4,352 results on '"O'Beirne A"'
Search Results
2. An Australian Community-Based Metabolic Dysfunction-Associated Steatotic Liver Disease Care Pathway for People with Type 2 Diabetes: Barriers and Considerations
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Gracen L, Aikebuse M, Sarraf B, McPhail SM, Russell AW, O’Beirne J, Irvine KM, Williams S, Valery PC, and Powell EE
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nafld ,primary care ,chronic liver disease ,fibroscan ,Medicine (General) ,R5-920 - Abstract
Lucy Gracen,1 Melanie Aikebuse,2,3 Babak Sarraf,2– 4 Steven M McPhail,5 Anthony W Russell,6 James O’Beirne,7 Katharine M Irvine,8 Suzanne Williams,9 Patricia C Valery,4,* Elizabeth E Powell2– 4,* 1Department of Gastroenterology and Hepatology, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia; 2Department of Gastroenterology and Hepatology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia; 3Centre for Liver Disease Research, Faculty of Medicine, Translational Research Institute, The University of Queensland, Woolloongabba, QLD, Australia; 4QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; 5Australian Centre for Health Services Innovation School of Public Health, Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Brisbane, QLD, Australia; 6Endocrinology and Diabetes, the Alfred Hospital, Melbourne, VIC, Australia; 7Department of Gastroenterology and Hepatology, Sunshine Coast University Hospital, Birtinya, QLD, Australia; 8Mater Research, Translational Research Institute, Brisbane, QLD, Australia; 9Inala Primary Care General Practice, Inala, QLD, Australia*These authors contributed equally to this workCorrespondence: Elizabeth E Powell, Centre for Liver Disease Research, Faculty of Medicine, Translational, Research Institute, The University of Queensland, Level 5, West Wing, 37, Kent Street, Woolloongabba, Brisbane, QLD, 4102, Australia, Tel +61 412 014 337, Email e.powell@uq.edu.auBackground: Although clinical guidelines endorse screening for metabolic dysfunction-associated steatotic liver disease (MASLD) with advanced fibrosis in people with type 2 diabetes (T2D), the feasibility of and barriers and considerations relevant to implementing this approach in the community remain unclear.Methods: Sequential adults with T2D attending selected community clinics during 2021– 2023 were invited to receive a “liver health check” (n=543). A further 95 participants were referred directly from their general practitioner (GP) or self-referred to the study. A total of 302 participants underwent a point of care assessment of hepatic steatosis and stiffness (FibroScan) and were advised to see their GP to discuss the results. “Template” letters containing key results, their interpretation and advice about management of cardiometabolic risk, patient follow-up and referral criteria, were sent to participants’ GPs.Results: Referral to a tertiary liver clinic was advised in GP letters for 45 (15%) participants with an increased risk of clinically significant fibrosis (liver stiffness measurement ≥ 8), 15 participants with ‘red flags’ (eg splenomegaly, thrombocytopenia) and 2 with unsuccessful FibroScan examinations. A referral from GPs to the liver clinic was received for 27 (44%) of these 62 participants. Approximately 90% of GPs rated the “template” letters favourably on a Likert rating scale.Conclusion: The low rate of participation in the “liver health check” and liver clinic referral reflects a real-world scenario and may stem from societal under-recognition and engagement with MASLD, competing health priorities or under-appreciation of the link between liver fibrosis severity and mortality risk. Further studies need to address strategies to enhance participation in liver health assessments and determine their impact on liver-related morbidity/mortality and overall survival.Keywords: NAFLD, primary care, chronic liver disease, FibroScan
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- 2024
3. ChatGPT and Excel -- trust, but verify
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O'Beirne, Patrick
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Computer Science - Software Engineering - Abstract
This paper adopts a critical approach to ChatGPT, showing how its huge reach makes it a useful tool for people with simple requirements but a bad, even misleading guide to those with more complex problems which are more rarely present in the training data and even more rarely have straightforward solutions. It works through four exercises in creating lookup formulas using chatbots, showing the need to test the offered solutions. They are a simple lookup, a lookup to the left, a match of two values at the same time, and intentionally confusing the models by using common language with technical meaning in Excel. It concludes with a practical guide for how to add an Excelscript button, with system and user prompts, to the ChatGPT API into the Excel desktop environment, supported by a blog post giving the technical details for those interested., Comment: 15 pages, 3 figures
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- 2023
4. A randomised controlled trial of Standard Of Care versus RadioAblaTion in Early Stage HepatoCellular Carcinoma (SOCRATES HCC)
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Wigg, Alan, Tibballs, Jonathan, Woodman, Richard, Stuart, Katherine, Le, Hien, Roberts, Stuart K., Olynyk, John K., Strasser, Simone I., Wallace, Michael, Martin, Jarad, Haworth, Annette, Hardcastle, Nicholas, Loo, Kee Fong, Tang, Colin, Lee, Yoo Young, Chu, Julie, De Abreu Lourenco, Richard, Koukourou, Adam, De Boo, Diederick, McLean, Kate, Buck, Jackie, Sawhney, Rohit, Nicoll, Amanda, Dev, Anouk, Wood, Marnie, Braund, Alicia, Weltman, Martin, Khor, Richard, Levy, Miriam, Wang, Tim, Potter, Michael, Haridy, James, Raj, Ashok, Duncan, Oliver, Zekry, Amany, Collier, Natalie, O’Beirne, James, Holliday, Catherine, Trada, Yuvnik, Tronidjaja, Jaw, George, Jacob, and Pryor, David
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- 2024
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5. High prevalence of diabetes among young First Nations Peoples with metabolic dysfunction-associated steatotic liver disease: a population-based study in Australia
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Valery, Patricia C., Roche, Shruti, Brown, Catherine, O’Beirne, James, Hartel, Gunter, Leggett, Barbara, Skoien, Richard, and Powell, Elizabeth E.
