4,342 results on '"MacIntyre, P."'
Search Results
2. Language Teacher Wellbeing: An Individual-Institutional Pact
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Tammy Gregersen and Peter MacIntyre
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Although positive psychology (PP) is characterized as a tripartite approach to human flourishing that considers emotions, traits, and institutions, to date the role of institutions has been relatively overlooked. This is particularly problematic when exploring language teacher wellbeing because a teacher's ability to thrive is also dependent upon the context in which they work. Combining the results of a web survey on teacher wellbeing with relevant concepts from PP on the collective responsibility of individuals and institutions, this study provides a podium from which teachers' voices can be heard. When asked for specific advice on positively confronting challenges (particularly stemming from the COVID-19 pandemic), teachers' recommendations coalesced around the four themes of doing your best: teaching practices, positive leadership, and positive attitudes and gratitude. The purpose of this study is to listen to teachers' voices and provide implications for making more positive institutions.
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- 2024
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3. Shared Ownership of an Engineering Success Centre to Support Students and Develop Leaders
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Osgood, Libby, MacIntyre, Rebecca, and Pollard-Feehan, Erin
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An Engineering Success Centre was formed with the long-term goals of providing targeted first-year support, increasing retention, and developing leaders. The novelty of the Centre is that the priorities and activities were defined by the students that were employed to run it in a shared leadership model. Student leaders were in various years of undergraduate and graduate engineering degrees, which provided multiple years for leadership opportunities and organizational memory. The priorities identified by the student leaders were to: (1) guide students through their time in engineering, (2) connect students with campus resources, (3) impact the overall experience for students in a positive way, and (4) assist students with educational needs such as tutoring, writing support, and CAD development. Between the drop-in hours and professional development programs, 145 students (55% of engineering students) interacted over 400 times in formal Centre activities throughout the year, and at least 77% of students engaged in online or asynchronous platforms. This paper was written by two of the student leaders and the faculty coordinator to document the motivations, successes, and challenges of the Centre in its inaugural year and promote shared ownership in academic support centres. Goals were derived, and a model was developed to map Centre activities, priorities, and goals to assess the success of the Centre.
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- 2023
4. Investigation and management of young-onset hypertension: British and Irish hypertension society position statement
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Kulkarni, Spoorthy, Faconti, Luca, Partridge, Sarah, Delles, Christian, Glover, Mark, Lewis, Philip, Gray, Asha, Hodson, Emma, Macintyre, Iain, Maniero, Carmen, McEniery, Carmel M., Sinha, Manish D., Walsh, Stephen B., and Wilkinson, Ian B.
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- 2024
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5. Persistence of left atrial thrombus in patients with hypertrophic cardiomyopathy and atrial fibrillation
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Burczak, Daniel R., Scott, Christopher G., Julakanti, Raghav R., Kara Balla, Abdalla, Swain, William H., Ismail, Khaled, Geske, Jeffrey B., Killu, Ammar M., Deshmukh, Abhishek J., MacIntyre, Ciorsti J., Ommen, Steve R., Nkomo, Vuyisile T., Gersh, Bernard J., Noseworthy, Peter A., and Siontis, Konstantinos C.
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- 2024
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6. Relation Extraction from News Articles (RENA): A Tool for Epidemic Surveillance
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Hong, Jaeff, Dung, Duong, Hutchinson, Danielle, Akhtar, Zubair, Chen, Rosalie, Dawson, Rebecca, Joshi, Aditya, Lim, Samsung, MacIntyre, C Raina, and Gurdasani, Deepti
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence - Abstract
Relation Extraction from News Articles (RENA) is a browser-based tool designed to extract key entities and their semantic relationships in English language news articles related to infectious diseases. Constructed using the React framework, this system presents users with an elegant and user-friendly interface. It enables users to input a news article and select from a choice of two models to generate a comprehensive list of relations within the provided text. As a result, RENA allows real-time parsing of news articles to extract key information for epidemic surveillance, contributing to EPIWATCH, an open-source intelligence-based epidemic warning system., Comment: Under review in AAAI 2024
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- 2023
7. Hydrodynamic Modeling of Stratification and Mixing in a Shallow, Tropical Floodplain Lake
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Zhou, Wencai, Melack, John M, MacIntyre, Sally, Barbosa, Pedro M, Amaral, Joao HF, and Cortés, Alicia
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Earth Sciences ,Atmospheric Sciences ,Affordable and Clean Energy ,Physical Geography and Environmental Geoscience ,Civil Engineering ,Environmental Engineering ,Hydrology ,Civil engineering ,Environmental engineering - Abstract
Abstract: Floodplain lakes are widespread and ecologically important throughout tropical river systems, however data are rare that describe how temporal variations in hydrological, meteorological and optical conditions moderate stratification and mixing in these shallow lakes. Using time series measurements of meteorology and water‐column temperatures from 17 several day campaigns spanning two hydrological years in a representative Amazon floodplain lake, we calculated surface energy fluxes and thermal stratification, and applied and evaluated a 3‐dimensional hydrodynamic model. The model successfully simulated diel cycles in thermal structure characterized by buoyancy frequency, depth of the actively mixing layer, and other terms associated with the surface energy budget. Diurnal heating with strong stratification and nocturnal mixing were common; despite considerable heat loss at night, the strong stratification during the day meant that mixing only infrequently extended to the bottom at night. Simulations indicated that the diurnal thermocline up and downwelled creating lake‐wide differences in near‐surface temperatures and mixing depths. Infrequent full mixing creates conditions conducive to anoxia in these shallow lakes given their warm temperatures.
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- 2024
8. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research
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Golob, Jonathan L, Oskotsky, Tomiko T, Tang, Alice S, Roldan, Alennie, Chung, Verena, Ha, Connie WY, Wong, Ronald J, Flynn, Kaitlin J, Parraga-Leo, Antonio, Wibrand, Camilla, Minot, Samuel S, Oskotsky, Boris, Andreoletti, Gaia, Kosti, Idit, Bletz, Julie, Nelson, Amber, Gao, Jifan, Wei, Zhoujingpeng, Chen, Guanhua, Tang, Zheng-Zheng, Novielli, Pierfrancesco, Romano, Donato, Pantaleo, Ester, Amoroso, Nicola, Monaco, Alfonso, Vacca, Mirco, De Angelis, Maria, Bellotti, Roberto, Tangaro, Sabina, Kuntzleman, Abigail, Bigcraft, Isaac, Techtmann, Stephen, Bae, Daehun, Kim, Eunyoung, Jeon, Jongbum, Joe, Soobok, Community, The Preterm Birth DREAM, Theis, Kevin R, Ng, Sherrianne, Lee, Yun S, Diaz-Gimeno, Patricia, Bennett, Phillip R, MacIntyre, David A, Stolovitzky, Gustavo, Lynch, Susan V, Albrecht, Jake, Gomez-Lopez, Nardhy, Romero, Roberto, Stevenson, David K, Aghaeepour, Nima, Tarca, Adi L, Costello, James C, and Sirota, Marina
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Paediatrics ,Biomedical and Clinical Sciences ,Infant Mortality ,Prevention ,Genetics ,Perinatal Period - Conditions Originating in Perinatal Period ,Pediatric ,Human Genome ,Preterm ,Low Birth Weight and Health of the Newborn ,Reproductive health and childbirth ,Good Health and Well Being ,Pregnancy ,Female ,Infant ,Newborn ,Humans ,Premature Birth ,Crowdsourcing ,Phylogeny ,Vagina ,Microbiota ,Preterm Birth DREAM Community ,16S harmonization ,DREAM challenge ,crowdsourced ,machine learning ,microbiome ,predictive modeling ,preterm birth ,vaginal microbiome ,Biomedical and clinical sciences - Abstract
Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB;
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- 2024
9. Patterns of patient-reported outcomes (PROs) in a diverse group of gynecologic cancer survivors
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Gerrity, Charlotte, Sinno, Abdulrahman, Natori, Akina, Sookdeo, Vandana, MacIntyre, Jessica, George, Sophia, Calfa, Carmen, Crane, Tracy E., Penedo, Frank J., and Schlumbrecht, Matthew
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- 2024
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10. Improved influenza vaccine responses after expression of multiple viral glycoproteins from a single mRNA
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Rebecca A. Leonard, Kaitlyn N. Burke, Rachel L. Spreng, Andrew N. Macintyre, Ying Tam, Mohamad-Gabriel Alameh, Drew Weissman, and Nicholas S. Heaton
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Science - Abstract
Abstract Influenza viruses cause substantial morbidity and mortality every year despite seasonal vaccination. mRNA-based vaccines have the potential to elicit more protective immune responses, but for maximal breadth and durability, it is desirable to deliver both the viral hemagglutinin and neuraminidase glycoproteins. Delivering multiple antigens individually, however, complicates manufacturing and increases cost, thus it would be beneficial to express both proteins from a single mRNA. Here, we develop an mRNA genetic configuration that allows the simultaneous expression of unmodified, full-length NA and HA proteins from a single open reading frame. We apply this approach to glycoproteins from contemporary influenza A and B viruses and, after vaccination, observe high levels of functional antibodies and protection from disease in female mouse and male ferret challenge models. This approach may further efforts to utilize mRNA technology to improve seasonal vaccine efficacy by efficiently delivering multiple viral antigens simultaneously and in their native state.
