113 results on '"M. O'Rourke"'
Search Results
2. Coarse to superfine: can hyperspectral soil organic carbon models predict higher-resolution information?
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Shayan Kabiri and Sharon M. O’Rourke
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hyperspectral imaging ,soil organic carbon modeling ,soil core ,grassland soil organic carbon ,neural network modeling ,pedometrics, high resolution ,Environmental sciences ,GE1-350 - Abstract
Introduction: Modeling and mapping of soil organic carbon concentration and distribution at the pedon scale is a current knowledge gap that can be addressed by laboratory-based hyperspectral imaging and chemometric analysis of soil cores. Despite the advancements in soil organic carbon models based on hyperspectral images, it is not clear how these models will perform upon input with images at higher resolutions than those of their training sets. This study aims to measure the generalizability of a soil organic carbon model based on a test set with higher resolution hyperspectral images than that of its training set.Methods: Organic carbon contents were measured at 10 cm intervals on eight soil cores for use as the training set and at 1 cm intervals on a single core for use as the test set. Three regression models, namely, multilayer perceptron, partial least-squares, and support vector regressions, were trained and tested with the median of each hyperspectral image for each of these intervals as the training and test predictors. Permutation importance analysis was performed to explain the models.Results: The results show that although all three models had the same validation R2 of 0.92 for cross-validation on the 10 cm data, multilayer perceptron regression allowed the best generalization with a test R2 of 0.96 compared to the partial least-squares regression (0.81) and support vector regression (0.86). It was demonstrated that the multilayer perceptron model is more robust to soil surface anomalies and that it predicts soil organic carbon on the test set by learning the spectral features related to soil organic matter chromophore activity in the 950–1,150 nm region along with clay mineralogy derived from peaks at 1,400, 1,900, 2,200, 2,250, and 2,350 nm.Conclusions: This study shows that while the regression models based on hyperspectral images perform well at the 10-cm-resolution cross validation, multilayer perceptron regression shows superior generalization and robustness for a higher 1-cm-resolution test set without much loss of prediction power.
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- 2024
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3. Assessing social connection for long‐term care home residents: Systematic review using COnsensus‐based Standards for the selection of health Measurement INstruments guidelines
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Neha Dewan, Andrew Sommerlad, Hannah Chapman, Sube Banerjee, Kirsten Corazzini, David Edvardsson, Madalena P. Liougas, Gill Livingston, Katherine S. McGilton, Hannah M. O'Rourke, and Jennifer Bethell
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COSMIN ,dementia ,long‐term care home ,nursing home ,outcome measures ,psychometric properties ,Neurology. Diseases of the nervous system ,RC346-429 ,Geriatrics ,RC952-954.6 - Abstract
Abstract Social connection is important for long‐term care (LTC) residents' quality of life and care. However, there is a lack of consensus on how to measure it and this limits ability to find what improves and impairs social connection in LTC homes. We therefore aimed to systematically review and evaluate the measurement properties of existing measures of social connection for LTC residents, to identify which, if any, measures can be recommended. We searched eight electronic databases from inception to April 2022 for studies which reported on psychometric properties of a measure of any aspect(s) of social connection (including social networks, interaction, engagement, support, isolation, connectedness, and loneliness) for LTC residents. We used COnsensus‐based Standards for the selection of health Measurement INstruments (COSMIN) guidelines to evaluate the measurement properties reported for each identified measure and make recommendations. We identified 62 studies reporting on 38 measures; 21 measured quality of life, well‐being or life satisfaction and included a social connection subscale or standalone items and 17 measures specifically targeted social connection. We found there was little high‐quality evidence on psychometric properties such as sufficient content validity (n = 0), structural validity (n = 3), internal consistency (n = 3), reliability (n = 1), measurement error (n = 0), construct validity (n = 4), criterion validity (n = 0) and responsiveness (n = 0). No measures demonstrated satisfactory psychometric properties on all these aspects, so none could be recommended for use. Thirty‐four measures have the potential to be recommended but require further research to assess their quality and the remaining four are not recommended for use. Our review therefore found that no existing measures have sufficient evidence to be recommended for assessment of social connection in residents of LTC homes. Further validation and reliability studies of existing instruments or the development of new measures are needed to enable accurate measurement of social connection in LTC residents for future observational and interventional studies. Highlights Social connection is fundamental to person‐centered care in long‐term care homes. There is insufficient evidence for the reliability and validity of existing measures. No current measures can be recommended for use based on existing evidence. A reliable and valid measure of social connection is needed for future research.
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- 2024
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4. Assessing social connection for long‐term care home residents: A scoping review of measure content
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Madalena P. Liougas, Andrew Sommerlad, Hannah M. O'Rourke, Hannah Chapman, Neha Dewan, Katherine S. McGilton, and Jennifer Bethell
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Neurology. Diseases of the nervous system ,RC346-429 ,Geriatrics ,RC952-954.6 - Abstract
Abstract INTRODUCTION Social connection comprises distinct but interrelated aspects describing how individuals connect to each other. Various measures have assessed multiple aspects of social connection in long‐term care (LTC) home populations, but they use inconsistent terminology, making it unclear what aspects are measured. This scoping review describes how social connection is assessed by measures that have been used in LTC home residents. METHODS This review followed the Preferred Reporting Items for Systematic reviews and Meta‐Analyses extension for Scoping Reviews (PRISMA‐ScR) guidelines. Two systematic literature searches combining search terms for social connection AND LTC home residents AND measurement properties were conducted in eight electronic databases from inception to April 2022. Included studies reported the development or psychometric testing of measures which assessed social connection in LTC home residents. A content analysis with a deductive‐inductive approach was used to analyze the measures’ content and an adapted Framework Method was used for data management. Findings report each measure's items and the assessed aspects of social connection. Dementia and non‐dementia‐specific measures had content, administration, and scoring compared. RESULTS From 8753 records, 58 studies reporting on 14 dementia‐specific and 28 non‐dementia‐specific social connection measures were identified, including complete measures, subscales, and single items. These measures assessed social network (52.4%), social isolation (11.9%), social interaction (47.6%), social engagement (31.0%), social support (33.3%), social connectedness (21.4%), and loneliness (9.5%). A total of 27 (64.3%) of the measures included more than one aspect of social connection. Dementia‐specific measures most often assessed social interaction whereas non‐dementia‐specific measures most often assessed social network, social interaction, and social support. Dementia‐specific measures typically relied on a proxy response, whereas non‐dementia‐specific measures more often used self‐report. DISCUSSION Existing social connection measures in LTC home settings operationalize seven aspects of social connection and differ according to the target population (dementia or non‐dementia‐specific). These findings will inform future measure selection and development. Highlights Social connection is important to long‐term care (LTC) home residents’ quality of life. Social connection has been assessed by quantifying/describing relationships. Existing measures usually assess more than one aspect of social connection. These aspects cover several interlinked observed or experienced domains. Dementia and non‐dementia‐specific measures differ in assessing social connection.
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- 2024
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5. Social connection measures for older adults living in long-term care homes: a systematic review protocol
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Madalena P. Liougas, Andrew Sommerlad, Hannah M. O’Rourke, Katherine S. McGilton, and Jennifer Bethell
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Long-term care ,Measurement ,Social connection ,Medicine - Abstract
Abstract Background Various measures have assessed social connection in long-term care (LTC) home residents. However, they use inconsistent terminology, conceptualizations, and operationalizations of social connection. In this systematic review protocol, we propose a study that will characterize measures that assess aspects of LTC home residents’ social connection using a unified conceptual model. The objectives are to (1) describe and analyze the measures and (2) evaluate their measurement properties. Methods A literature search was conducted in MEDLINE ALL (Ovid), Embase Classic and Embase (Ovid), Emcare Nursing (Ovid), APA PsycInfo (Ovid), Scopus, CINAHL Complete (EBSCOhost), AgeLine (EBSCOhost), and Sociological Abstracts (ProQuest). We will include primary research papers with no language limit, published from database inception. We will include studies of a measure of any aspect of social connection in LTC home residents that report at least one measurement property. Independently, two reviewers will screen titles and abstracts, review full-text articles against eligibility criteria, and extract data from included studies. In objective 1, we will analyze identified tools using an adapted framework method. In objective 2, we will evaluate each measure’s measurement properties using COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) methodology. We will engage experts and stakeholders to assist with interpreting results and translating knowledge. Discussion Our findings will inform the social connection in long-term care home residents (SONNET) study’s development of a novel, person-centered measure for social connection in LTC home settings. We will present our findings in academic and non-academic forums, including conferences, peer-reviewed journals, and other publications. Systemic review registration Prospero—“Systematic review of measures of social connection used in long-term care home research.” CRD42022303526 .
