3,412 results on '"P. Heaney"'
Search Results
2. Estimating the Exposure-Response Relationship between Fine Mineral Dust Concentration and Coccidioidomycosis Incidence Using Speciated Particulate Matter Data: A Longitudinal Surveillance Study.
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Weaver, Amanda K, Keeney, Nicole, Head, Jennifer R, Heaney, Alexandra K, Camponuri, Simon K, Collender, Philip, Bhattachan, Abinash, Okin, Gregory S, Eisen, Ellen A, Sondermeyer-Cooksey, Gail, Yu, Alexander, Vugia, Duc J, Jain, Seema, Balmes, John, Taylor, John, Remais, Justin V, and Strickland, Matthew J
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Epidemiology ,Health Sciences ,Emerging Infectious Diseases ,Infectious Diseases ,Climate-Related Exposures and Conditions ,Valley Fever ,Rare Diseases ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Coccidioidomycosis ,Dust ,Humans ,California ,Incidence ,Particulate Matter ,Environmental Exposure ,Longitudinal Studies ,Air Pollutants ,Minerals ,Coccidioides ,Environmental Sciences ,Medical and Health Sciences ,Toxicology ,Biomedical and clinical sciences ,Environmental sciences ,Health sciences - Abstract
BackgroundCoccidioidomycosis, caused by inhalation of Coccidioides spp. spores, is an emerging infectious disease that is increasing in incidence throughout the southwestern US. The pathogen is soil-dwelling, and spore dispersal and human exposure are thought to co-occur with airborne mineral dust exposures, yet fundamental exposure-response relationships have not been conclusively estimated.ObjectivesWe estimated associations between fine mineral dust concentration and coccidioidomycosis incidence in California from 2000 to 2017 at the census tract level, spatiotemporal heterogeneity in exposure-response, and effect modification by antecedent climate conditions.MethodsWe acquired monthly census tract-level coccidioidomycosis incidence data and modeled fine mineral dust concentrations from 2000 to 2017. We fitted zero-inflated distributed-lag nonlinear models to estimate overall exposure-lag-response relationships and identified factors contributing to heterogeneity in exposure-responses. Using a random-effects meta-analysis approach, we estimated county-specific and pooled exposure-responses for cumulative exposures.ResultsWe found a positive exposure-response relationship between cumulative fine mineral dust exposure in the 1-3 months before estimated disease onset and coccidioidomycosis incidence across the study region [incidence rate ratio (IRR) for an increase from 0.1 to 1.1 μg/m3=1.60; 95% CI: 1.46, 1.74]. Positive, supralinear associations were observed between incidence and modeled fine mineral dust exposures 1 [IRR=1.13 (95% CI: 1.10, 1.17)], 2 [IRR=1.15 (95% CI: 1.09, 1.20)] and 3 [IRR=1.08 (95% CI: 1.04, 1.12)] months before estimated disease onset, with the highest exposures being particularly associated. The cumulative exposure-response relationship varied significantly by county [lowest IRR, western Tulare: 1.05 (95% CI: 0.54, 2.07); highest IRR, San Luis Obispo: 3.01 (95% CI: 2.05, 4.42)]. Season of exposure and prior wet winter were modest effect modifiers.DiscussionLagged exposures to fine mineral dust were strongly associated with coccidioidomycosis incidence in the endemic regions of California from 2000 to 2017. https://doi.org/10.1289/EHP13875.
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- 2025
3. Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes
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Vo, Peter, Imai-Leonard, Denise M, Yang, Benjamin, Briere, Andrew, Shao, Andy, Casanova, M Isabel, Adams, David, Amano, Takanori, Amarie, Oana, Berberovic, Zorana, Bower, Lynette, Braun, Robert, Brown, Steve, Burrill, Samantha, Cho, Soo Young, Clementson-Mobbs, Sharon, D’Souza, Abigail, Dickinson, Mary, Eskandarian, Mohammad, Flenniken, Ann M, Fuchs, Helmut, Gailus-Durner, Valerie, Heaney, Jason, Hérault, Yann, Angelis, Martin Hrabe de, Hsu, Chih-Wei, Jin, Shundan, Joynson, Russell, Kang, Yeon Kyung, Kim, Haerim, Masuya, Hiroshi, Meziane, Hamid, Murray, Steve, Nam, Ki-Hoan, Noh, Hyuna, Nutter, Lauryl MJ, Palkova, Marcela, Prochazka, Jan, Raishbrook, Miles Joseph, Riet, Fabrice, Ryan, Jennifer, Salazar, Jason, Seavey, Zachery, Seavitt, John Richard, Sedlacek, Radislav, Selloum, Mohammed, Seo, Kyoung Yul, Seong, Je Kyung, Shin, Hae-Sol, Shiroishi, Toshihiko, Stewart, Michelle, Svenson, Karen, Tamura, Masaru, Tolentino, Heather, Udensi, Uchechukwu, Wells, Sara, White, Jacqueline, Willett, Amelia, Wotton, Janine, Wurst, Wolfgang, Yoshiki, Atsushi, Lanoue, Louise, Lloyd, KC Kent, Leonard, Brian C, Roux, Michel J, McKerlie, Colin, and Moshiri, Ala
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Biological Sciences ,Bioinformatics and Computational Biology ,Biomedical and Clinical Sciences ,Ophthalmology and Optometry ,Biotechnology ,Genetics ,Eye Disease and Disorders of Vision ,2.1 Biological and endogenous factors ,Eye ,Animals ,Mice ,Knockout ,Phenotype ,Mice ,Humans ,Cornea ,Corneal Diseases ,Corneal dysmorphologies ,Corneal disease ,Corneal dystrophies ,International Mouse Phenotyping Consortium ,Information and Computing Sciences ,Medical and Health Sciences ,Bioinformatics ,Biological sciences ,Biomedical and clinical sciences - Abstract
PurposeCorneal dysmorphologies (CDs) are typically classified as either regressive degenerative corneal dystrophies (CDtrs) or defective growth and differentiation-driven corneal dysplasias (CDyps). Both eye disorders have multifactorial etiologies. While previous work has elucidated many aspects of CDs, such as presenting symptoms, epidemiology, and pathophysiology, the genetic mechanisms remain incompletely understood. The purpose of this study was to analyze phenotype data from 8,707 knockout mouse lines to identify new genes associated with the development of CDs in humans.Methods8,707 knockout mouse lines phenotyped by the International Mouse Phenotyping Consortium were queried for genes associated with statistically significant (P
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- 2025
4. Use of Learning Theories to Guide Simulation-Based Learning in Allied Health Student Professional Placements: A Narrative Review
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Kelly Squires, Susan Heaney, Lesley MacDonald-Wicks, Catherine Johnston, and Leanne Brown
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Using a learning theory is key when designing simulation-based learning linked to allied health professional placements to ensure the purposeful selection of educational methods and to understand how it may assist learners in achieving desired learning outcomes. A narrative review was undertaken to identify the learning theories reported in simulation-based learning linked to allied health professional placements and how the learning outcomes aligned with the reported theories. Only eight of the 25 reviewed studies explicitly reported a learning theory, with minimal attempt to link them to the learning experience. Educators are encouraged to develop an understanding of the breadth and depth of learning theories and how they can best align these with the desired learning outcomes to allow the best fit for purpose. As a result, the authors have developed a practical guide to assist educators in designing simulation-based learning to better understand how learning theories could be incorporated and the anticipated outcomes that could be measured.
