1,007 results on '"Clucas A"'
Search Results
2. Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children
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Baldi, Andrew, Braat, Sabine, Imrul Hasan, Mohammed, Bennett, Cavan, Barrios, Marilou, Jones, Naomi, Moir-Meyer, Gemma, Abdul Azeez, Imadh, Wilcox, Stephen, Saiful Alam Bhuiyan, Mohammad, Ataide, Ricardo, Clucas, Danielle, Harrison, Leonard C., Arifeen, Shams El, Bowden, Rory, Biggs, Beverley-Ann, Jex, Aaron, and Pasricha, Sant-Rayn
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- 2024
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3. The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment
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Kaczvinsky, Chloe, Levy, Hila, Preston, Stephen, Youngflesh, Casey, Clucas, Gemma, Lynch, Heather J., Hart, Tom, and Smith, Adrian L.
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- 2024
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4. What Should Be in an Assessment Professional's Toolkit? Perceptions of Need from the Field
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Christen, Nikki, Morrow, Jennifer Ann, Polychronopoulos, Gina B., and Leaderman, Emilie Clucas
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What professional development do assessment professionals need to succeed in higher education? To meet the rising demands in the field, assessment professionals seek ways to improve their skill sets. The current study utilized survey responses from over 200 higher education assessment professionals across the United States to assess the amount of training assessment professionals had when starting their position, the professional development they have sought since being in the position, and what training is still needed in the field. A thematic analysis of three open-ended survey questions revealed the eclectic backgrounds of assessment professionals, their preferred trainings while in the role, and the content and modalities requested for future professional development.
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- 2023
5. An additive manufacturing approach for fabrication of agarose hydrogel structures for protein sorption application
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Feng Cao, Hossein Najaf Zadeh, Klaudia Świacka, Jakub Maculewicz, Dan Bowles, Tim Huber, and Don Clucas
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Stencil additive manufacturing ,Agarose hydrogel ,Static protein binding ,Protein adsorption ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
Additive manufacturing of hydrogels is a rapidly evolving field due to the unique properties of hydrogels and their potential applications in various sectors. However, the low production rate and coarse resolution of current additive manufacturing methods limit their use. This article proposes a Stencil Additive Manufacturing (SAM) method to produce agarose hydrogel structures with horizontal and vertical resolutions of 500 and 80 μm using a novel SAM printer. Compared to peer methods, the shape fidelity of printed structures was improved and errors resulting from the Barus effect were minimized to 1.7 % and 7.1 %, depending on stencil patterns. Mechanical and thermal properties of agarose hydrogels were investigated by considering chemical crosslinking and agarose concentration, and the gelation and melting temperatures were determined. The analysis of hydrogel microstructures illustrated the change in porosity by regulating agarose concentration and the gelation rate. Static bovine serum albumin binding tests were performed using printed structures with varying concentrations and resolutions to explore the protein adsorption capacity. The results indicated that structure resolutions affect the adsorption capacity dramatically, which was increased from 100.44 to 144.13 mg/ml as resolutions were improved from 500 to 350 µm. Therefore, SAM-printing agarose hydrogels with periodic structures demonstrates potential in applications.
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- 2025
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6. A Snapshot of Needed Skills and Dispositions through the Lens of Assessment Professionals in Higher Education: Findings from a National Survey
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Morrow, Jennifer Ann, Polychronopoulos, Gina B., Leaderman, Emilie Clucas, and Christen, R. Nikki
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What skills and dispositions are most important for higher education assessment professionals to be successful in their work? Emerging professionals and their instructors must be cognizant of what skills and dispositions are necessary in order to be adequately prepared for this work. Utilizing a survey instrument that was developed based on recent research and validated by a panel of experts in higher education assessment, we surveyed 213 higher education assessment professionals from across the United States, assessing their perceptions on the importance of 92 skills and 52 dispositions. We analyzed responses by utilizing descriptive statistics for closed-ended items and thematic analysis of open-ended items. A discussion of the findings, including what skills and dispositions were deemed most important, as well as implications for future research and professional identity are discussed.
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- 2022
7. Seasonal variation in the ultrasonic vocal activity of Humboldt's flying squirrel (Glaucomys oregonensis)
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Travis A. Farwell and Barbara Clucas
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activity patterns ,communication ,function ,nocturnal ,small mammals ,ultrasonic vocalizations ,Ecology ,QH540-549.5 - Abstract
Abstract Most mammals rely on vocal communication to increase survival and reproductive success. While the functions of audible vocalizations have been well‐studied across mammal species, ultrasonic vocalizations in small mammals outside of bats are less understood. North American flying squirrel species (Glaucomys spp.), including the newly described Humboldt's flying squirrel (Glaucomys oregonensis), produce numerous call‐types that extend into the ultrasonic range. To investigate the potential function of ultrasonic call‐types in the Humboldt's flying squirrels, we used ultrasonic recorders to record squirrels in the wild across multiple seasons to determine if there are temporal and seasonal patterns in nightly vocal activity and rates of different call‐types. We recorded Humboldt's flying squirrels in two geographic locations ‐ Humboldt and San Bernardino counties—in California from 2018 to 2022 in the summer and winter across multiple study areas. We found that although seasonal weather conditions differ between locations, flying squirrels in Humboldt and San Bernardino had similar vocal activity patterns across nightly active periods between locations and between summer and winter. Nightly activity patterns of when the three main chirp‐like call‐types (arc chirps, tonal chirps, upsweeps) were given varied between seasons in both geographic locations, and these call‐types were given at greater rates in the summer in San Bernardino, but rates did not vary by season in Humboldt. Trills, the most structurally complex of the four main call‐types, were produced more in the summer than in winter, and also differed in their nightly activity patterns, in both geographic locations. Flying squirrels may use certain call‐types earlier or later in the nightly active period due to their potentially varying functions, and may produce more trills in the summer coinciding with the breeding season. Further understanding of the function of different call‐types can provide insight into social, foraging, and antipredator behavior of this nocturnal and elusive species.
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- 2024
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8. Black‐throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability
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Sara A. Kaiser, Lindsey E. Forg, Andrew N. Stillman, John F. Deitsch, T. Scott Sillett, and Gemma V. Clucas
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black‐throated blue warbler ,climate change ,diet flexibility ,fecal DNA metabarcoding ,phenology ,Ecology ,QH540-549.5 - Abstract
Abstract Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing “green” season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black‐throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a 2‐week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long‐legged cobweaver), and Philodromus rufus (white‐striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black‐throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate‐induced changes in insect communities with longer green seasons.
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- 2024
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9. Multiple methods of diet assessment reveal differences in Atlantic puffin diet between ages, breeding stages, and years
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William L. Kennerley, Gemma V. Clucas, and Donald E. Lyons
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Atlantic puffins ,Gulf of Maine ,DNA metabarcoding ,forage fish ,seabird diet ,optimal foraging theory (OFT) ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
IntroductionAtlantic puffin (Fratercula arctica, hereafter “puffin”) reproductive success in the Gulf of Maine (GoM) has declined following a recent oceanographic regime shift that has led to rapid warming and increasingly frequent marine heatwaves. Concurrent changes in both the regional forage fish community and puffin chick diets and provisioning rates suggest that inadequate prey resources may be driving this decline. Traditional, noninvasive methods of diet assessment, however, are unable to determine seabird diet at many age classes and breeding stages.MethodsTo determine what prey GoM puffins were feeding on during two years of marine heatwave conditions, we assessed puffin diet using two complementary methods: traditional, observational methods that utilize bill-load photography and emerging methods employing fecal DNA metabarcoding. We then examined the effect of methodology, age, breeding stage, and year on puffin diet composition. ResultsWe identified a strong correlation between the composition of chick diet as estimated through traditional and emerging methods, supporting the interpretation of DNA relative read abundance as a quantitative metric of diet composition. Both methods identified the same dominant prey groups yet metabarcoding identified a greater number of species and offered higher taxonomic resolution. Additionally, metabarcoding revealed adult puffin diet during the incubation period for the first time. Although puffin adults and chicks fed on many of the same prey types, adults consumed a greater variety of taxa and consumed more low quality prey types than they provisioned chicks.DiscussionFor both age classes, diet varied both between and within years, likely reflecting changes in the local forage fish community in response to environmental variability. Puffins exploited unusual abundances of typically-uncommon prey during these two years of marine heatwave conditions, yet low puffin productivity suggests the observed dietary plasticity was not fully able to compensate for apparent prey shortages. Continued refinement of molecular methods and the interpretation of the data they provide will enable better assessments of how seabirds of diverse ages and breeding stages are adapting to changing prey communities.
