612 results on '"Bria P"'
Search Results
2. Lift Every Voice in Tech: Co-Designed Recommendations to Support Black Workers and Learners Seeking to Enter and Advance in Technology Industry Career Pathways
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Digital Promise, Bria Carter, Britney Jacobs, Zohal Shah, and Chioma Aso-Hernandez
- Abstract
Research has shown that access to technology industry pathways and support for recruitment, retention, and advancement through technology careers remain inequitable for Black talent due to various systemic barriers. To help address this issue, Digital Promise conducted research that centers the voices and lived experiences of Black workers and learners seeking to enter and advance in the technology industry with the purpose of building awareness to the: (1) challenges and barriers they face navigating the U.S. technology learning and working ecosystem; (2) factors such as supports and services that have facilitated their technology career pathway entry, retention, and advancement; and (3) collaboratively designed recommendations for needed supports that they have identified that can better promote successful navigation and persistence within technology career pathways. This report further highlights actionable steps that various technology industry contributors can take to dismantle systemic barriers within the technology learning and workforce ecosystem and increase access to non-four-year-degree pathways to tech careers. [Funding for this project is provided by Walmart through the Walmart.org Center for Racial Equity.]
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- 2024
3. AXIAL: Attention-based eXplainability for Interpretable Alzheimer's Localized Diagnosis using 2D CNNs on 3D MRI brain scans
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Lozupone, Gabriele, Bria, Alessandro, Fontanella, Francesco, Meijer, Frederick J. A., and De Stefano, Claudio
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,41A05 41A10 65D05 65D17 - Abstract
This study presents an innovative method for Alzheimer's disease diagnosis using 3D MRI designed to enhance the explainability of model decisions. Our approach adopts a soft attention mechanism, enabling 2D CNNs to extract volumetric representations. At the same time, the importance of each slice in decision-making is learned, allowing the generation of a voxel-level attention map to produce an explainable MRI. To test our method and ensure the reproducibility of our results, we chose a standardized collection of MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). On this dataset, our method significantly outperforms state-of-the-art methods in (i) distinguishing AD from cognitive normal (CN) with an accuracy of 0.856 and Matthew's correlation coefficient (MCC) of 0.712, representing improvements of 2.4% and 5.3% respectively over the second-best, and (ii) in the prognostic task of discerning stable from progressive mild cognitive impairment (MCI) with an accuracy of 0.725 and MCC of 0.443, showing improvements of 10.2% and 20.5% respectively over the second-best. We achieved this prognostic result by adopting a double transfer learning strategy, which enhanced sensitivity to morphological changes and facilitated early-stage AD detection. With voxel-level precision, our method identified which specific areas are being paid attention to, identifying these predominant brain regions: the hippocampus, the amygdala, the parahippocampal, and the inferior lateral ventricles. All these areas are clinically associated with AD development. Furthermore, our approach consistently found the same AD-related areas across different cross-validation folds, proving its robustness and precision in highlighting areas that align closely with known pathological markers of the disease., Comment: 21 pages, 9 figures, 9 tables
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- 2024
4. The BabyView dataset: High-resolution egocentric videos of infants' and young children's everyday experiences
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Long, Bria, Xiang, Violet, Stojanov, Stefan, Sparks, Robert Z., Yin, Zi, Keene, Grace E., Tan, Alvin W. M., Feng, Steven Y., Zhuang, Chengxu, Marchman, Virginia A., Yamins, Daniel L. K., and Frank, Michael C.
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Computer Science - Computer Vision and Pattern Recognition - Abstract
Human children far exceed modern machine learning algorithms in their sample efficiency, achieving high performance in key domains with much less data than current models. This ''data gap'' is a key challenge both for building intelligent artificial systems and for understanding human development. Egocentric video capturing children's experience -- their ''training data'' -- is a key ingredient for comparison of humans and models and for the development of algorithmic innovations to bridge this gap. Yet there are few such datasets available, and extant data are low-resolution, have limited metadata, and importantly, represent only a small set of children's experiences. Here, we provide the first release of the largest developmental egocentric video dataset to date -- the BabyView dataset -- recorded using a high-resolution camera with a large vertical field-of-view and gyroscope/accelerometer data. This 493 hour dataset includes egocentric videos from children spanning 6 months - 5 years of age in both longitudinal, at-home contexts and in a preschool environment. We provide gold-standard annotations for the evaluation of speech transcription, speaker diarization, and human pose estimation, and evaluate models in each of these domains. We train self-supervised language and vision models and evaluate their transfer to out-of-distribution tasks including syntactic structure learning, object recognition, depth estimation, and image segmentation. Although performance in each scales with dataset size, overall performance is relatively lower than when models are trained on curated datasets, especially in the visual domain. Our dataset stands as an open challenge for robust, humanlike AI systems: how can such systems achieve human-levels of success on the same scale and distribution of training data as humans?, Comment: 9 pages, 2 figures, 4 tables and SI. Submitted to NeurIPS Datasets and Benchmarks
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- 2024
5. DevBench: A multimodal developmental benchmark for language learning
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Tan, Alvin Wei Ming, Yu, Sunny, Long, Bria, Ma, Wanjing Anya, Murray, Tonya, Silverman, Rebecca D., Yeatman, Jason D., and Frank, Michael C.