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- 2024
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6. Integrating imaging and genomic data for the discovery of distinct glioblastoma subtypes: a joint learning approach
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Jun Guo, Anahita Fathi Kazerooni, Erik Toorens, Hamed Akbari, Fanyang Yu, Chiharu Sako, Elizabeth Mamourian, Russell T. Shinohara, Constantinos Koumenis, Stephen J. Bagley, Jennifer J. D. Morrissette, Zev A. Binder, Steven Brem, Suyash Mohan, Robert A. Lustig, Donald M. O’Rourke, Tapan Ganguly, Spyridon Bakas, MacLean P. Nasrallah, and Christos Davatzikos
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Medicine ,Science - Abstract
Abstract Glioblastoma is a highly heterogeneous disease, with variations observed at both phenotypical and molecular levels. Personalized therapies would be facilitated by non-invasive in vivo approaches for characterizing this heterogeneity. In this study, we developed unsupervised joint machine learning between radiomic and genomic data, thereby identifying distinct glioblastoma subtypes. A retrospective cohort of 571 IDH-wildtype glioblastoma patients were included in the study, and pre-operative multi-parametric MRI scans and targeted next-generation sequencing (NGS) data were collected. L21-norm minimization was used to select a subset of 12 radiomic features from the MRI scans, and 13 key driver genes from the five main signal pathways most affected in glioblastoma were selected from the genomic data. Subtypes were identified using a joint learning approach called Anchor-based Partial Multi-modal Clustering on both radiomic and genomic modalities. Kaplan–Meier analysis identified three distinct glioblastoma subtypes: high-risk, medium-risk, and low-risk, based on overall survival outcome (p
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- 2024
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7. Counting what counts: assessing quality of life and its social determinants among nursing home residents with dementia
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Matthias Hoben, Emily Dymchuk, Malcolm B. Doupe, Janice Keefe, Katie Aubrecht, Christine Kelly, Kelli Stajduhar, Sube Banerjee, Hannah M. O’Rourke, Stephanie Chamberlain, Anna Beeber, Jordana Salma, Pamela Jarrett, Amit Arya, Kyle Corbett, Rashmi Devkota, Melissa Ristau, Shovana Shrestha, and Carole A. Estabrooks
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Quality of life ,Dementia ,Nursing homes ,Social determinants of health ,Geriatrics ,RC952-954.6 - Abstract
Abstract Background Maximizing quality of life (QoL) is a major goal of care for people with dementia in nursing homes (NHs). Social determinants are critical for residents' QoL. However, similar to the United States and other countries, most Canadian NHs routinely monitor and publicly report quality of care, but not resident QoL and its social determinants. Therefore, we lack robust, quantitative studies evaluating the association of multiple intersecting social determinants with NH residents’ QoL. The goal of this study is to address this critical knowledge gap. Methods We will recruit a random sample of 80 NHs from 5 Canadian provinces (Alberta, British Columbia, Manitoba, Nova Scotia, Ontario). We will stratify facilities by urban/rural location, for-profit/not-for-profit ownership, and size (above/below median number of beds among urban versus rural facilities in each province). In video-based structured interviews with care staff, we will complete QoL assessments for each of ~ 4,320 residents, using the DEMQOL-CH, a validated, feasible tool for this purpose. We will also assess resident’s social determinants of QoL, using items from validated Canadian population surveys. Health and quality of care data will come from routinely collected Resident Assessment Instrument – Minimum Data Set 2.0 records. Knowledge users (health system decision makers, Alzheimer Societies, NH managers, care staff, people with dementia and their family/friend caregivers) have been involved in the design of this study, and we will partner with them throughout the study. We will share and discuss study findings with knowledge users in web-based summits with embedded focus groups. This will provide much needed data on knowledge users' interpretations, usefulness and intended use of data on NH residents’ QoL and its health and social determinants. Discussion This large-scale, robust, quantitative study will address a major knowledge gap by assessing QoL and multiple intersecting social determinants of QoL among NH residents with dementia. We will also generate evidence on clusters of intersecting social determinants of QoL. This study will be a prerequisite for future studies to investigate in depth the mechanisms leading to QoL inequities in LTC, longitudinal studies to identify trajectories in QoL, and robust intervention studies aiming to reduce these inequities.
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- 2024
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8. Development and validation of risk of CPS decline (RCD): a new prediction tool for worsening cognitive performance among home care clients in Canada
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Dawn M. Guthrie, Nicole Williams, Hannah M. O’Rourke, Joseph B. Orange, Natalie Phillips, M. Kathleen Pichora-Fuller, Marie Y. Savundranayagam, and Rinku Sutradhar
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Prediction tool ,interRAI ,Home care ,Cognitive Performance Scale ,Standardized assessment ,Decision support ,Geriatrics ,RC952-954.6 - Abstract
Abstract Background To develop and validate a prediction tool, or nomogram, for the risk of a decline in cognitive performance based on the interRAI Cognitive Performance Scale (CPS). Methods Retrospective, population-based, cohort study using Canadian Resident Assessment Instrument for Home Care (RAI-HC) data, collected between 2010 and 2018. Eligible home care clients, aged 18+, with at least two assessments were selected randomly for model derivation (75%) and validation (25%). All clients had a CPS score of zero (intact) or one (borderline intact) on intake into the home care program, out of a possible score of six. All individuals had to remain as home care recipients for the six months observation window in order to be included in the analysis. The primary outcome was any degree of worsening (i.e., increase) on the CPS score within six months. Using the derivation cohort, we developed a multivariable logistic regression model to predict the risk of a deterioration in the CPS score. Model performance was assessed on the validation cohort using discrimination and calibration plots. Results We identified 39,292 eligible home care clients, with a median age of 79.0 years, 62.3% were female, 38.8% were married and 38.6% lived alone. On average, 30.3% experienced a worsening on the CPS score within the six-month window (i.e., a change from 0 or 1 to 2, 3, 4, 5, or 6). The final model had good discrimination (c-statistic of 0.65), with excellent calibration. Conclusions The model accurately predicted the risk of deterioration on the CPS score over six months among home care clients. This type of predictive model may provide useful information to support decisions for home care clinicians who use interRAI data internationally.
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- 2023
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9. Increasing access to palliative care for patients with advanced cancer of African and Latin American descent: a patient-oriented community-based study protocol
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Anna Santos Salas, Sharon M. Watanabe, Aynharan Sinnarajah, Nahyeni Bassah, Fleur Huang, Jill Turner, Jacqueline Alcalde Castro, Hannah M. O’Rourke, Pilar Camargo-Plazas, Bukola Salami, María Santana, Katy Campbell, Omar Abdel-Rahman, Tracy Wildeman, Lisa Vaughn, Harkeert Judge, Sadia Ahmed, Bisi Adewale, Iqmat Iyiola, and the Patient Advisory Council
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Advanced cancer ,Palliative care ,Black ,Latino ,Health services accessibility ,Healthcare disparities ,Special situations and conditions ,RC952-1245 - Abstract
Abstract Background Cancer disparities are a major public health concern in Canada, affecting racialized communities of Latin American and African descent, among others. This is evident in lower screening rates, lower access to curative, and palliative-intent treatments, higher rates of late cancer diagnoses and lower survival rates than the general Canadian population. We will develop an Access to Palliative Care Strategy informed by health equity and patient-oriented research principles to accelerate care improvements for patients with advanced cancer of African and Latin American descent. Methods This is a community-based participatory research study that will take place in two Canadian provinces. Patients and community members representatives have been engaged as partners in the planning and design of the study. We have formed a patient advisory council (PAC) with patient partners to guide the development of the Access to Palliative Care Strategy for people of African and Latin American descent. We will engage100 participants consisting of advanced cancer patients, families, and community members of African and Latin American descent, and health care providers. We will conduct in-depth interviews to delineate participants’ experiences of access to palliative care. We will explore the intersections of race, gender, socioeconomic status, language barriers, and other social categorizations to elucidate their role in diverse access experiences. These findings will inform the development of an action plan to increase access to palliative care that is tailored to our study population. We will then organize conversation series to examine together with community partners and healthcare providers the appropriateness, effectiveness, risks, requirements, and convenience of the strategy. At the end of the study, we will hold knowledge exchange gatherings to share findings with the community. Discussion This study will improve our understanding of how patients with advanced cancer from racialized communities in Canada access palliative care. Elements to address gaps in access to palliative care and reduce inequities in these communities will be identified. Based on the study findings a strategy to increase access to palliative care for this population will be developed. This study will inform ways to improve access to palliative care for racialized communities in other parts of Canada and globally.
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- 2023
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10. The global crisis of loneliness: a call for contextualised, mechanistic research
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Hannah M O'Rourke
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Geriatrics ,RC952-954.6 ,Medicine - Published
- 2024
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11. Live Organoid Cyclic Imaging
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David E. Reynolds, Yusha Sun, Xin Wang, Phoebe Vallapureddy, Jianhua Lim, Menghan Pan, Andres Fernandez Del Castillo, Jonathan C. T. Carlson, Mark A. Sellmyer, MacLean Nasrallah, Zev Binder, Donald M. O'Rourke, Guo‐li Ming, Hongjun Song, and Jina Ko
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biomarker discovery ,bioorthogonal click‐chemistry ,glioblastoma ,longitudinal monitoring ,multiplexing ,organoids ,Science - Abstract
Abstract Organoids are becoming increasingly relevant in biology and medicine for their physiological complexity and accuracy in modeling human disease. To fully assess their biological profile while preserving their spatial information, spatiotemporal imaging tools are warranted. While previously developed imaging techniques, such as four‐dimensional (4D) live imaging and light‐sheet imaging have yielded important clinical insights, these technologies lack the combination of cyclic and multiplexed analysis. To address these challenges, bioorthogonal click chemistry is applied to display the first demonstration of multiplexed cyclic imaging of live and fixed patient‐derived glioblastoma tumor organoids. This technology exploits bioorthogonal click chemistry to quench fluorescent signals from the surface and intracellular of labeled cells across multiple cycles, allowing for more accurate and efficient molecular profiling of their complex phenotypes. Herein, the versatility of this technology is demonstrated for the screening of glioblastoma markers in patient‐derived human glioblastoma organoids while conserving their viability. It is anticipated that the findings and applications of this work can be broadly translated into investigating physiological developments in other organoid systems.
