41,242 results on '"Hopper, A"'
Search Results
2. High-Transmission Mid-Infrared Bandpass Filters Using Hybrid Metal-Dielectric Metasurfaces for CO2 Sensing
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Soliman, Amr, Williams, C, Hopper, Richard, Udrea, Florin, Butt, Haider, and Wilkinson, Timothy D.
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Physics - Optics - Abstract
Mid-infrared (MIR) spectroscopy is a powerful technique employed for a variety of applications, including gas sensing, industrial inspection, astronomy, surveillance, and imaging. Thin-film narrowband interference filters, targeted to specific absorption bands of target molecules, are commonly deployed for cost-effective MIR sensing systems. These devices require complex and time-consuming fabrication processes. Also, their customization on the micro-scale for emerging miniaturized applications is challenging. Plasmonic nanostructure arrays operating in reflection and transmission modes have been developed for MIR. However, they experience undesirable characteristics, such as broad spectra and low reflection/transmission efficiencies. All-dielectric metasurfaces have low intrinsic losses and have emerged as a substitute for plasmonic metasurfaces in MIR spectroscopy. Nevertheless, they typically operate only in reflection mode. In this work, we present a hybrid metal-dielectric metasurface for MIR spectroscopy operating in transmission mode. The metasurface is composed of germanium (Ge) atop aluminum (Al) cylinders, and we show that the transmission response arises because of the hybridization of modes arising from the Ge and the Al structures. The presented metasurface has a high transmission efficiency of 80 % at $\lambda = 2.6\ \mu\text{m}$, and a narrow full-width-at-half-maximum of $0.4\ \mu\text{m}$. We show numerical simulations, successful fabrication using a straightforward fabrication method, and deployment as the in-line optical filter in a CO$_2$ gas detection with a limit of detection of ~0.04% (a few hundred ppm). Our work demonstrates the potential for hybrid metasurfaces as in-line gas sensing optical filters in MIR spectroscopy.
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- 2024
3. Ultrafast symmetry control in photoexcited quantum dots
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Guzelturk, Burak, Portner, Joshua, Ondry, Justin, Ghanbarzadeh, Samira, Tarantola, Mia, Jeong, Ahhyun, Field, Thomas, Chandler, Alicia M., Wieman, Eliza, Hopper, Thomas R., Watkins, Nicolas E., Yue, Jin, Cheng, Xinxin, Lin, Ming-Fu, Luo, Duan, Kramer, Patrick L., Shen, Xiaozhe, Reid, Alexander H., Borkiewicz, Olaf, Ruett, Uta, Zhang, Xiaoyi, Lindenberg, Aaron M., Ma, Jihong, Schaller, Richard, Talapin, Dmitri V., and Cotts, Benjamin L.
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Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Materials Science ,Physics - Optics - Abstract
Symmetry control is essential for realizing unconventional properties, such as ferroelectricity, nonlinear optical responses, and complex topological order, thus it holds promise for the design of emerging quantum and photonic systems. Nevertheless, fast and reversible control of symmetry in materials remains a challenge, especially for nanoscale systems. Here, we unveil reversible symmetry changes in colloidal lead chalcogenide quantum dots on picosecond timescales. Using a combination of ultrafast electron diffraction and total X-ray scattering, in conjunction with atomic-scale structural modeling and first-principles calculations, we reveal that symmetry-broken lead sulfide quantum dots restore to a centrosymmetric phase upon photoexcitation. The symmetry restoration is driven by photoexcited electronic carriers, which suppress lead off-centering for about 100 ps. Furthermore, the change in symmetry is closely correlated with the electronic properties as shown by transient optical measurements. Overall, this study elucidates reversible symmetry changes in colloidal quantum dots, and more broadly defines a new methodology to optically control symmetry in nanoscale systems on ultrafast timescales., Comment: 19 pages, 5 figures
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- 2024
4. Stratified Resistive Tearing Instability
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Hopper, Scott J., Wood, Toby S., and Bushby, Paul J.
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Physics - Fluid Dynamics ,Astrophysics - Solar and Stellar Astrophysics ,Mathematical Physics ,Physics - Plasma Physics ,Physics - Space Physics - Abstract
Resistive tearing instabilities are common in fluids that are highly electrically conductive and carry strong currents. We determine the effect of stable stratification on the tearing instability under the Boussinesq approximation. Our results generalise previous work that considered only specific parameter regimes, and we show that the length scale of the fastest growing mode depends non-monotonically on the stratification strength. We confirm our analytical results by solving the linearised equations numerically, and we discuss whether the instability could operate in the solar tachocline.
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- 2024
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5. Sliced Wasserstein Geodesics and Equivalence Wasserstein and Sliced Wasserstein metrics
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Hopper, John Seale
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Mathematics - Probability ,Mathematics - Optimization and Control ,49Q22, 46E27, 60A99 - Abstract
This paper will introduce a family of sliced Wasserstein geodesics which are not standard Wasserstein geodesics, objects yet to be discovered in the literature. These objects exhibit how the geometric structure of the Sliced Wasserstein space differs from the Wasserstein space, and provides a simple example of how solving the barycenter and gradient flow problems change when moving between these metrics. Some of these geodesics will only be H\"older continuous with respect to the Wasserstein metric and thus will provide a direct proof that Sliced-Wasserstein and regular Wasserstein metrics are not equivalent. Previous proofs of this were done for various cases in [2] and [5]. This paper, not only provides a direct proof, but also fills in gaps showing these metrics not equivalent in dimensions greater than 2., Comment: 6 pages, 1 figure, preprint
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- 2024
6. The IT-BME Project: Integrating Inclusive Teaching in Biomedical Engineering through Faculty/Graduate Partnerships
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Patricia Jaimes, Elizabeth Bottorff, Theo Hopper, Javiera Jilberto, Jessica King, Monica Wall, Maria Coronel, Karin Jensen, Elizabeth Mays, Aaron Morris, James Weiland, Melissa Wrobel, David Nordsletten, and Tershia Pinder-Grover
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To broaden efforts for improving diversity, equity, and inclusion (DEI) in biomedical engineering (BME) education--a key area of emphasis is the integration of inclusive teaching practices. While BME faculty generally support these efforts, translating support into action remains challenging. This project aimed to address this need through a 3-phase inclusive teaching training, consisting of graduate students, faculty, and engineering education consultants. In Phase I, graduate students and faculty participated in a 6-week learning community on inclusive teaching ("Foundational Learning"). In Phase II, graduate students were paired with faculty to modify or develop new inclusive teaching materials to be integrated into a BME course ("Experiential Learning"). Phase III was the implementation of these materials. To assess Phases I & II, graduate student participants reflected on their experiences on the project. To assess Phase III, surveys were administered to students in IT-BME-affiliated courses as well as those taking other BME-related courses. Phases I & II: graduate students responded positively to the opportunity to engage in this inclusive teaching experiential learning opportunity. Phase III: survey results indicated that the incorporation of inclusive teaching practices in BME courses enhanced the student learning experience. The IT-BME project supported graduate students and faculty in learning about, creating, and implementing inclusive teaching practices in a collaborative and supportive environment. This project will serve to both train the next class of instructors and use their study of inclusive teaching concepts to facilitate the creation of ideas and materials that will benefit the BME curriculum and students.
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- 2024
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7. Genome divergence and reproductive incompatibility among populations of Ganaspis near brasiliensis.
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Hopper, Keith, Wang, Xingeng, Kenis, Marc, Seehausen, M, Abram, Paul, Daane, Kent, Buffington, Matthew, Hoelmer, Kim, Kingham, Brewster, Shevchenko, Olga, and Bernberg, Erin
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Hymenoptera ,biological control ,genome annotation ,genome assembly ,parasitoid ,reproductive incompatibility ,Animals ,Drosophila ,Genome ,Insect ,Reproduction ,Reproductive Isolation ,Phylogeny ,Female ,Genetic Variation ,Genomics - Abstract
During the last decade, the spotted wing drosophila, Drosophila suzukii, has spread from eastern Asia to the Americas, Europe, and Africa. This fly attacks many species of cultivated and wild fruits with soft, thin skins, where its serrated ovipositor allows it to lay eggs in undamaged fruit. Parasitoids from the native range of D. suzukii may provide sustainable management of this polyphagous pest. Among these parasitoids, host-specificity testing has revealed a lineage of Ganaspis near brasiliensis, referred to in this paper as G1, that appears to be a cryptic species more host-specific to D. suzukii than other parasitoids. Differentiation among cryptic species is critical for introduction and subsequent evaluation of their impact on D. suzukii. Here, we present results on divergence in genomic sequences and architecture and reproductive isolation between lineages of Ganaspis near brasiliensis that appear to be cryptic species. We studied five populations, two from China, two from Japan, and one from Canada, identified as the G1 vs G3 lineages based on differences in cytochrome oxidase l sequences. We assembled and annotated the genomes of these populations and analyzed divergences in sequence and genome architecture between them. We also report results from crosses to test reproductive compatibility between the G3 lineage from China and the G1 lineage from Japan. The combined results on sequence divergence, differences in genome architectures, ortholog divergence, reproductive incompatibility, differences in host ranges and microhabitat preferences, and differences in morphology show that these lineages are different species. Thus, the decision to evaluate the lineages separately and only import and introduce the more host-specific lineage to North America and Europe was appropriate.