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Computer Science - Computation and Language ,Computer Science - Machine Learning - Abstract
How (dis)similar are the learning trajectories of vision-language models and children? Recent modeling work has attempted to understand the gap between models' and humans' data efficiency by constructing models trained on less data, especially multimodal naturalistic data. However, such models are often evaluated on adult-level benchmarks, with limited breadth in language abilities tested, and without direct comparison to behavioral data. We introduce DevBench, a multimodal benchmark comprising seven language evaluation tasks spanning the domains of lexical, syntactic, and semantic ability, with behavioral data from both children and adults. We evaluate a set of vision-language models on these tasks, comparing models and humans not only on accuracy but on their response patterns. Across tasks, models exhibit variation in their closeness to human response patterns, and models that perform better on a task also more closely resemble human behavioral responses. We also examine the developmental trajectory of OpenCLIP over training, finding that greater training results in closer approximations to adult response patterns. DevBench thus provides a benchmark for comparing models to human language development. These comparisons highlight ways in which model and human language learning processes diverge, providing insight into entry points for improving language models.
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- 2024
6. Understanding the Supports and Skills That Enable Successful Pathways for Black Learners and Workers into Non-Four-Year Degree Technology Careers: A Landscape Scan
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Digital Promise, Carter, Bria, Shah, Zohal, Tinsley, Brian, LeGrand-Dunn, Jhacole, and Luke Luna, Christina
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While diversity within the technology industry has been critical for developing robust and creative technology solutions, recruiting and retaining diverse tech talent in today's society has been a challenge worldwide, especially for Black learners and workers. Subsequently, the technology field is left lacking in diversity of thought and perspective among technology industry practitioners and leaders. By examining peer-reviewed journal articles, statistical data from research reports, and website material from professional associations, this landscape scan synthesizes existing research and curates programs, services, and supports that effectively promote the success of Black learners and workers within technology career pathways. [Funding for this project is provided by Walmart through the Walmart.org Center for Racial Equity.]
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- 2023
7. Learning Transition Design Principles for Learning and Employment Records: Co-Designing for Equity
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Digital Promise, Page, Kelly, Merritt Johnson, Alexandra, Franklin, Kristen, Carter, Bria, Galindo, Marilys, Solorzano, Teresa, Lee, Sangyeon, and Shah, Zohal
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With the emergence of digital credentialing and platforms to support learners and workers with entering and traversing the increasingly skill-based education and workforce ecosystem, Learning and Employment Record (LER) technologies have been identified as a promising solution for individuals to share and access their learning- and skills-data and to education and career opportunities. However, learning journeys are rarely continuous; opportunities, challenges, and evolving circumstances can result in both the development of skills and competencies and a change in the way in which individuals demonstrate and get recognized for their skills and competencies. Further, systemic barriers and inequities disproportionately impact learning transitions for historically and systematically excluded (HSE) communities, barring access to supports and resources to enter and persist in the education and workforce ecosystem. To help inform the the design of LER technologies to be of value and useful in supporting HSE learners and workers during learning transitions and along multiple pathways, this report highlights the following: (1) co-design methodologies and experiences that center HSE learners and workers in LER design, development, and testing; (2) recommendations and insights from HSE learners and workers on the opportunities and challenges of utilizing LERs through education and career pathways; and (3) seven learning transition design principles that support the multiple and often fluid transitions between education and the workforce that many HSE communities experience. These findings will inform the future work in developing a certification that guides developers to center HSE learners and workers as they design LER technologies to support individuals over time and through learning transitions. Based on these findings, LER developers, postsecondary education providers, and the workforce ecosystem, may develop a more inclusive skills-based learning and employment record system.
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- 2023
8. Trapping Defect Modes in a Quasi-Periodic Star Waveguide Structure Based on the Fibonacci Sequence
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Errouas, Younes, El Kadmiri, Ilyass, Ben-Ali, Youssef, and Bria, Driss
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- 2024
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9. Attrition between lines of therapy and real-world outcomes of patients with HER2-positive metastatic breast cancer in Europe: a cohort study leveraging electronic medical records
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Cottu, Paul, Cheeseman, Sue, Hall, Peter, Wöckel, Achim, Scholz, Christian W., Bria, Emilio, Orlandi, Armando, Ribelles, Nuria, Vallet, Mahéva, Niklas, Nicolas, Hogg, Catherine, Aggarwal, Shivani, Moreira, Joana, Lucerna, Markus, Collin, Simon M., Logue, Amanda, and Long, Gráinne H.
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- 2024
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10. Frequency Division Multiple Access with High Performance Based on Several Defect Resonators According to the Fibonacci Sequence in 1D Photonic Star Waveguide Structure
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Younes Errouas, El Kadmiri, Ilyass, Ben-Ali, Youssef, and Bria, Driss
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- 2024
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11. Transfer learning in breast mass detection and classification
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Ryspayeva, Marya, Bria, Alessandro, Marrocco, Claudio, Tortorella, Francesco, and Molinara, Mario
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- 2024
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12. Caring for community members during the COVID-19 pandemic: results of a statewide survey
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Jewell, Tess, Gillespie, Kate H., Schmuhl, Nicholas B., Gilbert, Sharon, Grant, Bria, Watts, Lakeeta, and Ehrenthal, Deborah B.
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- 2024
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13. Experiences and Comfort of Young Cancer Patients Discussing Cannabis with Their Providers: Insights from a Survey at an NCI-Designated Cancer Center
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Baral, Amrit, Diggs, Bria-Necole A., Aka, Anurag, Williams, Renessa, Ortega, Nicholas Hernandez, Fellah, Ranya Marrakchi El, Islam, Jessica Y., Camacho-Rivera, Marlene, Penedo, Frank J., and Vidot, Denise C.