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- 2024
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10. Suing for grace : the early modern rhetoric of petition
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Veronese-Clucas, Leah and McCullough, Peter
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Poetry ,Ireland ,Epistolary poetry, English ,Prayer in literature ,Authors and patrons ,English poetry--Early modern, 1500-1700--History and criticism ,Patron and client ,Manuscripts ,Petitions ,Sonnets ,Early modern, 1500-1700 ,Meditation ,Verse satire ,Rhetoric ,Spenser, Edmund, 1552?-1599--Characters - Abstract
Early modern petition was both a secular and spiritual mode. It was a distinct epistolary form, and a type of prayer. Both secular and spiritual petition share the same function: a request. This dual meaning did not escape early modern writers, who frequently exploited it for rhetorical effect. The thesis explores how early modern writers elaborated on petitionary metaphor, and to what ends; it considers the transfer between the formal characteristics of petition and literary forms which drew upon these conventions. The thesis compromises four chapters. Chapter One provides an example of real petitionary rhetoric in action in two petitions written in 1567 by John Appleyard of Bracon Ash (1529 - c.1574) to the Privy Council. The following chapters explore how early modern writers both employed, and put pressure on, the petitionary strategies Appleyard exemplifies. Chapter Two examines how Edmund Spenser exploits the connection between political, martial, religious, and romantic petition in the Amoretti. Paying greater heed to the political connotations of petition, especially in relation to the Smerwick massacre of 1580, enables a greater understanding of the Amoretti's colonial context. Chapter Three compares how Donne uses religious metaphor to negotiate hierarchy and petition for access in his verse-letters with his petitions to God in the Devotions Upon Emergent Occasions. In the Devotions, in his withdrawal from the world in his illness, he seems to expose and dismantle the patronage process; yet simultaneously the text itself is embroiled in patronage negotiations. Chapter Four studies the 'mock petition' for the first time. Tracing the circulation of the Jacobean verse-libel 'The Commons Petition to St Eliza' reveals an emerging tradition of mock-petitions running from the Spanish Match crisis to the Long Parliament. They highlight the prevalence and increasingly dramatic political significance of petitions during this period, and concomitantly how petitions directly inspired poetry.
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- 2022
11. Acceleration of Eulerian multi-material methods on highly parallel compute architectures
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Clucas, Robert, Nikiforakis, Nikolaos, and Blakely, Philip
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GPU ,Parallel Computing ,Finite Volume ,Multi-Material ,Level-set ,Ghost Fluid Method - Abstract
The aims of this thesis are to develop a framework, which we have named Ripple, for the efficient execution of general purpose computations on modern heterogeneous compute architectures, with a focus on multiple graphics processing units (GPUs), as well as to develop algorithms for the numerical simulation of multiple interacting materials on modern, massively parallel, computer hardware. The Ripple framework is applicable to a wide range of HPC problems, allowing programmers to concentrate on algorithm design, while the framework takes the high- level domain application logic and executes it with near optimal performance across all devices, handling data layout transformations, inter-device communication, and optimal scheduling of the computation sub-stages. To demonstrate the effectiveness of the framework, we develop efficient parallel algorithms for numerical schemes commonly used in finite-volume methods, the solution of the Eikonal equation in a narrow band, the Ghost Fluid Method (GFM), and signed-distance function generation from multiple external geometry file types. Additionally, we present the main problems involved in scaling multi-material interaction simulations across multiple GPUs, and provide solutions to these problems which allow multi-material simulations to scale almost linearly with the number of compute devices, enabling the simulation of prob- lems on massive domains. We also demonstrate how the Ripple framework improves on existing work in terms of performance and simplification of software development, and enables solutions to execute across multiple GPUs. The algorithms which we present are built around well developed methods for multi-material interaction. These methods currently require vast computational resources for simulation on domains of modest size-even when well developed adaptive mesh refinement (AMR) tech- niques are used-since they do not make use of modern GPUs. The work presented in this thesis demonstrates the benefits of utilising modern hardware, particularly GPUs, reduces com- putational time. To ensure that our algorithms are correct, we validate the developed code on standard test cases used for finite-volume methods, as well as for multi-material interaction problems in two- and three-dimensions involving gas-gas, gas-liquid, and gas-liquid-solid inter- faces. We then apply the developed techniques to novel, unvalidated real-world use cases to demonstrate the utility of the techniques. We performed comparison simulations using multi-GPU unigrid with the developed frame- work and multi-core CPU adaptive mesh refinement using existing implementation which have demonstrated good performance. While these are different algorithms executed on different hardware, the cost of execution per hour using a single NVIDIA A100 GPU and a 48 core Intel Xeon Cascade Lake is effectively equivalent on current cloud providers, such as AWS. This com- parison demonstrates the improvements in both performance and cost which can be achieved by adapting current state of the art scientific computing algorithms which have been designed for CPU execution, for execution on the GPU. For two-dimensional multi-material simulations, our framework is able to achieve up to a 24x improvement in performance and 3x reduction in cost using 8 GPUs without adaptive mesh refinement compared with a 48 core CPU implemen- tation using adaptive mesh refinement. While multi-GPU unigrid and multi-core CPU AMR are different algorithms executed on different hardware, the cost of execution for The algorithms developed in this thesis allow strong scaling of 6.95x across 8 GPUs, and the Ripple framework makes performance gains of this magnitude accessible to other computationally demanding scientific domains, with minimal effort. For novel three-dimensional blast problems involving complex geometries, we show that our signed-distance function generation for such geometries using the Ripple framework can be performed multiple orders of magnitude faster on the GPU than on the CPU, and that the overall simulation can be performed up to 35x faster on a single GPU without AMR than when using a 32 core CPU implementation with AMR, at a reduction in cost of 22x.
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- 2022
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12. Ripple : Simplified Large-Scale Computation on Heterogeneous Architectures with Polymorphic Data Layout
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Clucas, Robert, Blakely, Philip, and Nikiforakis, Nikolaos
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Computer Science - Distributed, Parallel, and Cluster Computing ,Computer Science - Performance - Abstract
GPUs are now used for a wide range of problems within HPC. However, making efficient use of the computational power available with multiple GPUs is challenging. The main challenges in achieving good performance are memory layout, affecting memory bandwidth, effective use of the memory spaces with a GPU, inter-GPU communication, and synchronization. We address these problems with the Ripple library, which provides a unified view of the computational space across multiple dimensions and multiple GPUs, allows polymorphic data layout, and provides a simple graph interface to describe an algorithm from which inter-GPU data transfers can be optimally scheduled. We describe the abstractions provided by Ripple to allow complex computations to be described simply, and to execute efficiently across many GPUs with minimal overhead. We show performance results for a number of examples, from particle motion to finite-volume methods and the eikonal equation, as well as showing good strong and weak scaling results across multiple GPUs., Comment: Preprint submitted to the Journal of Parallel and Distributed Computing
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- 2021
13. Humanizing the Assessment Process: How the RARE Model Informs Best Practices
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Leaderman, Emilie Clucas and Polychronopoulos, Gina B.
- Abstract
This paper introduces a conceptual framework for overcoming common assessment challenges and supporting a positive assessment culture in higher education through fostering collaborative relationships with faculty and staff. By using a lens that integrates concepts from person-centered and solution-focused counseling, positive psychology, and motivational interviewing, assessment practitioners can better understand what guides the cultivation of inclusive and participatory relationships in assessment. The RARE model provides a common set of strategies for implementing principles of effective assessment practice, developed by two assessment professionals from universities located in different accrediting regions: WASC (Western Senior College and University Commission) and SACSCOC (Southern Association of Colleges and Schools Commission on Colleges). In calling attention to the influence of their practitioner training and background, this model also highlights the benefit of exploring the disciplinary diversity that exists within the assessment field. Through exploration of this reflexive, strengths-based approach to assessment practice, the authors contribute to the discourse about professional identity in higher education assessment.
