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2,040 results on '"O'Leary, John"'

5. Reinterpretation of prostate cancer pathology by Appl1, Sortilin and Syndecan-1 biomarkers

Author

Logan, Jessica M., Martini, Carmela, Sorvina, Alexandra, Johnson, Ian R. D., Brooks, Robert D., Caruso, Maria C., Huzzell, Chelsea, Moore, Courtney R., Karageorgos, Litsa, Butler, Lisa M., Tewari, Prerna, Prabhakaran, Sarita, Hickey, Shane M., Klebe, Sonja, Samaratunga, Hemamali, Delahunt, Brett, Moretti, Kim, O’Leary, John J., Brooks, Douglas A., and Ung, Ben S.-Y.

Published
2024
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22. Dynamic interplay between sortilin and syndecan-1 contributes to prostate cancer progression

Author

Lazniewska, Joanna, Li, Ka Lok, Johnson, Ian R. D., Sorvina, Alexandra, Logan, Jessica M., Martini, Carmela, Moore, Courtney, Ung, Ben S.-Y., Karageorgos, Litsa, Hickey, Shane M., Prabhakaran, Sarita, Heatlie, Jessica K., Brooks, Robert D., Huzzell, Chelsea, Warnock, Nicholas I., Ward, Mark P., Mohammed, Bashir, Tewari, Prerna, Martin, Cara, O’Toole, Sharon, Edgerton, Laura Bogue, Bates, Mark, Moretti, Paul, Pitson, Stuart M., Selemidis, Stavros, Butler, Lisa M., O’Leary, John J., and Brooks, Douglas A.

Published
2023
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23. Ex vivo expansion of circulating tumour cells (CTCs)

Author

Mohamed, Bashir M., Ward, Mark P., Bates, Mark, Spillane, Cathy D., Kelly, Tanya, Martin, Cara, Gallagher, Michael, Heffernan, Sheena, Norris, Lucy, Kennedy, John, Saadeh, Feras Abu, Gleeson, Noreen, Brooks, Doug A., Brooks, Robert D., Selemidis, Stavros, O’Toole, Sharon, and O’Leary, John J.

Published
2023
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28. Exploring the role of sporadic BRAF and KRAS mutations during colorectal cancer pathogenesis: A spotlight on the contribution of the endosome-lysosome system

Author

Tang, Jingying, Lam, Giang T., Brooks, Robert D., Miles, Mark, Useckaite, Zivile, Johnson, Ian RD., Ung, Ben S.-Y., Martini, Carmela, Karageorgos, Litsa, Hickey, Shane M., Selemidis, Stavros, Hopkins, Ashley M., Rowland, Andrew, Vather, Ryash, O'Leary, John J., Brooks, Douglas A., Caruso, Maria C., and Logan, Jessica M.

Published
2024
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29. Couplings of the Random-Walk Metropolis algorithm

Author

O'Leary, John

Subjects
Statistics - Methodology, Statistics - Computation
Abstract

Couplings play a central role in contemporary Markov chain Monte Carlo methods and in the analysis of their convergence to stationarity. In most cases, a coupling must induce relatively fast meeting between chains to ensure good performance. In this paper we fix attention on the random walk Metropolis algorithm and examine a range of coupling design choices. We introduce proposal and acceptance step couplings based on geometric, optimal transport, and maximality considerations. We consider the theoretical properties of these choices and examine their implication for the meeting time of the chains. We conclude by extracting a few general principles and hypotheses on the design of effective couplings., Comment: 28 pages, 8 figures

Published
2021

31. Metropolis-Hastings transition kernel couplings

Author

O'Leary, John and Wang, Guanyang

Subjects
Mathematics - Statistics Theory, Mathematics - Probability, Statistics - Computation, 60J22, 65C05, 62D05
Abstract

Couplings play a central role in the analysis of Markov chain convergence and in the construction of novel Markov chain Monte Carlo estimators, diagnostics, and variance reduction techniques. The set of possible couplings is often intractable, frustrating the search for tight bounds and efficient estimators. To address this challenge for algorithms in the Metropolis-Hastings (MH) family, we establish a simple characterization of the set of MH transition kernel couplings. We then extend this result to describe the set of maximal couplings of the MH kernel, resolving an open question of O'Leary et al.. Our results represent an advance in understanding the MH transition kernel and a step forward for coupling this popular class of algorithms., Comment: 25 pages, 2 figures. Accepted, Annales de l'Institut Henri Poincar\'e, Probabilit\'es et Statistiques