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- 2024
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14. Two Frequency-Division Demultiplexing Using Photonic Waveguides by the Presence of Two Geometric Defects
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El-Aouni Mimoun, Youssef, Ben-Ali, Ilyass, El Kadmiri, Abdelaziz, Ouariach, and Driss, Bria
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- 2024
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15. On the Cross-Dataset Generalization of Machine Learning for Network Intrusion Detection
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Cantone, Marco, Marrocco, Claudio, and Bria, Alessandro
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Computer Science - Cryptography and Security ,Computer Science - Machine Learning ,Computer Science - Networking and Internet Architecture - Abstract
Network Intrusion Detection Systems (NIDS) are a fundamental tool in cybersecurity. Their ability to generalize across diverse networks is a critical factor in their effectiveness and a prerequisite for real-world applications. In this study, we conduct a comprehensive analysis on the generalization of machine-learning-based NIDS through an extensive experimentation in a cross-dataset framework. We employ four machine learning classifiers and utilize four datasets acquired from different networks: CIC-IDS-2017, CSE-CIC-IDS2018, LycoS-IDS2017, and LycoS-Unicas-IDS2018. Notably, the last dataset is a novel contribution, where we apply corrections based on LycoS-IDS2017 to the well-known CSE-CIC-IDS2018 dataset. The results show nearly perfect classification performance when the models are trained and tested on the same dataset. However, when training and testing the models in a cross-dataset fashion, the classification accuracy is largely commensurate with random chance except for a few combinations of attacks and datasets. We employ data visualization techniques in order to provide valuable insights on the patterns in the data. Our analysis unveils the presence of anomalies in the data that directly hinder the classifiers capability to generalize the learned knowledge to new scenarios. This study enhances our comprehension of the generalization capabilities of machine-learning-based NIDS, highlighting the significance of acknowledging data heterogeneity.
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- 2024
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16. Durability of Original Monovalent mRNA Vaccine Effectiveness Against COVID-19 Omicron-Associated Hospitalization in Children and Adolescents - United States, 2021-2023.
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Zambrano, Laura, Newhams, Margaret, Simeone, Regina, Payne, Amanda, Wu, Michael, Orzel-Lockwood, Amber, Halasa, Natasha, Calixte, Jemima, Pannaraj, Pia, Mongkolrattanothai, Kanokporn, Boom, Julie, Sahni, Leila, Kamidani, Satoshi, Chiotos, Kathleen, Cameron, Melissa, Maddux, Aline, Irby, Katherine, Schuster, Jennifer, Mack, Elizabeth, Biggs, Austin, Coates, Bria, Michelson, Kelly, Bline, Katherine, Nofziger, Ryan, Crandall, Hillary, Hobbs, Charlotte, Gertz, Shira, Heidemann, Sabrina, Bradford, Tamara, Walker, Tracie, Schwartz, Stephanie, Staat, Mary, Bhumbra, Samina, Hume, Janet, Kong, Michele, Stockwell, Melissa, Connors, Thomas, Cullimore, Melissa, Flori, Heidi, Levy, Emily, Cvijanovich, Natalie, Zinter, Matt, Maamari, Mia, Bowens, Cindy, Zerr, Danielle, Guzman-Cottrill, Judith, Gonzalez, Ivan, Campbell, Angela, and Randolph, Adrienne
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Humans ,Adolescent ,Child ,United States ,COVID-19 Vaccines ,COVID-19 ,mRNA Vaccines ,Vaccine Efficacy ,SARS-CoV-2 ,Hospitalization ,RNA ,Messenger - Abstract
Pediatric COVID-19 vaccination is effective in preventing COVID-19-related hospitalization, but duration of protection of the original monovalent vaccine during SARS-CoV-2 Omicron predominance merits evaluation, particularly given low coverage with updated COVID-19 vaccines. During December 19, 2021-October 29, 2023, the Overcoming COVID-19 Network evaluated vaccine effectiveness (VE) of ≥2 original monovalent COVID-19 mRNA vaccine doses against COVID-19-related hospitalization and critical illness among U.S. children and adolescents aged 5-18 years, using a case-control design. Too few children and adolescents received bivalent or updated monovalent vaccines to separately evaluate their effectiveness. Most case-patients (persons with a positive SARS-CoV-2 test result) were unvaccinated, despite the high frequency of reported underlying conditions associated with severe COVID-19. VE of the original monovalent vaccine against COVID-19-related hospitalizations was 52% (95% CI = 33%-66%) when the most recent dose was administered
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- 2024
17. Trauma, Policy, and Teaching English Language Learners
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Scarf, Bria, Millar, Nathan, Kostouros, Patricia, Crossman, Katie, and Abboud, Rida
- Abstract
The authors present findings that emphasize a need for trauma-informed policy to mitigate vicarious trauma transmission for teachers who work in English language learning (ELL) classrooms. Qualitative data was collected from 10 stakeholders in Canada using an interpretive-phenomenological methodology. Findings assisted to better understand the impact of institutional policy, or lack thereof, on trauma-informed practices within English language teacher work. Themes that emerged were settlement factors, roles, and responsibilities (personal and professional), and organizational policies. A scan of publicly available information on trauma-informed policy suggested a gap for English language teachers. Current literature on vicarious trauma stresses that trauma-informed practice necessitates an individual and systemic approach to mitigating its effects. A basic scan of potential trauma-informed frameworks was discussed as potential institutional approaches to reduce the impact of vicarious trauma on teachers.
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- 2023
18. Using 3MT Storytelling Approaches to Improve Science Communication
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Kristy L. Daniel, Ryan Ament, Myra McConnell, Bria Marty, and Jenn L. Idema
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Traditional academic communication practices tend to be jargon-heavy jargon and lack public relatability. Thus, it is paramount that scientists learn to develop effective communication skills. The Three Minute Thesis (3MT) competition is one avenue to refine and build science communications skills. Using one static slide as a visual supplement, competitors have three minutes to explain their research goals and relevance through easily comprehended vernacular. Using an observation protocol including three criteria: presentation framing, verbal, and non-verbal communication, we identified characteristics of prior successful 3MT presentations. We also tested the identified characteristics by observing 15 local 3MT presentations and found that all successful presentations contained similar communication patterns. For example, we found that using storytelling frames resulted in the most compelling and successful presentations. Our study offers implications on how these identified characteristics can be used to help budding scientists build critical communication skills for sharing their research with non-scientists. Scientists can apply our outcomes to build effective presentations and successfully deliver science messages helping create a more informed public.
