (PCa). Here, we assess whether presumed Agent Orange exposure is independently associated with increased risk of any metastatic or fatal PCa in a diverse Veteran cohort still alive in the modern era (at least 2011), when accounting for race/ethnicity, family history, and genetic risk.Patients and methodsParticipants in the Million Veteran Program (MVP; enrollment began in 2011) who were on active duty during the Vietnam War era (August 1964-April 1975) were included (n = 301,470). Agent Orange exposure was determined using the US government definition. Genetic risk was assessed via a validated polygenic hazard score. Associations with age at diagnosis of any PCa, metastatic PCa, and death from PCa were assessed via Cox proportional hazards models.Results and interpretationOn univariable analysis, exposure to Agent Orange was not associated with increased PCa (hazard ratio [HR]: 1.02, 95% confidence interval [CI]: 1.00-1.04, p = 0.06), metastatic PCa (HR: 0.98, 95% CI: 0.91-1.05, p = 0.55), or fatal PCa (HR: 0.94, 95% CI: 0.79-1.09, p = 0.41). When accounting for race/ethnicity and family history, Agent Orange exposure was independently associated with slightly increased risk of PCa (HR: 1.06, 95% CI: 1.04-1.09,

Published
2024

23. Phylogenomics and the rise of the angiosperms

Author

Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Epitawalage, Niroshini, Françoso, Elaine, Gallego-Paramo, Berta, McGinnie, Catherine, Negrão, Raquel, Roy, Shyamali R., Simpson, Lalita, Toledo Romero, Eduardo, Barber, Vanessa M. A., Botigué, Laura, Clarkson, James J., Cowan, Robyn S., Dodsworth, Steven, Johnson, Matthew G., Kim, Jan T., Pokorny, Lisa, Wickett, Norman J., Antar, Guilherme M., DeBolt, Lucinda, Gutierrez, Karime, Hendriks, Kasper P., Hoewener, Alina, Hu, Ai-Qun, Joyce, Elizabeth M., Kikuchi, Izai A. B. S., Larridon, Isabel, Larson, Drew A., de Lírio, Elton John, Liu, Jing-Xia, Malakasi, Panagiota, Przelomska, Natalia A. S., Shah, Toral, Viruel, Juan, Allnutt, Theodore R., Ameka, Gabriel K., Andrew, Rose L., Appelhans, Marc S., Arista, Montserrat, Ariza, María Jesús, Arroyo, Juan, Arthan, Watchara, Bachelier, Julien B., Bailey, C. Donovan, Barnes, Helen F., Barrett, Matthew D., Barrett, Russell L., Bayer, Randall J., Bayly, Michael J., Biffin, Ed, Biggs, Nicky, Birch, Joanne L., Bogarín, Diego, Borosova, Renata, Bowles, Alexander M. C., Boyce, Peter C., Bramley, Gemma L. C., Briggs, Marie, Broadhurst, Linda, Brown, Gillian K., Bruhl, Jeremy J., Bruneau, Anne, Buerki, Sven, Burns, Edie, Byrne, Margaret, Cable, Stuart, Calladine, Ainsley, Callmander, Martin W., Cano, Ángela, Cantrill, David J., Cardinal-McTeague, Warren M., Carlsen, Mónica M., Carruthers, Abigail J. A., de Castro Mateo, Alejandra, Chase, Mark W., Chatrou, Lars W., Cheek, Martin, Chen, Shilin, Christenhusz, Maarten J. M., Christin, Pascal-Antoine, Clements, Mark A., Coffey, Skye C., Conran, John G., Cornejo, Xavier, Couvreur, Thomas L. P., Cowie, Ian D., Csiba, Laszlo, Darbyshire, Iain, Davidse, Gerrit, Davies, Nina M. J., Davis, Aaron P., van Dijk, Kor-jent, Downie, Stephen R., Duretto, Marco F., Duvall, Melvin R., Edwards, Sara L., Eggli, Urs, Erkens, Roy H. J., Escudero, Marcial, de la Estrella, Manuel, Fabriani, Federico, Fay, Michael F., Ferreira, Paola de L., Ficinski, Sarah Z., Fowler, Rachael M., Frisby, Sue, Fu, Lin, Fulcher, Tim, Galbany-Casals, Mercè, Gardner, Elliot M., German, Dmitry A., Giaretta, Augusto, Gibernau, Marc, Gillespie, Lynn J., González, Cynthia C., Goyder, David J., Graham, Sean W., Grall, Aurélie, Green, Laura, Gunn, Bee F., Gutiérrez, Diego G., Hackel, Jan, Haevermans, Thomas, Haigh, Anna, Hall, Jocelyn C., Hall, Tony, Harrison, Melissa J., Hatt, Sebastian A., Hidalgo, Oriane, Hodkinson, Trevor R., Holmes, Gareth D., Hopkins, Helen C. F., Jackson, Christopher J., James, Shelley A., Jobson, Richard W., Kadereit, Gudrun, Kahandawala, Imalka M., Kainulainen, Kent, Kato, Masahiro, Kellogg, Elizabeth A., King, Graham J., Klejevskaja, Beata, Klitgaard, Bente B., Klopper, Ronell R., Knapp, Sandra, Koch, Marcus