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- 2024
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6. The HI in Ring Galaxies Survey (HI-RINGS) -- Effects of the bar on the HI gas in ring galaxies
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Murugeshan, Chandrashekar, Dzudzar, Robert, Bagge, Ryan, O'Beirne, Tamsyn, Wong, Ivy, Kilborn, Virginia, Cluver, Michelle, Lutz, Katharina, and Elagali, Ahmed
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Astrophysics - Astrophysics of Galaxies - Abstract
We present a new high-resolution neutral atomic hydrogen (HI) survey of ring galaxies using the Australia Telescope Compact Array (ATCA). We target a sample of 24 ring galaxies from the Buta (1995) Southern Ring Galaxy Survey Catalogue in order to study the origin of resonance-, collisional- and interaction-driven ring galaxies. In this work, we present an overview of the sample and study their global and resolved HI properties. In addition, we also probe their star formation properties by measuring their star formation rates (SFR) and their resolved SFR surface density profiles. We find that a majority of the barred galaxies in our sample are HI deficient, alluding to the effects of the bar in driving their HI deficiency. Furthermore, for the secularly evolving barred ring galaxies in our sample, we apply Lindblad's resonance theory to predict the location of the resonance rings and find very good agreement between predictions and observations. We identify rings of HI gas and/or star formation co-located at one or the other major resonances. Lastly, we measure the bar pattern speed ($\Omega_{\textrm{bar}}$) for a sub-sample of our galaxies and find that the values range from 10 -- 90 km s$^{-1}$ kpc$^{-1}$, in good agreement with previous studies., Comment: Accepted for publication in PASA
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- 2023
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7. A randomised controlled trial of Standard Of Care versus RadioAblaTion in Early Stage HepatoCellular Carcinoma (SOCRATES HCC)
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Alan Wigg, Jonathan Tibballs, Richard Woodman, Katherine Stuart, Hien Le, Stuart K. Roberts, John K. Olynyk, Simone I. Strasser, Michael Wallace, Jarad Martin, Annette Haworth, Nicholas Hardcastle, Kee Fong Loo, Colin Tang, Yoo Young Lee, Julie Chu, Richard De Abreu Lourenco, Adam Koukourou, Diederick De Boo, Kate McLean, Jackie Buck, Rohit Sawhney, Amanda Nicoll, Anouk Dev, Marnie Wood, Alicia Braund, Martin Weltman, Richard Khor, Miriam Levy, Tim Wang, Michael Potter, James Haridy, Ashok Raj, Oliver Duncan, Amany Zekry, Natalie Collier, James O’Beirne, Catherine Holliday, Yuvnik Trada, Jaw Tronidjaja, Jacob George, and David Pryor
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Early-stage hepatocellular carcinoma ,Stereotactic ablative radiotherapy ,SABR ,SBRT ,Thermal ablation ,Transarterial therapies ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Therapeutic options for early-stage hepatocellular carcinoma (HCC) in individual patients can be limited by tumor and location, liver dysfunction and comorbidities. Many patients with early-stage HCC do not receive curative-intent therapies. Stereotactic ablative body radiotherapy (SABR) has emerged as an effective, non-invasive HCC treatment option, however, randomized evidence for SABR in the first line setting is lacking. Methods Trans-Tasman Radiation Oncology Group (TROG) 21.07 SOCRATES-HCC is a phase II, prospective, randomised trial comparing SABR to other current standard of care therapies for patients with a solitary HCC ≤ 8 cm, ineligible for surgical resection or transplantation. The study is divided into 2 cohorts. Cohort 1 will compromise 118 patients with tumors ≤ 3 cm eligible for thermal ablation randomly assigned (1:1 ratio) to thermal ablation or SABR. Cohort 2 will comprise 100 patients with tumors > 3 cm up to 8 cm in size, or tumors ≤ 3 cm ineligible for thermal ablation, randomly assigned (1:1 ratio) to SABR or best other standard of care therapy including transarterial therapies. The primary objective is to determine whether SABR results in superior freedom from local progression (FFLP) at 2 years compared to thermal ablation in cohort 1 and compared to best standard of care therapy in cohort 2. Secondary endpoints include progression free survival, overall survival, adverse events, patient reported outcomes and health economic analyses. Discussion The SOCRATES-HCC study will provide the first randomized, multicentre evaluation of the efficacy, safety and cost effectiveness of SABR versus other standard of care therapies in the first line treatment of unresectable, early-stage HCC. It is a broad, multicentre collaboration between hepatology, interventional radiology and radiation oncology groups around Australia, coordinated by TROG Cancer Research. Trial registration anzctr.org.au, ACTRN12621001444875, registered 21 October 2021.
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- 2024
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8. Separating Technological and Clinical Safety Assurance for Medical Devices
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Deevy, Spencer, Machado, Tiago de Moraes, Modhafar, Amen, O'Beirne, Wesley, Paige, Richard, and Wassyng, Alan
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Computer Science - Computers and Society - Abstract
The safety and clinical effectiveness of medical devices are closely associated with their specific use in clinical treatments. Assuring safety and the desired clinical effectiveness is challenging. Different people may react differently to the same treatment due to variability in their physiology and genetics. Thus, we need to consider the outputs and behaviour of the device itself as well as the effect of using the device to treat a wide variety of patients. High-intensity focused ultrasound systems and radiation therapy machines are examples of systems in which this is a primary concern. Conventional monolithic assurance cases are complex, and this complexity affects our ability to address these concerns adequately. Based on the principle of separation of concerns, we propose separating the assurance of the use of these types of systems in clinical treatments into two linked assurance cases. The first assurance case demonstrates the safety of the manufacturer's device independent of the clinical treatment. The second demonstrates the safety and clinical effectiveness of the device when it is used in a specific clinical treatment. We introduce the idea of these separate assurance cases, and describe briefly how they are separated and linked.
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- 2023
9. Towards mapping the contemporary art world with ArtLM: an art-specific NLP model
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Chen, Qinkai, El-Mennaoui, Mohamed, Fosset, Antoine, Rebei, Amine, Cao, Haoyang, Bouscasse, Philine, O'Beirne, Christy Eóin, Shevchenko, Sasha, and Rosenbaum, Mathieu
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Computer Science - Computation and Language ,Computer Science - Machine Learning - Abstract
With an increasing amount of data in the art world, discovering artists and artworks suitable to collectors' tastes becomes a challenge. It is no longer enough to use visual information, as contextual information about the artist has become just as important in contemporary art. In this work, we present a generic Natural Language Processing framework (called ArtLM) to discover the connections among contemporary artists based on their biographies. In this approach, we first continue to pre-train the existing general English language models with a large amount of unlabelled art-related data. We then fine-tune this new pre-trained model with our biography pair dataset manually annotated by a team of professionals in the art industry. With extensive experiments, we demonstrate that our ArtLM achieves 85.6% accuracy and 84.0% F1 score and outperforms other baseline models. We also provide a visualisation and a qualitative analysis of the artist network built from ArtLM's outputs.
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- 2022
10. Patient perspectives on knowledge gaps in hypersensitivity pneumonitis
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Monika M Safford, Robert Kaner, Kerri Aronson, Janani Varadarajan, Armani Edgar, Ronan O'Beirne, Tessy K Paul, and Jamuna K Krishnan
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Medicine ,Diseases of the respiratory system ,RC705-779 - Abstract
Objectives Responding to prior research findings that lack of knowledge about their disease impacted patients’ quality of life, the objective of this study was to identify and prioritise information gaps about hypersensitivity pneumonitis (HP) from the perspective of patients living with the disease.Design This study used the nominal group technique, a semiquantitative and qualitative method to identify stakeholder priorities.Setting Virtual group sessions were conducted in an academic medical centre in the USA.Participants 21 patients diagnosed with HP participated in this study. Participants were eligible if they spoke English and had access to the internet and were excluded if they had cognitive impairment.Results The patient statements were grouped into seven themes that were prioritised by participants in the following order: (1) natural history and prognosis; (2) current treatment options and therapeutic research; (3) epidemiology and aetiology of HP; (4) living well with HP; (5) origin and management of symptoms; (6) identifying and mitigating exposures and (7) methods of educating patients, clinicians and others about HP.Conclusions This study provides an understanding of patients’ prioritisation of knowledge gaps in HP to inform targeted educational interventions and provide avenues for future research.