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- 2024
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12. Navigating the Virtual Landscape: Methodological Considerations for Qualitative Research in Long-Term Care
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Danielle T. Just, Hannah M. O’Rourke, Whitney B. Berta, and Lisa A. Cranley
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Social sciences (General) ,H1-99 - Abstract
With the COVID-19 pandemic halting all in-person research in March 2020, many researchers adopted virtual methods to continue their work amid this global crisis. As the pandemic persisted and the safety of participants and researchers remained a priority, virtual research grew in popularity for qualitative researchers. This in turn led to methodological insights on the application and advantages of conducting qualitative research using virtual methods. Virtual methods have been found to enhance participant comfort, facilitate open discussion of sensitive topics, alleviate fatigue in participants and researchers, and result in more engaging and focused interviews. While the body of evidence supporting virtual methods of data collection for nursing and other healthcare disciplines continues to grow, its application in the long-term care (LTC) setting remains underreported. In this paper, we discuss the virtual methods that we developed and implemented to successfully conduct a virtual qualitative single case study in a Canadian LTC home during the COVID-19 pandemic. Considerations from existing literature on virtual methods are discussed in parallel with strategies we implemented to successfully conduct a virtual study in LTC. This paper contributes to the growing body of literature on methodological insights into conducting virtual qualitative research in LTC. We provide evidence-based strategies for the virtual recruitment of study sites, study participants including residents, team members and families, and virtual data collection methods. These recommendations offer insights to overcome challenges and maximize the advantages of virtual methods, to enhance the quality and rigour of virtual qualitative research conducted within LTC settings.
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- 2024
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13. Closing the Ivory Validation Gates: A Historical Analysis of Achkasov's Data Association Filters.
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Sean M. O'Rourke
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- 2023
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14. HyperGUI: A Web Application for Hyperspectral Image Analysis and Data Extraction
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Shayan Kabiri and Sharon M. O’Rourke
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hyperspectral imaging ,hyperspectral image processing ,web apps ,shiny ,Computer software ,QA76.75-76.765 - Abstract
HyperGUI is an intuitive R-based web application crafted to streamline the loading of raw hyperspectral images while offering essential processing functions for exploring hyperspectral data. Users can easily load, process, and visualize benchtop or aerial hyperspectral images, with the flexibility to export them to R, Python, MATLAB, or raster data frames for further analysis. HyperGUI’s source code is available on GitHub, and it is accessible online via shinyapps.io.
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- 2024
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15. Distance interventions for enhancing preparedness in informal caregivers of older adults: A systematic review protocol.
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Fernanda L F Dal Pizzol, Kathleen F Hunter, Jennifer Baumbusch, and Hannah M O'Rourke
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Medicine ,Science - Abstract
IntroductionInformal caregivers provide care to older adults but report lack of preparedness to enact the role. Intervention programs delivered by distance offer one alternative to support preparedness. Three review studies conducted to date have highlighted the benefits of distance interventions for enhancing preparedness among informal caregivers of older adults. However, these reviews have been limited in presenting and discussing how intervention components influenced outcomes. Additionally, they have not compared different distance delivery approaches for informal caregivers of older adults or assessed their varying impact on preparedness outcomes. These limitations make the effectiveness of diverse distance approaches unclear.AimTo evaluate the effects of distance interventions aimed at enhancing preparedness among informal caregivers of older adults.MethodsThis protocol follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocols (PRISMA-P) guidelines and is guided by the Cochrane Handbook for Systematic Reviews of Interventions. It has been registered in PROSPERO (CRD42023400668). Databases used in the search will include CINAHL, Cochrane Library, EMBASE, MEDLINE, PsycINFO, Scopus, and ProQuest Theses and Dissertations Global. The search will not be restricted by publication year to include all relevant studies. Studies published in English and Portuguese will be included. Study quality will be assessed using Downs and Black's checklist. If metanalysis is possible, it will be performed using the ReviewManager (RevMan) software.ConclusionsThe study will be the first of its type to systematically review and synthesize components and approaches of distance interventions aimed at supporting preparedness of informal caregivers of older adults.
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- 2024
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16. IMPAACT: IMproving the PArticipAtion of older people in policy decision-making on common health CondiTions – a study protocol
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Simon Stewart, Michael Lawless, Renuka Visvanathan, Danielle Taylor, Mandy Archibald, Hannah M O'Rourke, Matthew J Leach, Mark Thompson, Justin Beilby, Rachel C Ambagtsheer, Kathy Williams, Annette Braunack-Mayer, Victoria Cornell, Catherine J Hurley, Elsa Dent, Lyn Whiteway, and Agnieszka Chudecka
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Medicine - Abstract
Introduction Rapid population ageing is a demographic trend being experienced and documented worldwide. While increased health screening and assessment may help mitigate the burden of illness in older people, issues such as misdiagnosis may affect access to interventions. This study aims to elicit the values and preferences of evidence-informed older people living in the community on early screening for common health conditions (cardiovascular disease, diabetes, dementia and frailty). The study will proceed in three Phases: (1) generating recommendations of older people through a series of Citizens’ Juries; (2) obtaining feedback from a diverse range of stakeholder groups on the jury findings; and (3) co-designing a set of Knowledge Translation resources to facilitate implementation into research, policy and practice. Conditions were chosen to reflect common health conditions characterised by increasing prevalence with age, but which have been underexamined through a Citizens’ Jury methodology.Methods and analysis This study will be conducted in three Phases—(1) Citizens’ Juries, (2) Policy Roundtables and (3) Production of Knowledge Translation resources. First, older people aged 50+ (n=80), including those from traditionally hard-to-reach and diverse groups, will be purposively recruited to four Citizen Juries. Second, representatives from a range of key stakeholder groups, including consumers and carers, health and aged care policymakers, general practitioners, practice nurses, geriatricians, allied health practitioners, pharmaceutical companies, private health insurers and community and aged care providers (n=40) will be purposively recruited for two Policy Roundtables. Finally, two researchers and six purposively recruited consumers will co-design Knowledge Translation resources. Thematic analysis will be performed on documentation and transcripts.Ethics and dissemination Ethical approval has been obtained through the Torrens University Human Research Ethics Committee. Participants will give written informed consent. Findings will be disseminated through development of a policy brief and lay summary, peer-reviewed publications, conference presentations and seminars.
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- 2024
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17. X-ray Fluorescence Core Scanning for High-Resolution Geochemical Characterisation of Soils
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Shayan Kabiri, Nick M. Holden, Rory P. Flood, Jonathan N. Turner, and Sharon M. O’Rourke
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XRF core scanning ,geochemistry ,calibration ,Physical geography ,GB3-5030 ,Chemistry ,QD1-999 - Abstract
X-ray fluorescence (XRF) core scanners are commonly used for fine-scale geochemical analysis in sediment studies, but data are semi-quantitative and require calibration to convert geochemical element counts to concentrations. Application of XRF core scanning in soil science remains largely untapped. This study employed an ITRAX core scanner to scan grassland soil cores and developed a novel calibration method based on a chemometric approach to characterise soil geochemistry. As soil samples are collected based on depth sampling, this study investigated whether higher resolution element concentrations could be inferred from lower resolution reference samples and if regression models from multiple cores could apply to a new core at the same resolution. Reference concentrations were obtained for all cores at 10 cm intervals, with validation conducted at 1 cm for a single core. Two calibration curve types were proposed: one based on the single core’s 10 cm data to validate references at 1 cm intervals; and another using all cores, with each core serving as a test item after exclusion from the training set. Various preprocessing measures and feature selection techniques were tested. Results showed successful calibration for elements Ca, P, Zn, Sr, and S, with high R2 values of 0.94, 0.93, 0.93, 0.92 and 0.91, respectively. The study presents a novel method for calibrating XRF core scanning element counts, demonstrating its potential for high-resolution soil analysis.