A., Leebens-Mack, James H., Lens, Frederic, Leon, Christine J., Léveillé-Bourret, Étienne, Lewis, Gwilym P., Li, De-Zhu, Li, Lan, Liede-Schumann, Sigrid, Livshultz, Tatyana, Lorence, David, Lu, Meng, Lu-Irving, Patricia, Luber, Jaquelini, Lucas, Eve J., Luján, Manuel, Lum, Mabel, Macfarlane, Terry D., Magdalena, Carlos, Mansano, Vidal F., Masters, Lizo E., Mayo, Simon J., McColl, Kristina, McDonnell, Angela J., McDougall, Andrew E., McLay, Todd G. B., McPherson, Hannah, Meneses, Rosa I., Merckx, Vincent S. F. T., Michelangeli, Fabián A., Mitchell, John D., Monro, Alexandre K., Moore, Michael J., Mueller, Taryn L., Mummenhoff, Klaus, Munzinger, Jérôme, Muriel, Priscilla, Murphy, Daniel J., Nargar, Katharina, Nauheimer, Lars, Nge, Francis J., Nyffeler, Reto, Orejuela, Andrés, Ortiz, Edgardo M., Palazzesi, Luis, Peixoto, Ariane Luna, Pell, Susan K., Pellicer, Jaume, Penneys, Darin S., Perez-Escobar, Oscar A., Persson, Claes, Pignal, Marc, Pillon, Yohan, Pirani, José R., Plunkett, Gregory M., Powell, Robyn F., Prance, Ghillean T., Puglisi, Carmen, Qin, Ming, Rabeler, Richard K., Rees, Paul E. J., Renner, Matthew, Roalson, Eric H., Rodda, Michele, Rogers, Zachary S., Rokni, Saba, Rutishauser, Rolf, de Salas, Miguel F., Schaefer, Hanno, Schley, Rowan J., Schmidt-Lebuhn, Alexander, Shapcott, Alison, Al-Shehbaz, Ihsan, Shepherd, Kelly A., Simmons, Mark P., Simões, André O., Simões, Ana Rita G., Siros, Michelle, Smidt, Eric C., Smith, James F., Snow, Neil, Soltis, Douglas E., Soltis, Pamela S., Soreng, Robert J., Sothers, Cynthia A., Starr, Julian R., Stevens, Peter F., Straub, Shannon C. K., Struwe, Lena, Taylor, Jennifer M., Telford, Ian R. H., Thornhill, Andrew H., Tooth, Ifeanna, Trias-Blasi, Anna, Udovicic, Frank, Utteridge, Timothy M. A., Del Valle, Jose C., Verboom, G. Anthony, Vonow, Helen P., Vorontsova, Maria S., de Vos, Jurriaan M., Al-Wattar, Noor, Waycott, Michelle, Welker, Cassiano A. D., White, Adam J., Wieringa, Jan J., Williamson, Luis T., Wilson, Trevor C., Wong, Sin Yeng, Woods, Lisa A., Woods, Roseina, Worboys, Stuart, Xanthos, Martin, Yang, Ya, Zhang, Yu-Xiao, Zhou, Meng-Yuan, Zmarzty, Sue, Zuloaga, Fernando O., Antonelli, Alexandre, Bellot, Sidonie, Crayn, Darren M., Grace, Olwen M., Kersey, Paul J., Leitch, Ilia J., Sauquet, Hervé, Smith, Stephen A., Eiserhardt, Wolf L., Forest, Félix, and Baker, William J.

Published
2024
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25. Real-time Likelihood Methods for Improved Gamma-ray Transient Detection and Localization

Author

Kerr, Matthew, Duvall, Wade, Johnson, Neil, Woolf, Richard, Grove, J. Eric, and Kim, Hannah

Subjects
Astrophysics - High Energy Astrophysical Phenomena, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

We present a maximum likelihood (ML) algorithm that is fast enough to detect gamma-ray transients in real time on low-performance processors often used for space applications. We validate the routine with simulations and find that, relative to algorithms based on excess counts, the ML method is nearly twice as sensitive, allowing detection of 240-280% more short gamma-ray bursts. We characterize a reference implementation of the code, estimating its computational complexity and benchmarking it on a range of processors. We exercise the reference implementation on archival data from the Fermi Gamma-ray Burst Monitor (GBM), verifying the sensitivity improvements. In particular, we show that the ML algorithm would have detected GRB 170817A even if it had been nearly four times fainter. We present an ad hoc but effective scheme for discriminating transients associated with background variations. We show that the on-board localizations generated by ML are accurate, but that refined off-line localizations require a detector response matrix with about ten times finer resolution than is current practice. Increasing the resolution of the GBM response matrix could substantially reduce the few-degree systematic uncertainty observed in the localizations of bright bursts., Comment: 18 pages, 11 figures