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- 2024
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11. An attention-based hybrid model for spatial and temporal sentiment analysis of COVID-19 related tweets in the contiguous United States
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Bingnan Li, Danielle Hutchinson, Samsung Lim, and Chandini Raina MacIntyre
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Sentiment analysis ,BiLSTM ,deep learning ,attention mechanism ,COVID-19 ,Mathematical geography. Cartography ,GA1-1776 ,Geodesy ,QB275-343 - Abstract
Understanding the sentiments of social media posts can help health authorities respond to disease outbreaks, through a proxy measure of fear, confidence, and community compliance. Sentiment analysis identifies a pattern of emotion through the written word and assigns a positive, neutral, or negative value to it. As of February 2023, there were 677.7 million confirmed cases of coronavirus disease (COVID-19) and more than 6.7 million confirmed deaths. In this paper, around 170,000 COVID-19-related tweets were collected between September 2020 and January 2021 in the contiguous United States. Data preprocessing and exploratory investigation were completed for analysis of the collected dataset. Further, a novel and unified architecture called attention-based one-dimensional convolution with bidirectional long short-term memory layers (CNN-BiLSTM-ATT) is proposed to classify people’s sentiments as positive, neutral, and negative based on COVID-19-related tweets. In the CNN-BiLSTM-ATT model, the CNN layer can extract the low-level semantic features from textual data, and the BiLSTM layer can extract both the previous and future contextual representations. The attention module can improve the information focus from the outputted layer of the BiLSTM. The proposed method can extract both the local phrase representations and the global feature of sentences. Numerical experiments were conducted on COVID-19-related tweets using the proposed method and other baseline models to compare their performances. Our experimental results demonstrate that the CNN-BiLSTM-ATT model achieves an average accuracy of 95.16% and a macro-average F1-score of 95.12%, which outperforms the baseline models.
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- 2024
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12. Glycomics of cervicovaginal fluid from women at risk of preterm birth reveals immuno-regulatory epitopes that are hallmarks of cancer and viral glycosylation
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Gang Wu, Paola Grassi, Belen Gimeno Molina, David A. MacIntyre, Lynne Sykes, Phillip R. Bennett, Anne Dell, and Stuart M. Haslam
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Medicine ,Science - Abstract
Abstract During pregnancy the immune system needs to maintain immune tolerance of the foetus while also responding to infection, which can cause premature activation of the inflammatory pathways leading to the onset of labour and preterm birth. The vaginal microbiome is an important modifier of preterm birth risk, with Lactobacillus dominance during pregnancy associated with term delivery while high microbial diversity is associated with an increased risk of preterm birth. Glycans on glycoproteins along the lower female reproductive tract are fundamental to microbiota-host interactions and the mediation of inflammatory responses. However, the specific glycan epitopes involved in these processes are not well understood. To address this, we conducted glycomic analyses of cervicovaginal fluid (CVF) from 36 pregnant women at high risk of preterm birth and 4 non-pregnant women. Our analysis of N- and O-glycans revealed a rich CVF glycome. While O-glycans were shown to be the main carriers of ABO blood group epitopes, the main features of N-glycans were the presence of abundant paucimannose and high mannose glycans, and a remarkable diversity of complex bi-, tri-, and tetra-antennary glycans decorated with fucose and sialic acid. We identified immuno-regulatory epitopes, such as Lewis antigens, and found that fucosylation was negatively correlated to pro-inflammatory factors, such as IL-1β, MMP-8, C3a and C5a, while glycans with only sialylated antennae were mainly positively correlated to those. Similarly, paucimannose glycans showed a positive correlation to pro-inflammatory factors. We revealed a high abundance of glycans which have previously been identified as hallmarks of cancer and viral glycosylation, such as Man8 and Man9 high mannose glycans. Although each pregnant woman had a unique glycomic profile, longitudinal studies showed that the main glycosylation features were consistent throughout pregnancy in women who delivered at term, whereas women who experienced extreme preterm birth exhibited sharp changes in the CVF glycome shortly before delivery. These findings shed light on the processes underlying the role of glycosylation in maintaining a healthy vaginal microbiome and associated host immune responses. In addition, these discoveries facilitate our understanding of the lower female reproductive tract which has broad implications for women’s health.
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- 2024
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13. Use of Open-Source Epidemic Intelligence for Infectious Disease Outbreaks, Ukraine, 2022
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Anjali Kannan, Rosalie Chen, Zubair Akhtar, Braidy Sutton, Ashley Quigley, Margaret J. Morris, and C. Raina MacIntyre
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artificial intelligence ,open source ,epidemics ,outbreaks ,Ukraine ,bacteria ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
Formal infectious disease surveillance in Ukraine has been disrupted by Russia’s 2022 invasion, leading to challenges with tracking and containing epidemics. To analyze the effects of the war on infectious disease epidemiology, we used open-source data from EPIWATCH, an artificial intelligence early-warning system. We analyzed patterns of infectious diseases and syndromes before (November 1, 2021–February 23, 2022) and during (February 24–July 31, 2022) the conflict. We compared case numbers for the most frequently reported diseases with numbers from formal sources and found increases in overall infectious disease reports and in case numbers of cholera, botulism, tuberculosis, HIV/AIDS, rabies, and salmonellosis during compared with before the invasion. During the conflict, although open-source intelligence captured case numbers for epidemics, such data (except for diphtheria) were unavailable/underestimated by formal surveillance. In the absence of formal surveillance during military conflicts, open-source data provide epidemic intelligence useful for infectious disease control.