Published
2021

33. P53 and TLR4 expression are prognostic markers informing progression free survival of advanced stage high grade serous ovarian cancer

Author

Bates, Mark, Mullen, Dorinda, Lee, Eimear, Costigan, Danielle, Heron, Elizabeth A., Kernan, Niamh, Barry-O’Crowley, Jacqui, Martin, Cara, Keegan, Helen, Malone, Victoria, Brooks, Robert D., Brooks, Doug A., Logan, Jessica M., Martini, Carmela, Selemidis, Stavros, McFadden, Julie, O’Riain, Ciaran, Spillane, Cathy D., Gallagher, Michael F., McCann, Amanda, O’Toole, Sharon, and O’Leary, John J.

Published
2024
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34. Maximal couplings of the Metropolis-Hastings algorithm

Author

O'Leary, John, Wang, Guanyang, and Jacob, Pierre E.

Subjects
Statistics - Computation, Statistics - Methodology
Abstract

Couplings play a central role in the analysis of Markov chain Monte Carlo algorithms and appear increasingly often in the algorithms themselves, e.g. in convergence diagnostics, parallelization, and variance reduction techniques. Existing couplings of the Metropolis-Hastings algorithm handle the proposal and acceptance steps separately and fall short of the upper bound on one-step meeting probabilities given by the coupling inequality. This paper introduces maximal couplings which achieve this bound while retaining the practical advantages of current methods. We consider the properties of these couplings and examine their behavior on a selection of numerical examples.

Published
2020

35. Learning Concise Models from Long Execution Traces

Author

Jeppu, Natasha Yogananda, Melham, Tom, Kroening, Daniel, and O'Leary, John

Subjects
Computer Science - Formal Languages and Automata Theory, Computer Science - Software Engineering
Abstract

Abstract models of system-level behaviour have applications in design exploration, analysis, testing and verification. We describe a new algorithm for automatically extracting useful models, as automata, from execution traces of a HW/SW system driven by software exercising a use-case of interest. Our algorithm leverages modern program synthesis techniques to generate predicates on automaton edges, succinctly describing system behaviour. It employs trace segmentation to tackle complexity for long traces. We learn concise models capturing transaction-level, system-wide behaviour--experimentally demonstrating the approach using traces from a variety of sources, including the x86 QEMU virtual platform and the Real-Time Linux kernel.

Published
2020

36. Hardware/Software Co-verification Using Path-based Symbolic Execution

Author

Mukherjee, Rajdeep, Joshi, Saurabh, O'Leary, John, Kroening, Daniel, and Melham, Tom

Subjects
Computer Science - Formal Languages and Automata Theory, Computer Science - Logic in Computer Science
Abstract

Conventional tools for formal hardware/software co-verification use bounded model checking techniques to construct a single monolithic propositional formula. Formulas generated in this way are extremely complex and contain a great deal of irrelevant logic, hence are difficult to solve even by the state-of-the-art Satis ability (SAT) solvers. In a typical hardware/software co-design the firmware only exercises a fraction of the hardware state-space, and we can use this observation to generate simpler and more concise formulas. In this paper, we present a novel verification algorithm for hardware/software co-designs that identify partitions of the firmware and the hardware logic pertaining to the feasible execution paths by means of path-based symbolic simulation with custom path-pruning, property-guided slicing and incremental SAT solving. We have implemented this approach in our tool COVERIF. We have experimentally compared COVERIF with HW-CBMC, a monolithic BMC based co-verification tool, and observed an average speed-up of 5X over HW-CBMC for proving safety properties as well as detecting critical co-design bugs in an open-source Universal Asynchronous Receiver Transmitter design and a large SoC design., Comment: 6 pages, 3 tables, 5 figures

Published
2020

37. Evaluating Drought Impact on Postfire Recovery of Chaparral Across Southern California

Author

Storey, Emanuel A, Stow, Douglas A, Roberts, Dar A, O’Leary, John F, and Davis, Frank W