- Published
- 2019
14. Multisite assessment of reproducibility in high‐content cell migration imaging data
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Jianjiang Hu, Xavier Serra‐Picamal, Gert‐Jan Bakker, Marleen Van Troys, Sabina Winograd‐Katz, Nil Ege, Xiaowei Gong, Yuliia Didan, Inna Grosheva, Omer Polansky, Karima Bakkali, Evelien Van Hamme, Merijn van Erp, Manon Vullings, Felix Weiss, Jarama Clucas, Anna M Dowbaj, Erik Sahai, Christophe Ampe, Benjamin Geiger, Peter Friedl, Matteo Bottai, and Staffan Strömblad
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batch effect removal ,cell migration ,high‐content imaging ,reproducibility ,variability ,Biology (General) ,QH301-705.5 ,Medicine (General) ,R5-920 - Abstract
Abstract High‐content image‐based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular relevance for high‐quality open‐access data sharing and meta‐analysis. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta‐analysis of results from live‐cell microscopy, have not been systematically investigated. Here, using high‐content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells, and time points. Significant technical variability occurred between laboratories and, to lesser extent, between persons, providing low value to direct meta‐analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image‐based datasets of perturbation experiments. Thus, reproducible quantitative high‐content cell image analysis of perturbation effects and meta‐analysis depend on standardized procedures combined with batch correction.
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- 2023
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15. Iron homeostasis governs erythroid phenotype in polycythemia vera
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Bennett, Cavan, Jackson, Victoria E., Pettikiriarachchi, Anne, Hayman, Thomas, Schaeper, Ute, Moir-Meyer, Gemma, Fielding, Katherine, Ataide, Ricardo, Clucas, Danielle, Baldi, Andrew, Garnham, Alexandra L., Li-Wai-Suen, Connie S. N., Loughran, Stephen J., Baxter, E. Joanna, Green, Anthony R., Alexander, Warren S., Bahlo, Melanie, Burbury, Kate, Ng, Ashley P., and Pasricha, Sant-Rayn
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- 2023
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16. Let's Connect: Maintaining and Strengthening Collaborative Relationships in a Remote Environment
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Polychronopoulos, Gina B. and Leaderman, Emilie Clucas
- Abstract
The RARE Model (Clucas Leaderman & Polychronopoulos, 2019) is a framework for nurturing collaborative relationships in assessment practice. The four components (R- relate, A- acknowledge, R- reflect, E- Empower), which are based in humanistic and postmodern counseling theories, outline interpersonal strategies to support and strengthen relationships with our faculty and staff colleagues. Previous experiences employing this approach with colleagues and clients were primarily in person. While reflecting upon our assessment practices throughout this time, we wondered: "how do these strategies translate to a virtual environment?" Throughout this experience, we have found ourselves prioritizing the strategies to Relate and Acknowledge; now more than ever, it is critical to focus on building and nurturing relationships with our assessment partners. A more detailed outline of adapted RARE Model strategies is forthcoming; here, we offer a few examples of what has worked so far, as we continue to navigate the remote environment.
- Published
- 2020
17. Correction: Tamadon et al. Flow-Based Anatomy of Bobbin Friction-Stirred Weld; AA6082-T6 Aluminium Plate and Analogue Plasticine Model. Appl. Mech. 2020, 1, 3–19
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Abbas Tamadon, Dirk J. Pons, and Don Clucas
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n/a ,Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
In the original publication [...]
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- 2024
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18. Ten Simple Rules for Open Health Research
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Bafeta, Aïda, Bobe, Jason, Clucas, Jon, Gonsalves, Pattie Pramila, Gruson-Daniel, Célya, Hudson, Kathy, Klein, Arno, Krishnakumar, Anirudh, McCollister-Slipp, Anna, Lindner, Ariel, Misevic, Dusan, Naslund, John, Nebeker, Camille, Nikolaidis, Aki, Pasquetto, Irene, Sanchez, Gabriela, Schapira, Matthieu, Scheininger, Tohar, Schoeller, Félix, Sólon, Anibal, and Taddei, François
- Published
- 2019
19. Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation
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Frugone, María José, Cole, Theresa L., López, María Eugenia, Clucas, Gemma, Matos-Maraví, Pável, Lois, Nicolás A., Pistorius, Pierre, Bonadonna, Francesco, Trathan, Phil, Polanowski, Andrea, Wienecke, Barbara, Raya-Rey, Andrea, Pütz, Klemens, Steinfurth, Antje, Bi, Ke, Wang-Claypool, Cynthia Y., Waters, Jonathan M., Bowie, Rauri C. K., Poulin, Elie, and Vianna, Juliana A.
- Published
- 2021
20. Insectivorous bat occupancy is mediated by drought and agricultural land use in a highly modified ecoregion
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Smith, Trinity N., Furnas, Brett J., Nelson, Misty D., Barton, Daniel C., and Clucas, Barbara
- Published
- 2021
21. Correction: Tamadon et al. Development of Metallographic Etchants for the Microstructure Evolution of A6082-T6 BFSW Welds. Metals 2017, 7, 423
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Abbas Tamadon, Dirk J. Pons, Kamil Sued, and Don Clucas
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n/a ,Mining engineering. Metallurgy ,TN1-997 - Abstract
In the original publication [...]
- Published
- 2024
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22. Correction: Tamadon, A.; et al. Internal Material Flow Layers in AA6082-T6 Butt-Joints during Bobbin Friction Stir Welding. Metals 2019, 9, 1059
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Abbas Tamadon, Dirk J. Pons, Don Clucas, and Kamil Sued
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n/a ,Mining engineering. Metallurgy ,TN1-997 - Abstract
In the original publication [...]
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- 2024
- Full Text
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23. An open resource for transdiagnostic research in pediatric mental health and learning disorders.
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Alexander, Lindsay, Escalera, Jasmine, Ai, Lei, Andreotti, Charissa, Febre, Karina, Mangone, Alexander, Vega-Potler, Natan, Langer, Nicolas, Alexander, Alexis, Kovacs, Meagan, Litke, Shannon, OHagan, Bridget, Andersen, Jennifer, Bronstein, Batya, Bui, Anastasia, Bushey, Marijayne, Butler, Henry, Castagna, Victoria, Camacho, Nicolas, Chan, Elisha, Citera, Danielle, Clucas, Jon, Cohen, Samantha, Dufek, Sarah, Eaves, Megan, Fradera, Brian, Gardner, Judith, Grant-Villegas, Natalie, Green, Gabriella, Gregory, Camille, Hart, Emily, Harris, Shana, Horton, Megan, Kahn, Danielle, Kabotyanski, Katherine, Karmel, Bernard, Kelly, Simon, Kleinman, Kayla, Koo, Bonhwang, Kramer, Eliza, Lennon, Elizabeth, Lord, Catherine, Mantello, Ginny, Margolis, Amy, Merikangas, Kathleen, Milham, Judith, Minniti, Giuseppe, Neuhaus, Rebecca, Levine, Alexandra, Osman, Yael, Parra, Lucas, Pugh, Ken, Racanello, Amy, Restrepo, Anita, Saltzman, Tian, Septimus, Batya, Tobe, Russell, Waltz, Rachel, Williams, Anna, Yeo, Anna, Castellanos, Francisco, Klein, Arno, Paus, Tomas, Leventhal, Bennett, Craddock, R, Koplewicz, Harold, and Milham, Michael
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Adolescent ,Child ,Databases ,Factual ,Electroencephalography ,Humans ,Learning Disabilities ,Mental Health ,Multimodal Imaging ,Neuroimaging ,Young Adult - Abstract
Technological and methodological innovations are equipping researchers with unprecedented capabilities for detecting and characterizing pathologic processes in the developing human brain. As a result, ambitions to achieve clinically useful tools to assist in the diagnosis and management of mental health and learning disorders are gaining momentum. To this end, it is critical to accrue large-scale multimodal datasets that capture a broad range of commonly encountered clinical psychopathology. The Child Mind Institute has launched the Healthy Brain Network (HBN), an ongoing initiative focused on creating and sharing a biobank of data from 10,000 New York area participants (ages 5-21). The HBN Biobank houses data about psychiatric, behavioral, cognitive, and lifestyle phenotypes, as well as multimodal brain imaging (resting and naturalistic viewing fMRI, diffusion MRI, morphometric MRI), electroencephalography, eye-tracking, voice and video recordings, genetics and actigraphy. Here, we present the rationale, design and implementation of HBN protocols. We describe the first data release (n=664) and the potential of the biobank to advance related areas (e.g., biophysical modeling, voice analysis).