Published
2023
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28. Discretization-independent surrogate modeling of physical fields around variable geometries using coordinate-based networks

Author

James Duvall and Karthik Duraisamy

Subjects
aerodynamics, hypernetworks, neural networks, surrogate model, Engineering (General). Civil engineering (General), TA1-2040
Abstract

Numerical solutions of partial differential equations require expensive simulations, limiting their application in design optimization, model-based control, and large-scale inverse problems. Surrogate modeling techniques aim to decrease computational expense while retaining dominant solution features and characteristics. Existing frameworks based on convolutional neural networks and snapshot-matrix decomposition often rely on lossy pixelization and data-preprocessing, limiting their effectiveness in realistic engineering scenarios. Recently, coordinate-based multilayer perceptron networks have been found to be effective at representing 3D objects and scenes by regressing volumetric implicit fields. These concepts are leveraged and adapted in the context of physical-field surrogate modeling. Two methods toward generalization are proposed and compared: design-variable multilayer perceptron (DV-MLP) and design-variable hypernetworks (DVH). Each method utilizes a main network which consumes pointwise spatial information to provide a continuous representation of the solution field, allowing discretization independence and a decoupling of solution and model size. DV-MLP achieves generalization through the use of a design-variable embedding vector, while DVH conditions the main network weights on the design variables using a hypernetwork. The methods are applied to predict steady-state solutions around complex, parametrically defined geometries on non-parametrically-defined meshes, with model predictions obtained in less than a second. The incorporation of random Fourier features greatly enhanced prediction and generalization accuracy for both approaches. DVH models have more trainable weights than a similar DV-MLP model, but an efficient batch-by-case training method allows DVH to be trained in a similar amount of time as DV-MLP. A vehicle aerodynamics test problem is chosen to assess the method’s feasibility. Both methods exhibit promising potential as viable options for surrogate modeling, being able to process snapshots of data that correspond to different mesh topologies.

Published
2025
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29. Novel recombinant vaccinia virus-vectored vaccine affords complete protection against homologous Borrelia burgdorferi infection in mice

Author

Annabelle Pfeifle, Wanyue Zhang, Jingxin Cao, Sathya N. Thulasi Raman, Rose Anderson-Duvall, Levi Tamming, Caroline Gravel, Heather Coatsworth, Wangxue Chen, Michael J. W. Johnston, Simon Sauve, Michael Rosu-Myles, Lisheng Wang, and Xuguang Li

Subjects
Vaccinia virus, viral-vector vaccine, Borrelia burgdorferi, outer surface protein C, Lyme disease, antibodies, Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502
Abstract

The rising prevalence of Lyme disease (LD) in North America and Europe has emerged as a pressing public health concern. Despite the availability of veterinary LD vaccines, no vaccine is currently available for human use. Outer surface protein C (OspC) found on the outer membrane of the causative agent, Borrelia burgdorferi, has been identified as a promising target for LD vaccine development due to its sustained expression during mammalian infection. However, the efficacy and immunological mechanisms of LD vaccines solely targeting OspC are not well characterized. In this study, we developed an attenuated Vaccinia virus (VV) vectored vaccine encoding type A OspC (VV-OspC-A). Two doses of the VV-OspC-A vaccine conferred complete protection against homologous B. burgdorferi challenge in mice. Furthermore, the candidate vaccine also prevented the development of carditis and lymph node hyperplasia associated with LD. When investigating the humoral immune response to vaccination, VV-OspC-A was found to induce a robust antibody response predominated by the IgG2a subtype, indicating a Th1-bias. Using a novel quantitative flow cytometry assay, we also determined that elicited antibodies were capable of inducing antibody-dependent cellular phagocytosis in vitro. Finally, we demonstrated that VV-OspC-A vaccination generated a strong antigen-specific CD4+ T-cell response characterized by the secretion of numerous cytokines upon stimulation of splenocytes with OspC peptides. This study suggests a promising avenue for LD vaccine development utilizing viral vectors targeting OspC and provides insights into the immunological mechanisms that confer protection against B. burgdorferi infection.

Published
2024
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30. Actionable Genomic Alterations in Prostate Cancer Among Black and White United States Veterans.