Subjects
Vegetation change, Fire recovery, Time series analysis, Drought impact, Aridification, Ecological management, Environmental Sciences, Biological Sciences, Ecology
Abstract

Chaparral shrubs in southern California may be vulnerable to frequent fire and severe drought. Drought may diminish postfire recovery or worsen impact of short-interval fires. Field-based studies have not shown the extent and magnitude of drought effects on recovery, which may vary among chaparral types and climatic zones. We tracked regional patterns of shrub cover based on June-solstice Landsat Normalized Difference Vegetation Index series, compared between the periods 1984-1989 and 2014-2018. High spatial resolution ortho-imagery was used to map shrub cover in distributed sample plots, to empirically constrain the Landsat-based estimates of mature-stage lateral canopy recovery. We evaluated precipitation, climatic water deficit (CWD), and Palmer Drought Severity Index in summer and wet seasons preceding and following fire, as regional predictors of recovery in 982 locations between the Pacific Coast and inland deserts. Wet-season CWD was the strongest drought-metric predictor of recovery, contributing 34-43 % of explanatory power in multivariate regressions (R2 =0.16-0.42). Limited recovery linked to drought was most prevalent in transmontane chamise chaparral; impacts were minor in montane areas, and in mixed and montane chaparral types. Elevation was correlated negatively to recovery of transmontane chamise; this may imply acute drought sensitivity in resprouts which predominate seedlings at higher elevations. Landsat Visible Atmospherically Resistant Index (sensitive to live-fuel moisture) was evaluated as a landscape-scale predictor of recovery and explained the greatest amount of variance in a multivariate regression (R2 = 0.53). We find that drought severity was more closely related to recovery differences among twice-burned sites than was fire-return interval. Summarily, drought has a major role in long-term shrub cover reduction within xeric chaparral ecotones bounding the Mojave Desert and Colorado Desert, likely in tandem with other global change stressors.

Published
2021

41. Appl1, Sortilin and Syndecan-1 immunohistochemistry on intraductal carcinoma of the prostate provides evidence of retrograde spread

Author

Sorvina, Alexandra, Martini, Carmela, Prabhakaran, Sarita, Logan, Jessica M., S-Y. Ung, Benjamin, Moore, Courtney, Johnson, Ian R.D., Lazniewska, Joanna, Tewari, Prerna, Malone, Victoria, Brooks, Robert D., Hickey, Shane M., Caruso, Maria C., Klebe, Sonja, Karageorgos, Litsa, O'Leary, John J., Delahunt, Brett, Samaratunga, Hemamali, and Brooks, Doug A.

Published
2023
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42. Altered endosomal-lysosomal biogenesis in melanoma

Author

Lam, Giang T., Sorvina, Alexandra, Martini, Carmela, Prabhakaran, Sarita, Ung, Ben S.-Y., Lazniewska, Joanna, Moore, Courtney R., Beck, Andrew R., Hopkins, Ashley M., Johnson, Ian R.D., Caruso, Maria C., Hickey, Shane M., Brooks, Robert D., Jackett, Louise, Karageorgos, Litsa, Foster-Smith, Erwin J., Malone, Victoria, Klebe, Sonja, O'Leary, John J., Brooks, Douglas A., and Logan, Jessica M.

Published
2023
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43. Does short-interval fire inhibit postfire recovery of chaparral across southern California?

Author

Storey, Emanuel A, Stow, Douglas A, O'Leary, John F, Davis, Frank W, and Roberts, Dar A

Subjects
California, Climate, Ecosystem, Fires, Soil, Fire regime, Postfire recovery, Time series, Chaparral succession, Desertification, Environmental Sciences
Abstract