- Published
- 2017
24. 5610437 HLA TISSUE TYPING AND HSCT FOR THE SICKLE CELL DISEASE COHORT AT THE ROYAL CHILDREN’S HOSPITAL (MELBOURNE, AUSTRALIA): AN AUDIT
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A. Duncan, L. Clucas, E. O’Reilly, and A. Greenway
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Diseases of the blood and blood-forming organs ,RC633-647.5 - Published
- 2023
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25. Drought and coyotes mediate mesopredator response to human disturbance
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Molly K. Parren, Brett J. Furnas, Daniel C. Barton, Misty D. Nelson, and Barbara Clucas
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bobcat ,California ,Central Valley ,coyote ,detection probability ,drought ,Ecology ,QH540-549.5 - Abstract
Abstract Mesopredators in western North America are facing major changes to their ecosystems, including drought and the expansion of human disturbance. To balance resource needs and risk‐taking on the landscape, mesopredators are likely to shift their habitat use and interspecies interactions. As part of a large‐scale study to help evaluate responses of terrestrial wildlife to severe drought, the California Department of Fish and Wildlife surveyed mesopredator presence across 585 sites in the Mojave Desert (MD) and Central Valley (CV) ecoregions of California. This study spanned a drought year (2016) and a post‐drought year (2017), providing the opportunity to investigate how drought and interspecific interactions may mediate spatial patterns of mesopredator occurrence across a continuum of human disturbance levels. We used single‐season, single‐species, and conditional two‐species occupancy models to elucidate these relationships in both ecoregions. We examined the occupancy and detection of coyotes (Canis latrans) and smaller mesopredators, including bobcats (Lynx rufus) in both ecoregions, raccoons (Procyon lotor) in the CV, and desert kit foxes in the MD (Vulpes macrotis arsipus). The presence of coyotes influenced the detection probability of all other mesopredator species, and the influence of drought varied by species and ecoregion. Detection of mesopredators in the CV was typically higher in 2016, especially at low disturbance sites, suggesting species may have become more active during the drought to meet resource needs. However, detection of mesopredators in the MD tended to increase after the drought, suggesting a response to an increase in resources (e.g., prey). Coyotes in the MD became more detectable in high human disturbance in 2016 and less detectable in 2017, possibly increasing activity during the drought in human‐disturbed areas to obtain anthropogenic resources. Drought not only affects individual species and their relationships to human disturbance, but it can also influence their interspecies interactions and use of different landscape features.
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- 2022
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26. MESOPELAGIC DIET AS PATHWAY OF HIGH MERCURY LEVELS IN BODY FEATHERS OF THE ENDANGERED BLACK-CAPPED PETREL (DIABLOTIN) PTERODROMA HASITATA.
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SATGÉ, YVAN G., JANSSEN, SARAH E., CLUCAS, GEMMA, RUPP, ERNST, PATTESON, J. BRIAN, and JODICE, PATRICK G. R.
- Subjects
FISHERIES ,SMALL-scale fisheries ,PETRELS ,MERCURY ,POLLUTANTS ,FEATHERS - Abstract
The Diablotin or Black-capped Petrel Pterodroma hasitata is an endangered gadfly petrel found in the western North Atlantic, Caribbean Sea, and northern Gulf of Mexico. An estimated ~2000 pairs nest at five known sites on Hispaniola, Greater Antilles, although only 120 nests have been located to date. We collected breast feathers and feces from breeding adults in the Dominican Republic in April 2018 (n = 10) and from non-breeding adults at sea offshore of North Carolina, USA, in May 2019 (n = 10). We measured mercury burden in feathers and used fecal DNA metabarcoding to compare diets. We found higher concentrations of total mercury compared to other Pterodroma petrels worldwide, with mean concentrations of 30.3 ± 11.1 ppm dry weight (range: 15.2-53.9; n = 20). Diet was dominated by fish, including a high proportion of mesopelagic groups such as myctophids, as well as fishes of interest to artisanal and commercial Caribbean fisheries. These results confirm earlier suggestions of elevated ingestion of mercury by Black-capped Petrels, likely through the consumption of mesopelagic prey or fishery discards. [ABSTRACT FROM AUTHOR]
- Published
- 2024
27. Seasonal variation in the ultrasonic vocal activity of Humboldt's flying squirrel (Glaucomys oregonensis).
- Author
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Farwell, Travis A. and Clucas, Barbara
- Subjects
ANTIPREDATOR behavior ,WEATHER ,BIOLOGICAL fitness ,SQUIRRELS ,ULTRASONICS - Abstract
Most mammals rely on vocal communication to increase survival and reproductive success. While the functions of audible vocalizations have been well‐studied across mammal species, ultrasonic vocalizations in small mammals outside of bats are less understood. North American flying squirrel species (Glaucomys spp.), including the newly described Humboldt's flying squirrel (Glaucomys oregonensis), produce numerous call‐types that extend into the ultrasonic range. To investigate the potential function of ultrasonic call‐types in the Humboldt's flying squirrels, we used ultrasonic recorders to record squirrels in the wild across multiple seasons to determine if there are temporal and seasonal patterns in nightly vocal activity and rates of different call‐types. We recorded Humboldt's flying squirrels in two geographic locations ‐ Humboldt and San Bernardino counties—in California from 2018 to 2022 in the summer and winter across multiple study areas. We found that although seasonal weather conditions differ between locations, flying squirrels in Humboldt and San Bernardino had similar vocal activity patterns across nightly active periods between locations and between summer and winter. Nightly activity patterns of when the three main chirp‐like call‐types (arc chirps, tonal chirps, upsweeps) were given varied between seasons in both geographic locations, and these call‐types were given at greater rates in the summer in San Bernardino, but rates did not vary by season in Humboldt. Trills, the most structurally complex of the four main call‐types, were produced more in the summer than in winter, and also differed in their nightly activity patterns, in both geographic locations. Flying squirrels may use certain call‐types earlier or later in the nightly active period due to their potentially varying functions, and may produce more trills in the summer coinciding with the breeding season. Further understanding of the function of different call‐types can provide insight into social, foraging, and antipredator behavior of this nocturnal and elusive species. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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28. Black‐throated blue warblers (Setophaga caerulescens) exhibit diet flexibility and track seasonal changes in insect availability.
- Author
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Kaiser, Sara A., Forg, Lindsey E., Stillman, Andrew N., Deitsch, John F., Sillett, T. Scott, and Clucas, Gemma V.
- Subjects
PREY availability ,CRAB spiders ,SPRING ,AUTUMN ,INSECT communities ,MIGRATORY birds ,WARBLERS - Abstract
Changes in leaf phenology from warming spring and autumn temperatures have lengthened the temperate zone growing "green" season and breeding window for migratory birds in North America. However, the fitness benefits of an extended breeding season will depend, in part, on whether species have sufficient dietary flexibility to accommodate seasonal changes in prey availability. We used fecal DNA metabarcoding to test the hypothesis that seasonal changes in the diets of the insectivorous, migratory black‐throated blue warbler (Setophaga caerulescens) track changes in the availability of arthropod prey at the Hubbard Brook Experimental Forest, New Hampshire, USA. We examined changes across the breeding season and along an elevation gradient encompassing a 2‐week difference in green season length. From 98 fecal samples, we identified 395 taxa from 17 arthropod orders; 242 were identified to species, with Cecrita guttivitta (saddled prominent moth), Theridion frondeum (eastern long‐legged cobweaver), and Philodromus rufus (white‐striped running crab spider) occurring at the highest frequency. We found significant differences in diet composition between survey periods and weak differences among elevation zones. Variance in diet composition was highest late in the season, and diet richness and diversity were highest early in the season. Diet composition was associated with changes in prey availability surveyed over the green season. However, several taxa occurred in diets more or less than expected relative to their frequency of occurrence from survey data, suggesting that prey selection or avoidance sometimes accompanies opportunistic foraging. This study demonstrates that black‐throated blue warblers exhibit diet flexibility and track seasonal changes in prey availability, which has implications for migratory bird responses to climate‐induced changes in insect communities with longer green seasons. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
29. Humans Are More Influential Than Coyotes on Mammalian Mesopredator Spatiotemporal Activity Across an Urban Gradient
- Author
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Chad W. Moura, Barbara Clucas, and Brett J. Furnas
- Subjects
human presence ,mesopredators ,overlap ,spatiotemporal activity ,urban gradient ,Evolution ,QH359-425 ,Ecology ,QH540-549.5 - Abstract
For mammalian mesopredators, human-dominated landscapes offer a mosaic of risk and reward. While the reward of anthropogenic food resources may attract mesopredators to human-dominated areas, increased mesopredator activity and abundance in these areas may cause interspecific conflict. For smaller-bodied mesopredators, the perceived risk of intraguild predation by larger mesopredators may be enough to drive spatial and temporal avoidance strategies to reduce risk while still benefiting from anthropogenic resources. We evaluated how the spatiotemporal activity of four non-canid mammalian mesopredators – raccoon (Procyon lotor), striped skunk (Mephitis mephitis), opossum (Didelphis virginiana), and domestic cat (Felis catus) – might change in the presence of an intraguild predator, the coyote (Canis latrans), and a “super predator,” humans. We quantified mesopredator activity by deploying camera traps at 110 sites across an urban gradient in the Sacramento Metropolitan Area in central California, USA. We hypothesized that mesopredators would likely change their spatiotemporal activity in response to urban intensity (H1), coyotes (H2), human presence (H3), and if urban intensity might mediate the response to humans and coyotes (H4). We used single-species occupancy models to test how mesopredators responded to different spatial scales of urbanization, as well as the temporal presence of coyotes and humans. Top single-species models then informed two-species conditional occupancy models to evaluate how mesopredators responded to “dominant” coyotes. Finally, we used temporal overlap analyzes to evaluate whether activity patterns of mesopredators changed in response to humans and coyotes across three levels of urban intensity. Mesopredators did not change their spatial or temporal activity across the urban gradient when coyotes were present. Additionally, coyotes did not influence mesopredator temporal activity at 1-3-day scales; however, raccoons and cats may avoid coyotes at finer scales. Humans influenced mesopredator detectability, as cats and coyotes avoided humans after 1 and 2 days respectively, and opossums avoided urban areas when humans were present within 3 days. Coyotes may play a limited role in altering smaller-bodied mesopredator activity, especially when humans are present. While the impacts of human presence and urban features are often linked, mesopredators may perceive the risk each poses differently, and adjust their activity accordingly.