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- 2024
5. Are Confident Parents Really Aware of Children's Online Risks? A Conceptual Model and Validation of Parental Self-Efficacy, Mediation, and Awareness Scales
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Seffetullah Kuldas, Aikaterini Sargioti, Elisabeth Staksrud, Darran Heaney, and James O'Higgins Norman
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Children's use of the Internet comes with both risks and opportunities. To minimize risks and maximize opportunities, parents may choose to observe, enable, and/or restrict their children's Internet use. However, parents' high confidence in their children's online safety can itself be a risk factor inhibiting parental awareness of online risks. This research aims to test whether confident parents are accurately aware of how frequently their child has experienced risks online. To this end, construct validity and reliability of scales measuring parental self-efficacy, restrictive-enabling-observant mediation, awareness, and Internet use were established first. Next, a conceptual model of parental awareness was proposed. These results were based on a two-parameter-logistic-model of item response theory, minimum-rank factor analysis, and parallel-mediation analysis of self-reports by a convenience sample of 388 parents in Ireland (Autumn 2019). Confident parents mostly reported their child experienced no online risk in the past couple of months, whereas unconfident parents reported their child experienced an online risk once, twice, or more times. Results of the mediation analysis indicated that confident parents likely underestimated, whereas unconfident parents overestimated, how frequently their child experienced an online risk. The accuracy of parental awareness depended on their mediation strategies, particularly restrictive mediation. Further research is needed to test whether training parents on self-efficacy and mediation of children's Internet use raises their awareness of the children's online risks.
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- 2024
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6. Improved Clinical Outcomes During Long-term Osilodrostat Treatment of Cushing Disease With Normalization of Late-night Salivary Cortisol and Urinary Free Cortisol.
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Newell-Price, John, Fleseriu, Maria, Pivonello, Rosario, Feelders, Richard, Gadelha, Mônica, Lacroix, André, Witek, Przemysław, Heaney, Anthony, Piacentini, Andrea, Pedroncelli, Alberto, and Biller, Beverly
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Cushing disease ,cortisol normalization ,hypercortisolism ,long-term treatment ,osilodrostat - Abstract
PURPOSE: To assess whether simultaneous normalization of late-night salivary cortisol (LNSC) and mean urinary free cortisol (mUFC) in patients with Cushing disease treated with osilodrostat is associated with better clinical outcomes than control of mUFC or LNSC alone. METHODS: Pooled data from two phase III osilodrostat studies (LINC 3 and LINC 4) were analyzed. Both comprised a 48-week core phase and an optional open-label extension. Changes in cardiovascular/metabolic-related parameters, physical manifestations of hypercortisolism, and quality of life (QoL) were evaluated across the following patient subgroups: both LNSC and mUFC controlled, only mUFC controlled, only LNSC controlled, and neither controlled. RESULTS: Of 160 patients included in the analysis, 85.0% had both LNSC and mUFC uncontrolled at baseline. At week 72, 48.6% of patients had both LNSC and mUFC controlled; these patients generally exhibited greater improvements in cardiovascular/metabolic-related parameters than those with only mUFC controlled or both LNSC and mUFC uncontrolled: systolic/diastolic blood pressure, -7.4%/-4.9%, -6.0%/-5.5%, and 2.3%/0.8%, respectively; fasting plasma glucose, -5.0%, -4.8%, and 1.9%; glycated hemoglobin, -5.1%, -4.8%, and -1.3%. Weight, waist circumference, and body mass index improved with control of LNSC and/or mUFC; physical manifestations of hypercortisolism generally improved regardless of LNSC/mUFC control. Patients with both LNSC and mUFC controlled or only mUFC controlled had the greatest improvement from baseline to week 72 in QoL. CONCLUSION: In osilodrostat-treated patients with Cushing disease, normalization of LNSC and mUFC led to improvements in long-term outcomes, indicating that treatment should aim for normalization of both parameters for optimal patient outcomes. CLINICAL TRIAL IDENTIFIERS: NCT02180217 (LINC 3); NCT02697734 (LINC 4).
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- 2024
7. Coccidioidomycosis seasonality in California: a longitudinal surveillance study of the climate determinants and spatiotemporal variability of seasonal dynamics, 2000–2021
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Heaney, Alexandra K, Camponuri, Simon K, Head, Jennifer R, Collender, Philip, Weaver, Amanda, Cooksey, Gail Sondermeyer, Yu, Alexander, Vugia, Duc, Jain, Seema, Bhattachan, Abinash, Taylor, John, and Remais, Justin V
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Biological Sciences ,Ecology ,Climate-Related Exposures and Conditions ,2.2 Factors relating to the physical environment ,Climate Action ,Coccidioidomycosis ,Coccidioides ,Emerging infectious disease ,Drought ,Seasonality ,Fungal infections - Abstract
BackgroundCoccidioidomycosis, an emerging fungal disease in the western USA, exhibits seasonal patterns that are poorly understood, including periods of strong cyclicity, aseasonal intervals, and variation in seasonal timing that have been minimally characterized, and unexplained as to their causal factors. Coccidioidomycosis incidence has increased markedly in recent years, and our limited understanding of intra- and inter-annual seasonality has hindered the identification of important drivers of disease transmission, including climate conditions. In this study, we aim to characterize coccidioidomycosis seasonality in endemic regions of California and to estimate the relationship between drought conditions and coccidioidomycosis seasonal periodicity and timing.MethodsWe analysed data on all reported incident cases of coccidioidomycosis in California from 2000 to 2021 to characterize seasonal patterns in incidence, and conducted wavelet analyses to assess the dominant periodicity, power, and timing of incidence for 17 counties with consistently high incidence rates. We assessed associations between seasonality parameters and measures of drought in California using a distributed lag nonlinear modelling framework.FindingsAll counties exhibited annual cyclicity in incidence (i.e., a dominant wavelet periodicity of 12 months), but there was considerable heterogeneity in seasonal strength and timing across regions and years. On average, 12-month periodicity was most pronounced in the Southern San Joaquin Valley and Central Coast. Further, the annual seasonal cycles in the Southern San Joaquin Valley and the Southern Inland regions occurred earlier than those in coastal and northern counties, yet the timing of annual cycles became more aligned among counties by the end of the study period. Drought conditions were associated with a strong attenuation of the annual seasonal cycle, and seasonal peaks became more pronounced in the 1-2 years after a drought ended.InterpretationWe conclude that drought conditions do not increase the risk of coccidioidomycosis onset uniformly across the year, but instead promote increased risk concentrated within a specific calendar period (September to December). The findings have important implications for public health preparedness, and for how future shifts in seasonal climate patterns and extreme events may impact spatial and temporal coccidioidomycosis risk.FundingNational Institutes of Health.
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- 2024
8. 7 days of L-citrulline supplementation does not improve running performance in the heat whilst in a hypohydrated state
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Cable, Thomas G., Funnell, Mark P., Reynolds, Kirsty M., Hudson, Ella F., Macrae, Heather Z., Johnson, Drusus A., Taylor, Lee, Heaney, Liam M., Mears, Stephen A., Bailey, Stephen J., and James, Lewis J.
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- 2024
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9. Rapid modelling of reactive transport in porous media using machine learning: limitations and solutions
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Silva, Vinicius L S, Regnier, Geraldine, Salinas, Pablo, Heaney, Claire E, Jackson, Matthew D, and Pain, Christopher C
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Computer Science - Computational Engineering, Finance, and Science - Abstract
Reactive transport in porous media plays a pivotal role in subsurface reservoir processes, influencing fluid properties and geochemical characteristics. However, coupling fluid flow and transport with geochemical reactions is computationally intensive, requiring geochemical calculations at each grid cell and each time step within a discretized simulation domain. Although recent advancements have integrated machine learning techniques as surrogates for geochemical simulations, ensuring computational efficiency and accuracy remains a challenge. This chapter investigates machine learning models as replacements for a geochemical module in a reactive transport in porous media simulation. We test this approach on a well-documented cation exchange problem. While the surrogate models excel in isolated predictions, they fall short in rollout predictions over successive time steps. By introducing modifications, including physics-based constraints and tailored dataset generation strategies, we show that machine learning surrogates can achieve accurate rollout predictions. Our findings emphasize that, when judiciously designed, machine learning surrogates can substantially expedite the cation exchange problem without compromising accuracy, offering significant potential for a range of reactive transport applications.