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- 2023
19. State of the Science: Health Care Provider Communication of Cannabis Use Among Adults Living with Cancer
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Baral, Amrit, Diggs, Bria-Necole A., Greengold, Judith, Foronda, Cynthia, Anglade, Debbie, Camacho-Rivera, Marlene, Islam, Jessica Y., and Vidot, Denise C.
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- 2024
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20. Growing Up Intersex: A Thematic Analysis of Intersex Emerging Adults’ Key Socialization Experiences in Childhood and Adolescence
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Astle, Shelby, Pariera, Katrina, Anders, Kristin M., Brown-King, Bria, and Adams, Marissa
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- 2024
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21. The BabyView camera: Designing a new head-mounted camera to capture children’s early social and visual environments
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Long, Bria, Goodin, Sarah, Kachergis, George, Marchman, Virginia A., Radwan, Samaher F., Sparks, Robert Z., Xiang, Violet, Zhuang, Chengxu, Hsu, Oliver, Newman, Brett, Yamins, Daniel L. K., and Frank, Michael C.
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- 2024
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22. Kilometer-precise (UII) Umbriel physical properties from the multichord stellar occultation on 2020 September 21
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Assafin, M., Santos-Filho, S., Morgado, B. E., Gomes-Júnior, A. R., Sicardy, B., Margoti, G., Benedetti-Rossi, G., Braga-Ribas, F., Laidler, T., Camargo, J. I. B., Vieira-Martins, R., Swift, T., Dunham, D., George, T., Bardecker, J., Anderson, C., Nolthenius, R., Bender, K., Viscome, G., Oesper, D., Dunford, R., Getrost, K., Kitting, C., Green, K., Bria, R., Olsen, A., Scheck, A., Billard, B., Wasiuta, M. E., Tatum, R., Maley, P., di Cicco, D., Gamble, D., Ceravolo, P., Ceravolo, D., Hanna, W., Smith, N., Carlson, N., Messner, S., Bean, J., Moore, J., and Venable, R.
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
We report the results of the stellar occultation by (UII) Umbriel on September 21st, 2020. The shadow crossed the USA and Canada, and 19 positive chords were obtained. A limb parameter accounted for putative topographic features in the limb fittings. Ellipse fittings were not robust - only upper limits were derived for the true size/shape of a putative Umbriel ellipsoid. The adopted spherical solution gives radius = 582.4 +/- 0.8 km, smaller/close to 584.7 +/- 2.8 km from Voyager II. The apparent ellipse fit results in a true semi-major axis of 584.9 +/- 3.8 km, semi-minor axes of 582.3 +/- 0.6 km and true oblateness of 0.004 +/- 0.008 for a putative ellipsoid. The geometric albedo was pV = 0.26 +/- 0.01. The density was rho = 1.54 +/- 0.04 g cm-3. The surface gravity was 0.251 +/- 0.006 m s-2 and the escape velocity 0.541 +/- 0.006 km s-1 . Upper limits of 13 and 72 nbar (at 1 sigma and 3 sigma levels, respectively) were obtained for the surface pressure of a putative isothermal CO2 atmosphere at T = 70 K. A milliarcsecond precision position was derived: RA = 02h 30m 28.84556s +/- 0.1 mas, DE = 14o 19' 36.5836" +/- 0.2 mas. A large limb parameter of 4.2 km was obtained, in striking agreement with opposite southern hemisphere measurements by Voyager II in 1986. Occultation and Voyager results indicate that the same strong topography variation in the surface of Umbriel is present on both hemispheres.
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- 2023
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23. Gravity Network for end-to-end small lesion detection
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Russo, Ciro, Bria, Alessandro, and Marrocco, Claudio
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence - Abstract
This paper introduces a novel one-stage end-to-end detector specifically designed to detect small lesions in medical images. Precise localization of small lesions presents challenges due to their appearance and the diverse contextual backgrounds in which they are found. To address this, our approach introduces a new type of pixel-based anchor that dynamically moves towards the targeted lesion for detection. We refer to this new architecture as GravityNet, and the novel anchors as gravity points since they appear to be "attracted" by the lesions. We conducted experiments on two well-established medical problems involving small lesions to evaluate the performance of the proposed approach: microcalcifications detection in digital mammograms and microaneurysms detection in digital fundus images. Our method demonstrates promising results in effectively detecting small lesions in these medical imaging tasks.
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- 2023
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24. Parallel developmental changes in childrens production and recognition of line drawings of visual concepts.
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Chai, Zixian, Frank, Michael, Long, Bria, Fan, Judith, and Huey, Holly
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Childhood is marked by the rapid accumulation of knowledge and the prolific production of drawings. We conducted a systematic study of how children create and recognize line drawings of visual concepts. We recruited 2-10-year-olds to draw 48 categories via a kiosk at a childrens museum, resulting in >37K drawings. We analyze changes in the category-diagnostic information in these drawings using vision algorithms and annotations of object parts. We find developmental gains in childrens inclusion of category-diagnostic information that are not reducible to variation in visuomotor control or effort. Moreover, even unrecognizable drawings contain information about the animacy and size of the category children tried to draw. Using guessing games at the same kiosk, we find that children improve across childhood at recognizing each others line drawings. This work leverages vision algorithms to characterize developmental changes in childrens drawings and suggests that these changes reflect refinements in childrens internal representations.