Author

Valle, Luca F, Nickols, Nicholas G, Hausler, Ryan, Alba, Patrick R, Anglin-Foote, Tori, Perez, Cristina, Yamoah, Kosj, Rose, Brent S, Kelley, Michael J, DuVall, Scott L, Garraway, Isla P, Maxwell, Kara N, and Lynch, Julie A

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Aging, Clinical Research, Human Genome, Clinical Trials and Supportive Activities, Prostate Cancer, Genetics, Urologic Diseases, Cancer, Good Health and Well Being, Male, Humans, United States, Retrospective Studies, Black or African American, Veterans, Precision Medicine, Prostatic Neoplasms, Genomics, White, metastatic prostate cancer, actionable alterations, next-generation sequencing, disparities, race, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

Black Veterans have higher a incidence of localized and metastatic prostate cancer compared to White Veterans yet are underrepresented in reports of frequencies of somatic and germline alterations. This retrospective analysis of somatic and putative germline alterations was conducted in a large cohort of Veterans with prostate cancer (N = 835 Black, 1613 White) who underwent next generation sequencing through the VA Precision Oncology Program, which facilitates molecular testing for Veterans with metastatic cancer. No differences were observed in gene alterations for FDA approved targetable therapies (13.5% in Black Veterans vs. 15.5% in White Veterans, P = .21), nor in any potentially actionable alterations (25.5% vs. 28.7%, P =.1). Black Veterans had higher rates of BRAF (5.5% vs. 2.6%, P < .001) alterations, White Veterans TMPRSS2 fusions (27.2% vs. 11.7%, P < .0001). Putative germline alteration rates were higher in White Veterans (12.0% vs. 6.1%, P < .0001). Racial disparities in outcome are unlikely attributable to acquired somatic alterations in actionable pathways.

Published
2023

31. Blockchain-enabled immutable, distributed, and highly available clinical research activity logging system for federated COVID-19 data analysis from multiple institutions

Author

Kuo, Tsung-Ting, Pham, Anh, Edelson, Maxim E, Kim, Jihoon, Chan, Jason, Gupta, Yash, Ohno-Machado, Lucila, Anderson, David M, Balacha, Chandrasekar, Bath, Tyler, Baxter, Sally L, Becker-Pennrich, Andrea, Bell, Douglas S, Bernstam, Elmer V, Ngan, Chau, Day, Michele E, Doctor, Jason N, DuVall, Scott, El-Kareh, Robert, Florian, Renato, Follett, Robert W, Geisler, Benjamin P, Ghigi, Alessandro, Gottlieb, Assaf, Hinske, Ludwig C, Hu, Zhaoxian, Ir, Diana, Jiang, Xiaoqian, Kim, Katherine K, Knight, Tara K, Koola, Jejo D, Lee, Nelson, Mansmann, Ulrich, Matheny, Michael E, Meeker, Daniella, Mou, Zongyang, Neumann, Larissa, Nguyen, Nghia H, Nick, Anderson, Park, Eunice, Paul, Paulina, Pletcher, Mark J, Post, Kai W, Rieder, Clemens, Scherer, Clemens, Schilling, Lisa M, Soares, Andrey, SooHoo, Spencer, Soysal, Ekin, Steven, Covington, Tep, Brian, Toy, Brian, Wang, Baocheng, Wu, Zhen R, Xu, Hua, Yong, Choi, Zheng, Kai, Zhou, Yujia, and Zucker, Rachel A

Subjects
Distributed Computing and Systems Software, Information and Computing Sciences, Infectious Diseases, Emerging Infectious Diseases, Coronaviruses, Humans, Blockchain, COVID-19, Research, electronic health record, blockchain distributed ledger technology, clinical information systems, decision support systems, R2D2 Consortium, Engineering, Medical and Health Sciences, Medical Informatics, Biomedical and clinical sciences, Health sciences, Information and computing sciences
Abstract

ObjectiveWe aimed to develop a distributed, immutable, and highly available cross-cloud blockchain system to facilitate federated data analysis activities among multiple institutions.Materials and methodsWe preprocessed 9166 COVID-19 Structured Query Language (SQL) code, summary statistics, and user activity logs, from the GitHub repository of the Reliable Response Data Discovery for COVID-19 (R2D2) Consortium. The repository collected local summary statistics from participating institutions and aggregated the global result to a COVID-19-related clinical query, previously posted by clinicians on a website. We developed both on-chain and off-chain components to store/query these activity logs and their associated queries/results on a blockchain for immutability, transparency, and high availability of research communication. We measured run-time efficiency of contract deployment, network transactions, and confirmed the accuracy of recorded logs compared to a centralized baseline solution.ResultsThe smart contract deployment took 4.5 s on an average. The time to record an activity log on blockchain was slightly over 2 s, versus 5-9 s for baseline. For querying, each query took on an average less than 0.4 s on blockchain, versus around 2.1 s for baseline.DiscussionThe low deployment, recording, and querying times confirm the feasibility of our cross-cloud, blockchain-based federated data analysis system. We have yet to evaluate the system on a larger network with multiple nodes per cloud, to consider how to accommodate a surge in activities, and to investigate methods to lower querying time as the blockchain grows.ConclusionBlockchain technology can be used to support federated data analysis among multiple institutions.