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- 2024
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14. Estimation accuracy of bean bags as portion size estimation aids for amorphous foods
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Friedeburg Anna Maria Wenhold and Una Elizabeth MacIntyre
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dietary assessment ,portion size estimation ,portion size estimation aids ,accuracy ,amorphous foods ,bean bags ,Nutrition. Foods and food supply ,TX341-641 ,Nutritional diseases. Deficiency diseases ,RC620-627 - Abstract
Objective: A study was undertaken to explore the portion size estimation accuracy of bean bags as low-cost volumetric portion size estimation aids for amorphous foods.Designs: Three observational, cross-sectional and three experimental/quasi-experimental developmental evaluation sub-studies were carried out.Settings: Observational, cross-sectional: one retirement village and four schools. Experimental/quasi-experimental: one South African university.Participants: Observational, cross-sectional: elderly persons, adult women (school educators), schoolchildren. Experimental/quasi-experimental: university students. In total N = 541; > 3 800 observations.Variables measured: Using a standardised set of bean bags (test object; volume range: 60–625 ml), volumes of different amorphous foods (reference objects: actual foods or representations) in varying portion sizes had to be estimated. Accuracy (outcome measure) was perfect if volumes of test and reference object were identical. Acceptable estimation accuracy allowed for misestimation by one bean bag size. Test–retest reproducibility was also assessed.Analysis: Descriptive statistics (proportions perfect and acceptable accuracy).Results: Across the sub-studies, perfect accuracy ranged from 22–65% depending on participants, reference food and portion size. Irrespective thereof, acceptable accuracy was noted in > 70% of observations. Reproducibility varied (range: 28–67% agreement).Conclusions and implications: Perfect portion size estimation of amorphous foods remains challenging. When misestimation by 60–125 ml still serves the purpose of a dietary assessment, bean bags show promise for cost-effective food volume quantification, especially on group level in resource-limited settings.
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- 2024
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15. A Regenerative Decolonization Perspective on ESD from Latin America
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Thomas Macintyre, Daniele Tubino de Souza, and Arjen Evert Jan Wals
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This paper provides a Latin American perspective on ESD, with a focus on transformative and participatory learning in community contexts. With a long history of critical pedagogies, Latin America provides a fertile ground for exploring alternative forms of education as a means to address deep-rooted challenges in western traditional strands of education. We start by providing an overview of pertinent educational currents present in Latin America, then ground these perspectives in two case studies carried out by the authors -- one from Colombia, the other from Brazil -- which explore grassroots initiatives in community settings that utilise different forms of education and learning. We then propose an integrative model to foster alternative educational approaches that might lead to decolonial and regenerative praxis, finishing with a discussion on how Latin American-rooted regenerative decolonisation perspective and praxis can inform global ESD discourses.
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- 2024
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16. Willingness to Communicate in a Multilingual Context: Part One, a Time-Serial Study of Developmental Dynamics
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Alastair Henry, Cecilia Thorsen, and Peter D. MacIntyre
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In many contexts of multilingualism, language learners can initiate communication in the target language (TL), or a contact language (such as English). Patterns of use emerging from these choices affect TL development. They also vary between individuals. Willingness to communicate (WTC) needs to be investigated in ways that capture these variations. So far, WTC has not been studied in multilingual contexts, or using individual-level longitudinal designs. Employing a single-case, time-serial design and focused on a critical period of TL growth, this study explores WTC trajectories of adult learners of Swedish for whom the TL and English provide viable communication options in community interaction. Change point and moving window correlational analyses reveal the operation of mutually interacting influences that shape WTC and have system-level effects. With light shed on processes at the developmental timescale, findings are discussed in the context of language choice, co-evolution, and the trait--state dichotomy.
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- 2024
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17. Willingness to Communicate in a Multilingual Context: Part Two, Person-Context Dynamics
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Alastair Henry, Cecilia Thorsen, and Peter D. MacIntyre
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In many contexts of multilingualism, language learners can initiate communication in the target language (TL), or a contact language (such as English). Patterns of use emerging from these choices vary between individuals and affect TL development. Willingness to communicate (WTC) needs to be investigated in ways that capture these variations. So far, WTC has not been studied in multilingual contexts, or using individual-level designs. This case study explores intraindividual variability in the WTC propensities of adult learners of Swedish for whom the TL and English provide viable communication options in community interaction. Carried out over a period where TL skills began to develop, the purpose was to explore the process characteristics of changes in communication-initiation propensities. A person-context dynamics perspective was employed, and analyses of time-serial data were combined with analyses of concurrently generated interview data. Results reveal how changes in WTC could be gradual and nongradual, continuous and discontinuous.
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- 2024
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18. A Good Return on Investment? Cultural Identification through Learning Traditional Music and Language in Gaelic Nova Scotia
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Susan C. Baker, Heather Sparling, and Peter D. MacIntyre
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Language is often used to demonstrate group membership and to establish cultural identity. When the language is not readily available or is at risk, individuals tend to turn to other markers to develop their cultural identity. Using Leximancer for thematic and conceptual analyses of interviews with ten accomplished musicians in Nova Scotia, Canada, we argue that the commitment to learning music and dance may act as a channel to learning Scottish Gaelic, a threatened local heritage language. Drawing on Norton's construct of investment in language learning, we consider the extent to which participants commit to learning the language and the music/dance for their identification to the Gaelic culture. Given that Gaelic music and dance traditions remain healthy, even as the language is declining, the results of our research have significant implications for language revitalisation efforts.
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- 2024
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19. A Tartan Weave: Connecting the Experience of Flow in Traditional Music and Gaelic Language in Pursuit of Heritage Language Survival
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Heather Sparling and Peter MacIntyre
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Gaelic is an endangered language, but the traditional music associated with it thrives. Among individuals committed to learning Gaelic as a heritage language who also engage in traditional music-making, intense experiences shape the connection between language and music. The present study examines the connection between intensely motivating 'flow' experiences in music and language using qualitative data. In this context, flow is defined both at the individual level, consistent with much of the literature, but also at the group level which contributes a more nuanced, group-oriented conceptualisation of flow experiences. Data come from a sample of 54 participants recruited via social media and associated with traditional music and Gaelic language. The results show the depth of connection to traditional music developed over years that appears to feed into a motivation for language learning. The concept of group flow is prevalent in the descriptions, even though it was not measured directly. Group flow offers a nuanced lens through which to view how the connection between music and language developed in a context where language revitalisation is taking place.
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- 2024
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20. Commutative unital rings elementarily equivalent to prescribed product rings
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D'Aquino, Paola and Macintyre, Angus
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Mathematics - Logic - Abstract
The classical work of Feferman Vaught gives a powerful, constructive analysis of definability in (generalized) product structures, and certain associated enriched Boolean structures. %structures in terms of definability in the component structures. Here, by closely related methods, but in the special setting of commutative unital rings, we obtain a kind of converse allowing us to determine in interesting cases, when a commutative unital R is elementarily equivalent to a nontrivial product of a family of commutative unital rings R_i. We use this in the model theoretic analysis of residue rings of models of Peano Arithmetic.
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- 2023
21. Improved influenza vaccine responses after expression of multiple viral glycoproteins from a single mRNA
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Leonard, Rebecca A., Burke, Kaitlyn N., Spreng, Rachel L., Macintyre, Andrew N., Tam, Ying, Alameh, Mohamad-Gabriel, Weissman, Drew, and Heaton, Nicholas S.
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- 2024
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22. Glycomics of cervicovaginal fluid from women at risk of preterm birth reveals immuno-regulatory epitopes that are hallmarks of cancer and viral glycosylation
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Wu, Gang, Grassi, Paola, Molina, Belen Gimeno, MacIntyre, David A., Sykes, Lynne, Bennett, Phillip R., Dell, Anne, and Haslam, Stuart M.