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- 2024
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11. WALLABY Pilot Survey: Public release of HI data for almost 600 galaxies from phase 1 of ASKAP pilot observations
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Westmeier, T., Deg, N., Spekkens, K., Reynolds, T. N., Shen, A. X., Gaudet, S., Goliath, S., Huynh, M. T., Venkataraman, P., Lin, X., O'Beirne, T., Catinella, B., Cortese, L., Dénes, H., Elagali, A., For, B. -Q., Józsa, G. I. G., Howlett, C., van der Hulst, J. M., Jurek, R. J., Kamphuis, P., Kilborn, V. A., Kleiner, D., Koribalski, B. S., Lee-Waddell, K., Murugeshan, C., Rhee, J., Serra, P., Shao, L., Staveley-Smith, L., Wang, J., Wong, O. I., Zwaan, M. A., Allison, J. R., Anderson, C. S., Ball, Lewis, Bock, D. C. -J., Brodrick, D., Bunton, J. D., Cooray, F. R., Gupta, N., Hayman, D. B., Mahony, E. K., Moss, V. A., Ng, A., Pearce, S. E., Raja, W., Roxby, D. N., Voronkov, M. A., Warhurst, K. A., Courtois, H. M., and Said, K.
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Astrophysics - Astrophysics of Galaxies - Abstract
We present WALLABY pilot data release 1, the first public release of HI pilot survey data from the Wide-field ASKAP L-band Legacy All-sky Blind Survey (WALLABY) on the Australian Square Kilometre Array Pathfinder. Phase 1 of the WALLABY pilot survey targeted three $60~{\rm deg}^2$ regions on the sky in the direction of the Hydra and Norma galaxy clusters and the NGC 4636 galaxy group, covering the redshift range of z < 0.08. The source catalogue, images and spectra of nearly 600 extragalactic HI detections and kinematic models for 109 spatially resolved galaxies are available. As the pilot survey targeted regions containing nearby group and cluster environments, the median redshift of the sample of z ~ 0.014 is relatively low compared to the full WALLABY survey. The median galaxy HI mass is $2.3 \times 10^{9}~M_{\odot}$. The target noise level of 1.6 mJy per $30''$ beam and 18.5 kHz channel translates into a $5\sigma$ HI mass sensitivity for point sources of about $5.2 \times 10^{8} \, (D_{\rm L} / \mathrm{100~Mpc})^{2} \, M_{\odot}$ across 50 spectral channels (~200 km/s) and a $5\sigma$ HI column density sensitivity of about $8.6 \times 10^{19} \, (1 + z)^{4}~\mathrm{cm}^{-2}$ across 5 channels (~20 km/s) for emission filling the $30''$ beam. As expected for a pilot survey, several technical issues and artefacts are still affecting the data quality. Most notably, there are systematic flux errors of up to several 10% caused by uncertainties about the exact size and shape of each of the primary beams as well as the presence of sidelobes due to the finite deconvolution threshold. In addition, artefacts such as residual continuum emission and bandpass ripples have affected some of the data. The pilot survey has been highly successful in uncovering such technical problems, most of which are expected to be addressed and rectified before the start of the full WALLABY survey., Comment: 24 pages, 13 figures, 5 tables, accepted for publication in PASA
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- 2022
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12. High prevalence of diabetes among young First Nations Peoples with metabolic dysfunction-associated steatotic liver disease: a population-based study in Australia
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Patricia C. Valery, Shruti Roche, Catherine Brown, James O’Beirne, Gunter Hartel, Barbara Leggett, Richard Skoien, and Elizabeth E. Powell
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Type 2 diabetes ,Cirrhosis ,Population ,Epidemiology ,NAFLD ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background Liver disease is an important contributor to the mortality gap between First Nations Peoples and non-Indigenous Australian adults. Despite a high burden of metabolic comorbidities among First Nations Peoples, data about the epidemiology of metabolic dysfunction-associated steatotic liver disease (MASLD) in this population is scarce. Methods A retrospective analysis of all adults hospitalized with MASLD or metabolic dysfunction-associated steatohepatitis (MASH) with/without cirrhosis during 2007–2019 in the state of Queensland was performed. Patients were followed from the first admission with MASLD/MASH (identified based on validated algorithms) to decompensated cirrhosis and overall mortality. We explored differences according to Indigenous status using Multivariable Cox regression. Findings 439 First Nations Peoples and 7,547 non-Indigenous Australians were followed for a median of 4.6 years (interquartile range 2.7–7.2). Overall, women were overrepresented, but more so in the First Nations cohort (72.7% vs. 57.0%, p
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- 2024
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13. Australians with metabolic dysfunction‐associated steatotic liver disease have a twofold increase in the incidence of cancer
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Elizabeth E Powell, Shruti Roche, Babak Sarraf, Gunter Hartel, Richard Skoien, Barbara Leggett, James O'Beirne, and Patricia C Valery
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cirrhosis ,diabetes ,extrahepatic cancer ,liver disease ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Abstract Background and Aim Metabolic dysfunction‐associated steatotic liver disease (MASLD) is associated with an increased risk of extrahepatic morbidity. We compared the incidence of cancers in adults admitted to Queensland hospitals with MASLD with that for the Queensland population and examined the association between cirrhosis and type 2 diabetes and the development of extrahepatic cancers. Methods In this retrospective study, we identified all cancers (Queensland Cancer Registry) after the first hospitalization with MASLD during Jul‐2007 to Dec‐2019, estimated age‐standardized incidence (ASI) of cancers, and compared that with the ASI in the Queensland population (incidence rate ratios [IRR]). Among the MASLD cohort, we examined the association between diabetes and cancer risk (Cox regression). Median follow‐up was 3.8 years (54 204 person‐years). Results Totally 1104 new cancers were diagnosed in 1018 patients (8.9% of 9771 non‐cirrhotic and 1712 adults with cirrhosis). The ASI (all cancers) of 1668.2 per 100 000 person‐years in men (95% CI 1523.7–1827.4) and 1284.0 per 100 000 person‐years in women (95% CI 1169.6–1408.2) was 2‐fold higher than that of the Queensland population (IRR = 1.94, 95% CI 1.75–2.16 and IRR = 1.99, 95% CI 1.78–2.22, respectively). Incidence of stomach cancer, unknown primary, and pancreas was 3‐ to 5‐fold higher compared to the general population (all P
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- 2024
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14. Maternal pre-pregnancy BMI influences the associations between bisphenol and phthalate exposures and maternal weight changes and fat accumulation
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Kaplan, B.J., Field, C.J., Bell, R.C., Bernier, F.P., Cantell, M., Casey, L.M., Eliasziw, M., Farmer, A., Gagnon, L., Giesbrecht, G.F., Goonewardene, L., Johnston, D., Kooistra, L., Letourneau, N., Manca, D.P., Martin, J.W., McCargar, L.J., O'Beirne, M., Pop, V.J., Deane, A.J., Singhal, N., Letourneau (current Pi), N., Dewey, D., Forbes, L., Giesbrecht, G., Lebel, C., Leung, B., McMorris, C., Ross, K., Irvine, Nathalie, Bell, Rhonda C., Subhan, Fatheema B., Field, Catherine J., Liu, Jiaying, MacDonald, Amy M., Kinniburgh, David W., Martin, Jonathan W., Dewey, Deborah, and England-Mason, Gillian
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- 2024
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15. The Irish Republican Brotherhood, 1914-1924
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John O'Beirne Ranelagh
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- 2024
16. Decoding paleomire conditions of paleogene superhigh-organic-sulfur coals
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Adsul, Tushar, O'Beirne, Molly D., Fike, David A., Ghosh, Santanu, Werne, Josef P., Gilhooly, William P., III, Hackley, Paul C., Hatcherian, Javin J., Philip, Bright, Hazra, Bodhisatwa, Bhattacharyya, Sudip, Konar, Ritam, and Varma, Atul Kumar
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- 2024
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17. Defining the Denominator for Measuring Quality of End-of-Life Care in Children with Cancer: Results of a Nominal Group Technique
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Johnston, Emily E., Tefera, Raba, Ananth, Prasanna, Martinez, Isaac, Porter, Amy, Snaman, Jennifer M., Thienprayoon, Rachel, Asch, Steve, Bhatia, Smita, and O'Beirne, Ronan
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- 2024
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18. Rising hospital admissions for alcohol-related cirrhosis and the impact of sex and comorbidity – a data linkage study
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Sarraf, B., Skoien, R., Hartel, G., O'Beirne, J., Clark, P.J., Collins, L., Leggett, B., Powell, E.E., and Valery, P.C.