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- 2024
25. Novel and reported compensatory mutations in rpoABC genes found in drug resistant tuberculosis outbreaks
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Conkle-Gutierrez, Derek, Ramirez-Busby, Sarah M, Gorman, Bria M, Elghraoui, Afif, Hoffner, Sven, Elmaraachli, Wael, and Valafar, Faramarz
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Medical Microbiology ,Biomedical and Clinical Sciences ,Clinical Sciences ,Biological Sciences ,Emerging Infectious Diseases ,Tuberculosis ,Infectious Diseases ,Antimicrobial Resistance ,Genetics ,Prevention ,Rare Diseases ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Good Health and Well Being ,Environmental Science and Management ,Soil Sciences ,Microbiology ,Medical microbiology - Abstract
Background: Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by Mycobacterium tuberculosis. RIF resistance is caused by mutations in rpoB, at the cost of slower growth and reduced transcription efficiency. Antibiotic resistance to RIF is prevalent despite this fitness cost. Compensatory mutations in rpoABC genes have been shown to alleviate the fitness cost of rpoB:S450L, explaining how RIF resistant strains harbor this mutation can spread so rapidly. Unfortunately, the full set of RIF compensatory mutations is still unknown, particularly those compensating for rarer RIF resistance mutations. Objectives: We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations. Results and conclusions: Of the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in rpoABC for which no strong prior evidence of their compensatory role exists. Of these, 35 have previously been reported. As such, our independent corroboration adds to the mounting evidence that these 35 also carry a compensatory role. The remaining 11 are novel putative compensatory markers, reported here for the first time. Six of these 11 novel putative compensatory mutations had two or more mutation events. Most compensatory mutations appear to be specifically compensating for the fitness loss due to rpoB:S450L. However, an outbreak of 22 closely related isolates each carried three rpoB mutations, the rare RIFR markers D435G and L452P and the putative compensatory mutation I1106T. This suggests compensation may require specific combinations of rpoABC mutations. Here, we report only mutations that met our very strict criteria. It is highly likely that many additional rpoABC mutations compensate for rare resistance-causing mutations and therefore did not carry the statistical power to be reported here. These findings aid in the identification of RIF resistant M. tuberculosis strains with restored fitness, which pose a greater risk of causing resistant outbreaks.
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- 2024
26. Characterizing Contextual Variation in Children's Preschool Language Environment Using Naturalistic Egocentric Videos
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Sparks, Robert Z., Long, Bria, Keene, Grace E, Perez, Malia J., Tan, Alvin Wei Ming, Marchman, Virginia A, and Frank, Michael C.
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Cognitive development ,Language development ,Language learning ,Classroom studies ,Corpus studies - Abstract
What structures children's early language environment? Large corpora of child-centered naturalistic recordings provide an important window into this question, but most available data centers on young children within the home or in lab contexts interacting primarily with a single caregiver. Here, we characterize children's language experience in a very different kind of environment: the preschool classroom. Children ages 3 – 5 years (N = 26) wore a head-mounted camera in their preschool class, yielding a naturalistic, egocentric view of children's everyday experience across many classroom activity contexts (e.g., sand play, snack time), with >30 hours of video data. Using semi-automatic transcriptions (227,624 words), we find that activity contexts in the preschool classroom vary in both the quality and quantity of the language that children both hear and produce. Together, these findings reinforce prior theories emphasizing the contribution of activity contexts in structuring the variability in children's early learning environments.
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- 2024
27. Retronychia: the importance of proper footwear
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Riopelle, Alexandria M, Rajanala, Susruthi, Khan, Saara, Kosuru, Sindhu B, Bryant, Bria, Adigun, Chris G, and Kuchnir, Louis
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avulsion ,paronychia ,prevention ,retronychia ,treatment - Abstract
Retronychia is commonly underdiagnosed and exhibits classic features of proximal nail fold elevation and nail plate layering. Herein we summarize the literature and discuss cause, diagnosis, and treatment of this condition.
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- 2024
28. Validation and positive predictive values of diagnostic codes for Vulvar Lichen sclerosus
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Midgette, Bria, Cohn, Erica, Strunk, Andrew, Shah, Pooja R., and Garg, Amit
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- 2024
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29. External immunity in ant societies: sociality and colony size do not predict investment in antimicrobials
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Clint A. Penick, Omar Halawani, Bria Pearson, Stephanie Mathews, Margarita M. López-Uribe, Robert R. Dunn, and Adrian A. Smith
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antimicrobial secretions ,antibiotics ,social immunity ,social insects ,ants ,entomopathogens ,Science - Abstract
Social insects live in dense groups with a high probability of disease transmission and have therefore faced strong pressures to develop defences against pathogens. For this reason, social insects have been hypothesized to invest in antimicrobial secretions as a mechanism of external immunity to prevent the spread of disease. However, empirical studies linking the evolution of sociality with increased investment in antimicrobials have been relatively few. Here we quantify the strength of antimicrobial secretions among 20 ant species that cover a broad spectrum of ant diversity and colony sizes. We extracted external compounds from ant workers to test whether they inhibited the growth of the bacterium Staphylococcus epidermidis. Because all ant species are highly social, we predicted that all species would exhibit some antimicrobial activity and that species that form the largest colonies would exhibit the strongest antimicrobial response. Our comparative approach revealed that strong surface antimicrobials are common to particular ant clades, but 40% of species exhibited no antimicrobial activity at all. We also found no correlation between antimicrobial activity and colony size. Rather than relying on antimicrobial secretions as external immunity to control pathogen spread, many ant species have probably developed alternative strategies to defend against disease pressure.