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- 2024
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23. Microbial signatures and continuum in endometrial cancer and benign patients
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Semertzidou, Anita, Whelan, Eilbhe, Smith, Ann, Ng, Sherrianne, Roberts, Lauren, Brosens, Jan J., Marchesi, Julian R., Bennett, Phillip R., MacIntyre, David A., and Kyrgiou, Maria
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- 2024
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24. Impact of vaccine coverage and disruption to health services on COVID-19 in Ukraine
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Costantino, Valentina and MacIntyre, Chandini R.
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- 2024
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25. Predicting vaccine effectiveness for mpox
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Berry, Matthew T., Khan, Shanchita R., Schlub, Timothy E., Notaras, Adriana, Kunasekaran, Mohana, Grulich, Andrew E., MacIntyre, C. Raina, Davenport, Miles P., and Khoury, David S.
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- 2024
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26. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus
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Lin, Gu-Lung, Drysdale, Simon B., Snape, Matthew D., O’Connor, Daniel, Brown, Anthony, MacIntyre-Cockett, George, Mellado-Gomez, Esther, de Cesare, Mariateresa, Ansari, M. Azim, Bonsall, David, Bray, James E., Jolley, Keith A., Bowden, Rory, Aerssens, Jeroen, Bont, Louis, Openshaw, Peter J. M., Martinon-Torres, Federico, Nair, Harish, Golubchik, Tanya, and Pollard, Andrew J.
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- 2024
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27. scAbsolute: measuring single-cell ploidy and replication status
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Schneider, Michael P., Cullen, Amy E., Pangonyte, Justina, Skelton, Jason, Major, Harvey, Van Oudenhove, Elke, Garcia, Maria J., Chaves Urbano, Blas, Piskorz, Anna M., Brenton, James D., Macintyre, Geoff, and Markowetz, Florian
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- 2024
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28. Assessing the effects of population-level political, economic and social exposures, interventions and policies on inclusive economy outcomes for health equity in high-income countries: a systematic review of reviews
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Macintyre, Anna K., Shipton, Deborah, Sarica, Shifa, Scobie, Graeme, Craig, Neil, and McCartney, Gerry
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- 2024
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29. Effectiveness of vaccination, travel load, and facemask use control strategies for controlling COVID Delta variant: the case of Sydney Metropolitan Area
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Tabasi, Maliheh, Najmi, Ali, Miller, Eric J., MacIntyre, C. Raina, and Rashidi, Taha H.
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- 2024
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30. Emotion Controllability Beliefs and Young People’s Anxiety and Depression Symptoms: A Systematic Review
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Somerville, Matthew P., MacIntyre, Helen, Harrison, Amy, and Mauss, Iris B.
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- 2024
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31. Investigating image-based fallow weed detection performance on Raphanus sativus and Avena sativa at speeds up to 30 km h$^{-1}$
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Coleman, Guy R. Y., Macintyre, Angus, Walsh, Michael J., and Salter, William T.
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Computer Science - Computer Vision and Pattern Recognition ,C.3 ,I.4.8 ,J.3 - Abstract
Site-specific weed control (SSWC) can provide considerable reductions in weed control costs and herbicide usage. Despite the promise of machine vision for SSWC systems and the importance of ground speed in weed control efficacy, there has been little investigation of the role of ground speed and camera characteristics on weed detection performance. Here, we compare the performance of four camera-software combinations using the open-source OpenWeedLocator platform - (1) default settings on a Raspberry Pi HQ camera, (2) optimised software settings on a HQ camera, (3) optimised software settings on the Raspberry Pi v2 camera, and (4) a global shutter Arducam AR0234 camera - at speeds ranging from 5 km h$^{-1}$ to 30 km h$^{-1}$. A combined excess green (ExG) and hue, saturation, value (HSV) thresholding algorithm was used for testing under fallow conditions using tillage radish (Raphanus sativus) and forage oats (Avena sativa) as representative broadleaf and grass weeds, respectively. ARD demonstrated the highest recall among camera systems, with up to 95.7% of weeds detected at 5 km h$^{-1}$ and 85.7% at 30 km h$^{-1}$. HQ1 and V2 cameras had the lowest recall of 31.1% and 26.0% at 30 km h$^{-1}$, respectively. All cameras experienced a decrease in recall as speed increased. The highest rate of decrease was observed for HQ1 with 1.12% and 0.90% reductions in recall for every km h$^{-1}$ increase in speed for tillage radish and forage oats, respectively. Detection of the grassy forage oats was worse (P<0.05) than the broadleaved tillage radish for all cameras. Despite the variations in recall, HQ1, HQ2, and V2 maintained near-perfect precision at all tested speeds. The variable effect of ground speed and camera system on detection performance of grass and broadleaf weeds, indicates that careful hardware and software considerations must be made when developing SSWC systems., Comment: 15 pages, 9 figures, 3 tables
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- 2023
32. Peroxisomal cholesterol metabolism regulates yap-signaling, which maintains intestinal epithelial barrier function and is altered in Crohn’s disease
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Marinella Pinelli, Stephanie Makdissi, Michal Scur, Brendon D. Parsons, Kristi Baker, Anthony Otley, Brad MacIntyre, Huong D. Nguyen, Peter K. Kim, Andrew W. Stadnyk, and Francesca Di Cara
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Cytology ,QH573-671 - Abstract
Abstract Intestinal epithelial cells line the luminal surface to establish the intestinal barrier, where the cells play essential roles in the digestion of food, absorption of nutrients and water, protection from microbial infections, and maintaining symbiotic interactions with the commensal microbial populations. Maintaining and coordinating all these functions requires tight regulatory signaling, which is essential for intestinal homeostasis and organismal health. Dysfunction of intestinal epithelial cells, indeed, is linked to gastrointestinal disorders such as irritable bowel syndrome, inflammatory bowel disease, and gluten-related enteropathies. Emerging evidence suggests that peroxisome metabolic functions are crucial in maintaining intestinal epithelial cell functions and intestinal epithelium regeneration and, therefore, homeostasis. Here, we investigated the molecular mechanisms by which peroxisome metabolism impacts enteric health using the fruit fly Drosophila melanogaster and murine model organisms and clinical samples. We show that peroxisomes control cellular cholesterol, which in turn regulates the conserved yes-associated protein-signaling and contributes to intestinal epithelial structure and epithelial barrier function. Moreover, analysis of intestinal organoid cultures derived from biopsies of patients affected by Crohn’s Disease revealed that the dysregulation of peroxisome number, excessive cellular cholesterol, and inhibition of Yap-signaling are markers of disease and could be novel diagnostic and/or therapeutic targets for treating Crohn’s Disease. Our studies provided mechanistic insights on peroxisomal signaling in intestinal epithelial cell functions and identified cholesterol as a novel metabolic regulator of yes-associated protein-signaling in tissue homeostasis.