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- 2024
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18. Emergency nurses’ triage narrative data, their uses and structure: a scoping review protocol
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Hannah M O'Rourke, Matthew J Douma, Colleen M Norris, Christopher Thomas Picard, and Manal Kleib
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Medicine - Abstract
Introduction The first clinical interaction most patients have in the emergency department occurs during triage. An unstructured narrative is generated during triage and is the first source of in-hospital documentation. These narratives capture the patient’s reported reason for the visit and the initial assessment and offer significantly more nuanced descriptions of the patient’s complaints than fixed field data. Previous research demonstrated these data are useful for predicting important clinical outcomes. Previous reviews examined these narratives in combination or isolation with other free-text sources, but used restricted searches and are becoming outdated. Furthermore, there are no reviews focused solely on nurses’ (the primary collectors of these data) narratives.Methods and analysis Using the Arksey and O’Malley scoping review framework and PRISMA-ScR reporting guidelines, we will perform structured searches of CINAHL, Ovid MEDLINE, ProQuest Central, Ovid Embase and Cochrane Library (via Wiley). Additionally, we will forward citation searches of all included studies. No geographical or study design exclusion criteria will be used. Studies examining disaster triage, published before 1990, and non-English language literature will be excluded. Data will be managed using online management tools; extracted data will be independently confirmed by a separate reviewer using prepiloted extraction forms. Cohen’s kappa will be used to examine inter-rater agreement on pilot and final screening. Quantitative data will be expressed using measures of range and central tendency, counts, proportions and percentages, as appropriate. Qualitative data will be narrative summaries of the authors’ primary findings.Patient and public involvement No patients involved.Ethics and dissemination No ethics approval is required. Findings will be submitted to peer-reviewed conferences and journals. Results will be disseminated using individual and institutional social media platforms.
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- 2022
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19. Assessment of treatment response to dendritic cell vaccine in patients with glioblastoma using a multiparametric MRI-based prediction model
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Laiz Laura de Godoy, Sanjeev Chawla, Steven Brem, Sumei Wang, Donald M O’Rourke, MacLean P. Nasrallah, Arati Desai, Laurie A. Loevner, Linda M. Liau, and Suyash Mohan
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Cancer Research ,Neurology ,Oncology ,Neurology (clinical) - Abstract
Purpose Autologous tumor lysate-loaded dendritic cell vaccine (DCVax-L) is a promising treatment modality for glioblastomas. The purpose of this study was to investigate the potential utility of multiparametric MRI-based prediction model in evaluating treatment response in glioblastoma patients treated with DCVax-L. Methods Seventeen glioblastoma patients treated with standard-of-care therapy + DCVax-L were included. When tumor progression was suspected and repeat surgery was being contemplated, we sought to ascertain the number of cases correctly classified as true progression (TP) + mixed response or pseudoprogression (PsP) from multiparametric MRI-based prediction model using histopathology/mRANO criteria as ground truth. Multiparametric MRI model consisted of predictive probabilities (PP) of tumor progression computed from diffusion and perfusion MRI-derived parameters. A comparison of overall survival (OS) was performed between patients treated with standard-of-care therapy + DCVax-L and standard-of-care therapy alone (external controls). Additionally, Kaplan-Meier analyses were performed to compare OS between two groups of patients using PsP, Ki-67, and MGMT methylation status as stratification variables. Results Multiparametric MRI model correctly predicted TP + mixed response in 72.7% of cases (8/11) and PsP in 83.3% (5/6) with an overall concordance rate of 76.5% with final diagnosis as determined by histopathology/mRANO criteria. There was a significant concordant correlation coefficient between PP values and histopathology/mRANO criteria (r = 0.54; p = 0.026). DCVax-L-treated patients had significantly prolonged OS than those treated with standard-of-care therapy (22.38 ± 12.8 vs. 13.8 ± 9.5months, p = 0.040). Additionally, glioblastomas with PsP, MGMT methylation status, and Ki-67 values below median had longer OS than their counterparts. Conclusion Multiparametric MRI-based prediction model can assess treatment response to DCVax-L in patients with glioblastoma.
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- 2023
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20. The IAP antagonist birinapant enhances chimeric antigen receptor T cell therapy for glioblastoma by overcoming antigen heterogeneity
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Edward Z. Song, Xin Wang, Benjamin I. Philipson, Qian Zhang, Radhika Thokala, Logan Zhang, Charles-Antoine Assenmacher, Zev A. Binder, Guo-li Ming, Donald M. O’Rourke, Hongjun Song, and Michael C. Milone
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Cancer Research ,Oncology ,Molecular Medicine ,Pharmacology (medical) - Abstract
Antigen heterogeneity that results in tumor antigenic escape is one of the major obstacles to successful chimeric antigen receptor (CAR) T cell therapies in solid tumors including glioblastoma multiforme (GBM). To address this issue and improve the efficacy of CAR T cell therapy for GBM, we developed an approach that combines CAR T cells with inhibitor of apoptosis protein (IAP) antagonists, a new class of small molecules that mediate the degradation of IAPs, to treat GBM. Here, we demonstrated that the IAP antagonist birinapant could sensitize GBM cell lines and patient-derived primary GBM organoids to apoptosis induced by CAR T cell-derived cytokines, such as tumor necrosis factor. Therefore, birinapant could enhance CAR T cell-mediated bystander death of antigen-negative GBM cells, thus preventing tumor antigenic escape in antigen-heterogeneous tumor models
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- 2022
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21. Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California
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Yingxin Su, Peter B. Moyle, Matthew A. Campbell, Amanda J. Finger, Sean M. O'Rourke, Jason Baumsteiger, and Michael R. Miller
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population genomics ,Life on Land ,Human Genome ,Fisheries ,population genetics ,taxonomy and systematics ,RAD sequencing ,Aquatic Science ,genetics and genomics ,Fisheries Sciences ,conservation management ,conservation genetics ,conservation genomics ,Genetics ,Ecology, Evolution, Behavior and Systematics ,Biotechnology - Abstract
Objective: Speckled Dace Rhinichthys osculus is small cyprinoid fish that is widespread in western North America. In California and elsewhere it is currently treated as a single species with multiple subspecies, many undescribed. However, these subspecies may represent evolutionary lineages that are cryptic species because they cannot be distinguished using standard morphometric techniques. In this study, we attempt to determine evolutionary lineages within California populations of Speckled Dace using the population genetic and genomic information. Methods: We used restriction site-associated DNA sequencing to extract thousands of single-nucleotide polymorphisms across the genome to identify genetic differences among all the samples from 38 locations in the western USA, with a focus on California. We performed principal component analysis, admixture analysis, estimated pairwise values of the genetic differentiation index FST, and constructed molecular phylogenies to characterize population genetic and phylogenetic relationships among sampled Speckled Dace populations. Result: Our analyses detected three major lineages of Speckled Dace in California that align with geography: (1) Sacramento River, central California coast, Klamath River, and Warner Basin; (2) Death Valley and Lahontan Basin; and (3) Santa Ana River basin, in southern California. These lineages fit well with the geologic history of California, which has promoted long isolation of populations of Speckled Dace and other fishes. Conclusion: The presence of distinct evolutionary lineages indicates that Speckled Dace in California should be managed with distinct population segments to preserve within-species diversity. This study highlights the importance of genetic analyses for conservation and management of freshwater fishes.
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- 2022
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22. EGFR, the Lazarus target for precision oncology in glioblastoma
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Benjamin Lin, Julia Ziebro, Erin Smithberger, Kasey R Skinner, Eva Zhao, Timothy F Cloughesy, Zev A Binder, Donald M O’Rourke, David A Nathanson, Frank B Furnari, and C Ryan Miller
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Cancer Research ,Oncology ,Neurology (clinical) - Abstract
The Lazarus effect is a rare condition that happens when someone seemingly dead shows signs of life. The epidermal growth factor receptor (EGFR) represents a target in the fatal neoplasm glioblastoma (GBM) that through a series of negative clinical trials has prompted a vocal subset of the neuro-oncology community to declare this target dead. However, an argument can be made that the core tenets of precision oncology were overlooked in the initial clinical enthusiasm over EGFR as a therapeutic target in GBM. Namely, the wrong drugs were tested on the wrong patients at the wrong time. Furthermore, new insights into the biology of EGFR in GBM vis-à-vis other EGFR-driven neoplasms, such as non-small cell lung cancer, and development of novel GBM-specific EGFR therapeutics resurrects this target for future studies. Here, we will examine the distinct EGFR biology in GBM, how it exacerbates the challenge of treating a CNS neoplasm, how these unique challenges have influenced past and present EGFR-targeted therapeutic design and clinical trials, and what adjustments are needed to therapeutically exploit EGFR in this devastating disease.