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- 2018
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30. Augmentation of light therapy in difficult-to-treat depressed patients: an open-label trial in both unipolar and bipolar patients
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Camardese G, Leone B, Serrani R, Walstra C, Di Nicola M, Della Marca G, Bria P, and Janiri L
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Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Giovanni Camardese,1 Beniamino Leone,1 Riccardo Serrani,1 Coco Walstra,1 Marco Di Nicola,1 Giacomo Della Marca,2 Pietro Bria,1 Luigi Janiri1 1Institute of Psychiatry and Psychology, 2Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy Objectives: We investigated the clinical benefits of bright light therapy (BLT) as an adjunct treatment to ongoing psychopharmacotherapy, both in unipolar and bipolar difficult-to-treat depressed (DTD) outpatients.Methods: In an open-label study, 31 depressed outpatients (16 unipolar and 15 bipolar) were included to undergo 3 weeks of BLT. Twenty-five completed the treatment and 5-week follow-up.Main outcome measures: Clinical outcomes were evaluated by the Hamilton Depression Rating Scale (HDRS). The Snaith–Hamilton Pleasure Scale and the Depression Retardation Rating Scale were used to assess changes in anhedonia and psychomotor retardation, respectively.Results: The adjunctive BLT seemed to influence the course of the depressive episode, and a statistically significant reduction in HDRS scores was reported since the first week of therapy. The treatment was well-tolerated, and no patients presented clinical signs of (hypo)manic switch during the overall treatment period. At the end of the study (after 5 weeks from BLT discontinuation), nine patients (36%, eight unipolar and one bipolar) still showed a treatment response. BLT augmentation also led to a significant improvement of psychomotor retardation.Conclusion: BLT combined with the ongoing pharmacological treatment offers a simple approach, and it might be effective in rapidly ameliorating depressive core symptoms of vulnerable DTD outpatients. These preliminary results need to be confirmed in placebo-controlled, randomized, double-blind clinical trial on larger samples. Keywords: light therapy, unipolar depression, bipolar depression, anhedonia, psychomotor dysfunction
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- 2015
31. Characterization of two transcriptomic subtypes of marker-null large cell carcinoma of the lung suggests different origin and potential new therapeutic perspectives
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Simbolo, Michele, Centonze, Giovanni, Gkountakos, Anastasios, Monti, Valentina, Maisonneuve, Patrick, Golovco, Stela, Sabella, Giovanna, Del Gobbo, Alessandro, Gobbo, Stefano, Ferrero, Stefano, Fabbri, Alessandra, Pardo, Carlotta, Garzone, Giovanna, Prinzi, Natalie, Pusceddu, Sara, Testi, Adele, Rolli, Luigi, Mangogna, Alessandro, Bercich, Luisa, Benvenuti, Mauro Roberto, Bria, Emilio, Pilotto, Sara, Berruti, Alfredo, Pastorino, Ugo, Capella, Carlo, Infante, Maurizio, Milella, Michele, Scarpa, Aldo, and Milione, Massimo
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- 2024
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32. “Support the Shit Out of Them:” Intersex Emerging Adults’ Recommendations for Caregivers of an Intersex Child
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Astle, Shelby, Pariera, Katrina, Anders, Kristin M., Brown-King, Bria, and Adams, Marissa
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- 2024
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33. Developmental Changes in Drawing Production under Different Memory Demands in a U.S. and Chinese Sample
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Long, Bria, Wang, Ying, Christie, Stella, Frank, Michael C., and Fan, Judith E.
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Children's drawings of common object categories become dramatically more recognizable across childhood. What are the major factors that drive developmental changes in children's drawings? To what degree are children's drawings a product of their changing internal category representations versus limited by their visuomotor abilities or their ability to recall the relevant visual information? To explore these questions, we examined the degree to which developmental changes in drawing recognizability vary across different drawing tasks that vary in memory demands (i.e., drawing from verbal vs. picture cues) and with children's shape-tracing abilities across two geographical locations (San Jose, United States, and Beijing, China). We collected digital shape tracings and drawings of common object categories (e.g., cat, airplane) from 4- to 9-year-olds (N = 253). The developmental trajectory of drawing recognizability was remarkably similar when children were asked to draw from pictures versus verbal cues and across these two geographical locations. In addition, our Beijing sample produced more recognizable drawings but showed similar tracing abilities to children from San Jose. Overall, this work suggests that the developmental trajectory of children's drawings is remarkably consistent and not easily explainable by changes in visuomotor control or working memory; instead, changes in children's drawings over development may at least partly reflect changes in the internal representations of object categories.
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- 2023
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34. BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
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Manubens-Gil, Linus, Zhou, Zhi, Chen, Hanbo, Ramanathan, Arvind, Liu, Xiaoxiao, Liu, Yufeng, Bria, Alessandro, Gillette, Todd, Ruan, Zongcai, Yang, Jian, Radojević, Miroslav, Zhao, Ting, Cheng, Li, Qu, Lei, Liu, Siqi, Bouchard, Kristofer E, Gu, Lin, Cai, Weidong, Ji, Shuiwang, Roysam, Badrinath, Wang, Ching-Wei, Yu, Hongchuan, Sironi, Amos, Iascone, Daniel Maxim, Zhou, Jie, Bas, Erhan, Conde-Sousa, Eduardo, Aguiar, Paulo, Li, Xiang, Li, Yujie, Nanda, Sumit, Wang, Yuan, Muresan, Leila, Fua, Pascal, Ye, Bing, He, Hai-yan, Staiger, Jochen F, Peter, Manuel, Cox, Daniel N, Simonneau, Michel, Oberlaender, Marcel, Jefferis, Gregory, Ito, Kei, Gonzalez-Bellido, Paloma, Kim, Jinhyun, Rubel, Edwin, Cline, Hollis T, Zeng, Hongkui, Nern, Aljoscha, Chiang, Ann-Shyn, Yao, Jianhua, Roskams, Jane, Livesey, Rick, Stevens, Janine, Liu, Tianming, Dang, Chinh, Guo, Yike, Zhong, Ning, Tourassi, Georgia, Hill, Sean, Hawrylycz, Michael, Koch, Christof, Meijering, Erik, Ascoli, Giorgio A, and Peng, Hanchuan
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Biological Sciences ,Bioengineering ,Networking and Information Technology R&D (NITRD) ,Neurosciences ,Benchmarking ,Microscopy ,Imaging ,Three-Dimensional ,Neurons ,Algorithms ,Technology ,Medical and Health Sciences ,Developmental Biology ,Biological sciences - Abstract
BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.