- Published
- 2022
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30. Correction: Tamadon et al. Flow-Based Anatomy of Bobbin Friction-Stirred Weld; AA6082-T6 Aluminium Plate and Analogue Plasticine Model. Appl. Mech. 2020, 1, 3–19
- Author
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Tamadon, Abbas, primary, Pons, Dirk J., additional, and Clucas, Don, additional
- Published
- 2024
- Full Text
- View/download PDF
31. Receding ice drove parallel expansions in Southern Ocean penguins
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Cole, Theresa L., Dutoit, Ludovic, Dussex, Nicolas, Hart, Tom, Alexander, Alana, Younger, Jane L., Clucas, Gemma V., Frugone, María José, Cherel, Yves, Cuthbert, Richard, Ellenberg, Ursula, Fiddaman, Steven R., Hiscock, Johanna, Houston, David, Jouventin, Pierre, Mattern, Thomas, Miller, Gary, Miskelly, Colin, Nolan, Paul, Polito, Michael J., Quillfeldt, Petra, Ryan, Peter G., Smith, Adrian, Tennyson, Alan J. D., Thompsona, David, Wieneckeb, Barbara, Viannac, Juliana A., and Waters, Jonathan M.
- Published
- 2019
32. Gene flow and glacial history : investigating the processes shaping the population structure of penguins in the Southern Ocean
- Author
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Clucas, Gemma
- Subjects
598.4 - Abstract
Penguins in Antarctica and the sub-Antarctic have survived multiple glacial to inter-glacial transitions. However, anthropogenic climate change may exceed this natural variability in the rate and extent of warming. To accurately monitor the effects of climate change on natural populations, predict their local or global extinction risk, and design effective conservation management plans, we must first be able to define the borders of breeding populations. Regular dispersal of individuals from their natal colony to breed at another colony may mean that multiple colonies constitute a breeding population. By investigating patterns of intraspecific genetic variation, we can estimate the dispersal of individuals between colonies and identify any barriers to gene flow. Barriers to gene flow may be permanent or transient. Permanent barriers to gene flow may ultimately lead to speciation if populations diverge sufficiently, and so by investigating intraspecific population differentiation, we can potentially gain a window into the speciation process. Using both mitochondrial and nuclear genomic markers (single nucleotide polymorphisms, SNPs), and by comparing closely related species with different life histories across a range of habitats, I identify the historical and contemporary barriers to gene flow in emperor, king, gentoo, chinstrap and Adélie penguins. I find that historical glaciation during the last glacial period was significant in driving population divergence among small, refugial populations of Antarctic emperor penguins, but there was no evidence for this in their congener the sub- Antarctic king penguin. This is likely a result of the greater effects of glaciation in the Antarctic compared to the sub-Antarctic. I also show that high levels of contemporary dispersal among emperor penguin colonies has created at least four metapopulations, which span thousands of kilometres of coastline, and that dispersal between these metapopulations has largely eroded the historical population differentiation. King, chinstrap, and Adélie penguins also showed high levels of dispersal across distances of thousands of kilometres. This is in stark contrast to the gentoo penguin, in which colonies separated by less than 50 km were genetically differentiated, and large stretches of open-ocean appear to form permanent barriers to gene flow, promoting allopatric speciation in gentoo penguins. I find that the at-sea range of these species appears to determine these dispersal patterns. The pelagic foraging emperor, king, chinstrap and Adélie penguins, which range from hundreds to thousands of kilometres away from their colonies during the nonbreeding season, show high levels of dispersal and gene flow between colonies. However the coastal foraging gentoo penguin, which is resident at or near colonies year-round, shows very little dispersal and gene flow between colonies. Other barriers to gene flow identified were the Polar Front, which restricts gene flow among king and gentoo penguin colonies, and natal philopatry, which also appears to play a role in restricting gene flow among gentoo penguin colonies. The implications of these patterns of dispersal are discussed with respect to monitoring and management, and taxonomic revision is advised to recognise the incipient allopatric speciation identified between populations of gentoo penguins.
- Published
- 2016
33. Elucidating the role of radixin in prostate cancer progression
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Clucas, Jarama
- Subjects
616.99 - Abstract
Introduction: Radixin (RDX) is a member of the ezrin-radixin-moesin (ERM) family of cytoskeletal linkers that have been implicated in cancer progression. Prostate cancer (PC) is the most common cancer of males in the UK. Patients with high grade prostatic intraepithelial neoplasia (HGPIN), the predicted precursor to PC, have shown a significant elevation of RDX expression compared to both normal adjacent tissue and PC samples but its influence in prostate cancer progression remains unclear. Aim: The aim of this thesis was to investigate the role of RDX in the earlier stages of PC progression (such as HGPIN) using 3D cell culture models, microscopy techniques and molecular tools to test the hypothesis that RDX aids the progression of epithelial prostatic cells to a more mesenchymal-like phenotype, in the early stages of PC development. Results: An inducible shRNA system was optimised to successfully knock down RDX expression. The tumourigenic cells WPE-1 NB26, had significantly higher expression of RDX and were chosen to study HGPIN in combination with two improved 3D cell culture models. RDX knock down induced polarisation of WPE-1 NB26-derived spheroids, affecting cell morphology, E-cadherin localisation and laminin 332 expression. Overexpression of a constitutively active RDX mutant in the non-neoplastic cell line, RWPE-1, induced a more mesenchymal-like phenotype. Pharmacological inhibition of atypical protein kinase C (aPKC) reduced the phosphorylation levels of RDX in WPE-1 NB26 cells and localised E-cadherin to the plasma membrane in WPE-1 NB26-derived spheroids. Conclusion: The tools generated and optimised enabled RDX's role in HGPIN to be investigated. RDX was found to maintain the mesenchymal phenotype of acini-like spheroids derived from tumourigenic cells. This phenotype appeared to be aPKC-dependent. Preliminary data indicated the activity of RDX, rather than its expression, mediated a mesenchymal phenotype in non-neoplastic cells. The potential aPKC/RDX/E-cadherin pathway presented in this thesis may provide a therapeutic target to prevent further tumour progression in PC.
- Published
- 2016
34. Morphometric and genetic evidence for four species of gentoo penguin
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Joshua Tyler, Matthew T. Bonfitto, Gemma V. Clucas, Sushma Reddy, and Jane L. Younger
- Subjects
Antarctica ,integrative taxonomy ,new species ,Pygoscelis ,Southern Ocean ,Ecology ,QH540-549.5 - Abstract
Abstract Gentoo penguins (Pygoscelis papua) are found across the Southern Ocean with a circumpolar distribution and notable genetic and morphological variation across their geographic range. Whether this geographic variation represents species‐level diversity has yet to be investigated in an integrative taxonomic framework. Here, we show that four distinct populations of gentoo penguins (Iles Kerguelen, Falkland Islands, South Georgia, and South Shetlands/Western Antarctic Peninsula) are genetically and morphologically distinct from one another. We present here a revised taxonomic treatment including formal nomenclatural changes. We suggest the designation of four species of gentoo penguin: P. papua in the Falkland Islands, P. ellsworthi in the South Shetland Islands/Western Antarctic Peninsula, P. taeniata in Iles Kerguelen, and a new gentoo species P. poncetii, described herein, in South Georgia. These findings of cryptic diversity add to many other such findings across the avian tree of life in recent years. Our results further highlight the importance of reassessing species boundaries as methodological advances are made, particularly for taxa of conservation concern. We recommend reassessment by the IUCN of each species, particularly P. taeniata and P. poncetii, which both show evidence of decline.