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- 2024
8. 2024 RECOVER Guidelines: Updated treatment recommendations for CPR in dogs and cats
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Burkitt‐Creedon, Jamie M, Boller, Manuel, Fletcher, Daniel J, Brainard, Benjamin M, Buckley, Gareth J, Epstein, Steven E, Fausak, Erik D, Hopper, Kate, Lane, Selena L, Rozanski, Elizabeth A, and Wolf, Jacob
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Veterinary Sciences ,Agricultural ,Veterinary and Food Sciences ,Dogs ,Animals ,Cats ,Cardiopulmonary Resuscitation ,Cat Diseases ,Dog Diseases ,Heart Arrest ,canine ,cardiopulmonary resuscitation ,clinical trials ,consensus guidelines ,critical care ,evidence-based medicine ,feline ,evidence‐based medicine ,Veterinary sciences - Abstract
ObjectiveAfter the 2012 Reassessment Campaign on Veterinary Resuscitation (RECOVER) CPR Guidelines, this is an update of evidence-based consensus guidelines for Basic Life Support (BLS), advanced life support (ALS), and periarrest monitoring.DesignThese RECOVER CPR Guidelines were generated using a modified version of the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system for evidence evaluation and translation of this evidence into clear and actionable clinical instructions. Prioritized clinical questions in the Population, Intervention, Comparator, and Outcome (PICO) format were used as the basis to conduct systematic literature searches by information specialists, to extract information from relevant publications, to assess this evidence for quality, and finally to translate the findings into treatment recommendations. These recommendations were reviewed by the RECOVER writing group and opened for comment by veterinary professionals for 4 weeks.SettingTransdisciplinary, international collaboration in university, specialty, and emergency practice.ResultsA total of 40 worksheets were prepared to evaluate questions across the 3 domains of BLS, ALS and Monitoring, resulting in 90 individual treatment recommendations. High-dose epinephrine is no longer recommended, and atropine, if used, is only administered once. Bag-mask ventilation is prioritized over mouth-to-nose ventilation in nonintubated animals. In addition, an algorithm for initial assessment, an updated CPR algorithm, a rhythm diagnosis tool, and an updated drug dosing table are provided.ConclusionsWhile the majority of the BLS and ALS recommendations remain unchanged, some noteworthy changes were made due to new evidence that emerged over the past 10 years. Indirectness of evidence remains the largest impediment to the certainty of guidelines formulation and underscores an urgent need for more studies in the target species of dogs and cats.
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- 2024
9. 2024 RECOVER Guidelines: Methods, evidence identification, evaluation, and consensus process for development of treatment recommendations
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Fletcher, Daniel J, Boller, Manuel, Burkitt‐Creedon, Jamie M, Fausak, Erik, Van Noord, Megan G, Mears, Kim, Hopper, Kate, and Epstein, Steven E
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Veterinary Sciences ,Agricultural ,Veterinary and Food Sciences ,Prevention ,Animals ,Veterinary Medicine ,Consensus ,Practice Guidelines as Topic ,Evidence-Based Medicine ,Cardiopulmonary Resuscitation ,Heart Arrest ,cardiopulmonary resuscitation ,clinical trials ,consensus guidelines ,critical care ,development and evaluation ,evidence-based medicine ,GRADE ,grading of recommendations assessment ,evidence‐based medicine ,Veterinary sciences - Abstract
ObjectiveTo describe the methodology used by the Reassessment Campaign on Veterinary Resuscitation (RECOVER) to re-evaluate the scientific evidence relevant to CPR in small and large animals, to newborn resuscitation, and to first aid and to formulate the respective consensus-based clinical guidelines.DesignThis report describes the evidence-to-guidelines process employed by RECOVER that is based on the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach and includes Information Specialist-driven systematic literature search, evidence evaluation conducted by more than 200 veterinary professionals, and provision of clinical guidelines in the domains of Preparedness and Prevention, Basic Life Support, Advanced Life Support, Post-cardiac Arrest Care, Newborn Resuscitation, First Aid, and Large Animal CPR.SettingTransdisciplinary, international collaboration in academia, referral practice, and general practice.ResultsFor this update to the RECOVER 2012 CPR guidelines, we answered 135 Population, Intervention, Comparator, and Outcome (PICO) questions with the help of a team of Domain Chairs, Information Specialists, and more than 200 Evidence Evaluators. Most primary contributors were veterinary specialists or veterinary technician specialists. The RECOVER 2024 Guidelines represent the first veterinary application of the GRADE approach to clinical guideline development. We employed an iterative process that follows a predefined sequence of steps designed to reduce bias of Evidence Evaluators and to increase the repeatability of the quality of evidence assessments and ultimately the treatment recommendations. The process also allowed numerous important knowledge gaps to emerge that form the foundation for prioritizing research efforts in veterinary resuscitation science.ConclusionsLarge collaborative, volunteer-based development of evidence- and consensus-based clinical guidelines is challenging and complex but feasible. The experience gained will help refine the process for future veterinary guidelines initiatives.
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- 2024
10. 2024 RECOVER Guidelines: Basic Life Support. Evidence and knowledge gap analysis with treatment recommendations for small animal CPR
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Hopper, Kate, Epstein, Steven E, Burkitt‐Creedon, Jamie M, Fletcher, Daniel J, Boller, Manuel, Fausak, Erik D, Mears, Kim, Crews, Molly, and Evaluators, the RECOVER Basic Life Support Domain Evidence
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Veterinary Sciences ,Agricultural ,Veterinary and Food Sciences ,Animals ,Dogs ,Cats ,Cardiopulmonary Resuscitation ,Veterinary Medicine ,Cat Diseases ,Heart Arrest ,Evidence-Based Medicine ,Dog Diseases ,canine ,cardiopulmonary resuscitation ,clinical trials ,consensus guidelines ,critical care ,evidence-based medicine ,feline ,RECOVER Basic Life Support Domain Evidence Evaluators ,evidence‐based medicine ,Veterinary sciences - Abstract
ObjectiveTo systematically review evidence and devise treatment recommendations for basic life support (BLS) in dogs and cats and to identify critical knowledge gaps.DesignStandardized, systematic evaluation of literature pertinent to BLS following Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) methodology. Prioritized questions were each reviewed by 2 Evidence Evaluators, and findings were reconciled by BLS Domain Chairs and Reassessment Campaign on Veterinary Resuscitation (RECOVER) Co-Chairs to arrive at treatment recommendations commensurate to quality of evidence, risk to benefit relationship, and clinical feasibility. This process was implemented using an Evidence Profile Worksheet for each question that included an introduction, consensus on science, treatment recommendations, justification for these recommendations, and important knowledge gaps. A draft of these worksheets was distributed to veterinary professionals for comment for 4 weeks prior to finalization.SettingTransdisciplinary, international collaboration in university, specialty, and emergency practice.ResultsTwenty questions regarding animal position, chest compression point and technique, ventilation strategies, as well as the duration of CPR cycles and chest compression pauses were examined, and 32 treatment recommendations were formulated. Out of these, 25 addressed chest compressions and 7 informed ventilation during CPR. The recommendations were founded predominantly on very low quality of evidence and expert opinion. These new treatment recommendations continue to emphasize the critical importance of high-quality, uninterrupted chest compressions, with a modification suggested for the chest compression technique in wide-chested dogs. When intubation is not possible, bag-mask ventilation using a tight-fitting facemask with oxygen supplementation is recommended rather than mouth-to-nose ventilation.ConclusionsThese updated RECOVER BLS treatment recommendations emphasize continuous chest compressions, conformation-specific chest compression techniques, and ventilation for all animals. Very low quality of evidence due to absence of clinical data in dogs and cats consistently compromised the certainty of recommendations, emphasizing the need for more veterinary research in this area.
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- 2024
11. Hardware Trojan Detection Potential and Limits with the Quantum Diamond Microscope
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Lenz, Jacob N., Perryman, Scott K., Martynowych, Dmitro J., Hopper, David A., and Oliver, Sean M.