Published
2023

32. The Impact of Insulin Resistance on Loss of Lung Function and Response to Treatment in Asthma.

Author

Peters, Michael C, Schiebler, Mark L, Cardet, Juan Carlos, Johansson, Mats W, Sorkness, Ronald, DeBoer, Mark D, Bleecker, Eugene R, Meyers, Deborah A, Castro, Mario, Sumino, Kaharu, Erzurum, Serpil C, Tattersall, Matthew C, Zein, Joe G, Hastie, Annette T, Moore, Wendy, Levy, Bruce D, Israel, Elliot, Duvall, Melody G, Phillips, Brenda R, Mauger, David T, Wenzel, Sally E, Fajt, Merritt L, Koliwad, Suneil K, Denlinger, Loren C, Woodruff, Prescott G, Jarjour, Nizar N, Fahy, John V, Schiebler, Mark, Carlos Cardet, Juan, and Duvall, Melody

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Clinical Trials and Supportive Activities, Clinical Research, Lung, Asthma, Obesity, Respiratory, Humans, Insulin Resistance, Cross-Sectional Studies, Bronchodilator Agents, Adrenal Cortex Hormones, Forced Expiratory Volume, asthma, obesity, insulin resistance, lung function, National Heart, Lung, and Blood Institute Severe Asthma Research Program-3, Medical and Health Sciences, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

Rationale: The role of obesity-associated insulin resistance (IR) in airflow limitation in asthma is uncertain. Objectives: Using data in the Severe Asthma Research Program 3 (SARP-3), we evaluated relationships between homeostatic measure of IR (HOMA-IR), lung function (cross-sectional and longitudinal analyses), and treatment responses to bronchodilators and corticosteroids. Methods: HOMA-IR values were categorized as without (5.0). Lung function included FEV1 and FVC measured before and after treatment with inhaled albuterol and intramuscular triamcinolone acetonide and yearly for 5 years. Measurements and Main Results: Among 307 participants in SARP-3, 170 (55%) were obese and 140 (46%) had IR. Compared with patients without IR, those with IR had significantly lower values for FEV1 and FVC, and these lower values were not attributable to obesity effects. Compared with patients without IR, those with IR had lower FEV1 responses to β-adrenergic agonists and systemic corticosteroids. The annualized decline in FEV1 was significantly greater in patients with moderate IR (-41 ml/year) and severe IR (-32 ml/year,) than in patients without IR (-13 ml/year, P

Published
2022

36. Reproducible variability: assessing investigator discordance across 9 research teams attempting to reproduce the same observational study.

Author

Ostropolets, Anna, Albogami, Yasser, Conover, Mitchell, Banda, Juan, Baumgartner, William, Blacketer, Clair, Desai, Priyamvada, DuVall, Scott, Fortin, Stephen, Gilbert, James, Golozar, Asieh, Ide, Joshua, Kanter, Andrew, Kern, David, Kim, Chungsoo, Lai, Lana, Li, Chenyu, Liu, Feifan, Lynch, Kristine, Minty, Evan, Neves, Maria, Ng, Ding, Obene, Tontel, Pera, Victor, Pratt, Nicole, Rao, Gowtham, Rappoport, Nadav, Reinecke, Ines, Saroufim, Paola, Shoaibi, Azza, Simon, Katherine, Swerdel, Joel, Voss, Erica, Weaver, James, Zhang, Linying, Hripcsak, George, Ryan, Patrick, and Suchard, Marc

Subjects
credibility, observational data, open science, reproducibility, Humans, Research Personnel, Databases, Factual
Abstract

OBJECTIVE: Observational studies can impact patient care but must be robust and reproducible. Nonreproducibility is primarily caused by unclear reporting of design choices and analytic procedures. This study aimed to: (1) assess how the study logic described in an observational study could be interpreted by independent researchers and (2) quantify the impact of interpretations variability on patient characteristics. MATERIALS AND METHODS: Nine teams of highly qualified researchers reproduced a cohort from a study by Albogami et al. The teams were provided the clinical codes and access to the tools to create cohort definitions such that the only variable part was their logic choices. We executed teams cohort definitions against the database and compared the number of subjects, patient overlap, and patient characteristics. RESULTS: On average, the teams interpretations fully aligned with the master implementation in 4 out of 10 inclusion criteria with at least 4 deviations per team. Cohorts size varied from one-third of the master cohort size to 10 times the cohort size (2159-63 619 subjects compared to 6196 subjects). Median agreement was 9.4% (interquartile range 15.3-16.2%). The teams cohorts significantly differed from the master implementation by at least 2 baseline characteristics, and most of the teams differed by at least 5. CONCLUSIONS: Independent research teams attempting to reproduce the study based on its free-text description alone produce different implementations that vary in the population size and composition. Sharing analytical code supported by a common data model and open-source tools allows reproducing a study unambiguously thereby preserving initial design choices.