- Published
- 2020
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35. A novel method using camera traps to record effectiveness of artificial perches for raptors
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Barbara Clucas, Trinity N. Smith, Jaime Carlino, Sarah Daniel, Anna Davis, Leigh Douglas, Masha M. Gulak, Sarah L. Kanga Livingstone, Skyler Lopez, Kyra J. Kerr, Kelly M. Koehn, Kathryn A. Lloyd, Joseph A. Medina, Evan A. S. Miller, Alyssa M. Prior, Marilyn Sandoval, Alexandria Shedlock, and Shaun Thornton
- Subjects
griculture ,artificial perches ,buteo jamaicensis ,buteo lineatus ,camera traps ,falco sparverius ,foraging ,pests ,raptors ,rodents ,Science - Abstract
Agricultural areas can benefit from the reduction of rodents by raptors, yet many croplands and pastures do not provide adequate perching structures needed by raptors to hunt effectively. Many artificial raptor perches have been constructed as a solution to this deficiency, however, monitoring the benefits of these perches has proved challenging. We developed a method using artificial perches and camera traps mounted on poles that allows for 24-hour monitoring of perch utilization. We tested the new method in an agricultural area in northern California and demonstrated its ability to facilitate accurate species identification and to quantify raptor use and activity. Three of the six raptor species observed at the site utilized the artificial perches: American kestrels (Falco sparverius), red-tailed hawks (Buteo jamaicensis), and red-shouldered hawks (B. lineatus). We did not document any rodent predation events from the perches; but we did observe American kestrels using perches to hunt for invertebrates. Overall, we found that using camera traps mounted on poles can successfully monitor artificial perches and can be easily used to study the effectiveness of hunting perches for raptors in agricultural areas.
- Published
- 2020
- Full Text
- View/download PDF
36. Problematic internet use in children and adolescents: associations with psychiatric disorders and impairment
- Author
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Anita Restrepo, Tohar Scheininger, Jon Clucas, Lindsay Alexander, Giovanni A. Salum, Kathy Georgiades, Diana Paksarian, Kathleen R. Merikangas, and Michael P. Milham
- Subjects
Internet addiction ,Pediatric ,Depression ,ADHD ,ASD ,Impairment ,Psychiatry ,RC435-571 - Abstract
Abstract Background Problematic internet use (PIU) is an increasingly worrisome issue, as youth population studies are establishing links with internalizing and externalizing problems. There is a need for a better understanding of psychiatric diagnostic profiles associated with this issue, as well as its unique contributions to impairment. Here, we leveraged the ongoing, large-scale Child Mind Institute Healthy Brain Network, a transdiagnostic self-referred, community sample of children and adolescents (ages 5–21), to examine the associations between PIU and psychopathology, general impairment, physical health and sleep disturbances. Methods A total sample of 564 (190 female) participants between the ages of 7–15 (mean = 10.80, SD = 2.16), along with their parents/guardians, completed diagnostic interviews with clinicians, answered a wide range of self-report (SR) and parent-report (PR) questionnaires, including the Internet Addiction Test (IAT) and underwent physical testing as part of the Healthy Brain Network protocol. Results PIU was positively associated with depressive disorders (SR: aOR = 2.43, CI: 1.22–4.74, p = .01; PR: aOR = 2.56, CI: 1.31–5.05, p = .01), the combined presentation of ADHD (SR: aOR = 1.91, CI: 1.14–3.22, p = .01; PR: n.s.), Autism Spectrum Disorder (SR: n.s.; PR: aOR = 2.24, CI: 1.34–3.73, p
- Published
- 2020
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37. ChemoKnowings as Part of 21st Century Bildung and Subject Didaktik
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Merve Yavuzkaya, Paul Clucas, and Jesper Sjöström
- Subjects
didaktik ,Anthropocene ,powerful knowings ,eco-reflexive Bildung ,embodied knowledge ,chemistry education ,Education (General) ,L7-991 - Abstract
In this article, we elaborate on the construct ChemoKnowings as subject-specific powerful knowings for chemical agency in the Anthropocene era. Related to constructs such as critical chemical literacy, ChemoCapabilities, and eco-reflexive chemical thinking, we unpack the construct as an example of Carlgren’s powerful knowings, which relates Young’s powerful knowledge to the idea and tradition of Bildung. It means powerful knowledge containing embodied and relational (or tacit) dimensions. ChemoKnowings can therefore be described as embodied and relational knowledge in and about chemistry – (critical) chemical knowledge that matters meaningfully to the student, connecting them to themselves and the world, and conferring an ethical compass. By situating the teaching of ChemoKnowings within a vision for chemistry teaching as a part of a world-centered vision for schooling in the Anthropocene, ChemoKnowings are viewed as having the capacity to mobilise an ethico-socio-political action, that is, chemical agency. By focusing on student transformation of content for ChemoKnowings and integrating elements of a theoretical didaktik model for eco-reflexive chemistry education, we develop a vision-oriented didaktik model for ChemoKnowings. More generally, we argue that didaktik models for supporting teachers’ consideration of student transformation of content for powerful subject-knowings are an important part of general subject didaktik. We present in the article vignettes that detail personal accounts for each of the three authors describing examples of chemistry-specific knowings that matter meaningfully to each of us, and which articulate our own embodied ethico-socio-political actions as students, teachers, researchers, and consumers. Inspired by Klafki’s didaktik analysis, we end the article by proposing four areas of questions that the teacher can use in guiding their preparation and transformation of the content they bring into the classroom for promoting students’ ChemoKnowings, and thus Bildung in the 21st century.
- Published
- 2022
- Full Text
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38. High burden of infectious disease and antibiotic use in early life in Australian Aboriginal communities
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Cuningham, Will, McVernon, Jodie, Lydeamore, Michael J., Andrews, Ross M., Carapetis, Jonathan, Kearns, Therese, Clucas, Danielle, Dhurrkay, Roslyn Gundjirryirr, Tong, Steven Y.C., and Campbell, Patricia T.
- Published
- 2019
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- View/download PDF
39. Raman spectroscopic analysis of skin as a diagnostic tool for Human African Trypanosomiasis.
- Author
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Alexandre Girard, Anneli Cooper, Samuel Mabbott, Barbara Bradley, Steven Asiala, Lauren Jamieson, Caroline Clucas, Paul Capewell, Francesco Marchesi, Matthew P Gibbins, Franziska Hentzschel, Matthias Marti, Juan F Quintana, Paul Garside, Karen Faulds, Annette MacLeod, and Duncan Graham
- Subjects
Immunologic diseases. Allergy ,RC581-607 ,Biology (General) ,QH301-705.5 - Abstract
Human African Trypanosomiasis (HAT) has been responsible for several deadly epidemics throughout the 20th century, but a renewed commitment to disease control has significantly reduced new cases and motivated a target for the elimination of Trypanosoma brucei gambiense-HAT by 2030. However, the recent identification of latent human infections, and the detection of trypanosomes in extravascular tissues hidden from current diagnostic tools, such as the skin, has added new complexity to identifying infected individuals. New and improved diagnostic tests to detect Trypanosoma brucei infection by interrogating the skin are therefore needed. Recent advances have improved the cost, sensitivity and portability of Raman spectroscopy technology for non-invasive medical diagnostics, making it an attractive tool for gambiense-HAT detection. The aim of this work was to assess and develop a new non-invasive diagnostic method for T. brucei through Raman spectroscopy of the skin. Infections were performed in an established murine disease model using the animal-infective Trypanosoma brucei brucei subspecies. The skin of infected and matched control mice was scrutinized ex vivo using a confocal Raman microscope with 532 nm excitation and in situ at 785 nm excitation with a portable field-compatible instrument. Spectral evaluation and Principal Component Analysis confirmed discrimination of T. brucei-infected from uninfected tissue, and a characterisation of biochemical changes in lipids and proteins in parasite-infected skin indicated by prominent Raman peak intensities was performed. This study is the first to demonstrate the application of Raman spectroscopy for the detection of T. brucei by targeting the skin of the host. The technique has significant potential to discriminate between infected and non-infected tissue and could represent a unique, non-invasive diagnostic tool in the goal for elimination of gambiense-HAT as well as for Animal African Trypanosomiasis (AAT).