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- 2024
10. Coccidioidomycosis seasonality in California: climate determinants and spatiotemporal variability of seasonal dynamics, 2000-2021
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Heaney, Alexandra K, Campo, Simon K, Head, Jennifer R, Collender, Phillip, Weaver, Amanda, Sondermeyer Cooksey, Gail, Yu, Alexander, Jain, Seema, Vugia, Duc, Bhattachan, Abinash, Taylor, John, and Remais, Justin V
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Biological Sciences ,Ecology ,Commerce ,Management ,Tourism and Services ,Emerging Infectious Diseases ,Infectious Diseases ,Valley Fever ,Rare Diseases ,Climate Action - Published
- 2024
11. Plasma cell disorders supress mucosal anti-bacterial immunity: another dimension of immunoparesis in plasma cell neoplasms
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Faustini, Sian, Chan, Y. L. Tracey, Evans, Lilli, Collman, Emily, Rapson, Alec, Backhouse, Claire, Emery, Annabelle, Campbell, John P., Moore, Sally, Richter, Alex, Pratt, Guy, Drayson, Mark T., and Heaney, Jennifer L. J.
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- 2024
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12. Using AI libraries for Incompressible Computational Fluid Dynamics
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Chen, Boyang, Heaney, Claire E., and Pain, Christopher C.
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Physics - Fluid Dynamics ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Recently, there has been a huge effort focused on developing highly efficient open source libraries to perform Artificial Intelligence (AI) related computations on different computer architectures (for example, CPUs, GPUs and new AI processors). This has not only made the algorithms based on these libraries highly efficient and portable between different architectures, but also has substantially simplified the entry barrier to develop methods using AI. Here, we present a novel methodology to bring the power of both AI software and hardware into the field of numerical modelling by repurposing AI methods, such as Convolutional Neural Networks (CNNs), for the standard operations required in the field of the numerical solution of Partial Differential Equations (PDEs). The aim of this work is to bring the high performance, architecture agnosticism and ease of use into the field of the numerical solution of PDEs. We use the proposed methodology to solve the advection-diffusion equation, the non-linear Burgers equation and incompressible flow past a bluff body. For the latter, a convolutional neural network is used as a multigrid solver in order to enforce the incompressibility constraint. We show that the presented methodology can solve all these problems using repurposed AI libraries in an efficient way, and presents a new avenue to explore in the development of methods to solve PDEs and Computational Fluid Dynamics problems with implicit methods., Comment: 24 pages, 6 figures
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- 2024
13. Solving the Discretised Multiphase Flow Equations with Interface Capturing on Structured Grids Using Machine Learning Libraries
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Chen, Boyang, Heaney, Claire E., Gomes, Jefferson L. M. A., Matar, Omar K., and Pain, Christopher C.
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Physics - Fluid Dynamics ,Computer Science - Machine Learning - Abstract
This paper solves the discretised multiphase flow equations using tools and methods from machine-learning libraries. The idea comes from the observation that convolutional layers can be used to express a discretisation as a neural network whose weights are determined by the numerical method, rather than by training, and hence, we refer to this approach as Neural Networks for PDEs (NN4PDEs). To solve the discretised multiphase flow equations, a multigrid solver is implemented through a convolutional neural network with a U-Net architecture. Immiscible two-phase flow is modelled by the 3D incompressible Navier-Stokes equations with surface tension and advection of a volume fraction field, which describes the interface between the fluids. A new compressive algebraic volume-of-fluids method is introduced, based on a residual formulation using Petrov-Galerkin for accuracy and designed with NN4PDEs in mind. High-order finite-element based schemes are chosen to model a collapsing water column and a rising bubble. Results compare well with experimental data and other numerical results from the literature, demonstrating that, for the first time, finite element discretisations of multiphase flows can be solved using an approach based on (untrained) convolutional neural networks. A benefit of expressing numerical discretisations as neural networks is that the code can run, without modification, on CPUs, GPUs or the latest accelerators designed especially to run AI codes., Comment: 34 pages, 18 figures, 4 tables
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- 2024
14. A cluster-randomized trial of water, sanitation, handwashing and nutritional interventions on stress and epigenetic programming.
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Lin, Audrie, Fernald, Lia, Kim, Lisa, Yan, Liying, Meyer, Ann, Karim, Md, Shahriar, Sunny, Shuman, Gabrielle, Famida, Syeda, Akther, Salma, Hossen, Md, Mutsuddi, Palash, Shoab, Abul, Shalev, Idan, Rahman, Mahbubur, Unicomb, Leanne, Heaney, Christopher, Kariger, Patricia, Rahman, Md, Tan, Sophia, Ilyasova, Dora, Spasojevic, Ivan, Ali, Shahjahan, Luby, Stephen, Colford, John, Hubbard, Alan, Stewart, Christine, Granger, Douglas, Arnold, Benjamin, and Mertens, Andrew
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Humans ,Hand Disinfection ,Female ,Sanitation ,Bangladesh ,Male ,DNA Methylation ,Infant ,Epigenesis ,Genetic ,Child ,Preschool ,Pregnancy ,Oxidative Stress ,Stress ,Physiological ,Rural Population ,Adult ,Diarrhea ,Receptors ,Glucocorticoid - Abstract
A regulated stress response is essential for healthy child growth and development trajectories. We conducted a cluster-randomized trial in rural Bangladesh (funded by the Bill & Melinda Gates Foundation, ClinicalTrials.gov NCT01590095) to assess the effects of an integrated nutritional, water, sanitation, and handwashing intervention on child health. We previously reported on the primary outcomes of the trial, linear growth and caregiver-reported diarrhea. Here, we assessed additional prespecified outcomes: physiological stress response, oxidative stress, and DNA methylation (N = 759, ages 1-2 years). Eight neighboring pregnant women were grouped into a study cluster. Eight geographically adjacent clusters were block-randomized into the control or the combined nutrition, water, sanitation, and handwashing (N + WSH) intervention group (receiving nutritional counseling and lipid-based nutrient supplements, chlorinated drinking water, upgraded sanitation, and handwashing with soap). Participants and data collectors were not masked, but analyses were masked. There were 358 children (68 clusters) in the control group and 401 children (63 clusters) in the intervention group. We measured four F2-isoprostanes isomers (iPF(2α)-III; 2,3-dinor-iPF(2α)-III; iPF(2α)-VI; 8,12-iso-iPF(2α)-VI), salivary alpha-amylase and cortisol, and methylation of the glucocorticoid receptor (NR3C1) exon 1F promoter including the NGFI-A binding site. Compared with control, the N + WSH group had lower concentrations of F2-isoprostanes isomers (differences ranging from -0.16 to -0.19 log ng/mg of creatinine, P
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- 2024
15. Application of machine learning algorithms to identify serological predictors of COVID-19 severity and outcomes
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Dhakal, Santosh, Yin, Anna, Escarra-Senmarti, Marta, Demko, Zoe O., Pisanic, Nora, Johnston, Trevor S., Trejo-Zambrano, Maria Isabel, Kruczynski, Kate, Lee, John S., Hardick, Justin P., Shea, Patrick, Shapiro, Janna R., Park, Han-Sol, Parish, Maclaine A., Caputo, Christopher, Ganesan, Abhinaya, Mullapudi, Sarika K., Gould, Stephen J., Betenbaugh, Michael J., Pekosz, Andrew, Heaney, Christopher D., Antar, Annukka A. R., Manabe, Yukari C., Cox, Andrea L., Karaba, Andrew H., Andrade, Felipe, Zeger, Scott L., and Klein, Sabra L.