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- 2023
35. Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets
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Manubens-Gil, Linus, Zhou, Zhi, Chen, Hanbo, Ramanathan, Arvind, Liu, Xiaoxiao, Liu, Yufeng, Bria, Alessandro, Gillette, Todd, Ruan, Zongcai, Yang, Jian, Radojević, Miroslav, Zhao, Ting, Cheng, Li, Qu, Lei, Liu, Siqi, Bouchard, Kristofer E., Gu, Lin, Cai, Weidong, Ji, Shuiwang, Roysam, Badrinath, Wang, Ching-Wei, Yu, Hongchuan, Sironi, Amos, Iascone, Daniel Maxim, Zhou, Jie, Bas, Erhan, Conde-Sousa, Eduardo, Aguiar, Paulo, Li, Xiang, Li, Yujie, Nanda, Sumit, Wang, Yuan, Muresan, Leila, Fua, Pascal, Ye, Bing, He, Hai-yan, Staiger, Jochen F., Peter, Manuel, Cox, Daniel N., Simonneau, Michel, Oberlaender, Marcel, Jefferis, Gregory, Ito, Kei, Gonzalez-Bellido, Paloma, Kim, Jinhyun, Rubel, Edwin, Cline, Hollis T., Zeng, Hongkui, Nern, Aljoscha, Chiang, Ann-Shyn, Yao, Jianhua, Roskams, Jane, Livesey, Rick, Stevens, Janine, Liu, Tianming, Dang, Chinh, Guo, Yike, Zhong, Ning, Tourassi, Georgia, Hill, Sean, Hawrylycz, Michael, Koch, Christof, Meijering, Erik, Ascoli, Giorgio A., and Peng, Hanchuan
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- 2024
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36. Faculty and Advisor Advice for Cybersecurity Students: Liberal Arts, Interdisciplinarity, Experience, Lifelong Learning, Technical Skills, and Hard Work
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Payne, Brian K., Cross, Bria, and Vandecar-Burdin, Tancy
- Abstract
The value of academic advising has been increasingly emphasized in higher education. In this study, attention is given to the most significant types of advice that a sample of cybersecurity faculty and advisors from the Commonwealth of Virginia recommend giving to cybersecurity students. The results show that faculty and advisors recommended that students be aware of six different aspects of cybersecurity education including the value of experience, the need for lifelong learning, the importance of hard work, the need to develop technical skills, the interdisciplinary nature of cybersecurity, and the need to develop liberal arts or professional/soft skills. Implications of the findings include the need to embrace the advising of cybersecurity students, the importance of helping cybersecurity faculty and advisors deliver effective advising, and recognition that good advising is more than simply telling students which classes to take.
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- 2022
37. PowToon as an Innovation in Improving Grade 4 Learners' Story Analysis and Reading Comprehension
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Samosa, Resty, Ilagan, Clariza, Ballaran, Bria Clorris, Margallo, Saira, and Sunga, Rhona May
- Abstract
This study is intended on the development of the learners' reading comprehension and story analysis skills under the implementation of PowToon as an innovative instructional material for learners' development in reading comprehension and story analysis skills. This study provided various evidence on how innovation can be a great step in developing the learners reading comprehension and story analysis skills. The purpose of this action research is to determine or evaluate the effectiveness of using PowToon as an innovative instructional material to improve and develop learners' reading comprehension and fluency. Various test and data gathering procedures showed promising data on the success of the implementation of the said instructional material where thirty (30) students assessed under the supervision of the chosen master teachers and grade 4 teachers with the use of learning materials evaluated by the teachers using LRMDS tool. The data that this study generated in terms of the success it shown over the development of the learners were significant in terms of their level of reading and analysis skills. Furthermore the information gained from this study will benefit English teachers by yielding information about the effectiveness of using PowToon as an innovative instructional material to develop learners' reading and analyzing skills.
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- 2021
38. Altered States of Consciousness during an Extreme Ritual.
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Ellen M Lee, Kathryn R Klement, James K Ambler, Tonio Loewald, Evelyn M Comber, Sarah A Hanson, Bria Pruitt, and Brad J Sagarin
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Medicine ,Science - Abstract
Extreme rituals (body-piercing, fire-walking, etc.) are anecdotally associated with altered states of consciousness-subjective alterations of ordinary mental functioning (Ward, 1984)-but empirical evidence of altered states using both direct and indirect measures during extreme rituals in naturalistic settings is limited. Participants in the "Dance of Souls", a 3.5-hour event during which participants received temporary piercings with hooks or weights attached to the piercings and danced to music provided by drummers, responded to measures of two altered states of consciousness. Participants also completed measures of positive and negative affect, salivary cortisol (a hormone associated with stress), self-reported stress, sexual arousal, and intimacy. Both pierced participants (pierced dancers) and non-pierced participants (piercers, piercing assistants, observers, drummers, and event leaders) showed evidence of altered states aligned with transient hypofrontality (Dietrich, 2003; measured with a Stroop test) and flow (Csikszentmihalyi, 1990; Csikszentmihalyi & Csikszentmihalyi, 1990; measured with the Flow State Scale). Both pierced and non-pierced participants also reported decreases in negative affect and psychological stress and increases in intimacy from before to after the ritual. Pierced and non-pierced participants showed different physiological reactions, however, with pierced participants showing increases in cortisol and non-pierced participants showing decreases from before to during the ritual. Overall, the ritual appeared to induce different physiological effects but similar psychological effects in focal ritual participants (i.e., pierced dancers) and in participants adopting other roles.