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Physics - Instrumentation and Detectors ,Quantum Physics - Abstract
The Quantum Diamond Microscope (QDM) is an instrument with a demonstrated capability to image electrical current in integrated circuits (ICs), which shows promise for detection of hardware Trojans. The anomalous current activity caused by hardware Trojans manifests through a magnetic field side channel that can be imaged with the QDM, potentially allowing for detection and localization of the effects of tampering. This paper seeks to identify the capabilities of the QDM for hardware Trojan detection through the analysis of previous QDM work as well as QDM physical limits and potential Trojan behaviors. QDM metrics of interest are identified, such as spatial resolution, sensitivity, time-to-result, and field-of-view. Rare event detection on an FPGA is demonstrated with the QDM. The concept of operations is identified for QDM utilization at different steps of IC development, noting necessary considerations and limiting factors for use at different development stages. Finally, the effects of hardware Trojans on IC current activity are estimated and compared to QDM sensitivities to project QDM detection potential for ICs of varying process sizes.
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- 2024
12. Resisting Concepts as Starting Points in a High School Leadership Pathway Alongside Indigenous Youth
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Dubnewick, Michael, Lessard, Sean, Hopper, Tristan, and Lewis, Brian
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This writing draws on an ongoing narrative inquiry with 10 Indigenous youth as they negotiated their lives within a high school leadership pathway. Our research demonstrates the need to resist starting in concepts as an intentional shift to being and becoming wakeful to storied lives on and off school landscapes. Three resonant threads are highlighted as we listened across the youths' lives. These threads are framed as pathways the youth asked us to consider in terms of reimagining schools as places of unfolding kinship, reimagining schools beyond notions of becoming responsible adults, and reimagining in-between spaces as landscapes that matter.
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- 2023
13. Students' and Teachers' Beliefs about Written Corrective Feedback: Perspectives on Amount, Type, and Focus of Feedback in an EFL Setting
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Derek Hopper and Neil Bowen
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Many writing teachers believe that giving written corrective feedback (WCF) is an important part of learning to write. Equally, students like to receive it. However, most previous research on WCF has looked at its overall effectiveness, with less attention paid to the differences of opinion between students and their teachers, and the implications of these differences. Accordingly, our aim was to investigate further these differences by carrying out a partial replication of Amrhein and Nassaji (2010). Using a combination of multiple-choice questions, Likert scale items, and open-ended questions, we sampled the beliefs of 469 undergraduates and 40 of their teachers at two public Thai universities. Our findings revealed significant differences of opinion between both groups when it came to the ideal amount of WCF, preferred type of WCF for grammatical errors, and the most useful WCF for specific error types. Qualitative comments also highlighted the affective side of WCF, the realities of the task-at-hand for teachers, and a misalignment between theory and practice. Based on our findings, we make recommendations for teacher development, cross-cultural awareness in teaching writing, increased communication between students, teachers, and theorists, and the importance of assessment rubrics in the feedback process.
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- 2023
14. NSQIP data collection up to 30 postoperative days is sufficient to capture some complications in orthopedic surgeries
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Hopper, Haleigh M., Nelson, Chase T., Satalich, James R., O’Neill, Conor N., and Vap, Alexander R.
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- 2024
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15. Admixture and reproductive skew shape the conservation value of ex situ populations of the Critically Endangered eastern black rhino
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Elsner-Gearing, Franziska, Kretzschmar, Petra, Shultz, Susanne, Pilgrim, Mark, Dawson, Deborah Ann, Horsburgh, Gavin John, Hruby, Jírí, Hopper, Jane, King, Tony, and Walton, Catherine
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- 2024
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16. Understanding the genetic complexity of puberty timing across the allele frequency spectrum
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Kentistou, Katherine A., Kaisinger, Lena R., Stankovic, Stasa, Vaudel, Marc, Mendes de Oliveira, Edson, Messina, Andrea, Walters, Robin G., Liu, Xiaoxi, Busch, Alexander S., Helgason, Hannes, Thompson, Deborah J., Santoni, Federico, Petricek, Konstantin M., Zouaghi, Yassine, Huang-Doran, Isabel, Gudbjartsson, Daniel F., Bratland, Eirik, Lin, Kuang, Gardner, Eugene J., Zhao, Yajie, Jia, Raina Y., Terao, Chikashi, Riggan, Marjorie J., Bolla, Manjeet K., Yazdanpanah, Mojgan, Yazdanpanah, Nahid, Bradfield, Jonathan P., Broer, Linda, Campbell, Archie, Chasman, Daniel I., Cousminer, Diana L., Franceschini, Nora, Franke, Lude H., Girotto, Giorgia, He, Chunyan, Järvelin, Marjo-Riitta, Joshi, Peter K., Kamatani, Yoichiro, Karlsson, Robert, Luan, Jian’an, Lunetta, Kathryn L., Mägi, Reedik, Mangino, Massimo, Medland, Sarah E., Meisinger, Christa, Noordam, Raymond, Nutile, Teresa, Concas, Maria Pina, Polašek, Ozren, Porcu, Eleonora, Ring, Susan M., Sala, Cinzia, Smith, Albert V., Tanaka, Toshiko, van der Most, Peter J., Vitart, Veronique, Wang, Carol A., Willemsen, Gonneke, Zygmunt, Marek, Ahearn, Thomas U., Andrulis, Irene L., Anton-Culver, Hoda, Antoniou, Antonis C., Auer, Paul L., Barnes, Catriona L. K., Beckmann, Matthias W., Berrington de Gonzalez, Amy, Bogdanova, Natalia V., Bojesen, Stig E., Brenner, Hermann, Buring, Julie E., Canzian, Federico, Chang-Claude, Jenny, Couch, Fergus J., Cox, Angela, Crisponi, Laura, Czene, Kamila, Daly, Mary B., Demerath, Ellen W., Dennis, Joe, Devilee, Peter, De Vivo, Immaculata, Dörk, Thilo, Dunning, Alison M., Dwek, Miriam, Eriksson, Johan G., Fasching, Peter A., Fernandez-Rhodes, Lindsay, Ferreli, Liana, Fletcher, Olivia, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A., González-Neira, Anna, Grallert, Harald, Guénel, Pascal, Haiman, Christopher A., Hall, Per, Hamann, Ute, Hakonarson, Hakon, Hart, Roger J., Hickey, Martha, Hooning, Maartje J., Hoppe, Reiner, Hopper, John L., Hottenga, Jouke-Jan, Hu, Frank B., Huebner, Hanna, Hunter, David J., Jernström, Helena, John, Esther M., Karasik, David, Khusnutdinova, Elza K., Kristensen, Vessela N., Lacey, James V., Lambrechts, Diether, Launer, Lenore J., Lind, Penelope A., Lindblom, Annika, Magnusson, Patrik K. E., Mannermaa, Arto, McCarthy, Mark I., Meitinger, Thomas, Menni, Cristina, Michailidou, Kyriaki, Millwood, Iona Y., Milne, Roger L., Montgomery, Grant W., Nevanlinna, Heli, Nolte, Ilja M., Nyholt, Dale R., Obi, Nadia, O’Brien, Katie M., Offit, Kenneth, Oldehinkel, Albertine J., Ostrowski, Sisse R., Palotie, Aarno, Pedersen, Ole B., Peters, Annette, Pianigiani, Giulia, Plaseska-Karanfilska, Dijana, Pouta, Anneli, Pozarickij, Alfred, Radice, Paolo, Rennert, Gad, Rosendaal, Frits R., Ruggiero, Daniela, Saloustros, Emmanouil, Sandler, Dale P., Schipf, Sabine, Schmidt, Carsten O., Schmidt, Marjanka K., Small, Kerrin, Spedicati, Beatrice, Stampfer, Meir, Stone, Jennifer, Tamimi, Rulla M., Teras, Lauren R., Tikkanen, Emmi, Turman, Constance, Vachon, Celine M., Wang, Qin, Winqvist, Robert, Wolk, Alicja, Zemel, Babette S., Zheng, Wei, van Dijk, Ko W., Alizadeh, Behrooz Z., Bandinelli, Stefania, Boerwinkle, Eric, Boomsma, Dorret I., Ciullo, Marina, Chenevix-Trench, Georgia, Cucca, Francesco, Esko, Tõnu, Gieger, Christian, Grant, Struan F. A., Gudnason, Vilmundur, Hayward, Caroline, Kolčić, Ivana, Kraft, Peter, Lawlor, Deborah A., Martin, Nicholas G., Nøhr, Ellen A., Pedersen, Nancy L., Pennell, Craig E., Ridker, Paul M., Robino, Antonietta, Snieder, Harold, Sovio, Ulla, Spector, Tim D., Stöckl, Doris, Sudlow, Cathie, Timpson, Nic J., Toniolo, Daniela, Uitterlinden, André, Ulivi, Sheila, Völzke, Henry, Wareham, Nicholas J., Widen, Elisabeth, Wilson, James F., Pharoah, Paul D. P., Li, Liming, Easton, Douglas F., Njølstad, Pål R., Sulem, Patrick, Murabito, Joanne M., Murray, Anna, Manousaki, Despoina, Juul, Anders, Erikstrup, Christian, Stefansson, Kari, Horikoshi, Momoko, Chen, Zhengming, Farooqi, I. Sadaf, Pitteloud, Nelly, Johansson, Stefan, Day, Felix R., Perry, John R. B., and Ong, Ken K.