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- 2024
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16. Impact of essential genes on the success of genome editing experiments generating 3313 new genetically engineered mouse lines
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Elrick, Hillary, Peterson, Kevin A., Willis, Brandon J., Lanza, Denise G., Acar, Elif F., Ryder, Edward J., Teboul, Lydia, Kasparek, Petr, Birling, Marie-Christine, Adams, David J., Bradley, Allan, Braun, Robert E., Brown, Steve D., Caulder, Adam, Codner, Gemma F., DeMayo, Francesco J., Dickinson, Mary E., Doe, Brendan, Duddy, Graham, Gertsenstein, Marina, Goodwin, Leslie O., Hérault, Yann, Lintott, Lauri G., Lloyd, K. C. Kent, Lorenzo, Isabel, Mackenzie, Matthew, Mallon, Ann-Marie, McKerlie, Colin, Parkinson, Helen, Ramirez-Solis, Ramiro, Seavitt, John R., Sedlacek, Radislav, Skarnes, William C., Smedley, Damien, Wells, Sara, White, Jacqueline K., Wood, Joshua A., Murray, Stephen A., Heaney, Jason D., and Nutter, Lauryl M. J.
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- 2024
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17. Perspectives of work readiness among Australian health students trained during the COVID-19 pandemic
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Podubinski, Tegan, Jessup, Belinda, Kirschbaum, Melissa, Bailie, Jodie, Heaney, Susan, Sheepway, Lyndal, and Bourke, Lisa
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- 2024
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18. Barriers to clinical remission in severe asthma
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Farinha, Inês and Heaney, Liam G
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- 2024
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19. A GREB1-steroid receptor feedforward mechanism governs differential GREB1 action in endometrial function and endometriosis
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Chadchan, Sangappa B., Popli, Pooja, Liao, Zian, Andreas, Eryk, Dias, Michelle, Wang, Tianyuan, Gunderson, Stephanie J., Jimenez, Patricia T., Lanza, Denise G., Lanz, Rainer B., Foulds, Charles E., Monsivais, Diana, DeMayo, Francesco J., Yalamanchili, Hari Krishna, Jungheim, Emily S., Heaney, Jason D., Lydon, John P., Moley, Kelle H., O’Malley, Bert W., and Kommagani, Ramakrishna
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- 2024
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20. The effects of short-term, progressive exercise training on disease activity in smouldering multiple myeloma and monoclonal gammopathy of undetermined significance: a single-arm pilot study
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Emery, A, Moore, S, Crowe, J, Murray, J, Peacock, O, Thompson, D, Betts, F, Rapps, S, Ross, L, Rothschild-Rodriguez, D, Arana Echarri, A, Davies, R, Lewis, R, Augustine, DX, Whiteway, A, Afzal, Z, Heaney, JLJ, Drayson, MT, Turner, JE, and Campbell, JP
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- 2024
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21. Time-Symmetric Resolutions of the Renninger Negative-Result Paradoxes
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Heaney, Michael B.
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Quantum Physics - Abstract
The 1953 and 1960 Renninger negative-result thought experiments illustrate conceptual paradoxes in the Copenhagen formulation of quantum mechanics. In the 1953 paradox we can infer the presence of a detector in one arm of a Mach-Zehnder interferometer without any particle interacting with the detector. In the 1960 paradox we can infer the collapse of a wavefunction without any change in the state of a detector. I resolve both of these paradoxes by using a time-symmetric formulation of quantum mechanics. I also describe a real experiment that can distinguish between the Copenhagen and time-symmetric formulations., Comment: 14 pages, 4 figures
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- 2023
22. Risk Factors Associated with Postoperative CSF Leak in Extrasellar Tumors.
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Zhang, Huan, Peeters, Sophie, Vengorivich, Gennadiy, Antoury, Layal, Park, Ki, Wells, Christine, Suh, Jeffrey, Lee, Jivianne, Bergsneider, Marvin, Wang, Marilene, Heaney, Anthony, and Kim, Won
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cerebrospinal fluid leak ,extrasellar ,repair ,skull base - Abstract
Objective While postoperative cerebrospinal fluid (CSF) leak rates of pituitary tumors have been frequently studied, there are fewer studies examining postoperative CSF leak rates for extrasellar tumors. The purpose of this study was to identify risk factors for the development of postoperative CSF leak in patients undergoing endoscopic surgery for extrasellar tumors. Methods A retrospective chart review was done for patients who underwent endoscopic resection for extrasellar tumors between 2008 and 2020. Age, gender, tumor type, tumor location, tumor size, reconstruction technique, medical comorbidities, and other potential risk factors were identified. Data was analyzed to identify significant risk factors for development of postoperative CSF leak. Results There were 100 patients with extrasellar tumors who developed intraoperative CSF leaks. Seventeen patients (17%) developed postoperative CSF leaks. Leaks occurred at a median of 2 days following surgery (range 0-34 days). Clival tumors had a significantly higher incidence of postoperative leak than those in other sites ( p
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- 2024
23. Testing the Influence of Tactics on an Intention to Participate in an Environmental Management Collaborative
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Heaney, Shannon, Plummer, Ryan, Baird, Julia, Bowen, Amy, and Dale, Gillian
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- 2024
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24. New valproate regulations, informed choice and seizure risk
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Angus-Leppan, Heather, Arkell, Rachel, Watkins, Lance, Heaney, Dominic, Cooper, Paul, and Shankar, Rohit
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- 2024
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25. Generation of a humanized mAce2 and a conditional hACE2 mouse models permissive to SARS-COV-2 infection
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Song, I-Wen, Washington, Megan, Leynes, Carolina, Hsu, Jason, Rayavara, Kempaiah, Bae, Yangjin, Haelterman, Nele, Chen, Yuqing, Jiang, Ming-Ming, Drelich, Aleksandra, Tat, Vivian, Lanza, Denise G., Lorenzo, Isabel, Heaney, Jason D., Tseng, Chien-Te Kent, Lee, Brendan, and Marom, Ronit
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- 2024
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26. Using Positioning Theory and Narrative to Explore Doctoral Students' Developing Understandings about Theory in Educational Research
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Cynthia Brock, Kate Muir Welsh, Cara Tarullo, Josh Montgomery, Avia Kelly, and April Heaney
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Doctoral students' ability to understand, use, and build on theory in educational research is a critical aspect of their learning to be successful scholars. Unfortunately, there is a paucity of work that explores the voices of graduate students articulating their experiences as they learn about theory. Using Positioning Theory to frame their work, the authors of this paper examined doctoral students' evolving understandings of theory and its uses in educational research. This work has important implications for concrete ways that senior faculty can work with doctoral students to foster their understanding of theory and its uses in educational research.
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- 2024
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27. FUSE Anti-Bullying and Online Safety Programme: Measuring Self-Efficacy amongst Post-Primary Students
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James O'Higgins Norman, Paloma Viejo Otero, Colm Canning, Angela Kinehan, Darran Heaney, and Aikaterini Sargioti
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'FUSE' is an anti-bullying and online safety programme developed to support schools in complying with the Action Plan Procedures (2013). Between 2019 and 2022, 56% of all Post-Primary Schools in Ireland registered for the programme. FUSE is designed to address two key concerns, (a) students tend not to report bullying, and (b) students are increasingly facing online risks. FUSE aims to increase student's self-efficacy to recognise and report bullying behaviour and online harms safely. The programme is informed by Latané and Darley's bystander intervention model which outlines five sequential steps that an individual needs to follow in order to take action. This paper reports on the implementation of FUSE in Post Primary Schools in Ireland, justifying its theoretical base and model, and conveying the results of an empirical study conducted amongst a sample of 1254 Post Primary students (14-15 years of age) in 41 schools upon completion of the programme. Upon completion of the programme students reported high levels of self-efficacy in relation to noticing, responding and willingness to report. Future research will implement a pre- and post-study design to draw firmer conclusions regarding the effectiveness of the intervention.