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- 2024
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33. Microbial signatures and continuum in endometrial cancer and benign patients
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Anita Semertzidou, Eilbhe Whelan, Ann Smith, Sherrianne Ng, Lauren Roberts, Jan J. Brosens, Julian R. Marchesi, Phillip R. Bennett, David A. MacIntyre, and Maria Kyrgiou
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Microbiome ,Female genital tract ,Endometrial cancer ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Endometrial cancer is a multifactorial disease with inflammatory, metabolic and potentially microbial cues involved in disease pathogenesis. The endometrial cancer microbiome has been poorly characterised so far and studies have often overestimated bacterial biomass due to lack of integration of appropriate contamination controls. There is also a scarcity of evidence on the functionality of microbial microenvironments in endometrial cancer. This work addresses that knowledge gap by interrogating the genuine, contamination-free microbial signatures in the female genital tract and rectum of women with endometrial cancer and the mechanistic role of microbiome on carcinogenic processes. Results Here we sampled different regions of the reproductive tract (vagina, cervix, endometrium, fallopian tubes and ovaries) and rectum of 61 patients (37 endometrial cancer; 24 benign controls). We performed 16S rRNA gene sequencing of the V1–V2 hypervariable regions and qPCR of the 16S rRNA gene to qualitatively and quantitatively assess microbial communities and used 3D benign and endometrial cancer organoids to evaluate the effect of microbial products of L. crispatus, which was found depleted in endometrial cancer patients following primary analysis, on endometrial cell proliferation and inflammation. We found that the upper genital tract of a subset of women with and without endometrial cancer harbour microbiota quantitatively and compositionally distinguishable from background contaminants. Endometrial cancer was associated with reduced cervicovaginal and rectal bacterial load together with depletion of Lactobacillus species relative abundance, including L. crispatus, increased bacterial diversity and enrichment of Porphyromonas, Prevotella, Peptoniphilus and Anaerococcus in the lower genital tract and endometrium. Treatment of benign and malignant endometrial organoids with L. crispatus conditioned media exerted an anti-proliferative effect at high concentrations but had minimal impact on cytokine and chemokine profiles. Conclusions Our findings provide evidence that the upper female reproductive tract of some women contains detectable levels of bacteria, the composition of which is associated with endometrial cancer. Whether this is a cause or consequence of cancer pathophysiology and what is the functional significance of this finding remain to be elucidated to guide future screening tools and microbiome-based therapeutics . Video Abstract
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- 2024
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34. Impact of vaccine coverage and disruption to health services on COVID-19 in Ukraine
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Valentina Costantino and Chandini R. MacIntyre
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Coronavirus ,Modelling ,Infectious diseases ,Outbreak response ,Ukraine, Masks ,Vaccination ,Medicine ,Science - Abstract
Abstract COVID-19 surveillance in Ukraine ceased after the Russian invasion of the country in 2022, on a background of low vaccination rates of 34.5% for two doses at this time. We conducted a modelling study to estimate the epidemic trajectory of SARS-COV-2 in Ukraine after the start of the war. We use a COVID-19 deterministic Susceptible-Exposed-Infected-Recovered (SEIR) model for Ukraine to estimate the impact of increased vaccination coverage and masking as public health interventions. We fit the model output to case notification data between 6 January and 25 February 2022, then we forecast the COVID-19 epidemic trajectory in different scenarios of mask use and vaccine coverage. In the best-case scenario, 69% of the Ukrainian population would have been infected in the first half of 2022. Increasing mask use from 50 to 80% reduces cases and deaths by 17% and 30% respectively, while increasing vaccination rates to 60% and 9.6% for two and three doses respectively results in a 3% reduction in cases and 28% in deaths. However, if vaccination is increased to a higher coverage of 80% with two doses and 12.8% with three, or mask effectiveness is reduced to 40%, increasing vaccination coverage is more effective. The loss of health services, displacement, and destruction of infrastructure will amplify the risk of COVID-19 in Ukraine and make vaccine programs less feasible. Masks do not need the health infrastructure or cold-chain logistics required for vaccines and are more feasible for rapid epidemic control during war. However, increasing vaccine coverage will save more lives. Vaccination of refugees who have fled to other countries can be more feasibly achieved.
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- 2024
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35. Oxygen depletion and sediment respiration in ice‐covered arctic lakes
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Schwefel, Robert, MacIntyre, Sally, Cortés, Alicia, and Sadro, Steven
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Earth Sciences ,Environmental Sciences ,Biological Sciences ,Marine Biology & Hydrobiology - Abstract
Processes regulating the rate of oxygen depletion determine whether hypoxia occurs and the extent to which greenhouse gases accumulate in seasonally ice-covered lakes. Here, we investigate the oxygen budget of four arctic lakes using high-frequency data during two winters in three shallow lakes (9–13 m maximal depth) and four winters in 24 m deep main basin of Toolik Lake. Incubation experiments measured sediment metabolism. Volume-averaged oxygen depletion measured in situ was independent of water temperature and duration of the ice-covered period. Average rates were between 0.2 and 0.39 g O2 m−2 d−1 in the shallow lakes and between 0.03 and 0.14 g O2 m−2 d−1 in Toolik Lake, with higher rates in smaller lakes with their larger sediment area to volume ratio. Rates decreased to ~ 20%–50% of initial values in late winter in the shallow lakes but less or not at all in Toolik. The lack of a decline in Toolik Lake points to continued oxygen transport to the sediment–water interface where oxygen consumption occurs. In all lakes, lower in situ oxygen depletion than in incubation measurements points toward increasing anoxia in the lower water column depressing loss rates. In Toolik, oxygen loss during early winter was less in years with minimal snow cover. Penetrative convection occurred, which could mix downwards oxygen produced by photosynthesis or excluded during ice formation. Estimates of these terms exceeded photosynthesis measured in sediment incubations. Modeling under ice-oxygen dynamics requires consideration of optical properties and biological and transport processes that modify oxygen concentrations and distributions.
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- 2023
36. Sentinel responses of Arctic freshwater systems to climate: linkages, evidence, and a roadmap for future research
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Saros, Jasmine E, Arp, Christopher D, Bouchard, Frédéric, Comte, Jérôme, Couture, Raoul-Marie, Dean, Joshua F, Lafrenière, Melissa, MacIntyre, Sally, McGowan, Suzanne, Rautio, Milla, Prater, Clay, Tank, Suzanne E, Walvoord, Michelle, Wickland, Kimberly P, Antoniades, Dermot, Ayala-Borda, Paola, Canario, Joao, Drake, Travis W, Folhas, Diogo, Hazuková, Václava, Kivilä, Henriikka, Klanten, Yohanna, Lamoureux, Scott, Laurion, Isabelle, Pilla, Rachel M, Vonk, Jorien E, Zolkos, Scott, and Vincent, Warwick F
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Climate Action ,Climate change ,climate indicators ,Arctic lakes ,Arctic rivers ,polar limnology - Abstract
While the sentinel nature of freshwater systems is now well recognized, widespread integration of freshwater processes and patterns into our understanding of broader climate-driven Arctic terrestrial ecosystem change has been slow. We review the current understanding across Arctic freshwater systems of key sentinel responses to climate, which are attributes of these systems with demonstrated and sensitive responses to climate forcing. These include ice regimes, temperature and thermal structure, river baseflow, lake area and water level, permafrost-derived dissolved ions and nutrients, carbon mobilization (dissolved organic carbon, greenhouse gases, and radiocarbon), dissolved oxygen concentrations, lake trophic state, various aquatic organisms and their traits, and invasive species. For each sentinel, our objectives are to clarify linkages to climate, describe key insights already gained, and provide suggestions for future research based on current knowledge gaps. We suggest that tracking key responses in Arctic freshwater systems will expand understanding of the breadth and depth of climate-driven Arctic ecosystem changes, provide early indicators of looming, broader changes across the landscape, and improve protection of freshwater biodiversity and resources.