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- 2024
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17. Familial confounding of internalising symptoms and obesity in adolescents and young adults; a co-twin analysis
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Campbell, Alexander Charles, Calais-Ferreira, Lucas, Hahn, Elisabeth, Spinath, Frank M., Hopper, John L., and Young, Jesse T.
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- 2024
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18. Room Temperature Dynamics of an Optically Addressable Single Spin in Hexagonal Boron Nitride
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Patel, Raj N., Fishman, Rebecca E. K., Huang, Tzu-Yung, Gusdorff, Jordan A., Fehr, David A., Hopper, David A., Breitweiser, S. Alex, Porat, Benjamin, Flatté, Michael E., and Bassett, Lee C.
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Condensed Matter - Mesoscale and Nanoscale Physics ,Quantum Physics - Abstract
Hexagonal boron nitride (h-BN) hosts pure single-photon emitters that have shown evidence of optically detected electronic spin dynamics. However, the electrical and chemical structure of these optically addressable spins is unknown, and the nature of their spin-optical interactions remains mysterious. Here, we use time-domain optical and microwave experiments to characterize a single emitter in h-BN exhibiting room temperature optically detected magnetic resonance. Using dynamical simulations, we constrain and quantify transition rates in the model, and we design optical control protocols that optimize the signal-to-noise ratio for spin readout. This constitutes a necessary step towards quantum control of spin states in h-BN., Comment: 15 pages, 15 figures. Updates in version 2 include modifications to figure 4, an updated estimate for T2*, and minor syntax edits to the main text and supplement for clarity
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- 2023
19. An Analysis of Shear-Dependent Mechanochemical Reaction Kinetics
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Rana, Resham, Hopper, Nicholas, Sidoroff, François, Cayer-Barrioz, Juliette, Mazuyer, Denis, and Tysoe, Wilfred T.
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- 2024
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20. Evaluation of European-based polygenic risk score for breast cancer in Ashkenazi Jewish women in Israel
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Levi, Hagai, Carmi, Shai, Rosset, Saharon, Yerushalmi, Rinat, Zick, Aviad, Yablonski-Peretz, Tamar, Consortium, The BCAC, Wang, Qin, Bolla, Manjeet K, Dennis, Joe, Michailidou, Kyriaki, Lush, Michael, Ahearn, Thomas, Andrulis, Irene L, Anton-Culver, Hoda, Antoniou, Antonis C, Arndt, Volker, Augustinsson, Annelie, Auvinen, Päivi, Freeman, Laura Beane, Beckmann, Matthias, Behrens, Sabine, Bermisheva, Marina, Bodelon, Clara, Bogdanova, Natalia V, Bojesen, Stig E, Brenner, Hermann, Byers, Helen, Camp, Nicola, Castelao, Jose, Chang-Claude, Jenny, Chirlaque, María-Dolores, Chung, Wendy, Clarke, Christine, Collaborators, NBCS, Collee, Margriet J, Colonna, Sarah, Consortium, CTS, Couch, Fergus, Cox, Angela, Cross, Simon S, Czene, Kamila, Daly, Mary, Devilee, Peter, Dork, Thilo, Dossus, Laure, Eccles, Diana M, Eliassen, A Heather, Eriksson, Mikael, Evans, Gareth, Fasching, Peter, Fletcher, Olivia, Flyger, Henrik, Fritschi, Lin, Gabrielson, Marike, Gago-Dominguez, Manuela, García-Closas, Montserrat, Garcia-Saenz, Jose Angel, Genkinger, Jeanine, Giles, Graham G, Goldberg, Mark, Guénel, Pascal, Hall, Per, Hamann, Ute, He, Wei, Hillemanns, Peter, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John, Investigators, ABCTB, Jakovchevska, Simona, Jakubowska, Anna, Jernström, Helena, John, Esther, Johnson, Nichola, Jones, Michael, Vijai, Joseph, Kaaks, Rudolf, Khusnutdinova, Elza, Kitahara, Cari, Koutros, Stella, Kristensen, Vessela, Kurian, Allison W, Lacey, James, Lambrechts, Diether, Le Marchand, Loic, Lejbkowicz, Flavio, Lindblom, Annika, Loibl, Sibylle, Lori, Adriana, Lubinski, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Mavroudis, Dimitrios, Menon, Usha, Mulligan, AnnaMarie, Murphy, Rachel, Nevelsteen, Ines, Newman, William G, and Obi, Nadia
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Biological Sciences ,Biomedical and Clinical Sciences ,Genetics ,Oncology and Carcinogenesis ,Breast Cancer ,Prevention ,Cancer ,Humans ,Female ,Breast Neoplasms ,Genome-Wide Association Study ,Jews ,Israel ,Genetic Predisposition to Disease ,Risk Factors ,Multifactorial Inheritance ,Transcription Factors ,Genomics ,Polymorphism ,Genetic ,BCAC Consortium ,NBCS Collaborators ,CTS Consortium ,ABCTB Investigators ,Polymorphism ,Genetic ,Medical and Health Sciences ,Genetics & Heredity ,Clinical sciences - Abstract
BackgroundPolygenic risk score (PRS), calculated based on genome-wide association studies (GWASs), can improve breast cancer (BC) risk assessment. To date, most BC GWASs have been performed in individuals of European (EUR) ancestry, and the generalisation of EUR-based PRS to other populations is a major challenge. In this study, we examined the performance of EUR-based BC PRS models in Ashkenazi Jewish (AJ) women.MethodsWe generated PRSs based on data on EUR women from the Breast Cancer Association Consortium (BCAC). We tested the performance of the PRSs in a cohort of 2161 AJ women from Israel (1437 cases and 724 controls) from BCAC (BCAC cohort from Israel (BCAC-IL)). In addition, we tested the performance of these EUR-based BC PRSs, as well as the established 313-SNP EUR BC PRS, in an independent cohort of 181 AJ women from Hadassah Medical Center (HMC) in Israel.ResultsIn the BCAC-IL cohort, the highest OR per 1 SD was 1.56 (±0.09). The OR for AJ women at the top 10% of the PRS distribution compared with the middle quintile was 2.10 (±0.24). In the HMC cohort, the OR per 1 SD of the EUR-based PRS that performed best in the BCAC-IL cohort was 1.58±0.27. The OR per 1 SD of the commonly used 313-SNP BC PRS was 1.64 (±0.28).ConclusionsExtant EUR GWAS data can be used for generating PRSs that identify AJ women with markedly elevated risk of BC and therefore hold promise for improving BC risk assessment in AJ women.
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- 2023
21. Ligand-induced conformational changes in the β1-adrenergic receptor revealed by hydrogen-deuterium exchange mass spectrometry
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Joanna Toporowska, Parth Kapoor, Maria Musgaard, Karolina Gherbi, Kathy Sengmany, Feng Qu, Mark Soave, Hsin-Yung Yen, Kjetil Hansen, Ali Jazayeri, Jonathan T. S. Hopper, and Argyris Politis
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Science - Abstract
Abstract G Protein Coupled Receptors (GPCRs) constitute the largest family of signalling proteins responsible for translating extracellular stimuli into intracellular functions. They play crucial roles in numerous physiological processes and are major targets for drug discovery. Dysregulation of GPCRs is implicated in various diseases, making understanding their structural dynamics critical for therapeutic development. Here, we use Hydrogen Deuterium Exchange Mass Spectrometry (HDX-MS) to explore the structural dynamics of the turkey β1-adrenergic receptor (tβ1AR) bound with nine different ligands, including agonists, partial agonists, and antagonists. We find that these ligands induce distinct dynamic patterns across the receptor, which can be grouped by compound modality. Notably, full agonist binding destabilises the intracellular loop 1 (ICL1), while antagonist binding stabilises it, highlighting ICL1’s role in G protein recruitment. Our findings indicate that the conserved L72 residue in ICL1 is crucial for maintaining receptor structural integrity and stabilising the GDP-bound state. Overall, our results provide a platform for determining drug modality and highlight how HDX-MS can be used to dissect receptor ligand interaction properties and GPCR mechanism.