Published
2023

39. Guselkumab in patients with moderately to severely active ulcerative colitis (QUASAR): phase 3 double-blind, randomised, placebo-controlled induction and maintenance studies

Author

Abrahamovych, Orest, Abu-farsakh, Niazy, Afanasieva, Halyna, Akpinar, Hale, Al Kharrat, Houssam, Altintas, Engin, Altwegg, Romain, Andreev, Pavel, Aomatsu, Kazuki, Araki, Hiroshi, Argollo, Marjorie, Ariel, Federico, Armuzzi, Alessandro, Ashida, Toshifumi, Augustyn, Monika, Aumais, Guy, Azum, Martín, Baert, Filip, Balaz, Jozef, Balderramo, Domingo, Begun, Jakob, Berova, Temenuzhka, Billiauws, Lore, Blanco, Antonio, Bortlik, Martin, Bossa, Fabrizio, Bunkova, Elena, Cabello, Mercedes, Cao, Qian, Caprioli, Flavio, Cerqueira, Rute, Chachu, Karen, Chamouard, Patrick, Chen, Chunxiao, Chen, Yan, Chen, Baili, Chen, Dongfeng, Chen, Hong, Chen, Youxiang, Chen, Chou-chen, Cheon, Jaehee, Chen, Minhu, Chiu, Cheng-tang, Choi, Changhwan, Chow, Elizabeth, Cicala, Michele, Cintra, Aderson, Danilkiewicz, Wit, Datsenko, Olena, De Hertogh, Gert, De María, Julio, Del Valle Torrealba Medina, Leyanira, Deliang, Liu, Desreumaux, Pierre, Dewint, Pieter, Ding, Shigang, Doherty, Glen, Draganova, Raina, Dutré, Joris, Duvall, George, Egan, Laurence, Fahed, Julien, Fechner, Lars, Fedurco, Miroslav, Ferhat Celik, Aykut, Fernandez, Juan, Filip, Rafal, Fishman, Sigal, Flores, Cristina, Fogel, Ronald, Fowler, Sharyle, Francesconi, Carlos, Fujii, Toshimitsu, Fujiya, Mikihiro, Fukata, Masayuki, Fukuhara, Seiichiro, Furumoto, Yohei, G.Kiss, Gyula, Gachowski, Waldemar, Gao, Xiang, Gasbarrini, Antonio, Gawdis-wojnarska, Beata, Gaya, Daniel, Geccherle, Andrea, Gilletta De Saint Joseph, Cyrielle, Gimenez, Edgardo, Gionchetti, Paolo, Goldin, Eran, Golovchenko, Oleksandr, Gonciarz, Maciej, Gonen, Can, Gonzales, Chad, Gonzalez, Raquel, Gonzalez Segura, Gaston Julian, Gridnyev, Oleksiy, Gu, Fang, Gupta, Nitin, Gyokeres, Tibor, Haines, Melissa, Hebuterne, Xavier, Hedin, Charlotte, Hellstrom, Per, Hilmi, Ida Normiha, Hirai, Fumihito, Hisabe, Takashi, Hlavaty, Tibor, Hoentjen, Frank, Holtmann, Gerald, Horiki, Noriyuki, Horny, Ivo, Horvat, Gyula, Horvath, Frantisek, Hoshi, Namiko, Hosomi, Shuhei, Hospodarskyy, Ihor, Hou, Xiaohua, Hrdlicka, Ludek, Hu, Naizhong, Huang, Vivian, Huang, Caibin, Inaba, Tomoki, Ishiguro, Yoh, Ishihara, Shunji, Ishikawa, Takeshi, Iskandar, Heba, Israeli, Eran, Itaba, Soichi, Ivanishyn, Olha, Izbéki, Ferenc, Jain, Animesh, Jairath, Vipul, Jang, Byung Ik, Jiang, Chunmeng, Jones, Michael, Kagaya, Takashi, Kalimullina, Dilara, Karakina, Marina, Karatas, Ali, Kashimura, Hiroshi, Keret, Dan, Khovaeva, Yaroslava, Kierkus, Jaroslaw, Kim, Taeoh, Kim, Youngho, Kim, Hyo Jong, Klaus, Jochen, Kleczkowski, Dariusz, Klopocka, Maria, Kobayashi, Taku, Kobielusz-gembala, Iwona, Kojima, Yuichiro, Koo, Ja Seol, Kopon, Adam, Kopp, James, Koyama, Fumikazu, Koynarski, Vasil, Kravchenko, Tetiana, Kudo, Masatoshi, Kusunoki, Ryusaku, Kwon, Kwangan, Laclav, Martin, Lago, Paula, Laharie, David, Lasa, Juan, Lateef, Syed, Latinovic Radakovic, Tatjana, Lee, Kang Moon, Leszczyszyn, Jaroslaw, Li, Yan, Liu, Mei, Liu, Eashen, Lobaton