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- 2022
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23. Non-invasive Assessment of IDH-mutant Gliomas Using Optimized Proton Magnetic Resonance Spectroscopy on a Routine Clinical 3-Tesla MRI
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De Godoy, Laiz Laura, primary, Choon Lim, Kheng, additional, Rajan, Archith, additional, Verma, Gaurav, additional, Hanaoka, Mauro, additional, M O’Rourke, Donald, additional, Lee, John, additional, Desai, Arati, additional, Chawla, Sanjeev, additional, and Mohan, Suyash, additional
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- 2023
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24. Locally secreted BiTEs complement CAR T cells by enhancing killing of antigen heterogeneous solid tumors
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Yibo Yin, Jesse L. Rodriguez, Nannan Li, Radhika Thokala, MacLean P. Nasrallah, Li Hu, Logan Zhang, Jiasi Vicky Zhang, Meghan T. Logun, Devneet Kainth, Leila Haddad, Yang Zhao, Tong Wu, Emily X. Johns, Yu Long, Hongsheng Liang, Jiping Qi, Xiangtong Zhang, Zev A. Binder, Zhiguo Lin, and Donald M. O’Rourke
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Pharmacology ,T-Lymphocytes ,Immunotherapy, Adoptive ,Xenograft Model Antitumor Assays ,ErbB Receptors ,Mice ,Cell Line, Tumor ,Drug Discovery ,Interleukin-13 Receptor alpha2 Subunit ,Genetics ,Animals ,Molecular Medicine ,Original Article ,Glioblastoma ,Molecular Biology - Abstract
Bispecific T cell engagers (BiTEs) are bispecific antibodies that redirect T cells to target antigen-expressing tumors. We hypothesized that BiTE-secreting T cells could be a valuable therapy in solid tumors, with distinct properties in mono- or multi-valent strategies incorporating chimeric antigen receptor (CAR) T cells. Glioblastomas represent a good model for solid tumor heterogeneity, representing a significant therapeutic challenge. We detected expression of tumor-associated epidermal growth factor receptor (EGFR), EGFR variant III, and interleukin-13 receptor alpha 2 (IL13Rα2) on glioma tissues and cancer stem cells. These antigens formed the basis of a multivalent approach, using a conformation-specific tumor-related EGFR targeting antibody (806) and Hu08, an IL13Rα2-targeting antibody, as the single chain variable fragments to generate new BiTE molecules. Compared with CAR T cells, BiTE T cells demonstrated prominent activation, cytokine production, and cytotoxicity in response to target-positive gliomas. Superior response activity was also demonstrated in BiTE-secreting bivalent T cells compared with bivalent CAR T cells in a glioma mouse model at early phase, but not in the long term. In summary, BiTEs secreted by mono- or multi-valent T cells have potent anti-tumor activity in vitro and in vivo with significant sensitivity and specificity, demonstrating a promising strategy in solid tumor therapy.
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- 2022
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25. Feasibility of Routine Quality of Life Measurement for People Living With Dementia in Long-Term Care
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Kyle Corbett, Hannah M O'Rourke, Kelli I. Stajduhar, Anna Song Beeber, Shovana Shrestha, Emily Dymchuk, Ian Simons, Carole A. Estabrooks, Matthias Hoben, Laura J Hughes, Rashmi Devkota, Jenny Lam, Sube Banerjee, and Stephanie A. Chamberlain
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Gerontology ,Canada ,Quality of life ,Surveys and Questionnaires ,Internal consistency ,medicine ,Humans ,Dementia ,General Nursing ,Reliability (statistics) ,Assisted living ,business.industry ,Health Policy ,Reproducibility of Results ,General Medicine ,medicine.disease ,Long-Term Care ,Confidence interval ,Long-term care ,Cross-Sectional Studies ,Quality of Life ,Feasibility Studies ,Geriatrics and Gerontology ,Nursing homes ,business - Abstract
OBJECTIVES Maximizing quality of life (QoL) is the ultimate goal of long-term dementia care. However, routine QoL measurement is rare in nursing home (NH) and assisted living (AL) facilities. Routine QoL measurement might lead to improvements in resident QoL. Our objective was to assess the feasibility of using DEMQOL-CH, completed by long-term care staff in video calls with researchers, to assess health-related quality of life (HrQoL) of NH and AL residents with dementia or other cognitive impairment. DESIGN Cross-sectional study. SETTING AND PARTICIPANTS We included a convenience sample of 5 NHs and 5 AL facilities in the Canadian province of Alberta. Forty-two care staff who had worked in the facility for ≥3 months completed DEMQOL-CH assessments of 183 residents who had lived in the facility for 3 months or more and were aged ≥65 years. Sixteen residents were assessed independently by 2 care staff to assess inter-rater reliability. METHODS We assessed HrQoL in people with dementia or other cognitive impairment using DEMQOL-CH, and assessed time to complete, inter-rater reliability, internal consistency reliability, and care staff ratings of feasibility of completing the DEMQOL-CH. RESULTS Average time to complete DEMQOL-CH was
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- 2022
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26. Image congruity in the love triangle among mega sport event organizer, sponsor, and consumers: the moderating effects of product involvement and consumer awareness
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Nicolas G. A. Lorgnier, Nicolas Chanavat, Che-Jen Su, and Shawn M. O’Rourke
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Strategy and Management ,Tourism, Leisure and Hospitality Management - Published
- 2022
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27. Risk of intracranial hemorrhage with direct oral anticoagulants vs low molecular weight heparin in glioblastoma: A retrospective cohort study
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Lauren Reed-Guy, Arati S Desai, Richard E Phillips, Desiree Croteau, Karen Albright, Meghan O’Neill, Steven Brem, Donald M O’Rourke, Nduka M Amankulor, and Stephen J Bagley
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Cohort Studies ,Cancer Research ,Oncology ,Clinical Investigations ,Humans ,Anticoagulants ,Venous Thromboembolism ,Neurology (clinical) ,Heparin, Low-Molecular-Weight ,Glioblastoma ,Intracranial Hemorrhages ,Retrospective Studies - Abstract
Background Glioblastoma (GBM) is associated with a high incidence of venous thromboembolism (VTE), but there are little data to guide anticoagulation in patients with GBM, in whom the risks of VTE must be balanced against the risk of intracranial hemorrhage (ICH). Methods We performed a single-institution retrospective cohort study of patients with GBM diagnosed with VTE from 2014 to 2021 who were treated with low molecular weight heparin (LMWH) or a direct oral anticoagulant (DOAC). The incidence of ICH was compared between the LMWH and DOAC groups. The primary outcome was clinically relevant ICH within the first 30 days of anticoagulation, defined as any ICH that was fatal, symptomatic, required surgical intervention, and/or led to cessation of anticoagulation. Secondary outcomes included clinically relevant ICH within 6 months, fatal ICH within 30 days and 6 months, and any bleeding within 30 days and 6 months. Results One hundred twenty-one patients were identified in the cohort for 30-day outcome analyses (DOAC, n = 33; LMWH, n = 88). For 6-month outcome analyses, the cohort included only patients who were maintained on their initial anticoagulant (DOAC, n = 32; LMWH, n = 75). The incidence of clinically relevant ICH at 30 days was 0% in the DOAC group and 9% in the LMWH group (P = .11). The cumulative incidence of clinically relevant ICH at 6 months was 0% in the DOAC group and 24% in the LMWH group (P = .001), with 4 fatal ICHs in the LMWH group. Conclusions DOACs are associated with a lower incidence of clinically relevant ICH in patients with GBM-associated VTE compared to LMWH.
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- 2022
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28. Glioblastoma: The Current State of Biology and Therapeutic Strategies
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Zev A. Binder and Donald M. O'Rourke
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Cancer Research ,Oncology ,Brain Neoplasms ,Humans ,Glioblastoma ,Biology ,Article - Abstract
Over the past two decades, there have been advances in surgical technologies and chemoradiation strategies for glioblastoma, yet durable remissions are rarely seen. As the biological challenges and genetic basis of glioblastoma have become more understood, new therapeutic strategies may lead to more durable clinical responses and long-term remissions. We believe specialized academic centers that form meaningful corporate partnerships to complement basic science infrastructure and use adaptive clinical trial designs will achieve more rapid translation of innovative approaches to glioblastoma. Here we outline the core biological challenges to be overcome in the management of glioblastoma.
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- 2022
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29. Enhancing CAR T function with the engineered secretion of C. perfringens neuraminidase
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Joseph S. Durgin, Zev A. Binder, Vijay Bhoj, Michael C. Milone, Donald M. O'Rourke, Radhika Thokala, Saba Ghassemi, Roddy S. O’Connor, Lexus R. Johnson, John Leferovich, and Edward Z Song
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Adoptive cell transfer ,Clostridium perfringens ,T cell ,Antigens, CD19 ,Cell ,Neuraminidase ,Immunotherapy, Adoptive ,Immune system ,Cell Line, Tumor ,Drug Discovery ,Genetics ,medicine ,Humans ,Molecular Biology ,Pharmacology ,Receptors, Chimeric Antigen ,biology ,Effector ,Chemistry ,Xenograft Model Antitumor Assays ,Immune checkpoint ,Cell biology ,Cytolysis ,medicine.anatomical_structure ,biology.protein ,Molecular Medicine - Abstract
Prior to adoptive transfer, CAR T cells are activated, lentivirally infected with CAR transgenes, and expanded over 9 to 11 days. An unintended consequence of this process is the progressive differentiation of CAR T cells over time in culture. Differentiated T cells engraft poorly, which limits their ability to persist and provide sustained tumor control in hematologic as well as solid tumors. Solid tumors include other barriers to CAR T cell therapies, including immune and metabolic checkpoints that suppress effector function and durability. Sialic acids are ubiquitous surface molecules with known immune checkpoint functions. The enzyme C. perfringens neuraminidase (CpNA) removes sialic acid residues from target cells, with good activity at physiologic conditions. In combination with galactose oxidase (GO), NA has been found to stimulate T cell mitogenesis and cytotoxicity in vitro. Here we determine whether CpNA alone and in combination with GO promotes CAR T cell antitumor efficacy. We show that CpNA restrains CAR T cell differentiation during ex vivo culture, giving rise to progeny with enhanced therapeutic potential. CAR T cells expressing CpNA have superior effector function and cytotoxicity in vitro. In a Nalm-6 xenograft model of leukemia, CAR T cells expressing CpNA show enhanced antitumor efficacy. Arming CAR T cells with CpNA also enhanced tumor control in xenograft models of glioblastoma as well as a syngeneic model of melanoma. Given our findings, we hypothesize that charge repulsion via surface glycans is a regulatory parameter influencing differentiation. As T cells engage target cells within tumors and undergo constitutive activation through their CARs, critical thresholds of negative charge may impede cell-cell interactions underlying synapse formation and cytolysis. Removing the dense pool of negative cell-surface charge with CpNA is an effective approach to limit CAR T cell differentiation and enhance overall persistence and efficacy.