- Published
- 2021
- Full Text
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40. Remote Digital Psychiatry for Mobile Mental Health Assessment and Therapy: MindLogger Platform Development Study
- Author
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Arno Klein, Jon Clucas, Anirudh Krishnakumar, Satrajit S Ghosh, Wilhelm Van Auken, Benjamin Thonet, Ihor Sabram, Nino Acuna, Anisha Keshavan, Henry Rossiter, Yao Xiao, Sergey Semenuta, Alessandra Badioli, Kseniia Konishcheva, Sanu Ann Abraham, Lindsay M Alexander, Kathleen R Merikangas, Joel Swendsen, Ariel B Lindner, and Michael P Milham
- Subjects
Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundUniversal access to assessment and treatment of mental health and learning disorders remains a significant and unmet need. There are many people without access to care because of economic, geographic, and cultural barriers, as well as the limited availability of clinical experts who could help advance our understanding and treatment of mental health. ObjectiveThis study aims to create an open, configurable software platform to build clinical measures, mobile assessments, tasks, and interventions without programming expertise. Specifically, our primary requirements include an administrator interface for creating and scheduling recurring and customized questionnaires where end users receive and respond to scheduled notifications via an iOS or Android app on a mobile device. Such a platform would help relieve overwhelmed health systems and empower remote and disadvantaged subgroups in need of accurate and effective information, assessment, and care. This platform has the potential to advance scientific research by supporting the collection of data with instruments tailored to specific scientific questions from large, distributed, and diverse populations. MethodsWe searched for products that satisfy these requirements. We designed and developed a new software platform called MindLogger, which exceeds the requirements. To demonstrate the platform’s configurability, we built multiple applets (collections of activities) within the MindLogger mobile app and deployed several of them, including a comprehensive set of assessments underway in a large-scale, longitudinal mental health study. ResultsOf the hundreds of products we researched, we found 10 that met our primary requirements with 4 that support end-to-end encryption, 2 that enable restricted access to individual users’ data, 1 that provides open-source software, and none that satisfy all three. We compared features related to information presentation and data capture capabilities; privacy and security; and access to the product, code, and data. We successfully built MindLogger mobile and web applications, as well as web browser–based tools for building and editing new applets and for administering them to end users. MindLogger has end-to-end encryption, enables restricted access, is open source, and supports a variety of data collection features. One applet is currently collecting data from children and adolescents in our mental health study, and other applets are in different stages of testing and deployment for use in clinical and research settings. ConclusionsWe demonstrated the flexibility and applicability of the MindLogger platform through its deployment in a large-scale, longitudinal, mobile mental health study and by building a variety of other mental health–related applets. With this release, we encourage a broad range of users to apply the MindLogger platform to create and test applets to advance health care and scientific research. We hope that increasing the availability of applets designed to assess and administer interventions will facilitate access to health care in the general population.
- Published
- 2021
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41. Correction: Tamadon, A.; et al. Internal Material Flow Layers in AA6082-T6 Butt-Joints during Bobbin Friction Stir Welding. Metals 2019, 9, 1059
- Author
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Tamadon, Abbas, primary, Pons, Dirk J., additional, Clucas, Don, additional, and Sued, Kamil, additional
- Published
- 2024
- Full Text
- View/download PDF
42. Correction: Tamadon et al. Development of Metallographic Etchants for the Microstructure Evolution of A6082-T6 BFSW Welds. Metals 2017, 7, 423
- Author
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Tamadon, Abbas, primary, Pons, Dirk J., additional, Sued, Kamil, additional, and Clucas, Don, additional
- Published
- 2024
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- View/download PDF
43. Age at First Return to the Breeding Colony and Juvenile Survival of Sooty Shearwaters
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Fletcher, David, Moller, Henrik, Clucas, Rosemary, Bragg, Corey, Scott, Darren, Scofield, Paul, Hunter, Christine M., Win, Ilka, Newman, Jamie, McKechnie, Sam, de Cruz, Justine, and Lyver, Philip
- Published
- 2013
- Full Text
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44. Multiple methods of diet assessment reveal differences in Atlantic puffin diet between ages, breeding stages, and years.
- Author
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Kennerley, William L., Clucas, Gemma V., and Lyons, Donald E.
- Subjects
MARINE heatwaves ,DIET ,FORAGE fishes ,FISH communities ,BIOLOGICAL fitness - Abstract
Introduction: Atlantic puffin (Fratercula arctica, hereafter "puffin") reproductive success in the Gulf of Maine (GoM) has declined following a recent oceanographic regime shift that has led to rapid warming and increasingly frequent marine heatwaves. Concurrent changes in both the regional forage fish community and puffin chick diets and provisioning rates suggest that inadequate prey resources may be driving this decline. Traditional, noninvasive methods of diet assessment, however, are unable to determine seabird diet at many age classes and breeding stages. Methods: To determine what prey GoM puffins were feeding on during two years of marine heatwave conditions, we assessed puffin diet using two complementary methods: traditional, observational methods that utilize billload photography and emerging methods employing fecal DNA metabarcoding. We then examined the effect of methodology, age, breeding stage, and year on puffin diet composition. Results: We identified a strong correlation between the composition of chick diet as estimated through traditional and emerging methods, supporting the interpretation of DNA relative read abundance as a quantitative metric of diet composition. Both methods identified the same dominant prey groups yet metabarcoding identified a greater number of species and offered higher taxonomic resolution. Additionally, metabarcoding revealed adult puffin diet during the incubation period for the first time. Although puffin adults and chicks fed on many of the same prey types, adults consumed a greater variety of taxa and consumed more low quality prey types than they provisioned chicks. Discussion: For both age classes, diet varied both between and within years, likely reflecting changes in the local forage fish community in response to environmental variability. Puffins exploited unusual abundances of typically-uncommon prey during these two years of marine heatwave conditions, yet low puffin productivity suggests the observed dietary plasticity was not fully able to compensate for apparent prey shortages. Continued refinement of molecular methods and the interpretation of the data they provide will enable better assessments of how seabirds of diverse ages and breeding stages are adapting to changing prey communities. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
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45. Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole‐genome sequencing
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Gemma V. Clucas, R. Nicolas Lou, Nina O. Therkildsen, and Adrienne I. Kovach
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adaptive differentiation ,allochronic reproduction ,Atlantic cod ,chromosomal inversions ,fisheries management ,heat shock proteins ,Evolution ,QH359-425 - Abstract
Abstract Selection can create complex patterns of adaptive differentiation among populations in the wild that may be relevant to management. Atlantic cod in the Northwest Atlantic are at a fraction of their historical abundance and a lack of recovery within the Gulf of Maine has created concern regarding the misalignment of fisheries management structures with biological population structure. To address this and investigate genome‐wide patterns of variation, we used low‐coverage sequencing to perform a region‐wide, whole‐genome analysis of fine‐scale population structure. We sequenced 306 individuals from 20 sampling locations in U.S. and Canadian waters, including the major spawning aggregations in the Gulf of Maine in addition to spawning aggregations from Georges Bank, southern New England, the eastern Scotian Shelf, and St. Pierre Bank. With genotype likelihoods estimated at almost 11 million loci, we found large differences in haplotype frequencies of previously described chromosomal inversions between Canadian and U.S. sampling locations and also among U.S. sampling locations. Our whole‐genome resolution also revealed novel outlier peaks, some of which showed significant genetic differentiation among sampling locations. Comparisons between allochronic winter‐ and spring‐spawning populations revealed highly elevated relative (FST) and absolute (dxy) genetic differentiation near genes involved in reproduction, particularly genes associated with the brain‐pituitary‐gonadal axis, which likely control timing of spawning, contributing to prezygotic isolation. We also found genetic differentiation associated with heat shock proteins and other genes of functional relevance, with complex patterns that may point to multifaceted selection pressures and local adaptation among spawning populations. We provide a high‐resolution picture of U.S. Atlantic cod population structure, revealing greater complexity than is currently recognized in management. Our genome‐scan approach likely underestimates the full suite of adaptive differentiation among sampling locations. Nevertheless, it should inform the revision of stock boundaries to preserve adaptive genetic diversity and evolutionary potential of cod populations.