Ortega, Triana, Lopatin, Denis, Lopes, Susana, Lovric Jovanovic, Mileva, Lubini, Marcio, Lukas, Milan, Maaser, Christian, Machytka, Evzen, Maemoto, Atsuo, Magro, Fernando, Marcet, Jorge, Marini, Eduardo, Marusawa, Hiroyuki, Matous, Jan, Matsumoto, Takayuki, Mendu, Shoba, Miao, Yinglei, Mihaly, Emese, Miheller, Pal, Ministro, Paula, Miyabayashi, Hideharu, Mohl, Wolfgang, Molnar, Martin, Moore, Gregory, Moran Faienzo, Gabriela, Morral, Eugeni Domenech, Motoya, Satoshi, Murali, Narayanachar, Mustaffa, Nazri Mohamad, Naem, Mohamed, Nakai, Katsuhiko, Nakajima, Koichi, Nakamoto, Yasunari, Nakamura, Masanao, Nancey, Stephane, Navaneethan, Udayakumar, Nawawi, Khairul Najmi Muhammad, Ninomiya, Tomoyuki, Novak, Janos, Oki, Motoji, Oliveira Santana, Genoile, Onizawa, Michio, Ono, Yohei, Osada, Taro, Osipenko, Marina, Owczarek, Danuta, Parente, Jose Miguel, Patel, Kamal, Patel, Bhaktasharan, Pedersen, Peder, Petroniene, Rima, Petrov, Asen, Petrova, Elina, Piquet, Marie-astrid, Pokrotnieks, Juris, Poroshina, Elena, Portela, Francisco, Pruthi, Jatinder S., Prystupa, Lyudmila, Pukitis, Aldis, Qiu, Yun, Rafalsky, Vladimir, Rainis, Tova, Ramos Junior, Odery, Rashid, Mohammed, Rayyan, Yasser, Reshetko, Olga, Ribeiro, Tarsila, Rivero, Montserrat, Roblin, Xavier, Romatowski, Jacek, Rowbotham, David, Ruffinengo, Orlando Enrique, Rydzewska-wyszkowska, Grazyna, Sablin, Oleg, Sai, Souken, Saibeni, Simone, Said, Rosaida Hj. Md., Sakuraba, Hirotake, Samaan, Mark, Sandborn, William, Saruta, Masayuki, Sauk, Jenny, Savarino, Edoardo Vincenzo, Schultz, Michael, Schulze, Joerg, Sedghi, Shahriar, Seidler, Ursula, Seksik, Philippe, Senturk, Omer, Shelton, Edward, Shimizu, Masahito, Shin, Sungjae, Shukla, Richa, Sigal, Michael, Silva Junior, Roberto, Simoes Neto, Joaquim, Siroky Jr., Milan, Smajstrla, Vit, Smid, Vaclav, Smiley, Sarah, Soledad Brunatto, Luciana, Stanislavchuk, Mykola, Stokesberry, David, Stone, Christian, Suiter, Daniel, Suzuki, Takayoshi, Svorcan, Petar, Takagi, Sho, Takagi, Tomohisa, Takamura, Masaaki, Takayama, Tetsuji, Takeuchi, Ken, Tanaka, Akihito, Tanaka, Hiroki, Tanash, Omar, Tang, Wen, Tankova, Ludmila, Teixeira Campos, Luciana, Thin, Lena, Tkachev, Alexander, Tolmanis, Ivars, Tsarynna, Nataliia, Tsonev, Nikolay, Tulassay, Zsolt, Ueo, Tetsuya, Unal, Nalan, Valuyskikh, Ekaterina, Van Dop, Willemijn, Vasilevskaya, Olga, Venugopal, Kannan, Verstockt, Bram, Viamonte, Manuel, Vyshyvanyuk, Vira, Wang, Bangmao, Wang, Xiaoyan, Wang, Jiangbin, Wang, Yufang, Wei, Shu-chen, Weisshof, Roni, Wisam, Sbeit, Wojcik, Katarzyna, Yakovlev, Alexey, Yasuda, Hiroshi, Ye, Byongduk, Yen, Hsu-heng, Yilmaz, Hasan, Yokoyama, Yoko, Yoon, Hyuk, Yoshida, Takeshi, Yurkiv, Andriy, Zaha, Osamu, Zaltman, Cyrla, Zhan, Qiang, Zhang, Hongjie, Zhang, Shutian, Zhu, Lanxiang, Zou, Duowu, Zou, Xiaoping, Zureikat, Firas, Rubin, David T, Allegretti, Jessica R, Panés, Julián, Shipitofsky, Nicole, Yarandi, Shadi S, Huang, Kuan-Hsiang Gary, Germinaro, Matthew, Wilson, Rebbecca, Zhang, Hongyan, Johanns, Jewel, Feagan, Brian G, Hisamatsu, Tadakazu, Lichtenstein, Gary R, Bressler, Brian, Peyrin-Biroulet, Laurent, Sands, Bruce E, and Dignass, Axel