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- 2024
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19. A discrete choice experiment to elicit preferences for a liver screening programme in Queensland, Australia: a mixed methods study to select attributes and levels
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Allen, Michelle J, Doran, Rachael, Brain, David, Powell, Elizabeth E, O’Beirne, James, Valery, Patricia C, Barnett, Adrian, Hettiarachchi, Ruvini, Hickman, Ingrid J, and Kularatna, Sanjeewa
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- 2023
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20. Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms
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Hesketh-Best, Poppy J., Bosco-Santos, Alice, Garcia, Sofia L., O’Beirne, Molly D., Werne, Josef P., Gilhooly, III, William P., and Silveira, Cynthia B.
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- 2023
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21. A comparison of machine learning algorithms and traditional regression-based statistical modeling for predicting hypertension incidence in a Canadian population
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Chowdhury, Mohammad Ziaul Islam, Leung, Alexander A., Walker, Robin L., Sikdar, Khokan C., O’Beirne, Maeve, Quan, Hude, and Turin, Tanvir C.
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- 2023
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22. Life without an S-layer : the conditional genome of C. difficile
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O'Beirne, Shauna and Fagan, Robert
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571.6 - Abstract
Clostridium difficile is a Gram-positive spore-forming obligate anaerobe and the most common cause of antibiotic-associated infectious diarrhoea worldwide. C. difficile infection (CDI) has increased in severity and incidence over the last decade, representing a huge economic burden to healthcare systems. Two toxins elaborated by C. difficile are widely regarded as the major causes of CDI symptoms. However, little research has focused on the assembly of the cell envelope, which is the first point of contact with the host. Vegetative C. difficile are covered in a proteinaceous paracrystalline array, known as the S-layer. Production of the S-layer comes at an enormous metabolic cost to the cell and functional analysis of the major surface layer protein (SlpA) has uncovered roles in pathogenicity and sporulation. Using a C. difficile S-layer null strain, we examined the conditional genome of C. difficile in the absence of this major surface structure. This was achieved by creating a large library of mutants via insertional mutagenesis coupled to Transposon Directed Insertion Site Sequencing (TraDIS). We have identified 55 genes as conditionally essential and 20 genes as conditionally non-essential in the absence of SlpA. For example, we have demonstrated that secA2, encoding the SlpA translocase is dispensable for growth in an S-layer mutant. Interestingly, we have also demonstrated that in the absence of SlpA, several PSII biosynthetic genes, involved in S-layer surface attachment, are conditionally non-essential for growth in vitro. As conditionally non-essential genes represent potential targets for disrupting S-layer assembly, we investigated the phenotypic effects of gene silencing via CRISPR interference of conditionally non-essential genes identified in this study. We provide evidence that knock-down of secA2 in a WT background produces the same cell morphology as an S-layer mutant. Additionally, we show depletion of Era, a poly(A) polymerase and several PSII biosynthesis genes from cells has effects on cell shape, surface boundaries, membrane permeability and localisation of septas.
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- 2022
23. Distribution of branched glycerol dialkyl glycerol tetraether (brGDGT) lipids from soils and sediments from the same watershed are distinct regionally (central Chile) but not globally
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Molly D. O’Beirne, Wesley P. Scott, Sergio Contreras, A. Araneda, E. Tejos, J. Moscoso, and Josef P. Werne
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biomarker ,branched GDGTs ,lake ,soil ,Chile ,Science - Abstract
Quantitative reconstructions of past continental climates are vital for understanding contemporary and past climate change. Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are unique bacterial lipids that have been proposed as universal paleothermometers due to their correlation with temperature in modern settings. Thus, brGDGTs may serve as a crucial paleotemperature proxy for understanding past climate variations and improving regional climate projections, especially in critical but under constrained regions. That said, complications can arise in their application due to varying source contributions (e.g., soils vs. peats vs. lacustrine). As such, this study investigates brGDGT distributions in Chilean lake surface sediments and corresponding watershed soils to determine the source of brGDGTs to lake sediments. Global datasets of brGDGTs in lake sediments and soils were additionally compiled for comparison. Distinct brGDGT distributions in Chilean lakes and soils indicate minimal bias from soil inputs to the lacustrine sediments as well as in situ lacustrine production of brGDGTs, which supports the use of brGDGTs in lake sediments as reliable paleotemperature proxies in the region. The ΣIIIa/ΣIIa ratio, initially promising as a brGDGT source indicator in marine settings, shows global complexities in lacustrine settings, challenging the establishment of universal thresholds for source apportionment. That said, we show that the ratio can be successfully applied in Chilean lake surface sediments. Direct comparisons with watershed soils and further research are crucial for discerning brGDGT sources in lake sediments and improving paleotemperature reconstructions on regional and global scales moving forward. Overall, this study contributes valuable insights into brGDGT variability, essential for accurate paleoreconstructions.
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- 2024
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24. Moir\'e-localized interlayer exciton wavefunctions captured by imaging its electron and hole constituents
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Karni, Ouri, Barré, Elyse, Pareek, Vivek, Georgaras, Johnathan D., Man, Michael K. L., Sahoo, Chakradhar, Bacon, David R., Zhu, Xing, Ribeiro, Henrique B., O'Beirne, Aidan L., Hu, Jenny, Al-Mahboob, Abdullah, Abdelrasoul, Mohamed M. M., Chan, Nicholas S., Karmakar, Arka, Winchester, Andrew J., Kim, Bumho, Watanabe, Kenji, Taniguchi, Takashi, Barmak, Katayun, Madéo, Julien, da Jornada, Felipe H., Heinz, Tony F., and Dani, Keshav M.