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- 2022
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30. Validation of multiparametric MRI based prediction model in identification of pseudoprogression in glioblastomas
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Laiz Laura de Godoy, Suyash Mohan, Sumei Wang, MacLean P. Nasrallah, Yu Sakai, Donald M. O’Rourke, Stephen Bagley, Arati Desai, Laurie A. Loevner, Harish Poptani, and Sanjeev Chawla
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General Medicine ,General Biochemistry, Genetics and Molecular Biology - Abstract
Background Accurate differentiation of pseudoprogression (PsP) from tumor progression (TP) in glioblastomas (GBMs) is essential for appropriate clinical management and prognostication of these patients. In the present study, we sought to validate the findings of our previously developed multiparametric MRI model in a new cohort of GBM patients treated with standard therapy in identifying PsP cases. Methods Fifty-six GBM patients demonstrating enhancing lesions within 6 months after completion of concurrent chemo-radiotherapy (CCRT) underwent anatomical imaging, diffusion and perfusion MRI on a 3 T magnet. Subsequently, patients were classified as TP + mixed tumor (n = 37) and PsP (n = 19). When tumor specimens were available from repeat surgery, histopathologic findings were used to identify TP + mixed tumor (> 25% malignant features; n = 34) or PsP ( Results Multiparametric MRI model correctly predicted PsP in 95% (18/19) and TP+ mixed tumor in 57% of cases (21/37) with an overall concordance rate of 70% (39/56) with final diagnosis as determined by histopathology/mRANO criteria. There was a significant concordant correlation coefficient between PP values and histopathology/mRANO criteria (r = 0.56; p Conclusions Our multiparametric MRI based prediction model may be helpful in identifying PsP in GBM patients.
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- 2023
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31. Supplementary Figure from Immunologic Features in De Novo and Recurrent Glioblastoma Are Associated with Survival Outcomes
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Gregory L. Beatty, Donald M. O'Rourke, E. John Wherry, Jiasi Vicky Zhang, Logan Y. Zhang, Oliver Y. Tang, Joey H. Li, Devora Delman, MacLean P. Nasrallah, Renee B. Chang, Zev A. Binder, and Cécile Alanio
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Supplementary Figure from Immunologic Features in De Novo and Recurrent Glioblastoma Are Associated with Survival Outcomes
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- 2023
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32. Data from Immunologic Features in De Novo and Recurrent Glioblastoma Are Associated with Survival Outcomes
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Gregory L. Beatty, Donald M. O'Rourke, E. John Wherry, Jiasi Vicky Zhang, Logan Y. Zhang, Oliver Y. Tang, Joey H. Li, Devora Delman, MacLean P. Nasrallah, Renee B. Chang, Zev A. Binder, and Cécile Alanio
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Glioblastoma (GBM) is an immunologically “cold” tumor characterized by poor responsiveness to immunotherapy. Standard of care for GBM is surgical resection followed by chemoradiotherapy and maintenance chemotherapy. However, tumor recurrence is the norm, and recurring tumors are found frequently to have acquired molecular changes (e.g., mutations) that may influence their immunobiology. Here, we compared the immune contexture of de novo GBM and recurrent GBM (rGBM) using high-dimensional cytometry and multiplex IHC. Although myeloid and T cells were similarly abundant in de novo and rGBM, their spatial organization within tumors differed and was linked to outcomes. In rGBM, T cells were enriched and activated in perivascular regions and clustered with activated macrophages and fewer regulatory T cells. Moreover, a higher expression of phosphorylated STAT1 by T cells in these regions at recurrence was associated with a favorable prognosis. Together, our data identify differences in the immunobiology of de novo GBM and rGBM and identify perivascular T cells as potential therapeutic targets.See related Spotlight by Bayik et al., p. 787
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- 2023
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33. Supplementary Tables 1 and 2, Figures 1-9 from Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma
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Matthew J. Lazzara, Donald M. O'Rourke, M. Celeste Simon, Maria Martinez-Lage, Ramana V. Davuluri, Yingtao Bi, Lijoy K. Mathew, Janine M. Buonato, Gurpreet S. Kapoor, and Alice M. Walsh
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Supplementary Tables 1 and 2, Figures 1-9. Supplemental Table 1. H-score analysis for SPRY2 staining in 10 EGFRvIII-negative and 10 EGFRvIII-positive tumors. Supplemental Table 2. Upregulated genes shared by human GBMs expressing EGFRvIII and 9L.EGFRvIII rat tumors compared to wild-type EGFR human GBMs or 9L.EV rat tumors. Supplemental Figure 1. SPRY2 is efficiently knocked down by shRNA expression in GBM cell lines. Supplemental Figure 2. SPRY2 knockdown by a second non-overlapping shRNA reduces cellular proliferation, and SPRY2 knockdown by transient siRNA transfection reduces colony formation in soft agar in EGFRvIII-expressing cells. Supplemental Figure 3. SPRY2 knockdown increases cellular sensitivity to EGFR and c-MET co-inhibition. Supplemental Figure 4. SPRY2 knockdown promotes response to EGFR and c-MET coinhibition in GSC cells. Supplemental Figure 5. p38 and JNK control anchorage-independent growth and response to EGFR and c-MET co-inhibition. Supplemental Figure 6. shRNA-mediated knockdown of MKP-1 or MKP-5 reduces MKP-1 or MKP-5 mRNA level. Supplemental Figure 7. SPRY2 protein expression in kidney and cerebellum sections by immunohistochemical analysis. Supplemental Figure 8. SPRY2 correlates well with ERK phosphorylation in a panel of GBM cell lines. Supplemental Figure 9. TCGA GBM dataset analysis reveals that SPRY2 expression is associated with reduced patient survival.
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- 2023
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34. Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine
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John V. Dzimianski, Julianna Han, Giuseppe A. Sautto, Sara M. O’Rourke, Joseph M. Cruz, Spencer R. Pierce, Jeffrey W. Ecker, Michael A. Carlock, Kaito A. Nagashima, Jarrod J. Mousa, Ted M. Ross, Andrew B. Ward, and Rebecca M. DuBois
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Hemagglutinin Glycoproteins ,Influenza Virus ,Prevention ,Medicine (miscellaneous) ,General Biochemistry, Genetics and Molecular Biology ,Antibodies ,Influenza ,Vaccine Related ,Hemagglutinins ,Infectious Diseases ,Emerging Infectious Diseases ,Good Health and Well Being ,Orthomyxoviridae Infections ,Influenza Vaccines ,5.1 Pharmaceuticals ,Biodefense ,Influenza A Virus ,Pneumonia & Influenza ,Humans ,H1N1 Subtype ,Immunization ,Viral ,Development of treatments and therapeutic interventions ,General Agricultural and Biological Sciences ,Infection - Abstract
Influenza virus poses an ongoing human health threat with pandemic potential. Due to mutations in circulating strains, formulating effective vaccines remains a challenge. The use of computationally optimized broadly reactive antigen (COBRA) hemagglutinin (HA) proteins is a promising vaccine strategy to protect against a wide range of current and future influenza viruses. Though effective in preclinical studies, the mechanistic basis driving the broad reactivity of COBRA proteins remains to be elucidated. Here, we report the crystal structure of the COBRA HA termed P1 and identify antigenic and glycosylation properties that contribute to its immunogenicity. We further report the cryo-EM structure of the P1-elicited broadly neutralizing antibody 1F8 bound to COBRA P1, revealing 1F8 to recognize an atypical receptor binding site epitope via an unexpected mode of binding.