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- 2023
37. Higher Apparent Gas Transfer Velocities for CO2 Compared to CH4 in Small Lakes.
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Pajala, Gustav, Rudberg, David, Gålfalk, Magnus, Melack, John Michael, Macintyre, Sally, Karlsson, Jan, Sawakuchi, Henrique Oliveira, Schenk, Jonathan, Sieczko, Anna, Sundgren, Ingrid, Duc, Nguyen Thanh, and Bastviken, David
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Carbon Dioxide ,Gases ,Water ,Methane ,Lakes ,Greenhouse Gases ,carbon dioxide ,gas transfer ,greenhouse gas ,lake ,methane ,piston velocity ,Climate Action ,gastransfer ,Environmental Sciences - Abstract
Large greenhouse gas emissions occur via the release of carbon dioxide (CO2) and methane (CH4) from the surface layer of lakes. Such emissions are modeled from the air-water gas concentration gradient and the gas transfer velocity (k). The links between k and the physical properties of the gas and water have led to the development of methods to convert k between gases through Schmidt number normalization. However, recent observations have found that such normalization of apparent k estimates from field measurements can yield different results for CH4 and CO2. We estimated k for CO2 and CH4 from measurements of concentration gradients and fluxes in four contrasting lakes and found consistently higher (on an average 1.7 times) normalized apparent k values for CO2 than CH4. From these results, we infer that several gas-specific factors, including chemical and biological processes within the water surface microlayer, can influence apparent k estimates. We highlight the importance of accurately measuring relevant air-water gas concentration gradients and considering gas-specific processes when estimating k.
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- 2023
38. Dietary amino acids, macronutrients, vaginal birth, and breastfeeding are associated with the vaginal microbiome in early pregnancy
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Gillian A. Corbett, Rebecca Moore, Conor Feehily, Sarah Louise Killeen, Eileen O'Brien, Douwe Van Sinderen, Elizabeth Matthews, Roisin O'Flaherty, Pauline M. Rudd, Radka Saldova, Calum J. Walsh, Elaine M. Lawton, David A. MacIntyre, Siobhan Corcoran, Paul D. Cotter, and Fionnuala M. McAuliffe
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vagina ,microbiota ,pregnancy ,metagenomic sequencing ,beta diversity ,alpha diversity ,Microbiology ,QR1-502 - Abstract
ABSTRACT The vaginal microbiome is a key player in the etiology of spontaneous preterm birth. This study aimed to illustrate maternal environmental factors associated with vaginal microbiota composition and function in pregnancy. Women in healthy pregnancy had vaginal microbial sampling from the posterior vaginal fornix performed at 16 weeks gestation. After shotgun metagenomic sequencing, heatmaps of relative abundance data were generated. Community state type (CST) was assigned, and alpha diversity was calculated. Demography, obstetric history, well-being, exercise, and diet using food frequency questionnaires were collected and compared against microbial parameters. A total of 119 pregnant participants had vaginal metagenomic sequencing performed. Factors with strongest association with beta diversity were dietary lysine (adj-R2 0.113, P = 0.002), valine (adj-R2 0.096, P = 0.004), leucine (adj-R2 0.086, P = 0.003), and phenylalanine (adj-R2 0.085, P = 0.005, Fig. 2D). Previous vaginal delivery and breastfeeding were associated with vaginal beta diversity (adj-R2 0.048, P = 0.003; adj-R2 0.045, P = 0.004), accounting for 8.5% of taxonomy variation on redundancy analysis. Dietary fat, starch, and maltose were positively correlated with alpha diversity (fat +0.002 SD/g, P = 0.025; starch +0.002 SD/g, P = 0.043; maltose +0.440 SD/g, P = 0.013), particularly in secretor-positive women. Functional signature was associated with CST, maternal smoking, and dietary phenylalanine, accounting for 8.9%–11% of the variation in vaginal microbiome functional signature. Dietary amino acids, previous vaginal delivery, and breastfeeding history were associated with vaginal beta diversity. Functional signature of the vaginal microbiome differed with community state type, smoking, dietary phenylalanine, and vitamin K. Increased alpha diversity correlated with dietary fat and starch. These data provide a novel snapshot into the associations between maternal environment, nutrition, and the vaginal microbiome.IMPORTANCEThis secondary analysis of the MicrobeMom randomized controlled trial reveals that dietary amino acids, macronutrients, previous vaginal birth, and breastfeeding have the strongest associations with vaginal taxonomy in early pregnancy. Function of the vaginal niche is associated mainly by species composition, but smoking, vitamin K, and phenylalanine also play a role. These associations provide an intriguing and novel insight into the association between host factors and diet on the vaginal microbiome in pregnancy and highlight the need for further investigation into the complex interactions between the diet, human gut, and vaginal microbiome.
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- 2024
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39. Attitudes and Behaviours Regarding COVID‐19 Mitigation Strategies in Australians With an Underlying Health Condition: A Cross‐Sectional Study
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Sze‐Ee Soh, Darshini Ayton, Amelia Bevins, Helen Skouteris, Mallory Trent, and Raina MacIntyre
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attitudes ,Australia ,behaviours ,COVID‐19 ,health condition ,mitigation strategies ,Medicine (General) ,R5-920 ,Public aspects of medicine ,RA1-1270 - Abstract
ABSTRACT Background Public health strategies have focused on preventing and slowing the transmission of COVID‐19 by promoting the uptake of mitigation strategies. However, little is known about the uptake of these strategies in the presence of underlying health conditions. Objectives To describe the attitudes and behaviours of a sample of Australians towards COVID‐19 mitigation strategies, and determine if uptake of these strategies differed across different health conditions. Design Cross‐sectional study. Setting and Participants National survey of Australian residents over 18 years. Main Outcome Measures A purpose‐built survey was used to collect participants' attitudes and behaviours towards COVID‐19 mitigation strategies. Results Over half (53%) of the 2867 participants (99% completion rate) reported having one or more comorbidities. The most commonly self‐reported health condition was cardiometabolic conditions (28%). Most participants disagreed that masks were no longer needed (74%) and wanted the 5‐day isolation mandate (66%). More than one‐third would like masks to be mandated for indoor spaces (38%) and 25% avoided going to hospitals. Participants with allergies (OR 1.37; 95% CI 1.14, 1.65), cardiometabolic (OR 1.49; 95% CI 1.23, 1.79), respiratory (OR 1.32; 95% CI 1.07, 1.62) and neurological (OR 1.62; 95% CI 1.12, 2.32) conditions were more likely to avoid using public transport compared to those without. In contrast, participants with underlying mental health conditions were less likely to use N95/P2 facemasks in public spaces (OR 0.46; 95% CI 0.25, 0.87) compared to those without. Conclusions A substantial proportion of Australians continued to adopt COVID‐19 mitigation measures or expressed a desire for more mitigations, including mandatory isolation for COVID‐19, despite the lack of mandates. People with an underlying health condition who represent more than half of all adults appear to be more careful with mitigations to avoid COVID‐19. Patient or Public Contribution Members of the public were invited to participate in a soft launch of the survey between 4th and 5th January 2023 to test flow and functionality, and to allow the final wording of survey questions to be refined as required.
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- 2024
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40. Exploring longitudinal patterns of absences, exclusions and attainment in secondary schools in Scotland
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Morag Treanor, Patricio Troncoso, Lee Williamson, and Cecilia Macintyre
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Demography. Population. Vital events ,HB848-3697 - Abstract
Objective and Approach We seek to understand the impacts that absences and exclusions have on educational outcomes in secondary school pupils in Scotland. We adopt a Multilevel Structural Equations Modelling approach to analyse data from the newly linked administrative database created under the “Children’s Lives and Outcomes” research strand of the Scottish Centre for Administrative Data Research (SCADR), which includes data from Education Analytical Services (Scottish Government) and Public Health Scotland (NHS) from the period between 2007-2019, and the 2001 and 2011 Census. Results While exclusions, absences and attainment are known to be associated with each other and with individual and structural factors, less is known about how these phenomena play out over time in the Scottish education system. Our analyses focus on a particular cohort of students followed up over their entire schooling period to understand how longitudinal patterns of school absences and exclusions, and other relevant individual and structural factors are interrelated over time. We show that variation across schools and local authorities in these outcomes is significant and substantial in Scotland. We also analyse the impact of these longitudinal patterns on attainment, with an emphasis on mental health wellbeing and familial socioeconomic circumstances. Conclusions and Implications By elucidating further these relationships and interrelationships, we expect our findings to be pertinent to policymakers and practitioners, contributing to inform strategies, policies and/or interventions to reduce the inequalities in exclusions, absences and attainment, ultimately helping to improve children and young people’s school experiences and outcomes.