Published
2025
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40. Tamuzimod in patients with moderately-to-severely active ulcerative colitis: a multicentre, double-blind, randomised, placebo-controlled, phase 2 induction trial

Author

Sands, Bruce E, Panaccione, Remo, D'Haens, Geert, Schreiber, Stefan, Jairath, Vipul, DuVall, Aaron, Kierkus, Jaroslaw, Walczak, Michael, Naik, Snehal, Gilder, Kye, Lindstrom, Beatriz, Ogilvie, Kathleen, Sandborn, William J, Vermeire, Severine, Rubin, David T, Peyrin-Biroulet, Laurent, and Danese, Silvio

Published
2025
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43. Gated SPECT MPI

Author

Henzlova, Milena J., primary, McMahon, Sean R., additional, and Duvall, W. Lane, additional

Published
2024
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44. Temperature and photoperiod differentially impact maternal phenotypes in diapause egg-laying Aedes albopictus mosquitoes.

Author

In Hae Lee, Anthony S Lee, Helen V Kogan, Linhan Dong, and Laura B Duvall

Subjects
Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract

BackgroundAedes albopictus (Skuse 1894) mosquitoes can transmit deadly arboviruses and are globally invasive due to their ability to survive in both tropical and temperate climates. Although adults cannot survive harsh winters, females are capable of anticipating seasonal change and producing overwintering diapause (DP) eggs that remain in a state of arrested development over the winter and hatch when favorable conditions return in the spring. While low temperatures can facilitate DP entry under short photoperiods, temperature signals alone are not sufficient to induce DP.Methodology/principal findingsTo identify maternal phenotypes predictive of DP egg production in laboratory conditions, we characterized aspects of maternal physiology and behavior to identify those that correlate with DP egg production and changes in photoperiod, versus changes in temperature. Neither changes in temperature nor photoperiod impacted protein preference, blood meal consumption, or total number of eggs produced per female. Egg retention and oviposition timing were influenced by temperature, independent of DP egg production. However, females housed under short photoperiod conditions showed increased starvation resistance, despite showing similar levels of locomotor activity and internal stores of triacylglycerols, glucose, glycogen, and trehalose compared to females housed in long photoperiods.Conclusions/significanceThese results suggest that temperature and photoperiod differentially affect maternal phenotypes and identify starvation resistance as a maternal phenotype that is influenced by photoperiod and correlates with DP egg status.

Published
2024
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45. Effectiveness and comparative effectiveness of evidence-based psychotherapies for posttraumatic stress disorder in clinical practice.

Author

Maguen, Shira, Madden, Erin, Holder, Nicholas, Li, Yongmei, Seal, Karen H, Neylan, Thomas C, Lujan, Callan, Patterson, Olga V, DuVall, Scott L, and Shiner, Brian

Subjects
Humans, Treatment Outcome, Retrospective Studies, Stress Disorders, Post-Traumatic, Psychotherapy, Veterans, Electronic Health Records, Comparative Effectiveness, Effectiveness, Evidence-based psychotherapy, Posttraumatic Stress Disorder, Veteran, cognitive processing therapy, prolonged exposure therapy, Clinical Research, Behavioral and Social Science, Anxiety Disorders, Clinical Trials and Supportive Activities, Post-Traumatic Stress Disorder (PTSD), Mental Health, Comparative Effectiveness Research, Health Services, Brain Disorders, Mental health, Good Health and Well Being, Neurosciences, Public Health and Health Services, Psychology, Psychiatry
Abstract

BackgroundWhile evidence-based psychotherapy (EBP) for posttraumatic stress disorder (PTSD) is a first-line treatment, its real-world effectiveness is unknown. We compared cognitive processing therapy (CPT) and prolonged exposure (PE) each to an individual psychotherapy comparator group, and CPT to PE in a large national healthcare system.MethodsWe utilized effectiveness and comparative effectiveness emulated trials using retrospective cohort data from electronic medical records. Participants were veterans with PTSD initiating mental healthcare (N = 265 566). The primary outcome was PTSD symptoms measured by the PTSD Checklist (PCL) at baseline and 24-week follow-up. Emulated trials were comprised of 'person-trials,' representing 112 discrete 24-week periods of care (10/07-6/17) for each patient. Treatment group comparisons were made with generalized linear models, utilizing propensity score matching and inverse probability weights to account for confounding, selection, and non-adherence bias.ResultsThere were 636 CPT person-trials matched to 636 non-EBP person-trials. Completing ⩾8 CPT sessions was associated with a 6.4-point greater improvement on the PCL (95% CI 3.1-10.0). There were 272 PE person-trials matched to 272 non-EBP person-trials. Completing ⩾8 PE sessions was associated with a 9.7-point greater improvement on the PCL (95% CI 5.4-13.8). There were 232 PE person-trials matched to 232 CPT person-trials. Those completing ⩾8 PE sessions had slightly greater, but not statistically significant, improvement on the PCL (8.3-points; 95% CI 5.9-10.6) than those completing ⩾8 CPT sessions (7.0-points; 95% CI 5.5-8.5).ConclusionsPTSD symptom improvement was similar and modest for both EBPs. Although EBPs are helpful, research to further improve PTSD care is critical.

Published
2023

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