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- 2024
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22. DEK regulates B-cell proliferative capacity and is associated with aggressive disease in low-grade B-cell lymphomas
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Melissa A. Hopper, Abigail R. Dropik, Janek S. Walker, Joseph P. Novak, Miranda S. Laverty, Michelle K. Manske, Xiaosheng Wu, Kerstin Wenzl, Jordan E. Krull, Vivekananda Sarangi, Matthew J. Maurer, Zhi-Zhang Yang, Miles D. Del Busso, Thomas M. Habermann, Brian K. Link, Lisa M. Rimsza, Thomas E. Witzig, Stephen M. Ansell, James R. Cerhan, Dragan Jevremovic, and Anne J. Novak
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract This study sheds light on the pivotal role of the oncoprotein DEK in B-cell lymphoma. We reveal DEK expression correlates with increased tumor proliferation and inferior overall survival in cases diagnosed with low-grade B-cell lymphoma (LGBCL). We also found significant correlation between DEK expression and copy number alterations in LGBCL tumors, highlighting a novel mechanism of LGBCL pathogenesis that warrants additional exploration. To interrogate the mechanistic role of DEK in B-cell lymphoma, we generated a DEK knockout cell line model, which demonstrated DEK depletion caused reduced proliferation and altered expression of key cell cycle and apoptosis-related proteins, including Bcl-2, Bcl-xL, and p53. Notably, DEK depleted cells showed increased sensitivity to apoptosis-inducing agents, including venetoclax and staurosporine, which underscores the therapeutic potential of targeting DEK in B-cell lymphomas. Overall, our study contributes to a better understanding of DEK’s role as an oncoprotein in B-cell lymphomas, highlighting its potential as both a promising therapeutic target and a novel biomarker for aggressive LGBCL. Further research elucidating the molecular mechanisms underlying DEK-mediated tumorigenesis could pave the way for improved treatment strategies and better clinical outcomes for patients with B-cell lymphoma.
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- 2024
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23. Multi-channel portable odor delivery device for self-administered and rapid smell testing
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Richard Hopper, Daniel Popa, Emanuela Maggioni, Devarsh Patel, Marianna Obrist, Basile Nicolas Landis, Julien Wen Hsieh, and Florin Udrea
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Engineering (General). Civil engineering (General) ,TA1-2040 - Abstract
Abstract To improve our understanding of the perception of odors, researchers are often required to undertake experimental procedures with users exposed to multiple odors in a variety of settings, including to diagnose smell loss in clinics and care homes. Existing smell tests are typically administered using multiple sniffing pens, manually presented to patients by a highly specialized nurse using a time-consuming and complex testing paradigm. Automated odor delivery devices, such as olfactometer systems, exist but are expensive, bulky and typically lab based, making them difficult to use for on the ground odor delivery. Here we have developed a portable, affordable, odor delivery device that can deliver 24 odors through individual channels with high temporal precision and without cross-contamination. The device allows for the rapid, flexible sequencing of odors via digital control using a mobile application and has been experimentally validated in the lab, as well as tested on patients. The design provides several advantages for investigating olfactory perception and offers the possibility that users can one day self-administer smell tests in a range of settings, including at home, allowing smell healthcare services to evolve and become part of a routine practice and self-care culture.
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- 2024
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24. Reproductive factors and mammographic density within the International Consortium of Mammographic Density: A cross-sectional study
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Jessica O’Driscoll, Anya Burton, Gertraud Maskarinec, Beatriz Perez-Gomez, Celine Vachon, Hui Miao, Martín Lajous, Ruy López-Ridaura, A. Heather Eliassen, Ana Pereira, Maria Luisa Garmendia, Rulla M. Tamimi, Kimberly Bertrand, Ava Kwong, Giske Ursin, Eunjung Lee, Samera A. Qureshi, Huiyan Ma, Sarah Vinnicombe, Sue Moss, Steve Allen, Rose Ndumia, Sudhir Vinayak, Soo-Hwang Teo, Shivaani Mariapun, Farhana Fadzli, Beata Peplonska, Chisato Nagata, Jennifer Stone, John L. Hopper, Graham Giles, Vahit Ozmen, Mustafa Erkin Aribal, Joachim Schüz, Carla H. Van Gils, Johanna O. P. Wanders, Reza Sirous, Mehri Sirous, John Hipwell, Jisun Kim, Jong Won Lee, Mikael Hartman, Jingmei Li, Christopher Scott, Anna M. Chiarelli, Linda Linton, Marina Pollan, Anath Arzee Flugelman, Dorria Salem, Rasha Kamal, Norman Boyd, Isabel dos-Santos-Silva, Valerie McCormack, and Maeve Mullooly
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Mammographic density ,Reproductive factors ,Parity ,Age at first birth ,Breastfeeding ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Background Elevated mammographic density (MD) for a woman’s age and body mass index (BMI) is an established breast cancer risk factor. The relationship of parity, age at first birth, and breastfeeding with MD is less clear. We examined the associations of these factors with MD within the International Consortium of Mammographic Density (ICMD). Methods ICMD is a consortium of 27 studies with pooled individual-level epidemiological and MD data from 11,755 women without breast cancer aged 35–85 years from 22 countries, capturing 40 country-& ethnicity-specific population groups. MD was measured using the area-based tool Cumulus. Meta-analyses across population groups and pooled analyses were used to examine linear regression associations of square-root (√) transformed MD measures (percent MD (PMD), dense area (DA), and non-dense area (NDA)) with parity, age at first birth, ever/never breastfed and lifetime breastfeeding duration. Models were adjusted for age at mammogram, age at menarche, BMI, menopausal status, use of hormone replacement therapy, calibration method, mammogram view and reader, and parity and age at first birth when not the association of interest. Results Among 10,988 women included in these analyses, 90.1% (n = 9,895) were parous, of whom 13% (n = 1,286) had ≥ five births. The mean age at first birth was 24.3 years (Standard deviation = 5.1). Increasing parity (per birth) was inversely associated with √PMD (β: − 0.05, 95% confidence interval (CI): − 0.07, − 0.03) and √DA (β: − 0.08, 95% CI: − 0.12, − 0.05) with this trend evident until at least nine births. Women who were older at first birth (per five-year increase) had higher √PMD (β:0.06, 95% CI:0.03, 0.10) and √DA (β:0.06, 95% CI:0.02, 0.10), and lower √NDA (β: − 0.06, 95% CI: − 0.11, − 0.01). In stratified analyses, this association was only evident in women who were post-menopausal at MD assessment. Among parous women, no associations were found between ever/never breastfed or lifetime breastfeeding duration (per six-month increase) and √MD. Conclusions Associations with higher parity and older age at first birth with √MD were consistent with the direction of their respective associations with breast cancer risk. Further research is needed to understand reproductive factor-related differences in the composition of breast tissue and their associations with breast cancer risk.
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- 2024
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25. Poetry and Syllable-Stress Identification as the Means for Understanding Dyslexia and Reading-Related Difficulties
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Peter Richtsmeier, Matthew Hopper, Sheri Vasinda, Hannah Krimm, Michelle Moore, and Yu Zhang
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In young adults and adolescents, dyslexia typically is characterized by slow or laborious reading. These reading difficulties are underpinned at least partly by a phonological deficit that disrupts cognitive connections between spoken and written language. Prosodic stress is a phonological property of spoken language reflecting differences in syllable stress, for example, between the noun REC.ord and the verb re.CORD. Prosodic stress is not reflected in the written form "record," but evidence suggests that knowledge of prosodic stress is relatively weak in people with dyslexia. The present study examines the abilities of young adults with and without a history of dyslexia to identify stressed syllables in poems. In our main analysis, there was no significant difference for marking stressed syllables between the participants with and without dyslexia. However, accuracy for marking stress correlated with a measure of nonword reading, consistent with previous findings of overlapping segmental and prosodic deficits in dyslexia. Additional correlations of the task to both reading and language measures raise questions about the overlap between dyslexia and other disorders, particularly developmental language disorder. We also discuss how the poetry task could be used as an instructional intervention or treatment activity for people with limited awareness of prosodic stress.