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- 2024
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28. Effect of an acute session of intermittent exercise on trimethylamine N-oxide (TMAO) production following choline ingestion
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Ong, Marilyn L.Y., Green, Christopher G., Rowland, Samantha N., Rider, Katie, Sutcliffe, Harry, Funnell, Mark P., Salzano, Andrea, and Heaney, Liam M.
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- 2024
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29. Reducing Mass Confusion over the Microbiome.
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McAtamney, Allyson, Heaney, Casey, Lizama-Chamu, Itzel, and Sanchez, Laura
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Microbiota ,Fungi ,Bacteria ,Mass Spectrometry - Abstract
As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.
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- 2023
30. Specimen collection is essential for modern science.
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Nachman, Michael, Beckman, Elizabeth, Bowie, Rauri, Cicero, Carla, Conroy, Chris, Hayes, Tyrone, Koo, Michelle, Lacey, Eileen, Martin, Christopher, McGuire, Jimmy, Patton, James, Spencer, Carol, Wake, Marvalee, Wang, Ian, Achmadi, Anang, Álvarez-Castañeda, Sergio, Andersen, Michael, Arroyave, Jairo, Austin, Christopher, Barker, F, Barrow, Lisa, Barrowclough, George, Bates, John, Bauer, Aaron, Bell, Kayce, Bell, Rayna, Bronson, Allison, Brown, Rafe, Burbrink, Frank, Burns, Kevin, Cadena, Carlos, Cannatella, David, Castoe, Todd, Chakrabarty, Prosanta, Colella, Jocelyn, Cook, Joseph, Cracraft, Joel, Davis, Drew, Davis Rabosky, Alison, DElía, Guillermo, Dumbacher, John, Dunnum, Jonathan, Edwards, Scott, Esselstyn, Jacob, Faivovich, Julián, Fjeldså, Jon, Flores-Villela, Oscar, Ford, Kassandra, Fuchs, Jérôme, Fujita, Matthew, Good, Jeffrey, Greenbaum, Eli, Greene, Harry, Hackett, Shannon, Hamidy, Amir, Hanken, James, Haryoko, Tri, Hawkins, Melissa, Heaney, Lawrence, Hillis, David, Hollingsworth, Bradford, Hornsby, Angela, Hosner, Peter, Irham, Mohammad, Jansa, Sharon, Jiménez, Rosa, Joseph, Leo, Kirchman, Jeremy, LaDuc, Travis, Leaché, Adam, Lessa, Enrique, López-Fernández, Hernán, Mason, Nicholas, McCormack, John, McMahan, Caleb, Moyle, Robert, Ojeda, Ricardo, Olson, Link, Kin Onn, Chan, Parenti, Lynne, Parra-Olea, Gabriela, Patterson, Bruce, Pauly, Gregory, Pavan, Silvia, Peterson, A, Poe, Steven, Rabosky, Daniel, Raxworthy, Christopher, Reddy, Sushma, Rico-Guevara, Alejandro, Riyanto, Awal, Rocha, Luiz, Ron, Santiago, Rovito, Sean, Rowe, Kevin, Rowley, Jodi, Ruane, Sara, Salazar-Valenzuela, David, Shultz, Allison, and Sidlauskas, Brian
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Animals ,Museums ,Specimen Handling ,Natural History - Abstract
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.
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- 2023
31. Case Report: The Impact of Online Forum Use on Student Retention in a Level 1 Distance Learning Module
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Pinchbeck, Jessica and Heaney, Caroline
- Abstract
The importance of making online and distance education successful has been dramatically prioritized due to the COVID-19 pandemic. Student retention is a key performance indicator in online higher education. Evidence suggests that within online distance education the key to retaining students is to encourage an engaging and supportive online community. Online asynchronous forums are one method that has been employed to promote such engagement. This study investigated the relationship between online forum activity and student retention amongst 21 tutor groups on an Open University Level 1 module. It found that the volume of tutor group forum activity had a significant association with student retention (p<0.05 two-tailed, Pearson r=0.53), with student contributions having a greater impact on retention (p<0.01 two-tailed, Pearson r=0.628) than tutor contributions. Although tutor contributions did not appear to impact student retention directly the number of tutor and student posts were highly correlated (p<0.001, two tailed, Pearson r=0.86). Results indicate that asynchronous forums can be an effective tool in promoting student retention in an online distance learning environment. Important factors that impact on student retention within the educational medium of asynchronous forums are evidenced. The implications of these findings for educators are discussed. [Note: The page range (103-118) shown on the PDF is incorrect. The correct page range for this article is p103-117.]
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- 2022
32. Solving the Discretised Boltzmann Transport Equations using Neural Networks: Applications in Neutron Transport
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Phillips, T. R. F., Heaney, C. E., Boyang, C., Buchan, A. G., and Pain, C. C.
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Computer Science - Computational Engineering, Finance, and Science ,Computer Science - Machine Learning ,Physics - Computational Physics - Abstract
In this paper we solve the Boltzmann transport equation using AI libraries. The reason why this is attractive is because it enables one to use the highly optimised software within AI libraries, enabling one to run on different computer architectures and enables one to tap into the vast quantity of community based software that has been developed for AI and ML applications e.g. mixed arithmetic precision or model parallelism. Here we take the first steps towards developing this approach for the Boltzmann transport equation and develop the necessary methods in order to do that effectively. This includes: 1) A space-angle multigrid solution method that can extract the level of parallelism necessary to run efficiently on GPUs or new AI computers. 2) A new Convolutional Finite Element Method (ConvFEM) that greatly simplifies the implementation of high order finite elements (quadratic to quintic, say). 3) A new non-linear Petrov-Galerkin method that introduces dissipation anisotropically.
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- 2023
33. Solving the Discretised Neutron Diffusion Equations using Neural Networks
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Phillips, T. R. F., Heaney, C. E., Boyang, C., Buchan, A. G., and Pain, C. C.
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Computer Science - Computational Engineering, Finance, and Science ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning ,Physics - Computational Physics - Abstract
This paper presents a new approach which uses the tools within Artificial Intelligence (AI) software libraries as an alternative way of solving partial differential equations (PDEs) that have been discretised using standard numerical methods. In particular, we describe how to represent numerical discretisations arising from the finite volume and finite element methods by pre-determining the weights of convolutional layers within a neural network. As the weights are defined by the discretisation scheme, no training of the network is required and the solutions obtained are identical (accounting for solver tolerances) to those obtained with standard codes often written in Fortran or C++. We also explain how to implement the Jacobi method and a multigrid solver using the functions available in AI libraries. For the latter, we use a U-Net architecture which is able to represent a sawtooth multigrid method. A benefit of using AI libraries in this way is that one can exploit their power and their built-in technologies. For example, their executions are already optimised for different computer architectures, whether it be CPUs, GPUs or new-generation AI processors. In this article, we apply the proposed approach to eigenvalue problems in reactor physics where neutron transport is described by diffusion theory. For a fuel assembly benchmark, we demonstrate that the solution obtained from our new approach is the same (accounting for solver tolerances) as that obtained from the same discretisation coded in a standard way using Fortran. We then proceed to solve a reactor core benchmark using the new approach.
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- 2023
34. Refractory corticotroph adenomas
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Sumal, Amit KS, Zhang, Dongyun, and Heaney, Anthony P
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Biomedical and Clinical Sciences ,Clinical Sciences ,Cancer ,Clinical Research ,Humans ,ACTH-Secreting Pituitary Adenoma ,Adenoma ,Pituitary Neoplasms ,Refractory corticotroph adenomas ,Public Health and Health Services ,Endocrinology & Metabolism ,Clinical sciences - Abstract
The majority of corticotroph adenomas are benign but some are locally invasive, demonstrate high rates of recurrence, and exhibit a relatively poor response to often repeated surgical, medical, and radiation treatment. Herein, we summarize the currently known somatic and genetic mutations and other molecular factors that influence the pathogenesis of these tumors and discuss currently available therapies. Although recent molecular studies have advanced our understanding of the pathogenesis and behavior of these refractory corticotroph adenomas, these insights do not reliably guide treatment choices at present. Development of additional diagnostic tools and novel tumor-directed therapies that offer efficacious treatment choices for patients with refractory corticotroph adenomas are needed.