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Physics - Optics ,Condensed Matter - Materials Science ,Physics - Applied Physics ,Physics - Chemical Physics - Abstract
Interlayer excitons (ILXs) - electron-hole pairs bound across two atomically thin layered semiconductors - have emerged as attractive platforms to study exciton condensation, single-photon emission and other quantum-information applications. Yet, despite extensive optical spectroscopic investigations, critical information about their size, valley configuration and the influence of the moir\'e potential remains unknown. Here, we captured images of the time- and momentum-resolved distribution of both the electron and the hole that bind to form the ILX in a WSe2/MoS2 heterostructure. We thereby obtain a direct measurement of the interlayer exciton diameter of ~5.4 nm, comparable to the moir\'e unit-cell length of 6.1 nm. Surprisingly, this large ILX is well localized within the moir\'e cell to a region of only 1.8 nm - smaller than the size of the exciton itself. This high degree of localization of the interlayer exciton is backed by Bethe-Salpeter equation calculations and demonstrates that the ILX can be localized within small moir\'e unit cells. Unlike large moir\'e cells, these are uniform over large regions, thus allowing the formation of extended arrays of localized excitations for quantum technology., Comment: 4 figures
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- 2021
25. In the Echenozian Discomfort Zone: Desire and Creativity in the Shadow of Death
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O’Beirne, Emer
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- 2023
26. A discrete choice experiment to elicit preferences for a liver screening programme in Queensland, Australia: a mixed methods study to select attributes and levels
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Michelle J Allen, Rachael Doran, David Brain, Elizabeth E Powell, James O’Beirne, Patricia C Valery, Adrian Barnett, Ruvini Hettiarachchi, Ingrid J Hickman, and Sanjeewa Kularatna
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Non-alcoholic fatty liver disease ,Attribute Development ,Discrete choice experiment ,Patient preferences ,Community Screening ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background In Australia, the overall prevalence of liver disease is increasing. Maximising uptake of community screening programmes by understanding patient preferences is integral to developing consumer-centred care models for liver disease. Discrete choice experiments (DCEs) are widely used to elicit preferences for various healthcare services. Attribute development is a vital component of a well-designed DCE and should be described in sufficient detail for others to assess the validity of outcomes. Hence, this study aimed to create a list of potential attributes and levels which can be used in a DCE study to elicit preferences for chronic liver disease screening programmes. Methods Key attributes were developed through a multi-stage, mixed methods design. Focus groups were held with consumers and health care providers on attributes of community screening programmes for liver disease. Stakeholders then prioritised attributes generated from the focus group in order of importance via an online prioritisation survey. The outcomes of the prioritisation exercise were then reviewed and refined by an expert panel to ensure clinically meaningful levels and relevance for a DCE survey. Results Fifteen attributes were generated during the focus group sessions deemed necessary to design liver disease screening services. Outcomes of the prioritisation exercise and expert panel stages recognised five attributes, with three levels each, for inclusion in a DCE survey to elicit consumer preferences for community screening for liver disease. This study also highlights broader social issues such as the stigma around liver disease that require careful consideration by policy makers when designing or implementing a liver screening programme. Conclusions The attributes and levels identified will inform future DCE surveys to understand consumer preferences for community screening programmes for liver disease. In addition, the outcomes will help inform the implementation of the LOCATE-NAFLD programme in real-world practice, and could be relevant for other liver and non-liver related chronic disease screening programmes.
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- 2023
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27. A discrete choice experiment to elicit preferences for a chronic disease screening programme in Queensland, Australia
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Senanayake, S., Barnett, A., Brain, D., Allen, M., Powell, E.E., O'Beirne, J., Valery, P., Hickman, I.J., and Kularatna, S.
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- 2024
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28. Redesigning Medical Device Assurance: Separating Technological and Clinical Assurance Cases.
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Spencer Deevy, Tiago de Moraes Machado, Amen Modhafar, Wesley O'Beirne, Richard F. Paige, and Alan Wassyng
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- 2023
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29. Redesigning Medical Device Assurance: Separating Technological and Clinical Assurance Cases
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Deevy, Spencer, de Moraes Machado, Tiago, Modhafar, Amen, O’Beirne, Wesley, Paige, Richard F., Wassyng, Alan, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Guiochet, Jérémie, editor, Tonetta, Stefano, editor, and Bitsch, Friedemann, editor
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- 2023
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30. What's the harm? Results of an active surveillance adverse event reporting system for chiropractors and physiotherapists.
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Katherine A Pohlman, Martha Funabashi, Maeve O'Beirne, J David Cassidy, Michael D Hill, Eric L Hurwitz, Gregory Kawchuk, Silvano Mior, Quazi Ibrahim, Haymo Thiel, Michael Westaway, Jerome Yager, and Sunita Vohra
- Subjects
Medicine ,Science - Abstract
This prospective, community-based, active surveillance study aimed to report the incidence of moderate, severe, and serious adverse events (AEs) after chiropractic (n = 100) / physiotherapist (n = 50) visit in offices throughout North America between October-2015 and December-2017. Three content-validated questionnaires were used to collect AE information: two completed by the patient (pre-treatment [T0] and 2-7 days post-treatment [T2]) and one completed by the provider immediately post-treatment [T1]. Any new or worsened symptom was considered an AE and further classified as mild, moderate, severe or serious. From the 42 participating providers (31 chiropractors; 11 physiotherapists), 3819 patient visits had complete T0 and T1 assessments. The patients were on average 50±18 years of age and 62.5% females. Neck/back pain was the most common presenting condition (70.0%) with 24.3% of patients reporting no condition/preventative care. From the patients visits with a complete T2 assessment (n = 2136 patient visits, 55.9%), 21.3% reported an AE, of which: 7.9% were mild, 6.2% moderate, 3.7% severe, 1.5% serious, and 2.0% had missing severity rating. The most common symptoms reported with moderate or higher severity were discomfort/pain, stiffness, difficulty walking and headache. This study provides valuable information for patients and providers regarding incidence and severity of AEs following patient visits in multiple community-based professions. These findings can be used to inform patients of what AEs may occur and future research opportunities can focus on mitigating common AEs.
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- 2024
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31. Reconstruction of Upper Extremity Peripheral Nerve Injuries Using an Epineurial-Like Collagen Device—A Prospective Clinical Study
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Alex O'Beirne, Jaslyn Cullen, Euphemie Landao-Bassonga, Monica Zheng, Clair Lee, Priya Kaluskar, Andrew Tai, and Minghao Zheng
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nerve reconstruction ,epineurium ,nerve transfer ,upper extremity ,Surgery ,RD1-811 - Abstract
Background Epineurium acts as a barrier to protect nerves from injury and maintains its structural and functional integrity. A device was developed to mimic the native structure of epineurium. The aim of this study was to evaluate its biological characteristics and clinical performance in the reconstruction of upper extremity peripheral nerves.
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- 2024
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32. Accurate Machine Learning Atmospheric Retrieval via a Neural Network Surrogate Model for Radiative Transfer
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Himes, Michael D., Harrington, Joseph, Cobb, Adam D., Baydin, Atilim Gunes, Soboczenski, Frank, O'Beirne, Molly D., Zorzan, Simone, Wright, David C., Scheffer, Zacchaeus, Domagal-Goldman, Shawn D., and Arney, Giada N.