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- 2024
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26. Superintendents' Views of Principal Burnout amidst Change: A Narrative Inquiry
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Clinton Robert Hopper
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This study delves into the critical issue of principal burnout within Houston's uniquely challenging environment, marked by socioeconomic disparities, Hurricane Harvey's aftermath, and the COVID-19 pandemic. Utilizing Maslach's three dimensions of burnout model, it explores the manifestations of emotional exhaustion, depersonalization, and reduced personal accomplishment among principals, alongside superintendents' perceptions and strategies for addressing these issues. Through narrative inquiry, interviews with six superintendents within the Region 4 Educational Service Center's jurisdiction reveal the nuanced understanding and innovative strategies to combat principal burnout in the post-pandemic era. This comprehensive examination, grounded in Maslach's model, highlights the critical need for effective burnout mitigation strategies, informing policy reforms and interventions that promote principal retention and well-being. The findings offer insights into superintendent-principal dynamics, contributing to the broader understanding of leadership and well-being in education. This study's implications extend to guiding future research on school improvement and student achievement, ultimately aiming to enhance the sustainability of school leadership and the quality of education in Houston and beyond. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]
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- 2024
27. The Clinical Anatomy Fellowship: A Participants' Perspective
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Grace E. Thiel, Celeste M. Murtha, Jennifer F. Dennis, and Mari Hopper
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Kansas City University offers a Clinical Anatomy Fellowship which enrolls nine medical students during each academic year and provides training in research, teaching, and advanced anatomical topics. The Fellows practice as novice educators, working alongside Anatomy faculty to teach medical students in the Gross Anatomy laboratory. However, little has been reported related to Fellowship participation and success outcomes. This survey-based study was designed to explore (1) student motivation(s) for pursuing the Fellowship, (2) benefits of participation, and (3) the perceived impact on residency applications and career success. Three unique populations were surveyed. The most important factors driving application to the Fellowship were a desire to increase competitiveness in the residency application process (Likert mean score 4.7-5.0) and a passion for Anatomy (Likert mean score 4.3-4.7). Taking a year away from the College of Osteopathic Medicine curriculum (Likert mean score 4.4) and delaying clinical exposure (Likert mean score 4.2) were the most important deterrents to application. The most reported benefits after program completion included opportunities to build a strong residency application (44% and 50% of Fellows), conduct research (44% and 45% of Fellows), and participate in teaching (11% and 50% of Fellows). 73% of past Fellows matched into their top specialty of choice. Flexibility in the program allows participants to individualize their Fellowship experience to address their personal goals related to residency applications and careers as future physicians. As the results suggest, the Clinical Anatomy Fellowship benefits Fellows, signaling other medical institutions to consider adopting a similar program.
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- 2024
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28. The Clinical Anatomy Fellowship: Revolutionizing Curricular Experiences for Faculty and Students
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Celeste M. Murtha, Grace E. Thiel, Jennifer F. Dennis, and Mari Hopper
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Fellows completing the Clinical Anatomy Fellowship at Kansas City University assist Anatomy faculty in the Gross Anatomy laboratory, complete robust research projects, and support other departments. The program's positive impact on participants has been reported; however, the impact on individuals interfacing with Fellows has not been investigated. A follow-up, survey-based (Likert scale, multiple-choice, open-ended) study was conducted to evaluate faculty, staff, and student perceptions of the program. Ninety-five percent of surveyed faculty and staff (n = 22) perceived the Fellows as beneficial to students, faculty, and the university (p < 0.05) by acting as role models (95%) and mentors (90%), contributing to educational processes (90%), and reducing faculty work burden (81%) (p < 0.05). Student responses (n = 95) were also positive: 97% perceived interactions with Fellows as beneficial (p < 0.05). A passion for Anatomy (mean, 4.6; p < 0.05) and the opportunity to increase competitiveness for residency (mean, 4.5; p < 0.05) were the most important factors driving interest in the Fellowship (Cronbach's alpha, 0.766). In contrast, diverting a year from the school's curriculum (mean, 4.4; p < 0.05) and delaying clinical experiences (mean, 4.3; p < 0.05) were the most important deterrents (Cronbach's alpha, 0.505). Additionally, the financial investment required by the program is lower than that associated with hiring full-time faculty. Analysis comparing employment of Fellows versus associate-level faculty identified annual net savings of $370,000. Not only does the Fellowship augment faculty and student experiences at the university, but it also allows for substantial cost savings. Collectively, these data are evidence for other health professional institutions to consider adopting a similar program.
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- 2024
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29. Committee Moderation on Encrypted Messaging Platforms
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Pattison, Alistair and Hopper, Nicholas
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Computer Science - Cryptography and Security - Abstract
Encrypted messaging services like WhatsApp, Facebook Messenger, and Signal provide secure and deniable communication for billions across the world, but these exact properties prevent holding users accountable for sending messages that are abusive, misinformative, or otherwise harmful to society. Previous works have addressed this concern by allowing a moderator to verify the identity of a message's sender if a message is reported; if not reported, messages maintain all security guarantees. Using primitives from threshold cryptography, this work extends the message-reporting protocol Hecate from Issa, Alhaddad, and Varia to a setting in which consensus among a group of moderators is required to reveal and verify the identity of a message's sender., Comment: Presented at the 44th IEEE Symposium on Security and Privacy
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- 2023
30. A Likelihood Ratio Approach for Utilizing Case‐Control Data in the Clinical Classification of Rare Sequence Variants: Application to BRCA1 and BRCA2
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Zanti, Maria, O′Mahony, Denise G, Parsons, Michael T, Li, Hongyan, Dennis, Joe, Aittomäkkiki, Kristiina, Andrulis, Irene L, Anton-Culver, Hoda, Aronson, Kristan J, Augustinsson, Annelie, Becher, Heiko, Bojesen, Stig E, Bolla, Manjeet K, Brenner, Hermann, Brown, Melissa A, Buys, Saundra S, Canzian, Federico, Caputo, Sandrine M, Castelao, Jose E, Chang-Claude, Jenny, Collaborators, GC-HBOC study, Czene, Kamila, Daly, Mary B, De Nicolo, Arcangela, Devilee, Peter, Dörk, Thilo, Dunning, Alison M, Dwek, Miriam, Eccles, Diana M, Engel, Christoph, Evans, D Gareth, Fasching, Peter A, Gago-Dominguez, Manuela, García-Closas, Montserrat, García-Sáenz, José A, Gentry-Maharaj, Aleksandra, Giele, Willemina RR Geurts-, Giles, Graham G, Glendon, Gord, Goldberg, Mark S, Garcia, Encarna B Gómez, Güendert, Melanie, Guénel, Pascal, Hahnen, Eric, Haiman, Christopher A, Hall, Per, Hamann, Ute, Harkness, Elaine F, Hogervorst, Frans BL, Hollestelle, Antoinette, Hoppe, Reiner, Hopper, John L, Houdayer, Claude, Houlston, Richard S, Howell, Anthony, Investigators, ABCTB, Jakimovska, Milena, Jakubowska, Anna, Jernström, Helena, John, Esther M, Kaaks, Rudolf, Kitahara, Cari M, Koutros, Stella, Kraft, Peter, Kristensen, Vessela N, Lacey, James V, Lambrechts, Diether, Léoné, Melanie, Lindblom, Annika, Lubiński, Jan, Lush, Michael, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martinez, Maria Elena, Menon, Usha, Milne, Roger L, Monteiro, Alvaro N, Murphy, Rachel A, Neuhausen, Susan L, Nevanlinna, Heli, Newman, William G, Offit, Kenneth, Park, Sue K, James, Paul, Peterlongo, Paolo, Peto, Julian, Plaseska-Karanfilska, Dijana, Punie, Kevin, Radice, Paolo, Rashid, Muhammad U, Rennert, Gad, Romero, Atocha, Rosenberg, Efraim H, Saloustros, Emmanouil, Sandler, Dale P, Schmidt, Marjanka K, Schmutzler, Rita K, and Shu, Xiao-Ou
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Biological Sciences ,Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Genetics ,Biotechnology ,Genetic Testing ,Prevention ,Cancer ,Human Genome ,Women's Health ,Breast Cancer ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Humans ,Case-Control Studies ,BRCA2 Protein ,Genetic Predisposition to Disease ,Female ,BRCA1 Protein ,Breast Neoplasms ,Likelihood Functions ,Genetic Variation ,Penetrance ,GC-HBOC study Collaborators ,ABCTB Investigators ,ACMG/AMP ,BRCA ,PS4 ,VUS ,case-control ,likelihood ratio ,variant classification ,Clinical Sciences ,Genetics & Heredity ,Clinical sciences - Abstract
A large number of variants identified through clinical genetic testing in disease susceptibility genes, are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion), can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analyses of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC), and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity - findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared to classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and pre-formatted excel calculators for implementation of the method for rare variants in BRCA1, BRCA2 and other high-risk genes with known penetrance.