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- 2023
35. Supplementary Data 2 from A Randomized Double-Blind Placebo-Controlled Phase II Trial of Dendritic Cell Vaccine ICT-107 in Newly Diagnosed Patients with Glioblastoma
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John S. Yu, Radleigh G. Santos, Clemencia Pinilla, Alona Muzikansky, Santosh Kesari, Edward Pan, Glenn J. Lesser, Michael Gruber, Lyndon Kim, Karen Fink, Donald M. O'Rourke, Renato LaRocca, James M. Markert, David M. Peereboom, Michael Glantz, Jay-Jiguang Zhu, William T. Curry, Joseph C. Landolfi, Robert D. Aiken, Surasak Phuphanich, Terri S. Armstrong, David A. Reardon, and Patrick Y. Wen
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Supplemental Fig 2
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- 2023
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36. Table S1 from Clinical Utility of Plasma Cell-Free DNA in Adult Patients with Newly Diagnosed Glioblastoma: A Pilot Prospective Study
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Erica L. Carpenter, Arati S. Desai, Steven Brem, Andrew J. Cucchiara, Donald M. O'Rourke, Zev A. Binder, Jennifer J.D. Morrissette, MacLean P. Nasrallah, Stephanie S. Yee, Theresa Christensen, Samantha Guiry, Timothy Prior, Jasmin Hussain, Whitney Sarchiapone, Scott Levy, Jeffrey B. Ware, Jacob E. Till, Jazmine J. Mays, S. Ali Nabavizadeh, and Stephen J. Bagley
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Tissue next-generation sequencing gene coverage (152 genes)
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- 2023
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37. Figure S1 from Clinical Utility of Plasma Cell-Free DNA in Adult Patients with Newly Diagnosed Glioblastoma: A Pilot Prospective Study
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Erica L. Carpenter, Arati S. Desai, Steven Brem, Andrew J. Cucchiara, Donald M. O'Rourke, Zev A. Binder, Jennifer J.D. Morrissette, MacLean P. Nasrallah, Stephanie S. Yee, Theresa Christensen, Samantha Guiry, Timothy Prior, Jasmin Hussain, Whitney Sarchiapone, Scott Levy, Jeffrey B. Ware, Jacob E. Till, Jazmine J. Mays, S. Ali Nabavizadeh, and Stephen J. Bagley
- Abstract
Plasma cell-free DNA (cfDNA) concentration (ng/mL) is correlated with (A), total radiographic tumor burden (contrast-enhancing tumor + T2/FLAIR non-enhancing tumor) and (B), contrast-enhancing tumor burden at the first post-radiation MRI scan in patients with newly diagnosed glioblastoma
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- 2023
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38. Data from A Randomized Double-Blind Placebo-Controlled Phase II Trial of Dendritic Cell Vaccine ICT-107 in Newly Diagnosed Patients with Glioblastoma
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John S. Yu, Radleigh G. Santos, Clemencia Pinilla, Alona Muzikansky, Santosh Kesari, Edward Pan, Glenn J. Lesser, Michael Gruber, Lyndon Kim, Karen Fink, Donald M. O'Rourke, Renato LaRocca, James M. Markert, David M. Peereboom, Michael Glantz, Jay-Jiguang Zhu, William T. Curry, Joseph C. Landolfi, Robert D. Aiken, Surasak Phuphanich, Terri S. Armstrong, David A. Reardon, and Patrick Y. Wen
- Abstract
Purpose:To evaluate the results of the randomized, double-blind, placebo-controlled phase II clinical trial of ICT-107 in patients with newly diagnosed glioblastoma.Patients and Methods:We conducted a double-blinded randomized phase II trial of ICT-107 in newly diagnosed patients with glioblastoma (GBM) and tested efficacy, safety, quality of life (QoL), and immune response. HLA-A1+ and/or -A2+–resected patients with residual tumor ≤1 cm3 received radiotherapy and concurrent temozolomide. Following completion of radiotherapy, 124 patients, randomized 2:1, received ICT-107 [autologous dendritic cells (DC) pulsed with six synthetic peptide epitopes targeting GBM tumor/stem cell–associated antigens MAGE-1, HER-2, AIM-2, TRP-2, gp100, and IL13Rα2] or matching control (unpulsed DC). Patients received induction ICT-107 or control weekly × 4 followed by 12 months of adjuvant temozolomide. Maintenance vaccinations occurred at 1, 3, and 6 months and every 6 months thereafter.Results:ICT-107 was well tolerated, with no difference in adverse events between the treatment and control groups. The primary endpoint, median overall survival (OS), favored ICT-107 by 2.0 months in the intent-to-treat (ITT) population but was not statistically significant. Progression-free survival (PFS) in the ITT population was significantly increased in the ICT-107 cohort by 2.2 months (P = 0.011). The frequency of HLA-A2 primary tumor antigen expression was higher than that for HLA-A1 patients, and HLA-A2 patients had higher immune response (via Elispot). HLA-A2 patients achieved a meaningful therapeutic benefit with ICT-107, in both the MGMT methylated and unmethylated prespecified subgroups, whereas only HLA-A1 methylated patients had an OS benefit.Conclusions:PFS was significantly improved in ICT-107–treated patients with maintenance of QoL. Patients in the HLA-A2 subgroup showed increased ICT-107 activity clinically and immunologically.
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- 2023
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39. Figure S4 from In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The ϕ-Index
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Christos Davatzikos, Donald M. O'Rourke, Nadia Dahmane, Saima Rathore, Martin Rozycki, Maria Martinez-Lage, Jared Pisapia, Hamed Akbari, and Spyridon Bakas
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Leakage corrected rCBV distributions for each ROI of each subgroup (EGFRvIII+ and EGFRvIII-). We note although these rCBV results are consistent with those obtained via PHI, the separation between EGFRvIII+ and EGFRvIII- is notably weaker.
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- 2023
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40. Data from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy
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Andrew T. Parsa, Jeffrey N. Bruce, Anthony D'Ambrosio, Donald M. O'Rourke, John M. Abrahams, Ricardo J. Komotar, Michael E. Sughrue, Michael Lim, and Orin Bloch
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Purpose: Standard therapy for newly diagnosed glioblastoma (GBM) is surgical resection, followed by concurrent radiotherapy and temozolomide chemotherapy. In this phase II clinical trial, the addition of an autologous heat-shock protein vaccine to standard therapy was evaluated. Tumor-induced immunosuppression, mediated by expression of PD-L1 on tumor and circulating immune cells, may impact the efficacy of vaccination. Expression of PD-L1 on peripheral myeloid cells was evaluated for the first time as a predictor of survival.Experimental Design: In this single arm, phase II study, adult patients with GBM underwent surgical resection followed by standard radiation and chemotherapy. Autologous vaccine (Prophage) was generated from resected tumors and delivered in weekly vaccinations after completion of radiotherapy. The primary endpoint was overall survival.Results: Forty-six patients received the vaccine with a median overall survival of 23.8 months [95% confidence interval (CI), 19.8–30.2]. Median overall survival for patients with high PD-L1 expression on myeloid cells was 18.0 months (95% CI, 10.0–23.3) as compared with 44.7 months (95% CI, incalculable) for patients with low PD-L1 expression (hazard ratio 3.3; 95% CI, 1.4–8.6; P = 0.007). A multivariate proportional hazards model revealed MGMT methylation, Karnofsky performance status, and PD-L1 expression as the primary independent predictors of survival.Conclusions: Vaccination with autologous tumor-derived heat shock proteins may improve survival for GBM patients when combined with standard therapy and warrants further study. Systemic immunosuppression mediated by peripheral myeloid expression of PD-L1 is a recently identified factor that may significantly impact vaccine efficacy. Clin Cancer Res; 23(14); 3575–84. ©2017 AACR.
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- 2023
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41. Supplementary Table 1 from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy
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Andrew T. Parsa, Jeffrey N. Bruce, Anthony D'Ambrosio, Donald M. O'Rourke, John M. Abrahams, Ricardo J. Komotar, Michael E. Sughrue, Michael Lim, and Orin Bloch
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Criteria for determining first progression of GBM: modified from Response Assessment in Neuro-Oncology (RANO) criteria
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- 2023
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42. Data from Clinical Utility of Plasma Cell-Free DNA in Adult Patients with Newly Diagnosed Glioblastoma: A Pilot Prospective Study
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Erica L. Carpenter, Arati S. Desai, Steven Brem, Andrew J. Cucchiara, Donald M. O'Rourke, Zev A. Binder, Jennifer J.D. Morrissette, MacLean P. Nasrallah, Stephanie S. Yee, Theresa Christensen, Samantha Guiry, Timothy Prior, Jasmin Hussain, Whitney Sarchiapone, Scott Levy, Jeffrey B. Ware, Jacob E. Till, Jazmine J. Mays, S. Ali Nabavizadeh, and Stephen J. Bagley
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Purpose:The clinical utility of plasma cell-free DNA (cfDNA) has not been assessed prospectively in patients with glioblastoma (GBM). We aimed to determine the prognostic impact of plasma cfDNA in GBM, as well as its role as a surrogate of tumor burden and substrate for next-generation sequencing (NGS).Experimental Design:We conducted a prospective cohort study of 42 patients with newly diagnosed GBM. Plasma cfDNA was quantified at baseline prior to initial tumor resection and longitudinally during chemoradiotherapy. Plasma cfDNA was assessed for its association with progression-free survival (PFS) and overall survival (OS), correlated with radiographic tumor burden, and subjected to a targeted NGS panel.Results:Prior to initial surgery, GBM patients had higher plasma cfDNA concentration than age-matched healthy controls (mean 13.4 vs. 6.7 ng/mL, P < 0.001). Plasma cfDNA concentration was correlated with radiographic tumor burden on patients' first post-radiation magnetic resonance imaging scan (ρ = 0.77, P = 0.003) and tended to rise prior to or concurrently with radiographic tumor progression. Preoperative plasma cfDNA concentration above the mean (>13.4 ng/mL) was associated with inferior PFS (median 4.9 vs. 9.5 months, P = 0.038). Detection of ≥1 somatic mutation in plasma cfDNA occurred in 55% of patients and was associated with nonstatistically significant decreases in PFS (median 6.0 vs. 8.7 months, P = 0.093) and OS (median 5.5 vs. 9.2 months, P = 0.053).Conclusions:Plasma cfDNA may be an effective prognostic tool and surrogate of tumor burden in newly diagnosed GBM. Detection of somatic alterations in plasma is feasible when samples are obtained prior to initial surgical resection.