Regrowth after fire is critical to the persistence of chaparral shrub communities in southern California, which has been subject to frequent fire events in recent decades. Fires that recur at short intervals of 10 years or less have been considered an inhibitor of recovery and the major cause of 'community type-conversion' in chaparral, primarily based on studies of small extents and limited time periods. However, recent sub-regional investigations based on remote sensing suggest that short-interval fire (SIF) does not have ubiquitous impact on postfire chaparral recovery. A region-wide analysis including a greater spatial extent and time period is needed to better understand SIF impact on chaparral. This study evaluates patterns of postfire recovery across southern California, based on temporal trajectories of Normalized Difference Vegetation Index (NDVI) derived from June-solstice Landsat image series covering the period 1984-2018. High spatial resolution aerial images were used to calibrate Landsat NDVI trajectory-based estimates of change in fractional shrub cover (dFSC) for 294 stands. The objectives of this study were (1) to assess effects of time between fires and number of burns on recovery, using stand-aggregate samples (n = 294) and paired single- and multiple-burn sample plots (n = 528), and (2) to explain recovery variations among predominant single-burn locations based on shrub community type, climate, soils, and terrain. Stand-aggregate samples showed a significant but weak effect of SIF on recovery (p

Published
2021

45. CREST: Hardware Formal Verification with ANSI-C Reference Specifications

Author

Tiemeyer, Andreas, Melham, Tom, Kroening, Daniel, and O'Leary, John

Subjects
Computer Science - Programming Languages, Computer Science - Hardware Architecture, Computer Science - Symbolic Computation
Abstract

This paper presents CREST, a prototype front-end tool intended as an add-on to commercial EDA formal verifcation environments. CREST is an adaptation of the CBMC bounded model checker for C, an academic tool widely used in industry for software analysis and property verification. It leverages the capabilities of CBMC to process hardware datapath specifications written in arbitrary ANSI-C, without limiting restrictions to a synthesizable subset. We briefly sketch the architecture of our tool and show its use in a range of verification case studies., Comment: 4 pages

Published
2019

46. ExPeCT: a randomised trial examining the impact of exercise on quality of life in men with metastatic prostate cancer

Author

Sheill, Gráinne, Brady, Lauren, Hayes, Brian, Baird, Anne-Marie, Guinan, Emer, Vishwakarma, Rishabh, Brophy, Caroline, Vlajnic, Tatjana, Casey, Orla, Murphy, Verena, Greene, John, Allott, Emma, Hussey, Juliette, Cahill, Fidelma, Van Hemelrijck, Mieke, Peat, Nicola, Mucci, Lorelei, Cunningham, Moya, Grogan, Liam, Lynch, Thomas, Manecksha, Rustom P., McCaffrey, John, O’Donnell, Dearbhaile, Sheils, Orla, O’Leary, John, Rudman, Sarah, McDermott, Ray, and Finn, Stephen

Published
2023
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48. Aberrant protein expression of Appl1, Sortilin and Syndecan-1 during the biological progression of prostate cancer

Author

Martini, Carmela, Logan, Jessica M., Sorvina, Alexandra, Gordon, Colin, Beck, Andrew R., S-Y. Ung, Ben, Caruso, Maria C., Moore, Courtney, Hocking, Ashleigh, Johnson, Ian R.D., Li, Ka Lok, Karageorgos, Litsa, Hopkins, Ashley M., Esterman, Adrian J., Huzzell, Chelsea, Brooks, Robert D., Lazniewska, Joanna, Hickey, Shane M., Bader, Christie, Parkinson-Lawrence, Emma, Weigert, Roberto, Sorich, Michael J., Tewari, Prerna, Martin, Cara, O'Toole, Sharon, Bates, Mark, Ward, Mark, Mohammed, Bashir, Keegan, Helen, Watson, William, Prendergast, Sophie, Heffernan, Sheena, NiMhaolcatha, Sarah, O'Connor, Roisin, Malone, Victoria, Carter, Marguerite, Ryan, Katie, Brady, Nathan, Clarke, Andres, Sokol, Filip, Prabhakaran, Sarita, Stahl, Jürgen, Klebe, Sonja, Samaratunga, Hemamali, Delahunt, Brett, Selemidis, Stavros, Moretti, Kim L., Butler, Lisa M., O'Leary, John J., and Brooks, Douglas A.