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- 2023
31. Short-term adverse event rates and risk factors following total elbow arthroplasty for fracture and arthropathy: a matched analysis of nationally representative data
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Kiritsis, Nicholas R., Savsani, Kush, Hopper, Haleigh M., O’Neill, Conor N., Satalich, James R., Edge, Carl, and Vanderbeck, Jennifer L.
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- 2024
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32. Ligand-induced conformational changes in the β1-adrenergic receptor revealed by hydrogen-deuterium exchange mass spectrometry
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Toporowska, Joanna, Kapoor, Parth, Musgaard, Maria, Gherbi, Karolina, Sengmany, Kathy, Qu, Feng, Soave, Mark, Yen, Hsin-Yung, Hansen, Kjetil, Jazayeri, Ali, Hopper, Jonathan T. S., and Politis, Argyris
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- 2024
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33. Multi-channel portable odor delivery device for self-administered and rapid smell testing
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Hopper, Richard, Popa, Daniel, Maggioni, Emanuela, Patel, Devarsh, Obrist, Marianna, Landis, Basile Nicolas, Hsieh, Julien Wen, and Udrea, Florin
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- 2024
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34. DEK regulates B-cell proliferative capacity and is associated with aggressive disease in low-grade B-cell lymphomas
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Hopper, Melissa A., Dropik, Abigail R., Walker, Janek S., Novak, Joseph P., Laverty, Miranda S., Manske, Michelle K., Wu, Xiaosheng, Wenzl, Kerstin, Krull, Jordan E., Sarangi, Vivekananda, Maurer, Matthew J., Yang, Zhi-Zhang, Del Busso, Miles D., Habermann, Thomas M., Link, Brian K., Rimsza, Lisa M., Witzig, Thomas E., Ansell, Stephen M., Cerhan, James R., Jevremovic, Dragan, and Novak, Anne J.
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- 2024
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35. Reproductive factors and mammographic density within the International Consortium of Mammographic Density: A cross-sectional study
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O’Driscoll, Jessica, Burton, Anya, Maskarinec, Gertraud, Perez-Gomez, Beatriz, Vachon, Celine, Miao, Hui, Lajous, Martín, López-Ridaura, Ruy, Eliassen, A. Heather, Pereira, Ana, Garmendia, Maria Luisa, Tamimi, Rulla M., Bertrand, Kimberly, Kwong, Ava, Ursin, Giske, Lee, Eunjung, Qureshi, Samera A., Ma, Huiyan, Vinnicombe, Sarah, Moss, Sue, Allen, Steve, Ndumia, Rose, Vinayak, Sudhir, Teo, Soo-Hwang, Mariapun, Shivaani, Fadzli, Farhana, Peplonska, Beata, Nagata, Chisato, Stone, Jennifer, Hopper, John L., Giles, Graham, Ozmen, Vahit, Aribal, Mustafa Erkin, Schüz, Joachim, Van Gils, Carla H., Wanders, Johanna O. P., Sirous, Reza, Sirous, Mehri, Hipwell, John, Kim, Jisun, Lee, Jong Won, Hartman, Mikael, Li, Jingmei, Scott, Christopher, Chiarelli, Anna M., Linton, Linda, Pollan, Marina, Flugelman, Anath Arzee, Salem, Dorria, Kamal, Rasha, Boyd, Norman, dos-Santos-Silva, Isabel, McCormack, Valerie, and Mullooly, Maeve
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- 2024
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36. Comparison of AI-integrated pathways with human-AI interaction in population mammographic screening for breast cancer
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Frazer, Helen M. L., Peña-Solorzano, Carlos A., Kwok, Chun Fung, Elliott, Michael S., Chen, Yuanhong, Wang, Chong, Lippey, Jocelyn F., Hopper, John L., Brotchie, Peter, Carneiro, Gustavo, and McCarthy, Davis J.
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- 2024
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37. A diverse proteome is present and enzymatically active in metabolite extracts
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House, Rachel (Rae) J., Soper-Hopper, Molly T., Vincent, Michael P., Ellis, Abigail E., Capan, Colt D., Madaj, Zachary B., Wolfrum, Emily, Isaguirre, Christine N., Castello, Carlos D., Johnson, Amy B., Escobar Galvis, Martha L., Williams, Kelsey S., Lee, Hyoungjoo, and Sheldon, Ryan D.
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- 2024
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38. Multiomic analysis identifies a high-risk signature that predicts early clinical failure in DLBCL
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Wenzl, Kerstin, Stokes, Matthew E., Novak, Joseph P., Bock, Allison M., Khan, Sana, Hopper, Melissa A., Krull, Jordan E., Dropik, Abigail R., Walker, Janek S., Sarangi, Vivekananda, Mwangi, Raphael, Ortiz, Maria, Stong, Nicholas, Huang, C. Chris, Maurer, Matthew J., Rimsza, Lisa, Link, Brian K., Slager, Susan L., Asmann, Yan, Mondello, Patrizia, Morin, Ryan, Ansell, Stephen M., Habermann, Thomas M., Witzig, Thomas E., Feldman, Andrew L., King, Rebecca L., Nowakowski, Grzegorz, Cerhan, James R., Gandhi, Anita K., and Novak, Anne J.
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- 2024
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39. The impact of incident stroke on cognitive trajectories in later life
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Vishwanath, Swarna, Hopper, Ingrid, Cloud, Geoffrey C., Chong, Trevor T-J, Shah, Raj C., Donnan, Geoffrey A., Williamson, Jeff D., Eaton, Charles B., Wolfe, Rory, Reid, Christopher M., Tonkin, Andrew M., Orchard, Suzanne G., Fitzgerald, Sharyn, Murray, Anne M., Woods, Robyn L., Nelson, Mark R., Sood, Ajay, Steves, Claire J., and Ryan, Joanne
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- 2024
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40. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
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Chen, Zhishan, Guo, Xingyi, Tao, Ran, Huyghe, Jeroen R., Law, Philip J., Fernandez-Rozadilla, Ceres, Ping, Jie, Jia, Guochong, Long, Jirong, Li, Chao, Shen, Quanhu, Xie, Yuhan, Timofeeva, Maria N., Thomas, Minta, Schmit, Stephanie L., Díez-Obrero, Virginia, Devall, Matthew, Moratalla-Navarro, Ferran, Fernandez-Tajes, Juan, Palles, Claire, Sherwood, Kitty, Briggs, Sarah E. W., Svinti, Victoria, Donnelly, Kevin, Farrington, Susan M., Blackmur, James, Vaughan-Shaw, Peter G., Shu, Xiao-Ou, Lu, Yingchang, Broderick, Peter, Studd, James, Harrison, Tabitha A., Conti, David V., Schumacher, Fredrick R., Melas, Marilena, Rennert, Gad, Obón-Santacana, Mireia, Martín-Sánchez, Vicente, Oh, Jae Hwan, Kim, Jeongseon, Jee, Sun Ha, Jung, Keum Ji, Kweon, Sun-Seog, Shin, Min-Ho, Shin, Aesun, Ahn, Yoon-Ok, Kim, Dong-Hyun, Oze, Isao, Wen, Wanqing, Matsuo, Keitaro, Matsuda, Koichi, Tanikawa, Chizu, Ren, Zefang, Gao, Yu-Tang, Jia, Wei-Hua, Hopper, John L., Jenkins, Mark A., Win, Aung Ko, Pai, Rish K., Figueiredo, Jane C., Haile, Robert W., Gallinger, Steven, Woods, Michael O., Newcomb, Polly A., Duggan, David, Cheadle, Jeremy P., Kaplan, Richard, Kerr, Rachel, Kerr, David, Kirac, Iva, Böhm, Jan, Mecklin, Jukka-Pekka, Jousilahti, Pekka, Knekt, Paul, Aaltonen, Lauri A., Rissanen, Harri, Pukkala, Eero, Eriksson, Johan G., Cajuso, Tatiana, Hänninen, Ulrika, Kondelin, Johanna, Palin, Kimmo, Tanskanen, Tomas, Renkonen-Sinisalo, Laura, Männistö, Satu, Albanes, Demetrius, Weinstein, Stephanie J., Ruiz-Narvaez, Edward, Palmer, Julie R., Buchanan, Daniel D., Platz, Elizabeth A., Visvanathan, Kala, Ulrich, Cornelia M., Siegel, Erin, Brezina, Stefanie, Gsur, Andrea, Campbell, Peter T., Chang-Claude, Jenny, Hoffmeister, Michael, Brenner, Hermann, Slattery, Martha L., Potter, John D., Tsilidis, Kostas K., Schulze, Matthias B., Gunter, Marc J., Murphy, Neil, Castells, Antoni, Castellví-Bel, Sergi, Moreira, Leticia, Arndt, Volker, Shcherbina, Anna, Bishop, D. Timothy, Giles, Graham G., Southey, Melissa C., Idos, Gregory E., McDonnell, Kevin J., Abu-Ful, Zomoroda, Greenson, Joel K., Shulman, Katerina, Lejbkowicz, Flavio, Offit, Kenneth, Su, Yu-Ru, Steinfelder, Robert, Keku, Temitope O., van Guelpen, Bethany, Hudson, Thomas J., Hampel, Heather, Pearlman, Rachel, Berndt, Sonja I., Hayes, Richard B., Martinez, Marie Elena, Thomas, Sushma S., Pharoah, Paul D. P., Larsson, Susanna C., Yen, Yun, Lenz, Heinz-Josef, White, Emily, Li, Li, Doheny, Kimberly F., Pugh, Elizabeth, Shelford, Tameka, Chan, Andrew T., Cruz-Correa, Marcia, Lindblom, Annika, Hunter, David J., Joshi, Amit D., Schafmayer, Clemens, Scacheri, Peter C., Kundaje, Anshul, Schoen, Robert E., Hampe, Jochen, Stadler, Zsofia K., Vodicka, Pavel, Vodickova, Ludmila, Vymetalkova, Veronika, Edlund, Christopher K., Gauderman, W. James, Shibata, David, Toland, Amanda, Markowitz, Sanford, Kim, Andre, Chanock, Stephen J., van Duijnhoven, Franzel, Feskens, Edith J. M., Sakoda, Lori C., Gago-Dominguez, Manuela, Wolk, Alicja, Pardini, Barbara, FitzGerald, Liesel M., Lee, Soo Chin, Ogino, Shuji, Bien, Stephanie A., Kooperberg, Charles, Li, Christopher I., Lin, Yi, Prentice, Ross, Qu, Conghui, Bézieau, Stéphane, Yamaji, Taiki, Sawada, Norie, Iwasaki, Motoki, Le Marchand, Loic, Wu, Anna H., Qu, Chenxu, McNeil, Caroline E., Coetzee, Gerhard, Hayward, Caroline, Deary, Ian J., Harris, Sarah E., Theodoratou, Evropi, Reid, Stuart, Walker, Marion, Ooi, Li Yin, Lau, Ken S., Zhao, Hongyu, Hsu, Li, Cai, Qiuyin, Dunlop, Malcolm G., Gruber, Stephen B., Houlston, Richard S., Moreno, Victor, Casey, Graham, Peters, Ulrike, Tomlinson, Ian, and Zheng, Wei