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- 2023
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43. Figure A3 from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
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John H. Sampson, Thomas A. Davis, Tibor Keler, Christopher D. Turner, Michael J. Yellin, Jennifer A. Green, Yi He, Laura Vitale, Scott Cruickshank, Maciej M. Mrugala, J. Paul Duic, Lynn S. Ashby, Rimas V. Lukas, Daniela A. Bota, Gordon Li, Louis B. Nabors, Karen L. Fink, David D. Tran, Donald M. O'Rourke, James J. Vredenburgh, Annick Desjardins, and David A. Reardon
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Figure A3 from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
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- 2023
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44. Supplementary Data from A Randomized Double-Blind Placebo-Controlled Phase II Trial of Dendritic Cell Vaccine ICT-107 in Newly Diagnosed Patients with Glioblastoma
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John S. Yu, Radleigh G. Santos, Clemencia Pinilla, Alona Muzikansky, Santosh Kesari, Edward Pan, Glenn J. Lesser, Michael Gruber, Lyndon Kim, Karen Fink, Donald M. O'Rourke, Renato LaRocca, James M. Markert, David M. Peereboom, Michael Glantz, Jay-Jiguang Zhu, William T. Curry, Joseph C. Landolfi, Robert D. Aiken, Surasak Phuphanich, Terri S. Armstrong, David A. Reardon, and Patrick Y. Wen
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Text
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- 2023
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45. Supplementary Data from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
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John H. Sampson, Thomas A. Davis, Tibor Keler, Christopher D. Turner, Michael J. Yellin, Jennifer A. Green, Yi He, Laura Vitale, Scott Cruickshank, Maciej M. Mrugala, J. Paul Duic, Lynn S. Ashby, Rimas V. Lukas, Daniela A. Bota, Gordon Li, Louis B. Nabors, Karen L. Fink, David D. Tran, Donald M. O'Rourke, James J. Vredenburgh, Annick Desjardins, and David A. Reardon
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Web Extra Material - 2 tables and 3 figures
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46. Supplementary Figure 1 from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy
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Andrew T. Parsa, Jeffrey N. Bruce, Anthony D'Ambrosio, Donald M. O'Rourke, John M. Abrahams, Ricardo J. Komotar, Michael E. Sughrue, Michael Lim, and Orin Bloch
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Trial Screening and Enrollment
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- 2023
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47. Data from Rindopepimut with Bevacizumab for Patients with Relapsed EGFRvIII-Expressing Glioblastoma (ReACT): Results of a Double-Blind Randomized Phase II Trial
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John H. Sampson, Thomas A. Davis, Tibor Keler, Christopher D. Turner, Michael J. Yellin, Jennifer A. Green, Yi He, Laura Vitale, Scott Cruickshank, Maciej M. Mrugala, J. Paul Duic, Lynn S. Ashby, Rimas V. Lukas, Daniela A. Bota, Gordon Li, Louis B. Nabors, Karen L. Fink, David D. Tran, Donald M. O'Rourke, James J. Vredenburgh, Annick Desjardins, and David A. Reardon
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Purpose:Rindopepimut is a vaccine targeting the tumor-specific EGF driver mutation, EGFRvIII. The ReACT study investigated whether the addition of rindopepimut to standard bevacizumab improved outcome for patients with relapsed, EGFRvIII-positive glioblastoma.Patients and Methods:In this double-blind, randomized, phase II study (NCT01498328) conducted at 26 hospitals in the United States, bevacizumab-naïve patients with recurrent EGFRvIII-positive glioblastoma were randomized to receive rindopepimut or a control injection of keyhole limpet hemocyanin, each concurrent with bevacizumab. The primary endpoint was 6-month progression-free survival (PFS6) by central review with a one-sided significance of 0.2.Results:Between May 2012 and 2014, 73 patients were randomized (36 rindopepimut, 37 control). Rindopepimut toxicity included transient, low-grade local reactions. As primary endpoint, PFS6 was 28% (10/36) for rindopepimut compared with 16% (6/37) for control (P = 0.12, one-sided). Secondary and exploratory endpoints also favored the rindopepimut group including a statistically significant survival advantage [HR, 0.53; 95% confidence interval (CI), 0.32–0.88; two-sided log-rank P = 0.01], a higher ORR [30% (9/30) vs. 18% (6/34; P = 0.38)], median duration of response [7.8 months (95% CI, 3.5–22.2) vs. 5.6 (95% CI, 3.7–7.4)], and ability to discontinue steroids for ≥6 months [33% (6/18) vs. 0% (0/19)]. Eighty percent of rindopepimut-treated patients achieved robust anti-EGFRvIII titers (≥1:12,800), which were associated with prolonged survival (HR = 0.17; 95% CI, 0.07–0.45; P < 0.0001).Conclusions:Our randomized trial supports the potential for targeted immunotherapy among patients with GBM, but the therapeutic benefit requires validation due to the small sample size and potential heterogeneity of bevacizumab response among recurrent patients with GBM.See related commentary by Wick and Wagener, p. 1535
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48. Data from In Vivo Detection of EGFRvIII in Glioblastoma via Perfusion Magnetic Resonance Imaging Signature Consistent with Deep Peritumoral Infiltration: The ϕ-Index
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Christos Davatzikos, Donald M. O'Rourke, Nadia Dahmane, Saima Rathore, Martin Rozycki, Maria Martinez-Lage, Jared Pisapia, Hamed Akbari, and Spyridon Bakas
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Purpose: The epidermal growth factor receptor variant III (EGFRvIII) mutation has been considered a driver mutation and therapeutic target in glioblastoma, the most common and aggressive brain cancer. Currently, detecting EGFRvIII requires postoperative tissue analyses, which are ex vivo and unable to capture the tumor's spatial heterogeneity. Considering the increasing evidence of in vivo imaging signatures capturing molecular characteristics of cancer, this study aims to detect EGFRvIII in primary glioblastoma noninvasively, using routine clinically acquired imaging.Experimental Design: We found peritumoral infiltration and vascularization patterns being related to EGFRvIII status. We therefore constructed a quantitative within-patient peritumoral heterogeneity index (PHI/ϕ-index), by contrasting perfusion patterns of immediate and distant peritumoral edema. Application of ϕ-index in preoperative perfusion scans of independent discovery (n = 64) and validation (n = 78) cohorts, revealed the generalizability of this EGFRvIII imaging signature.Results: Analysis in both cohorts demonstrated that the obtained signature is highly accurate (89.92%), specific (92.35%), and sensitive (83.77%), with significantly distinctive ability (P = 4.0033 × 10−10, AUC = 0.8869). Findings indicated a highly infiltrative-migratory phenotype for EGFRvIII+ tumors, which displayed similar perfusion patterns throughout peritumoral edema. Contrarily, EGFRvIII− tumors displayed perfusion dynamics consistent with peritumorally confined vascularization, suggesting potential benefit from extensive peritumoral resection/radiation.Conclusions: This EGFRvIII signature is potentially suitable for clinical translation, since obtained from analysis of clinically acquired images. Use of within-patient heterogeneity measures, rather than population-based associations, renders ϕ-index potentially resistant to inter-scanner variations. Overall, our findings enable noninvasive evaluation of EGFRvIII for patient selection for targeted therapy, stratification into clinical trials, personalized treatment planning, and potentially treatment-response evaluation. Clin Cancer Res; 23(16); 4724–34. ©2017 AACR.
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49. Supplementary Table 3 from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy
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Andrew T. Parsa, Jeffrey N. Bruce, Anthony D'Ambrosio, Donald M. O'Rourke, John M. Abrahams, Ricardo J. Komotar, Michael E. Sughrue, Michael Lim, and Orin Bloch
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Proportional Hazards Model of Overall Survival
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- 2023
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50. Supplementary Figure Legend from Autologous Heat Shock Protein Peptide Vaccination for Newly Diagnosed Glioblastoma: Impact of Peripheral PD-L1 Expression on Response to Therapy
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Andrew T. Parsa, Jeffrey N. Bruce, Anthony D'Ambrosio, Donald M. O'Rourke, John M. Abrahams, Ricardo J. Komotar, Michael E. Sughrue, Michael Lim, and Orin Bloch
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Figure Legend
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- 2023
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