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- 2024
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41. Towards realistic simulations of human cough: effect of droplet emission duration and spread angle
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Li, Mogeng, Chong, Kai Leong, Ng, Chong Shen, Bahl, Prateek, de Silva, Charitha M., Verzicco, Roberto, Doolan, Con, MacIntyre, C. Raina, and Lohse, Detlef
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Physics - Fluid Dynamics - Abstract
Human respiratory events, such as coughing and sneezing, play an important role in the host-to-host airborne transmission of diseases. Thus, there has been a substantial effort in understanding these processes: various analytical or numerical models have been developed to describe them, but their validity has not been fully assessed due to the difficulty of a direct comparison with real human exhalations. In this study, we report a unique comparison between datasets that have both detailed measurements of a real human cough using spirometer and particle tracking velocimetry, and direct numerical simulation at similar conditions. By examining the experimental data, we find that the injection velocity at the mouth is not uni-directional. Instead, the droplets are injected into various directions, with their trajectories forming a cone shape in space. Furthermore, we find that the period of droplet emissions is much shorter than that of the cough: experimental results indicate that the droplets with an initial diameter $\gtrsim 10\mu$m are emitted within the first 0.05 s, whereas the cough duration is closer to 1 s. These two features (the spread in the direction of injection velocity and the short duration of droplet emission) are incorporated into our direct numerical simulation, leading to an improved agreement with the experimental measurements. Thus, to have accurate representations of human expulsions in respiratory models, it is imperative to include parametrisation of these two features.
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- 2022
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42. Prevalence of persistent SARS-CoV-2 in a large community surveillance study
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Ghafari, Mahan, Hall, Matthew, Golubchik, Tanya, Ayoubkhani, Daniel, House, Thomas, MacIntyre-Cockett, George, Fryer, Helen R., Thomson, Laura, Nurtay, Anel, Kemp, Steven A., Ferretti, Luca, Buck, David, Green, Angie, Trebes, Amy, Piazza, Paolo, Lonie, Lorne J., Studley, Ruth, Rourke, Emma, Smith, Darren L., Bashton, Matthew, Nelson, Andrew, Crown, Matthew, McCann, Clare, Young, Gregory R., Santos, Rui Andre Nunes dos, Richards, Zack, Tariq, Mohammad Adnan, Cahuantzi, Roberto, Barrett, Jeff, Fraser, Christophe, Bonsall, David, Walker, Ann Sarah, and Lythgoe, Katrina
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- 2024
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43. Understanding Language Teacher Wellbeing: An ESM Study of Daily Stressors and Uplifts
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Gregersen, Tammy, Mercer, Sarah, MacIntyre, Peter, Talbot, Kyle, and Banga, Claire Ann
- Abstract
This study focuses on understanding language teachers' lived experiences of their stressors and positive uplifts from a holistic perspective covering their professional lives in school, their personal lives beyond, and the connection between the two. The aim was to explore the nature of teachers' experiences of stress and how they spilled over from work into home domains. We also were keen to understand the dynamics of their experiences of stress and how their perception of daily stressors was related to their overall sense of wellbeing as well as their life and chronic stressors. The data were collected via a specially created app, which collected survey data and experience sampling method (ESM) data from language teachers across the globe. Teachers' wellbeing was investigated using the PERMA Profiler (Butler & Kern, 2016), their personality using Goldberg's (1992) Big Five measurement tool, and a questionnaire on chronic stressors and stressful life events. From a larger sample (n = 47), a set of 6 case studies of teachers who scored highly for wellbeing and those who scored low on wellbeing was examined to explore in depth and across time, the relationships between overall wellbeing, chronic stressors and stressful life events, the experience of daily stressors, and perceptions of health. The findings point to the complexity of the relationships between stress, wellbeing, and health as well as the dynamism of stress and the relationships between stress experienced in the workplace and at home. The study has important implications for research in this area and reveals the merits of working with this innovative data collection tool.
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- 2023
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44. Access to Healthcare Among US Adult Refugees: A Systematic Qualitative Review
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Ho, Chi H., Denton, Andrea H., Blackstone, Sarah R., Saif, Nadia, MacIntyre, Kara, Ozkaynak, Mustafa, Valdez, Rupa S., and Hauck, Fern R.
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- 2023
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45. Predicting vaccine effectiveness for mpox
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Matthew T. Berry, Shanchita R. Khan, Timothy E. Schlub, Adriana Notaras, Mohana Kunasekaran, Andrew E. Grulich, C. Raina MacIntyre, Miles P. Davenport, and David S. Khoury
- Subjects
Science - Abstract
Abstract The Modified Vaccinia Ankara vaccine developed by Bavarian Nordic (MVA-BN) was widely deployed to prevent mpox during the 2022 global outbreak. This vaccine was initially approved for mpox based on its reported immunogenicity (from phase I/II trials) and effectiveness in animal models, rather than evidence of clinical efficacy. However, no validated correlate of protection after vaccination has been identified. Here we performed a systematic search and meta-analysis of the available data to test whether vaccinia-binding ELISA endpoint titer is predictive of vaccine effectiveness against mpox. We observe a significant correlation between vaccine effectiveness and vaccinia-binding antibody titers, consistent with the existing assumption that antibody levels may be a correlate of protection. Combining this data with analysis of antibody kinetics after vaccination, we predict the durability of protection after vaccination and the impact of dose spacing. We find that delaying the second dose of MVA-BN vaccination will provide more durable protection and may be optimal in an outbreak with limited vaccine stock. Although further work is required to validate this correlate, this study provides a quantitative evidence-based approach for using antibody measurements to predict the effectiveness of mpox vaccination.
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- 2024
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46. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus
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Gu-Lung Lin, Simon B. Drysdale, Matthew D. Snape, Daniel O’Connor, Anthony Brown, George MacIntyre-Cockett, Esther Mellado-Gomez, Mariateresa de Cesare, M. Azim Ansari, David Bonsall, James E. Bray, Keith A. Jolley, Rory Bowden, Jeroen Aerssens, Louis Bont, Peter J. M. Openshaw, Federico Martinon-Torres, Harish Nair, Tanya Golubchik, Andrew J. Pollard, and RESCEU Consortium
- Subjects
Science - Abstract
Abstract Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants 100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03–9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.
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- 2024
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47. scAbsolute: measuring single-cell ploidy and replication status
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Michael P. Schneider, Amy E. Cullen, Justina Pangonyte, Jason Skelton, Harvey Major, Elke Van Oudenhove, Maria J. Garcia, Blas Chaves Urbano, Anna M. Piskorz, James D. Brenton, Geoff Macintyre, and Florian Markowetz
- Subjects
Single-cell DNA sequencing ,Singe-cell genomics ,Ploidy estimation ,Whole-genome doubling ,Whole-genome duplication ,Cell cycle stage ,Biology (General) ,QH301-705.5 ,Genetics ,QH426-470 - Abstract
Abstract Cancer cells often exhibit DNA copy number aberrations and can vary widely in their ploidy. Correct estimation of the ploidy of single-cell genomes is paramount for downstream analysis. Based only on single-cell DNA sequencing information, scAbsolute achieves accurate and unbiased measurement of single-cell ploidy and replication status, including whole-genome duplications. We demonstrate scAbsolute’s capabilities using experimental cell multiplets, a FUCCI cell cycle expression system, and a benchmark against state-of-the-art methods. scAbsolute provides a robust foundation for single-cell DNA sequencing analysis across different technologies and has the potential to enable improvements in a number of downstream analyses.