- Subjects
Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Earth and Planetary Astrophysics - Abstract
Atmospheric retrieval determines the properties of an atmosphere based on its measured spectrum. The low signal-to-noise ratio of exoplanet observations require a Bayesian approach to determine posterior probability distributions of each model parameter, given observed spectra. This inference is computationally expensive, as it requires many executions of a costly radiative transfer (RT) simulation for each set of sampled model parameters. Machine learning (ML) has recently been shown to provide a significant reduction in runtime for retrievals, mainly by training inverse ML models that predict parameter distributions, given observed spectra, albeit with reduced posterior accuracy. Here we present a novel approach to retrieval by training a forward ML surrogate model that predicts spectra given model parameters, providing a fast approximate RT simulation that can be used in a conventional Bayesian retrieval framework without significant loss of accuracy. We demonstrate our method on the emission spectrum of HD 189733 b and find good agreement with a traditional retrieval from the Bayesian Atmospheric Radiative Transfer (BART) code (Bhattacharyya coefficients of 0.9843--0.9972, with a mean of 0.9925, between 1D marginalized posteriors). This accuracy comes while still offering significant speed enhancements over traditional RT, albeit not as much as ML methods with lower posterior accuracy. Our method is ~9x faster per parallel chain than BART when run on an AMD EPYC 7402P central processing unit (CPU). Neural-network computation using an NVIDIA Titan Xp graphics processing unit is 90--180x faster per chain than BART on that CPU., Comment: 16 pages, 4 figures, submitted to PSJ 3/4/2020, revised 1/22/2021, accepted 2/4/2021, published 4/25/2022. Updated to match the published manuscript. Himes et al. 2022, PSJ, 3, 91
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- 2020
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33. Hip Sonography Training
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Scott, Sally, O’Beirne, Joseph, Dubs, Beat, Tarrant, Ailbhe, Kraus, Tanja, O'Beirne, Joseph, editor, and Chlapoutakis, Konstantinos, editor
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- 2022
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34. Clinical Examination
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Placzek, Richard, Placzek, Sonja, O’Beirne, Joseph, O'Beirne, Joseph, editor, and Chlapoutakis, Konstantinos, editor
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- 2022
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35. Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms
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Poppy J. Hesketh-Best, Alice Bosco-Santos, Sofia L. Garcia, Molly D. O’Beirne, Josef P. Werne, William P. Gilhooly, and Cynthia B. Silveira
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Geology ,QE1-996.5 ,Environmental sciences ,GE1-350 - Abstract
Abstract Viral infections modulate bacterial metabolism and ecology. Here, we investigated the hypothesis that viruses influence the ecology of purple and green sulfur bacteria in anoxic and sulfidic lakes, analogs of euxinic oceans in the geologic past. By screening metagenomes from lake sediments and water column, in addition to publicly-available genomes of cultured purple and green sulfur bacteria, we identified almost 300 high and medium-quality viral genomes. Viruses carrying the gene psbA, encoding the small subunit of photosystem II protein D1, were ubiquitous, suggesting viral interference with the light reactions of sulfur oxidizing autotrophs. Viruses predicted to infect these autotrophs also encoded auxiliary metabolic genes for reductive sulfur assimilation as cysteine, pigment production, and carbon fixation. These observations show that viruses have the genomic potential to modulate the production of metabolic markers of phototrophic sulfur bacteria that are used to identify photic zone euxinia in the geologic past.
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- 2023
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36. Lower prevalence of elevated liver stiffness measurements in people with type 2 diabetes taking sodium-glucose co-transporter 2 inhibitors or glucagon-like peptide-1 receptor agonists
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Gracen, Lucy, Muthukumara, Withma, Aikebuse, Melanie, Russell, Anthony, O'Beirne, James, Irvine, Katharine M., Williams, Suzanne, Puri, Gaurav, Valery, Patricia C., Hayward, Kelly L., and Powell, Elizabeth E.
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- 2023
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37. A critical assessment of lacustrine branched glycerol dialkyl glycerol tetraether (brGDGT) temperature calibration models
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O'Beirne, Molly D., Scott, Wesley P., and Werne, Josef P.
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- 2023
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38. Molecular fossil chronicles and geochemical probes of Paleogene coals from Meghalaya, India
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Adsul, Tushar, O'Beirne, Molly D., Ghosh, Santanu, Werne, Josef P., Mani, Devleena, Bhattacharyya, Sudip, and Varma, Atul Kumar
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- 2023
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39. An exploration of the development of a Network of Health Promoting Schools in the Mid-west region of Ireland, 2005-2015 : a complex adaptive systems approach
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O'Beirne, Alanna and Gray, John
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613.071 ,Health Promoting Schools ,Health Promoting Schools in Ireland ,Complex Adaptive Systems - Abstract
Alanna O'Beirne PHD THESIS ABSTRACT This thesis explores the development of a Network of Health Promoting Schools in the Midwest region of Ireland between 2005 and 2015. It identifies supports and barriers to developing the Health Promoting School concept and process with school communities. The study draws on the literature from the fields of education and health and in particular the sub-discipline of health promotion and includes an exploration of themes of leadership, collaborative working, change, systems theory and the concept of the Health Promoting School. The overarching conceptual framework of Complex Adaptive Systems is used to pull the different theories and models together. The research adopts a largely qualitative approach exploiting a case study methodology. Four cases are presented; one case focuses on the Health Promoting Partnership which was responsible for the governance and strategic direction of the Network and the remaining three cases focus on individual school sites. In the first case partners from the agencies represented in the Partnership were interviewed and these data are combined with information from steering group meetings to provide insights into the strategic supports and barriers to establishing and maintaining a Network of Health Promoting Schools. In the three school cases, stakeholders from the school communities (Principals, Health Promoting School Coordinators, Teachers, Parents and Pupils) were interviewed and these data were coupled with individual Health Promoting School Meeting records to identify supports and barriers for the implementation of Health Promoting Schools at the ground level. One of the key findings was that the promotion of the whole school's participation and engagement with the Health Promoting School concept was vital to successful implementation. However this was not unproblematic. While children's participation was supported and valued, responses relating to parental engagement were more ambivalent. Another finding was that strategic supports put in place by the Partnership were highly regarded by teachers, Principals and School Coordinators. The findings indicate that while stakeholders appreciated the need for schools to place an emphasis on health, the implementation of Health Promoting Schools had to compete with a myriad of other demands pressing on a finite amount of school time. This research is likely to be of interest to those involved in implementing a Health Promoting School Model and process at the individual school level or more strategically in developing a Network of Health Promoting Schools. Researchers interested in adopting a Complex Adaptive Systems approach in their investigation of Health Promoting Schools will also find this study informative.