- Published
- 2019
- Full Text
- View/download PDF
46. Divergent selection and drift shape the genomes of two avian sister species spanning a saline–freshwater ecotone
- Author
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Jennifer Walsh, Gemma V. Clucas, Matthew D. MacManes, W. Kelley Thomas, and Adrienne I. Kovach
- Subjects
adaptation ,Ammospiza caudacutus ,Ammospzia nelsoni ,demography ,ecological divergence ,ecological speciation ,Ecology ,QH540-549.5 - Abstract
Abstract The role of species divergence due to ecologically based divergent selection—or ecological speciation—in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline–freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes—the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)—to evaluate the influence of selective and demographic processes in shaping genome‐wide patterns of divergence. Genome‐wide divergence between these two recently diverged sister species was notably high (genome‐wide FST = 0.32). Against a background of high genome‐wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism—all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.
- Published
- 2019
- Full Text
- View/download PDF
47. Calculation of the age of the first infection for skin sores and scabies in five remote communities in northern Australia
- Author
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Lydeamore, M. J., Campbell, P. T., Cuningham, W., Andrews, R. M., Kearns, T., Clucas, D., Dhurrkay, R. Gundjirryirr, Carapetis, J., Tong, S. Y. C., McCaw, J. M., and McVernon, J.
- Published
- 2018
48. Romantic reclusion in the works of Cowper and Wordsworth
- Author
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Clucas, Tom and Newlyn, Lucy
- Subjects
820.9 ,English Language and Literature ,Romanticism ,Eighteenth Century ,Poetry ,William Wordsworth ,William Cowper ,Solitude ,Retirement ,Community ,Society - Abstract
The end of the eighteenth century witnessed an imaginative mass migration as authors wrote about withdrawing from society. This thesis traces the origins of 'Romantic reclusion' in the works of Cowper and Wordsworth, particularly Cowper's poem The Task and Wordsworth's unfinished masterwork The Recluse, which epitomise the tradition. Romantic reclusion differs from 'solitude' and 'retirement' in that its motives were social. Cowper and Wordsworth wrote about withdrawing in order to criticise the increasing commercialism and competition they saw in British society. Both poets imagined seceding into a community of individuals who would care for a shared set of values, envisaging this as a form of non-violent political protest leading to reform. The thesis builds on recent studies of Romantic community, and develops Raymond Williams's cultural criticism, to refute the New Historicist position that Romantic writing elides history. It proceeds by historicising Cowper's and Wordsworth's concepts of reclusion, tracing echoes of their extensive reading about this subject in what they wrote. Romantic reclusion emerges as an artistic attempt to defend the individual against the dehumanising effects of contemporary society. Its aims can be grouped under four interrelated headings-'creative', 'medical', 'political', and 'natural'-which form the basis of the chapter divisions. Chapter One argues that Cowper and Wordsworth both presented Milton as a precedent for their poetic reclusion. They withdrew from literary society and cut themselves off from the diction of eighteenth-century poetry, because they believed that it turned words into luxury items which could only be purchased by the imaginations of a few. Cowper's translations of Madame Guyon and Wordsworth's modernisations of Chaucer both attempted to develop a plain style which would unite a wider, non-hierarchical community of readers. Chapter Two explores the origins of Cowper's reclusion in his spiritual crisis of 1763-5. Beginning with a study of medical books owned by Cowper's doctor, Nathaniel Cotton, it argues that Cotton regarded Cowper's illness as a product of eighteenth-century models of sociability. Both Cowper and Wordsworth employed Robert Burton's concept of 'Honest Melancholy', or sorrow for the state of one's country, to critique social competition and call for new models of community. Chapter Three examines Cowper's and Wordsworth's presentations of reclusion as the best response to the violence of the American and French Revolutions. Drawing on the works of Classical and modern historians, both poets argued that political revolutions would only succeed once individuals learned to renounce self-interest and govern their selfish passions. The 'retired man' becomes the unexpected political hero of The Task, which in turn forms the basis for Wordsworth's conception of The Recluse. Finally, Chapter Four explores Cowper's and Wordsworth's interests in natural theology, arguing that both poets built on the works of writers including Calvin, David Hartley, and Joseph Butler to explain the psychological mechanism by which reclusion in nature could help to reform the mind, eliminating the selfish passions and teaching individuals to live in an active, mutually responsible community.
- Published
- 2014
49. Preanalytic and analytic factors affecting the measurement of haemoglobin concentration: impact on global estimates of anaemia prevalence
- Author
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Sabine Braat, Beverley-Ann Biggs, Jena Derakhshani Hamadani, Leila M Larson, Mohammed Imrul Hasan, Sheikh Jamal Hossain, Sant-Rayn Pasricha, Kamija S Phiri, Martin N Mwangi, Fernando Estepa, and Danielle Clucas
- Subjects
Medicine (General) ,R5-920 ,Infectious and parasitic diseases ,RC109-216 - Abstract
The accuracy of haemoglobin concentration measurements is crucial for deriving global anaemia prevalence estimates and monitoring anaemia reduction strategies. In this analysis, we examined and quantified the factors affecting preanalytic and analytic variation in haemoglobin concentrations. Using cross-sectional data from three field studies (in children, pregnant and nonpregnant women), we examined the difference in haemoglobin concentration between venous-drawn and capillary-drawn blood measured by HemoCue (ie, preanalytic) and modelled how the bias observed may affect anaemia prevalence estimates in population surveys and anaemia public health severity classification across countries. Using data from an international quality assurance programme, we examined differences due to instrumentation from 16 different haematology analyzers (ie, analytic). Results indicated that capillary and venous haemoglobin concentrations are not in agreement (bias +5.7 g/L (limits of agreement (LoA) −11.2, 22.6) in preschool age children; range from −28 g/L to +20 g/L in pregnant women; bias +8.8 g/L (LoA −5.2, 22.9) in non-pregnant women). The bias observed could introduce changes in population survey estimates of anaemia of up to −20.7 percentage points in children and −28.2 percentage points in non-pregnant women after venous adjustment. Analytic variation was minimal and unlikely to influence the diagnosis of anaemia. These findings suggest that global estimates of anaemia prevalence derived from capillary haemoglobin, as they often are, may be inaccurate and lead to erroneous public health severity classification, but that point-of-care, or other, instruments should not introduce variation if properly used.
- Published
- 2021
- Full Text
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50. Developing UAV Monitoring of South Georgia and the South Sandwich Islands’ Iconic Land-Based Marine Predators
- Author
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John Dickens, Philip R. Hollyman, Tom Hart, Gemma V. Clucas, Eugene J. Murphy, Sally Poncet, Philip N. Trathan, and Martin A. Collins
- Subjects
southern elephant seal ,wandering albatross ,penguin ,remote sensing ,unoccupied aerial vehicle ,drone ,Science ,General. Including nature conservation, geographical distribution ,QH1-199.5 - Abstract
Many remote islands present barriers to effective wildlife monitoring in terms of challenging terrain and frequency of visits. The sub-Antarctic islands of South Georgia and the South Sandwich Islands are home to globally significant populations of seabirds and marine mammals. South Georgia hosts the largest breeding populations of Antarctic fur seals, southern elephant seals and king penguins as well as significant populations of wandering, black-browed and grey-headed albatross. The island also holds important populations of macaroni and gentoo penguins. The South Sandwich Islands host the world’s largest colony of chinstrap penguins in addition to major populations of Adélie and macaroni penguins. A marine protected area was created around these islands in 2012 but monitoring populations of marine predators remains a challenge, particularly as these species breed over large areas in remote and often inaccessible locations. During the 2019/20 austral summer, we trialled the use of an unoccupied aerial vehicle (UAV; drone) to monitor populations of seals, penguins and albatross and here we report our initial findings, including considerations about the advantages and limitations of the methodology. Three extensive southern elephant seal breeding sites were surveyed with complete counts made around the peak pupping date, two of these sites were last surveyed 24 years ago. A total of nine islands, historically recorded as breeding sites for wandering albatross, were surveyed with 144 fledglings and 48 adults identified from the aerial imagery. The UAV was effective at surveying populations of penguins that nest on flat, open terrain, such as Adélie and chinstrap penguin colonies at the South Sandwich Islands, and an extensive king penguin colony on South Georgia, but proved ineffective for monitoring macaroni penguins nesting in tussock habitat on South Georgia as individuals were obscured or hidden by vegetation. Overall, we show that UAV surveys can allow regular and accurate monitoring of these important wildlife populations.
- Published
- 2021
- Full Text
- View/download PDF
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