Published
2023
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49. The impact of the 5:2 intermittent fasting diet on cognition in healthy adults

Author

O'Leary, John

Subjects
613.2
Abstract

Objectives: Research suggests that a reduction in calories may impact cognitive functioning in healthy adults. Despite studies that demonstrate changes to cognitive function following periods of fasting and continuous calorie restriction, any potential impact for those who follow intermittent fasting (IF) diets remains unclear. Among the most popular IF diet is the 5:2 fasting diet. Proponents of this dieting regime claims that it has numerous benefits to general health. Less in known about the impact of this diet on cognition. Given that some studies have shown cognition is impaired following acute fasting, concerns remain about the impact of a fasting diet that encourages high levels of intermittent calorie restriction. This study sought to understand the impact on specific areas of cognition for healthy adults who follow the 5:2 diet. Methods: Part A Using a within-subjects repeated measures design, 36 healthy adults who were following the 5:2 diet for more than four weeks were measured for cognitive performance on fasting and non-fasting days using a range of online cognitive tasks. Specifically, we measured cognitive flexibility, working and prospective memory, reflective impulsivity and psycho-motor speed. Part B Using a between-subjects design, mean performance on the cognitive tasks for healthy adults following the 5:2 diet (n=36), was compared to those following CCR diets (n=30). Both groups had been following their diets for more than four weeks. Results: Part A Cognitive flexibility, working and prospective memory was impaired on fasting days along with a reduction in impulsivity. Overall composite scores revealed impaired reaction time and accuracy on fasting days. Part B Participants following the 5:2 diet performed worse than those following CCR diets in tasks designed to measure psycho-motor speed and cognitive. Overall composite scores revealed impaired reaction time for those following 5:2 diets, compared with those following CCR diets. Conclusions Research that investigates the impact of calorie restriction and fasting on cognitive function should also consider the potential risks of cognitive impairment for those who choose to follow intermittent fasting diets. Future studies would benefit from longer term measurement of cognition for those following IF diets whilst accounting for potential confounding variables.

Published
2019

50. Fetal Deaths in Ireland Due to SARS-CoV-2 Placentitis Caused by SARS-CoV-2 Alpha

Author

Fitzgerald, Brendan, O'Donoghue, Keelin, McEntagart, Noel, Gillan, John E., Kelehan, Peter, O'Leary, John, Downey, Paul, Dean, Jonathan, De Gascun, Cillian F., Bermingham, John, Armstrong, Fionnvola, Fathil, Attia Al, Maher, Nicola, Murphy, Cliona, and Burke, Louise

Subjects
Fetal death -- Statistics -- Causes of -- Risk factors, Miscarriage -- Statistics -- Causes of -- Risk factors, Placental diseases -- Statistics -- Complications and side effects, Health
Abstract

Context.--A severe third wave of COVID-19 disease affected Ireland in the first 3 months of 2021. In this wave, 1 second-trimester miscarriage and 6 stillbirths were observed in the Irish population because of placental insufficiency as a result of SARS-CoV-2 placentitis. This observation was at odds with the country's previous experience with COVID-19 disease in pregnant mothers. Objective.--To describe the clinical and pathologic features of these pregnancy losses. Design.--Retrospective review of clinical and pathologic data of cases of second-trimester miscarriage, stillbirth, or neonatal death identified by perinatal pathologists as being due to SARS-CoV-2 placentitis during the third wave of COVID-19 in Ireland. Results.--Clinical and pathologic data were available for review in 6 pregnancies. Sequencing or genotyping of the virus identified SARS-CoV-2 alpha (B.1.1.7) in all cases. Three of the 6 cases had maternal thrombocytopenia, and fetal growth restriction was not prominent, suggesting a rapidly progressive placental disease. Conclusions.--The identification of SARS-CoV-2 alpha in all these cases suggests that the emergence of the variant was associated with an increased risk of fetal death due to SARS-CoV-2 placentitis when compared with the original virus. Maternal thrombocytopenia may have potential as a clinical marker of placentitis, but other inflammatory markers need investigation. Three of the 6 women had been assessed for reduced fetal movements in hospital some days before the fetal deaths actually occurred; this could suggest that there may be a window for intervention in some cases. (Arch Pathol Lab Med. 2022;146:529-537; doi: 10.5858/ arpa.2021-0586-SA), SARS-CoV-2 placentitis represents a readily recognizable pattern of placental injury occurring in some pregnant women who develop COVID-19. (1) Pregnant women are at increased risk of severe COVID-19-associated illness compared [...]

Published
2022

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