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- 2023
35. Low Cortisol in a Cushingoid Patient.
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Song, Lu, Sue, Laura Y, and Heaney, Anthony P
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Humans ,Prednisolone ,Hydrocortisone ,Kidney Transplantation ,Medical Biotechnology ,Medical Biochemistry and Metabolomics ,Clinical Sciences ,General Clinical Medicine - Published
- 2023
36. Outdoor education, environmental perceptions, and sustainability: Exploring relationships and opportunities
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Mallette, Angela, Heaney, Shannon, McGlynn, Bridget, Stuart, Savannah, Witkowski, Samantha, and Plummer, Ryan
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- 2024
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37. A Test of Dublin Anti-bullying Self-Efficacy Scale for Teachers (DABSE-T)
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Feijóo, Sandra, Kuldas, Seffetullah, Sargioti, Aikaterini, Kinahan, Angela, Heaney, Darran, Gorman, Alan, and O’Higgins Norman, James
- Published
- 2024
- Full Text
- View/download PDF
38. Point-Syn2Real: Semi-Supervised Synthetic-to-Real Cross-Domain Learning for Object Classification in 3D Point Clouds
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Wang, Ziwei, Arablouei, Reza, Liu, Jiajun, Borges, Paulo, Bishop-Hurley, Greg, and Heaney, Nicholas
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Multimedia - Abstract
Object classification using LiDAR 3D point cloud data is critical for modern applications such as autonomous driving. However, labeling point cloud data is labor-intensive as it requires human annotators to visualize and inspect the 3D data from different perspectives. In this paper, we propose a semi-supervised cross-domain learning approach that does not rely on manual annotations of point clouds and performs similar to fully-supervised approaches. We utilize available 3D object models to train classifiers that can generalize to real-world point clouds. We simulate the acquisition of point clouds by sampling 3D object models from multiple viewpoints and with arbitrary partial occlusions. We then augment the resulting set of point clouds through random rotations and adding Gaussian noise to better emulate the real-world scenarios. We then train point cloud encoding models, e.g., DGCNN, PointNet++, on the synthesized and augmented datasets and evaluate their cross-domain classification performance on corresponding real-world datasets. We also introduce Point-Syn2Real, a new benchmark dataset for cross-domain learning on point clouds. The results of our extensive experiments with this dataset demonstrate that the proposed cross-domain learning approach for point clouds outperforms the related baseline and state-of-the-art approaches in both indoor and outdoor settings in terms of cross-domain generalizability. The code and data will be available upon publishing.
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- 2022
39. Modeling in higher dimensions to improve diagnostic testing accuracy: theory and examples for multiplex saliva-based SARS-CoV-2 antibody assays
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Luke, Rayanne A., Kearsley, Anthony J., Pisanic, Nora, Manabe, Yukari C., Thomas, David L., Heaney, Christopher D., and Patrone, Paul N.
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Quantitative Biology - Quantitative Methods ,Mathematics - Optimization and Control ,Mathematics - Probability ,Physics - Biological Physics ,Statistics - Methodology - Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has emphasized the importance and challenges of correctly interpreting antibody test results. Identification of positive and negative samples requires a classification strategy with low error rates, which is hard to achieve when the corresponding measurement values overlap. Additional uncertainty arises when classification schemes fail to account for complicated structure in data. We address these problems through a mathematical framework that combines high dimensional data modeling and optimal decision theory. Specifically, we show that appropriately increasing the dimension of data better separates positive and negative populations and reveals nuanced structure that can be described in terms of mathematical models. We combine these models with optimal decision theory to yield a classification scheme that better separates positive and negative samples relative to traditional methods such as confidence intervals (CIs) and receiver operating characteristics. We validate the usefulness of this approach in the context of a multiplex salivary SARS-CoV-2 immunoglobulin G assay dataset. This example illustrates how our analysis: (i) improves the assay accuracy (e.g. lowers classification errors by up to 42 % compared to CI methods); (ii) reduces the number of indeterminate samples when an inconclusive class is permissible (e.g. by 40 % compared to the original analysis of the example multiplex dataset); and (iii) decreases the number of antigens needed to classify samples. Our work showcases the power of mathematical modeling in diagnostic classification and highlights a method that can be adopted broadly in public health and clinical settings., Comment: 14 pages, 4 figures, 1 table, 6 supplemental figures; fixed typos/updated table, corrected PDF in Appendix
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- 2022
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40. A Time-Symmetric Resolution of the Einstein's Boxes Paradox
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Heaney, Michael B.
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Quantum Physics - Abstract
The Einstein's Boxes paradox was developed by Einstein, de Broglie, Heisenberg, and others to demonstrate the incompleteness of the Copenhagen Formulation of quantum mechanics. I explain the paradox using the Copenhagen Formulation.~I then show how a time-symmetric formulation of quantum mechanics resolves the paradox in the way envisioned by Einstein and de Broglie. Finally, I describe an experiment that can distinguish between these two formulations., Comment: 10 pages, 3 figures
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- 2022
41. Long-term efficacy and safety of osilodrostat in patients with Cushings disease: results from the LINC 4 study extension.
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Gadelha, Mônica, Snyder, Peter, Witek, Przemysław, Bex, Marie, Belaya, Zhanna, Turcu, Adina, Feelders, Richard, Heaney, Anthony, Paul, Michaela, Pedroncelli, Alberto, and Auchus, Richard
- Subjects
11β-hydroxylase ,Cushing’s disease ,hypercortisolism ,long-term treatment ,osilodrostat ,Humans ,Pituitary ACTH Hypersecretion ,Hydrocortisone ,Quality of Life ,Adrenocortical Hyperfunction - Abstract
OBJECTIVE: To evaluate the long-term efficacy and safety of osilodrostat in patients with Cushings disease. METHODS: The multicenter, 48-week, Phase III LINC 4 clinical trial had an optional extension period that was initially intended to continue to week 96. Patients could continue in the extension until a managed-access program or alternative treatment became available locally, or until a protocol amendment was approved at their site that specified that patients should come for an end-of-treatment visit within 4 weeks or by week 96, whichever occurred first. Study outcomes assessed in the extension included: mean urinary free cortisol (mUFC) response rates; changes in mUFC, serum cortisol and late-night salivary cortisol (LNSC); changes in cardiovascular and metabolic-related parameters; blood pressure, waist circumference and weight; changes in physical manifestations of Cushings disease; changes in patient-reported outcomes for health-related quality of life; changes in tumor volume; and adverse events. Results were analyzed descriptively; no formal statistical testing was performed. RESULTS: Of 60 patients who entered, 53 completed the extension, with 29 patients receiving osilodrostat for more than 96 weeks (median osilodrostat duration: 87.1 weeks). The proportion of patients with normalized mUFC observed in the core period was maintained throughout the extension. At their end-of-trial visit, 72.4% of patients had achieved normal mUFC. Substantial reductions in serum cortisol and LNSC were also observed. Improvements in most cardiovascular and metabolic-related parameters, as well as physical manifestations of Cushings disease, observed in the core period were maintained or continued to improve in the extension. Osilodrostat was generally well tolerated; the safety profile was consistent with previous reports. CONCLUSION: Osilodrostat provided long-term control of cortisol secretion that was associated with sustained improvements in clinical signs and physical manifestations of hypercortisolism. Osilodrostat is an effective long-term treatment for patients with Cushings disease. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier NCT02180217.