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- 2020
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40. Lower prevalence of elevated liver stiffness measurements in people with type 2 diabetes taking sodium-glucose co-transporter 2 inhibitors or glucagon-like peptide-1 receptor agonists
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Lucy Gracen, Withma Muthukumara, Melanie Aikebuse, Anthony Russell, James O'Beirne, Katharine M. Irvine, Suzanne Williams, Gaurav Puri, Patricia C. Valery, Kelly L. Hayward, and Elizabeth E. Powell
- Subjects
Non-alcoholic fatty liver disease ,Diabetes mellitus, type 2 ,Sodium-glucose transporter 2 inhibitors ,Hypoglycemic Agents ,Glucagon-Like Peptide-1 Receptor ,Elasticity Imaging Techniques ,Specialties of internal medicine ,RC581-951 - Abstract
Introduction and Objectives: Among people with type 2 diabetes (T2D), non-alcoholic fatty liver disease (NAFLD) is very common and has an increased risk of clinically significant liver disease. The use of sodium-glucose co-transporter 2 (SGLT2i) inhibitors and glucagon-like peptide-1 (GLP-1a) receptor agonists is endorsed to reduce major cardiovascular events and/or progression of chronic kidney disease. Their prevalence of use in people with T2D and co-existent NAFLD remains unclear. We sought to determine the prevalence of use of these medications at two different time periods, and their association with prevalence of clinically significant liver disease. Materials and Methods: Consecutive people with type 2 diabetes (T2D) and non-alcoholic fatty liver disease (NAFLD) were recruited from diabetes clinics between Jun-2021 and Jun-2022 (‘current’ cohort). Liver stiffness measurements (LSM) using FibroScan were performed. Medication data were collected prospectively at recruitment and verified with the dispensing pharmacy or general practitioner medical records. Data for a historical cohort with NAFLD and T2D recruited from the same clinics during 2015–2017 (‘historical’ cohort) were available. Logistic regression was used to evaluate factors associated with LSM
- Published
- 2023
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41. An Ensemble of Bayesian Neural Networks for Exoplanetary Atmospheric Retrieval
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Cobb, Adam D., Himes, Michael D., Soboczenski, Frank, Zorzan, Simone, O'Beirne, Molly D., Baydin, Atılım Güneş, Gal, Yarin, Domagal-Goldman, Shawn D., Arney, Giada N., and Angerhausen, Daniel
- Subjects
Astrophysics - Earth and Planetary Astrophysics ,Computer Science - Machine Learning - Abstract
Machine learning is now used in many areas of astrophysics, from detecting exoplanets in Kepler transit signals to removing telescope systematics. Recent work demonstrated the potential of using machine learning algorithms for atmospheric retrieval by implementing a random forest to perform retrievals in seconds that are consistent with the traditional, computationally-expensive nested-sampling retrieval method. We expand upon their approach by presenting a new machine learning model, \texttt{plan-net}, based on an ensemble of Bayesian neural networks that yields more accurate inferences than the random forest for the same data set of synthetic transmission spectra. We demonstrate that an ensemble provides greater accuracy and more robust uncertainties than a single model. In addition to being the first to use Bayesian neural networks for atmospheric retrieval, we also introduce a new loss function for Bayesian neural networks that learns correlations between the model outputs. Importantly, we show that designing machine learning models to explicitly incorporate domain-specific knowledge both improves performance and provides additional insight by inferring the covariance of the retrieved atmospheric parameters. We apply \texttt{plan-net} to the Hubble Space Telescope Wide Field Camera 3 transmission spectrum for WASP-12b and retrieve an isothermal temperature and water abundance consistent with the literature. We highlight that our method is flexible and can be expanded to higher-resolution spectra and a larger number of atmospheric parameters.
- Published
- 2019
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42. Constraining alternative polarization states of gravitational waves from individual black hole binaries using pulsar timing arrays
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O'Beirne, Logan, Cornish, Neil J., Vigeland, Sarah J., and Taylor, Stephen R.
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General Relativity and Quantum Cosmology ,Astrophysics - High Energy Astrophysical Phenomena - Abstract
Pulsar timing arrays are sensitive to gravitational wave perturbations produced by individual supermassive black hole binaries during their early inspiral phase. Modified gravity theories allow for the emission of gravitational dipole radiation, which is enhanced relative to the quadrupole contribution for low orbital velocities, making the early inspiral an ideal regime to test for the presence of modified gravity effects. Using a theory-agnostic description of modified gravity theories based on the parametrized post-Einsteinian framework, we explore the possibility of detecting deviations from General Relativity using simulated pulsar timing array data, and provide forecasts for the constraints that can be achieved. We generalize the {\tt enterprise} pulsar timing software to account for possible additional polarization states and modifications to the phase evolution, and study how accurately the parameters of simulated signals can be recovered. We find that while a pure dipole model can partially recover a pure quadrupole signal, there is little possibility for confusion when the full model with all polarization states is used. With no signal present, and using noise levels comparable to those seen in contemporary arrays, we produce forecasts for the upper limits that can be placed on the amplitudes of alternative polarization modes as a function of the sky location of the source., Comment: 12 pages, 8 figures
- Published
- 2019
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43. Increased airway iron parameters and risk for exacerbation in COPD: an analysis from SPIROMICS.
- Author
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Zhang, William Z, Oromendia, Clara, Kikkers, Sarah Ann, Butler, James J, O'Beirne, Sarah, Kim, Kihwan, O'Neal, Wanda K, Freeman, Christine M, Christenson, Stephanie A, Peters, Stephen P, Wells, J Michael, Doerschuk, Claire, Putcha, Nirupama, Barjaktarevic, Igor, Woodruff, Prescott G, Cooper, Christopher B, Bowler, Russell P, Comellas, Alejandro P, Criner, Gerard J, Paine, Robert, Hansel, Nadia N, Han, Meilan K, Crystal, Ronald G, Kaner, Robert J, Ballman, Karla V, Curtis, Jeffrey L, Martinez, Fernando J, and Cloonan, Suzanne M
- Subjects
Lung ,Bronchoalveolar Lavage Fluid ,Humans ,Pulmonary Disease ,Chronic Obstructive ,Disease Progression ,Iron ,Iron-Binding Proteins ,Respiratory Function Tests ,Forced Expiratory Volume ,Severity of Illness Index ,Risk Factors ,Adult ,Aged ,Aged ,80 and over ,Middle Aged ,Female ,Male ,Ferritins ,Biomarkers - Abstract
Levels of iron and iron-related proteins including ferritin are higher in the lung tissue and lavage fluid of individuals with chronic obstructive pulmonary disease (COPD), when compared to healthy controls. Whether more iron in the extracellular milieu of the lung associates with distinct clinical phenotypes of COPD, including increased exacerbation susceptibility, is unknown. We measured iron and ferritin levels in the bronchoalveolar lavage fluid (BALF) of participants enrolled in the SubPopulations and InteRmediate Outcome Measures In COPD (SPIROMICS) bronchoscopy sub-study (n = 195). BALF Iron parameters were compared to systemic markers of iron availability and tested for association with FEV1 % predicted and exacerbation frequency. Exacerbations were modelled using a zero-inflated negative binomial model using age, sex, smoking, and FEV1 % predicted as clinical covariates. BALF iron and ferritin were higher in participants with COPD and in smokers without COPD when compared to non-smoker control participants but did not correlate with systemic iron markers. BALF ferritin and iron were elevated in participants who had COPD exacerbations, with a 2-fold increase in BALF ferritin and iron conveying a 24% and 2-fold increase in exacerbation risk, respectively. Similar associations were not observed with plasma ferritin. Increased airway iron levels may be representative of a distinct pathobiological phenomenon that results in more frequent COPD exacerbation events, contributing to disease progression in these individuals.