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- 2024
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41. Variability in the prevalence of depression among adults with chronic pain: UK Biobank analysis through clinical prediction models
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Chen, Lingxiao, Ashton-James, Claire E, Shi, Baoyi, Radojčić, Maja R, Anderson, David B, Chen, Yujie, Preen, David B, Hopper, John L, Li, Shuai, Bui, Minh, Beckenkamp, Paula R, Arden, Nigel K, Ferreira, Paulo H, Zhou, Hengxing, Feng, Shiqing, and Ferreira, Manuela L
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- 2024
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42. The online metacognitive control of decisions
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Bénon, Juliette, Lee, Douglas, Hopper, William, Verdeil, Morgan, Pessiglione, Mathias, Vinckier, Fabien, Bouret, Sebastien, Rouault, Marion, Lebouc, Raphael, Pezzulo, Giovanni, Schreiweis, Christiane, Burguière, Eric, and Daunizeau, Jean
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- 2024
- Full Text
- View/download PDF
43. Exploring the combinatorial explosion of amine–acid reaction space via graph editing
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Zhang, Rui, Mahjour, Babak, Outlaw, Andrew, McGrath, Andrew, Hopper, Tim, Kelley, Brian, Walters, W. Patrick, and Cernak, Tim
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- 2024
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- View/download PDF
44. Habitat engineering effects of freshwater mussels in rivers vary across spatial scales
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DuBose, Traci P., Vaughn, Caryn C., Hopper, Garrett W., Gido, Keith B., and Parr, Thomas B.
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- 2024
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- View/download PDF
45. Central Artery Hemodynamics in Angiotensin II-Induced Hypertension and Effects of Anesthesia
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Hopper, S. E., Weiss, D., Mikush, N., Jiang, B., Spronck, B., Cavinato, C., Humphrey, J. D., and Figueroa, C. A.
- Published
- 2024
- Full Text
- View/download PDF
46. Assessment of clinically significant urolithiasis positivity rate using CT KUB for suspected renal colic
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Anderson, Toni, Hopper, Carla, MacCraith, Eoin, McCabe, Aileen, and Shortt, Conor P.
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- 2024
- Full Text
- View/download PDF
47. Autoantibodies, antigen-autoantibody complexes and antigens complement CA125 for early detection of ovarian cancer
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Young Han, Chae, Bedia, Jacob S., Yang, Wei-Lei, Hawley, Sarah J., Bergan, Lindsay, Hopper, Marika, Celestino, Joseph, Guo, Jing, Gornet, Terrie G., Soosaipillai, Antoninus, Yang, Hailing, Doskocil, Samantha D., Lokshin, Anna E., Handy, Beverly C., Diamandis, Eleftherios P., Moore, Richard G., Lu, Karen H., Lu, Zhen, Anderson, Karen S., Drescher, Charles W., Skates, Steven J., and Bast, Jr, Robert C.
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- 2024
- Full Text
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48. Intratumoral presence of the genotoxic gut bacteria pks+E. coli, Enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum and their association with clinicopathological and molecular features of colorectal cancer
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Joo, Jihoon E., Chu, Yen Lin, Georgeson, Peter, Walker, Romy, Mahmood, Khalid, Clendenning, Mark, Meyers, Aaron L., Como, Julia, Joseland, Sharelle, Preston, Susan G., Diepenhorst, Natalie, Toner, Julie, Ingle, Danielle J., Sherry, Norelle L., Metz, Andrew, Lynch, Brigid M., Milne, Roger L., Southey, Melissa C., Hopper, John L., Win, Aung Ko, Macrae, Finlay A., Winship, Ingrid M., Rosty, Christophe, Jenkins, Mark A., and Buchanan, Daniel D.
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- 2024
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49. Poster: No safety in numbers: traffic analysis of sealed-sender groups in Signal
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Brigham, Eric and Hopper, Nicholas
- Subjects
Computer Science - Cryptography and Security - Abstract
Secure messaging applications often offer privacy to users by protecting their messages from would be observers through end-to-end encryption techniques. However, the metadata of who communicates with whom cannot be concealed by encryption alone. Signal's Sealed Sender mechanism attempts to enhance its protection of this data by obfuscating the sender of any message sent with the protocol. However, it was shown by Martiny et al. that due to the message delivery protocols in Signal, the record of who receives messages can be enough to recover this metadata. In this work we extend the attack presented from deanonymizing communicating pairs to deanonymizing entire group conversations., Comment: 2 page abstract for poster session at 44th IEEE Symposium on Security and Privacy
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- 2023
50. RADIFUSION: A multi-radiomics deep learning based breast cancer risk prediction model using sequential mammographic images with image attention and bilateral asymmetry refinement
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Yeoh, Hong Hui, Liew, Andrea, Phan, Raphaël, Strand, Fredrik, Rahmat, Kartini, Nguyen, Tuong Linh, Hopper, John L., and Tan, Maxine
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
Breast cancer is a significant public health concern and early detection is critical for triaging high risk patients. Sequential screening mammograms can provide important spatiotemporal information about changes in breast tissue over time. In this study, we propose a deep learning architecture called RADIFUSION that utilizes sequential mammograms and incorporates a linear image attention mechanism, radiomic features, a new gating mechanism to combine different mammographic views, and bilateral asymmetry-based finetuning for breast cancer risk assessment. We evaluate our model on a screening dataset called Cohort of Screen-Aged Women (CSAW) dataset. Based on results obtained on the independent testing set consisting of 1,749 women, our approach achieved superior performance compared to other state-of-the-art models with area under the receiver operating characteristic curves (AUCs) of 0.905, 0.872 and 0.866 in the three respective metrics of 1-year AUC, 2-year AUC and > 2-year AUC. Our study highlights the importance of incorporating various deep learning mechanisms, such as image attention, radiomic features, gating mechanism, and bilateral asymmetry-based fine-tuning, to improve the accuracy of breast cancer risk assessment. We also demonstrate that our model's performance was enhanced by leveraging spatiotemporal information from sequential mammograms. Our findings suggest that RADIFUSION can provide clinicians with a powerful tool for breast cancer risk assessment., Comment: v2
- Published
- 2023
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