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- 2023
42. Association between wildfires and coccidioidomycosis incidence in California, 2000–2018: a synthetic control analysis
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Phillips, Sophie, Jones, Isabel, Sondermyer-Cooksey, Gail, Yu, Alexander T, Heaney, Alexandra K, Zhou, Bo, Bhattachan, Abinash, Weaver, Amanda K, Campo, Simon K, Mgbara, Whitney, Wagner, Robert, Taylor, John, Lettenmaier, Dennis, Okin, Gregory S, Jain, Seema, Vugia, Duc, Remais, Justin V, and Head, Jennifer R
- Subjects
Agricultural ,Veterinary and Food Sciences ,Ecological Applications ,Environmental Sciences ,Infectious Diseases ,Valley Fever ,Biodefense ,Emerging Infectious Diseases ,Rare Diseases ,California ,Climate change ,Coccidioidomycosis ,Coccidioides ,Drought ,Synthetic control ,Valley fever ,Wildfires - Abstract
The frequency and severity of wildfires in the Western United States have increased over recent decades, motivating hypotheses that wildfires contribute to the incidence of coccidioidomycosis, an emerging fungal disease in the Western United States with sharp increases in incidence observed since 2000. While coccidioidomycosis outbreaks have occurred among wildland firefighters clearing brush, it remains unknown whether fires are associated with an increased incidence among the general population.MethodsWe identified 19 wildfires occurring within California's highly endemic San Joaquin Valley between 2003 and 2015. Using geolocated surveillance records, we applied a synthetic control approach to estimate the effect of each wildfire on the incidence of coccidioidomycosis among residents that lived within a hexagonal buffer of 20 km radii surrounding the fire.ResultsWe did not detect excess cases due to wildfires in the 12 months (pooled estimated percent change in cases: 2.8%; 95% confidence interval [CI] = -29.0, 85.2), 13-24 months (7.9%; 95% CI = -27.3, 113.9), or 25-36 months (17.4%; 95% CI = -25.1, 157.1) following a wildfire. When examined individually, we detected significant increases in incidence following three of the 19 wildfires, all of which had relatively large adjacent populations, high transmission before the fire, and a burn area exceeding 5,000 acres.DiscussionWe find limited evidence that wildfires drive increases in coccidioidomycosis incidence among the general population. Nevertheless, our results raise concerns that large fires in regions with ongoing local transmission of Coccidioides may be associated with increases in incidence, underscoring the need for field studies examining Coccidioides spp. in soils and air pre- and post-wildfires.
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- 2023
43. Whole genome analysis for 163 gRNAs in Cas9-edited mice reveals minimal off-target activity
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Peterson, Kevin A, Khalouei, Sam, Hanafi, Nour, Wood, Joshua A, Lanza, Denise G, Lintott, Lauri G, Willis, Brandon J, Seavitt, John R, Braun, Robert E, Dickinson, Mary E, White, Jacqueline K, Lloyd, KC Kent, Heaney, Jason D, Murray, Stephen A, Ramani, Arun, and Nutter, Lauryl MJ
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Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,2.1 Biological and endogenous factors ,1.1 Normal biological development and functioning ,Generic health relevance ,Mice ,Animals ,CRISPR-Cas Systems ,Gene Editing ,Genome ,Mutation ,Mutagenesis ,Biological sciences ,Biomedical and clinical sciences - Abstract
Genome editing with CRISPR-associated (Cas) proteins holds exceptional promise for "correcting" variants causing genetic disease. To realize this promise, off-target genomic changes cannot occur during the editing process. Here, we use whole genome sequencing to compare the genomes of 50 Cas9-edited founder mice to 28 untreated control mice to assess the occurrence of S. pyogenes Cas9-induced off-target mutagenesis. Computational analysis of whole-genome sequencing data detects 26 unique sequence variants at 23 predicted off-target sites for 18/163 guides used. While computationally detected variants are identified in 30% (15/50) of Cas9 gene-edited founder animals, only 38% (10/26) of the variants in 8/15 founders validate by Sanger sequencing. In vitro assays for Cas9 off-target activity identify only two unpredicted off-target sites present in genome sequencing data. In total, only 4.9% (8/163) of guides tested have detectable off-target activity, a rate of 0.2 Cas9 off-target mutations per founder analyzed. In comparison, we observe ~1,100 unique variants in each mouse regardless of genome exposure to Cas9 indicating off-target variants comprise a small fraction of genetic heterogeneity in Cas9-edited mice. These findings will inform future design and use of Cas9-edited animal models as well as provide context for evaluating off-target potential in genetically diverse patient populations.
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- 2023
44. Genome-wide screening reveals the genetic basis of mammalian embryonic eye development
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Chee, Justine M, Lanoue, Louise, Clary, Dave, Higgins, Kendall, Bower, Lynette, Flenniken, Ann, Guo, Ruolin, Adams, David J, Bosch, Fatima, Braun, Robert E, Brown, Steve DM, Chin, H-J Genie, Dickinson, Mary E, Hsu, Chih-Wei, Dobbie, Michael, Gao, Xiang, Galande, Sanjeev, Grobler, Anne, Heaney, Jason D, Herault, Yann, de Angelis, Martin Hrabe, Mammano, Fabio, Nutter, Lauryl MJ, Parkinson, Helen, Qin, Chuan, Shiroishi, Toshi, Sedlacek, Radislav, Seong, J-K, Xu, Ying, Brooks, Brian, McKerlie, Colin, Lloyd, KC Kent, Westerberg, Henrik, and Moshiri, Ala
- Subjects
Biological Sciences ,Genetics ,Pediatric ,Eye Disease and Disorders of Vision ,Rare Diseases ,Congenital Structural Anomalies ,Human Genome ,2.1 Biological and endogenous factors ,Eye ,Humans ,Mice ,Animals ,Eye Abnormalities ,Anophthalmos ,Microphthalmos ,Coloboma ,Mice ,Knockout ,Embryonic Development ,Phenotype ,Mammals ,MAC spectrum ,Eye development ,Mouse ,IMPC ,Serine-glycine biosynthesis ,CPLANE ,International Mouse Phenotyping Consortium ,Developmental Biology - Abstract
BackgroundMicrophthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome.ResultsQuery of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation.ConclusionsUsing genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.
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- 2023
45. Circulating FK506 binding protein 51 mRNA expression in patients with pituitary adenomas.
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Yang, Yingying, Babayan, Lilit, Mirzakhanian, Argishty, Sisliyan, Nvard, Zhang, Dongyun, Hurtado, Carolina, Zahid, Abdul, Bergsneider, Marvin, Kim, Won, Wang, Marilene B, and Heaney, Anthony P
- Subjects
Circulating biomarker ,Cushing disease ,FKBP5 ,Pituitary tumors ,Cancer ,Brain Disorders ,Clinical Research ,Genetics - Abstract
BackgroundFK506 binding protein 51 (FKBP5) is a co-chaperone regulator of the glucocorticoid receptor (GR). Recent studies have reported increased FKBP5 mRNA in the circulation from patients with Cushing disease (CD) which returned to comparable levels seen in healthy controls following successful trans-nasal trans-sphenoidal (TNTS) surgical corticotroph tumor removal. However, the expression of circulating FKBP5 mRNA levels in other pituitary tumor subtypes and its specificity to corticotroph tumors is unknown.MethodsPre-operative blood was collected from consecutive patients undergoing TNTS for pituitary tumors (n = 57) at our center between 2015 and 2019. Total RNA was isolated from whole blood using RiboPure blood RNA isolation kit and real-time qPCR was used to quantitate circulating FKBP5 mRNA expression.ResultsConsistent with the prior report, higher circulating FKBP5 mRNA levels were observed in 20 patients with CD prior to surgical tumor removal, compared to 21 healthy controls (p
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- 2023
46. Levoketoconazole treatment in endogenous Cushings syndrome: extended evaluation of clinical, biochemical, and radiologic outcomes.