- Published
- 2020
44. A comparison of machine learning algorithms and traditional regression-based statistical modeling for predicting hypertension incidence in a Canadian population
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Mohammad Ziaul Islam Chowdhury, Alexander A. Leung, Robin L. Walker, Khokan C. Sikdar, Maeve O’Beirne, Hude Quan, and Tanvir C. Turin
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Medicine ,Science - Abstract
Abstract Risk prediction models are frequently used to identify individuals at risk of developing hypertension. This study evaluates different machine learning algorithms and compares their predictive performance with the conventional Cox proportional hazards (PH) model to predict hypertension incidence using survival data. This study analyzed 18,322 participants on 24 candidate features from the large Alberta’s Tomorrow Project (ATP) to develop different prediction models. To select the top features, we applied five feature selection methods, including two filter-based: a univariate Cox p-value and C-index; two embedded-based: random survival forest and least absolute shrinkage and selection operator (Lasso); and one constraint-based: the statistically equivalent signature (SES). Five machine learning algorithms were developed to predict hypertension incidence: penalized regression Ridge, Lasso, Elastic Net (EN), random survival forest (RSF), and gradient boosting (GB), along with the conventional Cox PH model. The predictive performance of the models was assessed using C-index. The performance of machine learning algorithms was observed, similar to the conventional Cox PH model. Average C-indexes were 0.78, 0.78, 0.78, 0.76, 0.76, and 0.77 for Ridge, Lasso, EN, RSF, GB and Cox PH, respectively. Important features associated with each model were also presented. Our study findings demonstrate little predictive performance difference between machine learning algorithms and the conventional Cox PH regression model in predicting hypertension incidence. In a moderate dataset with a reasonable number of features, conventional regression-based models perform similar to machine learning algorithms with good predictive accuracy.
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- 2023
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45. Hip Sonography: Preparing for the Future
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O’Beirne, Joseph, Chlapoutakis, Konstantinos, O'Beirne, Joseph, editor, and Chlapoutakis, Konstantinos, editor
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- 2022
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46. Liver Transplantation
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Gupta, Rohit, O’Beirne, James, and Cross, Tim, editor
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- 2022
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47. Co-designing person-centred quality indicator implementation for primary care in Alberta: a consensus study
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Kimberly Manalili, Catherine M. Scott, Brenda Hemmelgarn, Maeve O’Beirne, Allan L. Bailey, Michel K. Haener, Cyrene Banerjee, Sue P. Peters, Mirella Chiodo, Fariba Aghajafari, and Maria J. Santana
- Subjects
Person-centred care ,Quality indicators ,Primary care ,Implementation ,Strategies ,Context consensus ,Medicine ,Medicine (General) ,R5-920 - Abstract
Plain English summary Person-centred care (PCC) is a model of care where patient needs and preferences are included in decisions about care and treatment. To improve PCC in primary care in Alberta, Canada, we plan to use person-centred quality indicators (PC-QIs). Using PC-QIs involves surveying patients about their care experiences and using this information to make improvements. For example, if 20% of patients do not feel they are getting enough information, the clinic may create a checklist for the providers so information is not missed. We engaged a panel of 11 people, including patients, family doctors, and staff who support quality improvement in clinics across the province to decide together which PC-QIs primary care clinics in Alberta should use. We also asked the panel to decide the most important strategies that would make using the PC-QIs more successful. The panel chose PC-QIs related to: patient and caregiver involvement in decisions about care and treatment, a trusting relationship with the healthcare provider, having health information technology to support PCC, partnering with communities in healthcare, and the patient’s overall experience. The most important strategies were: developing partnerships among people working in primary care in Alberta, discussing their needs and common efforts for improving PCC, engaging “champions,” and securing funding that would be needed. Finally, we asked the panelists to share their experiences with participating in this process. Panelists found the process useful and that their input was valued. Most panelists would also like to continue to work together to put the PC-QIs into practice.
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- 2022
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48. Monitoring quality of care in hepatocellular carcinoma: A modified Delphi consensus
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Ashika D. Maharaj, John Lubel, Eileen Lam, Paul J. Clark, Oliver Duncan, Jacob George, Gary P. Jeffrey, Lara Lipton, Howard Liu, Geoffrey McCaughan, Eu‐Ling Neo, Jennifer Philip, Simone I. Strasser, Katherine Stuart, Alexander Thompson, Jonathan Tibballs, Thomas Tu, Michael C. Wallace, Alan Wigg, Marnie Wood, Amany Zekry, Elysia Greenhill, Liane J. Ioannou, Golo Ahlenstiel, Kaye Bowers, Stephen J. Clarke, Anouk Dev, Michael Fink, Mark Goodwin, Christos S. Karapetis, Miriam T. Levy, Kate Muller, James O'Beirne, David Pryor, James Seow, Nicholas Shackel, Caroline Tallis, Nick Butler, John K. Olynyk, Kate Reed‐Cox, John R. Zalcberg, and Stuart K. Roberts
- Subjects
Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Abstract Although there are several established international guidelines on the management of hepatocellular carcinoma (HCC), there is limited information detailing specific indicators of good quality care. The aim of this study was to develop a core set of quality indicators (QIs) to underpin the management of HCC. We undertook a modified, two‐round, Delphi consensus study comprising a working group and experts involved in the management of HCC as well as consumer representatives. QIs were derived from an extensive review of the literature. The role of the participants was to identify the most important and measurable QIs for inclusion in an HCC clinical quality registry. From an initial 94 QIs, 40 were proposed to the participants. Of these, 23 QIs ultimately met the inclusion criteria and were included in the final set. This included (a) nine related to the initial diagnosis and staging, including timing to diagnosis, required baseline clinical and laboratory assessments, prior surveillance for HCC, diagnostic imaging and pathology, tumor staging, and multidisciplinary care; (b) thirteen related to treatment and management, including role of antiviral therapy, timing to treatment, localized ablation and locoregional therapy, surgery, transplantation, systemic therapy, method of response assessment, and supportive care; and (c) one outcome assessment related to surgical mortality. Conclusion: We identified a core set of nationally agreed measurable QIs for the diagnosis, staging, and management of HCC. The adherence to these best practice QIs may lead to system‐level improvement in quality of care and, ultimately, improvement in patient outcomes, including survival.
- Published
- 2022
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49. How Ready are Pediatricians and Family Physicians in Saudi Arabia to Perform Clinical Screening of Developmental Dysplasia of the Hip? [Letter]
- Author
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O'Beirne JG, Chlapoutakis K, and Aydingoz U
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hip dysplasia. ultrasound screening ,Medicine (General) ,R5-920 - Abstract
Joseph Gerard O’Beirne,1 Konstantinos Chlapoutakis,2 Ustun Aydingoz3 1Department of Orthopaedics, University Hospital Waterford, Waterford, Ireland; 2Vioapeikonisi Imaging Lab, Heraklion – Crete, Greece; 3Department of Radiology, Hacettepe University School of Medicine, Ankara, TurkeyCorrespondence: Joseph Gerard O’Beirne, Email jgobeirne@gmail.com
- Published
- 2023
50. Managing diabetes during treatment for breast cancer: oncology and primary care providers’ views on barriers and facilitators
- Author
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Pinheiro, Laura C., Cho, Jacklyn, Kern, Lisa M., Higgason, Noel, O’Beirne, Ronan, Tamimi, Rulla, and Safford, Monika
- Published
- 2022
- Full Text
- View/download PDF
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