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- 2024
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48. Public health management of pertussis in adults: Practical challenges and future strategies
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C Raina MacIntyre, Jaime Correia de Sousa, Ulrich Heininger, Peter Kardos, Andreas Konstantopoulos, Donald Middleton, Terry Nolan, Alberto Papi, Adrian Rendon, Albert Rizzo, Kim Sampson, Alessandro Sette, Elizabeth Sobczyk, Tina Tan, Catherine Weil-Olivier, Birgit Weinberger, Tom Wilkinson, and Carl Heinz Wirsing von König
- Subjects
Bordetella pertussis ,disease burden ,under-reporting ,Tdap vaccination ,adults ,comorbidities ,Immunologic diseases. Allergy ,RC581-607 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
A panel of 24 international experts met in July 2022 to discuss challenges associated with pertussis detection, monitoring, and vaccination in adults; conclusions from this meeting are presented. There has been a shift in the epidemiology of pertussis toward older children and adults. This shift has been attributed to the waning of infection- or vaccine-induced immunity, newer detection techniques causing detection bias, and possibly the replacement of whole-cell pertussis with acellular vaccines in high-income countries, which may lead to immunity waning more quickly. The burden of adult pertussis is still likely under-ascertained due to widespread under-recognition by healthcare professionals (HCPs), under-diagnosis, and under-reporting in this age group. Non-standardized testing guidance and varied case definitions have contributed to under-reporting. Key barriers to HCP engagement with the tetanus, diphtheria, and pertussis (Tdap) vaccine include low awareness, lack of time/funding, and lack of motivation due to low prioritization of Tdap.
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- 2024
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49. Management of patients with hypertension and chronic kidney disease referred to Hypertension Excellence Centres among 27 countries. On behalf of the European Society of Hypertension Working Group on Hypertension and the Kidney
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Jean-Michel Halimi, Pantelis Sarafidis, Michel Azizi, Grzegorz Bilo, Thilo Burkard, Michael Bursztyn, Miguel Camafort, Neil Chapman, Santina Cottone, Tine de Backer, Jaap Deinum, Philippe Delmotte, Maria Dorobantu, Michalis Doumas, Rainer Dusing, Béatrice Duly-Bouhanick, Jean-Pierre Fauvel, Pierre Fesler, Zbigniew Gaciong, Eugenia Gkaliagkousi, Daniel Gordin, Guido Grassi, Charalampos Grassos, Dominique Guerrot, Justine Huart, Raffaele Izzo, Fernando Jaén Águila, Zoltán Járai, Thomas Kahan, Ilkka Kantola, Eva Kociánová, FlorianP. Limbourg, Marilucy Lopez-Sublet, Francesca Mallamaci, Athanasios Manolis, Maria Marketou, Gert Mayer, Alberto Mazza, IainM. MacIntyre, Jean-Jacques Mourad, Maria Lorenza Muiesan, Edgar Nasr, Peter Nilsson, Anna Oliveras, Olivier Ormezzano, Vitor Paixão-Dias, Ioannis Papadakis, Dimitris Papadopoulos, Sabine Perl, Jorge Polónia, Roberto Pontremoli, Giacomo Pucci, Nicolás Roberto Robles, Sébastien Rubin, Luis Miguel Ruilope, Lars Christian Rump, Sahrai Saeed, Elias Sanidas, Riccardo Sarzani, Roland Schmieder, François Silhol, Sekib Sokolovic, Marit Solbu, Miroslav Soucek, George Stergiou, Isabella Sudano, Ramzi Tabbalat, Istemihan Tengiz, Helen Triantafyllidi, Konstontinos Tsioufis, Jan Václavík, Markus van der Giet, Patricia Van der Niepen, Franco Veglio, RetoM. Venzin, Margus Viigimaa, Thomas Weber, Jiri Widimsky, Gregoire Wuerzner, Parounak Zelveian, Pantelis Zebekakis, Stephan Lueders, Alexandre Persu, Reinhold Kreutz, and Liffert Vogt
- Subjects
Chronic kidney disease ,hypertension ,management ,RAS blockers ,hyperkalaemia ,SGLT2 inhibitors ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Objective Real-life management of patients with hypertension and chronic kidney disease (CKD) among European Society of Hypertension Excellence Centres (ESH-ECs) is unclear : we aimed to investigate it. Methods A survey was conducted in 2023. The questionnaire contained 64 questions asking ESH-ECs representatives to estimate how patients with CKD are managed. Results Overall, 88 ESH-ECS representatives from 27 countries participated. According to the responders, renin-angiotensin system (RAS) blockers, calcium-channel blockers and thiazides were often added when these medications were lacking in CKD patients, but physicians were more prone to initiate RAS blockers (90% [interquartile range: 70–95%]) than MRA (20% [10–30%]), SGLT2i (30% [20–50%]) or (GLP1-RA (10% [5–15%]). Despite treatment optimisation, 30% of responders indicated that hypertension remained uncontrolled (30% (15–40%) vs 18% [10%–25%]) in CKD and CKD patients, respectively). Hyperkalemia was the most frequent barrier to initiate RAS blockers, and dosage reduction was considered in 45% of responders when kalaemia was 5.5–5.9 mmol/L. Conclusions RAS blockers are initiated in most ESH-ECS in CKD patients, but MRA and SGLT2i initiations are less frequent. Hyperkalemia was the main barrier for initiation or adequate dosing of RAS blockade, and RAS blockers’ dosage reduction was the usual management.
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- 2024
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50. Understanding the impact of adult pertussis and current approaches to vaccination: A narrative review and expert panel recommendations
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Peter Kardos, Jaime Correia de Sousa, Ulrich Heininger, Andreas Konstantopoulos, C. Raina MacIntyre, Donald Middleton, Terry Nolan, Alberto Papi, Adrian Rendon, Albert Rizzo, Kim Sampson, Alessandro Sette, Elizabeth Sobczyk, Tina Tan, Catherine Weil-Olivier, Birgit Weinberger, Tom Wilkinson, and Carl Heinz Wirsing von König
- Subjects
Bordetella pertussis ,disease burden ,underreporting ,Tdap vaccination ,adults ,Immunologic diseases. Allergy ,RC581-607 ,Therapeutics. Pharmacology ,RM1-950 - Abstract
ABSTRACTPertussis has several notable consequences, causing economic burden, increased strain on healthcare facilities, and reductions in quality of life. Recent years have seen a trend toward an increase in pertussis cases affecting older children and adults. To boost immunity, and protect vulnerable populations, an enduring approach to vaccination has been proposed, but gaps remain in the evidence surrounding adult vaccination that are needed to inform such a policy. Gaps include: the true incidence of pertussis and its complications in adults; regional variations in disease recognition and reporting; and incidence of severe disease, hospitalizations, and deaths in older adults. Better data on the efficacy/effectiveness of pertussis vaccination in adults, duration of protection, and factors leading to poor vaccine uptake are needed. Addressing the critical evidence gaps will help highlight important areas of unmet need and justify the importance of adult pertussis vaccination to healthcare professionals, policymakers, and payers.
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- 2024
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