- Author
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Fleseriu, Maria, Auchus, Richard, Greenman, Yona, Zacharieva, Sabina, Geer, Eliza, Salvatori, Roberto, Pivonello, Rosario, Feldt-Rasmussen, Ulla, Kennedy, Laurence, Buchfelder, Michael, Biller, Beverly, Cohen, Fredric, and Heaney, Anthony
- Subjects
Humans ,Adrenal Insufficiency ,Cushing Syndrome ,Enzyme Inhibitors ,Hydrocortisone ,Pituitary ACTH Hypersecretion ,Somatostatin ,Treatment Outcome - Abstract
OBJECTIVE: This extended evaluation (EE) of the SONICS study assessed the effects of levoketoconazole for an additional 6 months following open-label, 6-month maintenance treatment in endogenous Cushings syndrome. DESIGN/METHODS: SONICS included dose-titration (150-600 mg BID), 6-month maintenance, and 6-month EE phases. Exploratory efficacy assessments were performed at months 9 and 12 (relative to the start of maintenance). For pituitary MRI in patients with Cushings disease, a threshold of ≥2 mm denoted change from baseline in the largest tumor diameter. RESULTS: Sixty patients entered EE at month 6; 61% (33/54 with data) exhibited normal mean urinary free cortisol (mUFC). At months 9 and 12, respectively, 55% (27/49) and 41% (18/44) of patients with data had normal mUFC. Mean fasting glucose, total and LDL-cholesterol, body weight, BMI, abdominal girth, hirsutism, CushingQoL, and Beck Depression Inventory-II scores improved from the study baseline at months 9 and 12. Forty-six patients completed month 12; four (6.7%) discontinued during EE due to adverse events. The most common adverse events in EE were arthralgia, headache, hypokalemia, and QT prolongation (6.7% each). No patient experienced alanine aminotransferase or aspartate aminotransferase >3× upper limit of normal, Fridericia-corrected QT interval >460 ms, or adrenal insufficiency during EE. Of 31 patients with tumor measurements at baseline and month 12 or follow-up, the largest tumor diameter was stable in 27 (87%) patients, decreased in one, and increased in three (largest increase 4 mm). CONCLUSION: In the first long-term levoketoconazole study, continued treatment through a 12-month maintenance period sustained the early clinical and biochemical benefits in most patients completing EE, without new adverse effects.
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- 2022
47. Audit of Postoperative Readmissions and Patient Messages following Endoscopic Transnasal Transsphenoidal Surgery
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Harary, Maya, Bommakanti, Krishna K, Nakhla, Morcos N, Kosaraju, Nikitha, Heaney, Anthony P, Kim, Won, Lee, Jivianne T, Suh, Jeffrey D, Bergsneider, Marvin, and Wang, Marilene B
- Subjects
Clinical Research ,Health Services ,Patient Safety ,Cancer ,8.1 Organisation and delivery of services ,Management of diseases and conditions ,7.1 Individual care needs ,Health and social care services research ,endoscopic skull base surgery ,TNTS ,discharge instructions ,readmissions ,Neurology & Neurosurgery - Abstract
Objectives The aim of this study was to identify the reasons for patient messages, phone calls, and emergency department (ED) visits prior to the first postoperative visit following discharge after endoscopic transnasal transsphenoidal (eTNTS) surgery. Design This is a retrospective review of patients at a tertiary care academic center who underwent eTNTS for resection of a sellar region tumor between May 2020 and August 2021. Patient, tumor, and surgical characteristics were collected, along with postoperative, postdischarge, and readmission information. Regression analyses were performed to investigate risk factors associated with postdischarge phone calls, messages, ED visits, and readmissions. Main Outcome Measures The main outcomes were the number of and reasons for phone calls, patient messages, and ED visits between hospital discharge and the first postoperative visit. We additionally determined whether these reasons were addressed in each patient's discharge instructions. Results A total of 98 patients underwent eTNTS during the study period. The median length of hospital stay was 2 days (interquartile range [IQR]: 1-4 days), at which point most patients (82%) were provided with eTNTS-specific discharge instructions. First postoperative visit took place 9 days after discharge (IQR: 7-10 days). Within that time, 54% of patients made at least one phone call or sent at least electronic message and 17% presented to the ED. Most common reasons for call/message were nasal care, appointment scheduling, and symptom and medication questions. Conclusion Through this work, we highlight the most common reasons for resource utilization via patient phone calls, messages, and ED visits among our cohort to better understand any shortfall or gap in the discharge process that may reduce these events.
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- 2022
48. Whole-exome sequencing reveals genetic variants that may play a role in neurocytomas
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Khowal, Sapna, Zhang, Dongyun, Yong, William H, and Heaney, Anthony P.
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- 2024
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49. Synthesis, characterisation, and solution behaviour of Ag(I) bis(phenanthroline-oxazine) complexes and the evaluation of their biological activity against the pathogenic yeast Candida albicans
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Evans, Clara, Ahmed, Muhib, Beirne, Darren F., McCann, Malachy, Kavanagh, Kevin, Devereux, Michael, Rooney, Denise, and Heaney, Frances
- Published
- 2023
- Full Text
- View/download PDF
50. Effects of precipitation, heat, and drought on incidence and expansion of coccidioidomycosis in western USA: a longitudinal surveillance study
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Head, Jennifer R, Sondermeyer-Cooksey, Gail, Heaney, Alexandra K, Yu, Alexander T, Jones, Isabel, Bhattachan, Abinash, Campo, Simon K, Wagner, Robert, Mgbara, Whitney, Phillips, Sophie, Keeney, Nicole, Taylor, John, Eisen, Ellen, Lettenmaier, Dennis P, Hubbard, Alan, Okin, Gregory S, Vugia, Duc J, Jain, Seema, and Remais, Justin V
- Subjects
Public Health ,Health Sciences ,Good Health and Well Being ,Coccidioidomycosis ,Droughts ,Hot Temperature ,Humans ,Incidence ,Seasons ,Climate change impacts and adaptation ,Environmental management ,Public health - Abstract
BackgroundDrought is an understudied driver of infectious disease dynamics. Amidst the ongoing southwestern North American megadrought, California (USA) is having the driest multi-decadal period since 800 CE, exacerbated by anthropogenic warming. In this study, we aimed to examine the influence of drought on coccidioidomycosis, an emerging infectious disease in southwestern USA.MethodsWe analysed California census tract-level surveillance data from 2000 to 2020 using generalised additive models and distributed monthly lags on precipitation and temperature. We then developed an ensemble prediction algorithm of incident cases of coccidioidomycosis per census tract to estimate the counterfactual incidence that would have occurred in the absence of drought.FindingsBetween April 1, 2000, and March 31, 2020, there were 81 448 reported cases of coccidioidomycosis throughout California. An estimated 1467 excess cases of coccidioidomycosis were observed in California in the 2 years following the drought that occurred between 2007 and 2009, and an excess 2649 drought-attributable cases of coccidioidomycosis were observed in the 2 years following the drought that occurred between 2012 and 2015. These increased numbers of cases more than offset the declines in cases that occurred during drought. An IQR increase in summer temperatures was associated with 2·02 (95% CI 1·84-2·22) times higher incidence in the following autumn (September to November), and an IQR increase in precipitation in the winter was associated with 1·45 (1·36-1·55) times higher incidence in the autumn. The effect of winter precipitation was 36% (25-48) stronger when preceded by two dry, rather than average, winters. Incidence in arid counties was most sensitive to precipitation fluctuations, while incidence in wetter counties was most sensitive to temperature.InterpretationIn California, multi-year cycles of dry conditions followed by a wet winter increases transmission of coccidioidomycosis, especially in historically wetter areas. With anticipated increasing frequency of drought in southwestern USA, continued expansion of coccidioidomycosis, along with more intense seasons, is expected. Our results motivate the need for heightened precautions against coccidioidomycosis in seasons that follow major droughts.FundingNational Institutes of Health.
- Published
- 2022
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