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- 2016
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39. NFKB2 haploinsufficiency identified via screening for IFN-α2 autoantibodies in children and adolescents hospitalized with SARS-CoV-2–related complications
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Bodansky, Aaron, Vazquez, Sara E, Chou, Janet, Novak, Tanya, Al-Musa, Amer, Young, Cameron, Newhams, Margaret, Kucukak, Suden, Zambrano, Laura D, Mitchell, Anthea, Wang, Chung-Yu, Moffitt, Kristin, Halasa, Natasha B, Loftis, Laura L, Schwartz, Stephanie P, Walker, Tracie C, Mack, Elizabeth H, Fitzgerald, Julie C, Gertz, Shira J, Rowan, Courtney M, Irby, Katherine, Sanders, Ronald C, Kong, Michele, Schuster, Jennifer E, Staat, Mary A, Zinter, Matt S, Cvijanovich, Natalie Z, Tarquinio, Keiko M, Coates, Bria M, Flori, Heidi R, Dahmer, Mary K, Crandall, Hillary, Cullimore, Melissa L, Levy, Emily R, Chatani, Brandon, Nofziger, Ryan, Investigators, Overcoming COVID-19 Network Study Group, Yates, Masson, Smith, Chelsea, Zinter, MattS, McLaughlin, Gwenn, Randolph, Adrienne G, Newhams, Margaret M, Moon, Hye Kyung, Kobayashi, Takuma, Melo, Jeni, Chen, Sabrina R, Behl, Supriya, Drapeau, Noelle M, McCulloh, Russell J, Nofziger, Ryan A, Staat, Mary Allen, Rohlfs, Chelsea C, Reed, Nelson, Geha, Raif S, DeRisi, Joseph, Campbell, Angela P, and Anderson, Mark
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Biomedical and Clinical Sciences ,Clinical Sciences ,Lung ,Vaccine Related ,Infectious Diseases ,Rare Diseases ,Pneumonia ,Clinical Research ,Prevention ,Emerging Infectious Diseases ,Biodefense ,Pediatric ,Genetics ,Autoimmune Disease ,Aetiology ,2.1 Biological and endogenous factors ,Inflammatory and immune system ,Good Health and Well Being ,Adult ,Humans ,Child ,Adolescent ,SARS-CoV-2 ,COVID-19 ,Autoantibodies ,NF-kappa B ,Haploinsufficiency ,Leukocytes ,Mononuclear ,Interferon Type I ,NF-kappa B p52 Subunit ,Anti-interferon autoantibody ,MIS-C ,NFKB2 ,inborn errors of immunity ,Overcoming COVID-19 Network Study Group Investigators ,Immunology ,Allergy - Abstract
BackgroundAutoantibodies against type I IFNs occur in approximately 10% of adults with life-threatening coronavirus disease 2019 (COVID-19). The frequency of anti-IFN autoantibodies in children with severe sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is unknown.ObjectiveWe quantified anti-type I IFN autoantibodies in a multicenter cohort of children with severe COVID-19, multisystem inflammatory syndrome in children (MIS-C), and mild SARS-CoV-2 infections.MethodsCirculating anti-IFN-α2 antibodies were measured by a radioligand binding assay. Whole-exome sequencing, RNA sequencing, and functional studies of peripheral blood mononuclear cells were used to study any patients with levels of anti-IFN-α2 autoantibodies exceeding the assay's positive control.ResultsAmong 168 patients with severe COVID-19, 199 with MIS-C, and 45 with mild SARS-CoV-2 infections, only 1 had high levels of anti-IFN-α2 antibodies. Anti-IFN-α2 autoantibodies were not detected in patients treated with intravenous immunoglobulin before sample collection. Whole-exome sequencing identified a missense variant in the ankyrin domain of NFKB2, encoding the p100 subunit of nuclear factor kappa-light-chain enhancer of activated B cells, aka NF-κB, essential for noncanonical NF-κB signaling. The patient's peripheral blood mononuclear cells exhibited impaired cleavage of p100 characteristic of NFKB2 haploinsufficiency, an inborn error of immunity with a high prevalence of autoimmunity.ConclusionsHigh levels of anti-IFN-α2 autoantibodies in children and adolescents with MIS-C, severe COVID-19, and mild SARS-CoV-2 infections are rare but can occur in patients with inborn errors of immunity.
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- 2023
40. Effect of a Randomized Controlled Trial of Housing Vouchers on Adolescent Risky Sexual Behavior Over a 15-Year Period
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Gresham, Bria, Thyden, Naomi H., Gailey, Samantha, and Osypuk, Theresa L.
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- 2024
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41. Torture and Metamorphosis in Exeter Book Riddle 261
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Bria, Jasmine
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- 2023
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42. Seamless Iterative Semi-Supervised Correction of Imperfect Labels in Microscopy Images
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Elbatel, Marawan, Bornberg, Christina, Kattel, Manasi, Almar, Enrique, Marrocco, Claudio, and Bria, Alessandro
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition - Abstract
In-vitro tests are an alternative to animal testing for the toxicity of medical devices. Detecting cells as a first step, a cell expert evaluates the growth of cells according to cytotoxicity grade under the microscope. Thus, human fatigue plays a role in error making, making the use of deep learning appealing. Due to the high cost of training data annotation, an approach without manual annotation is needed. We propose Seamless Iterative Semi-Supervised correction of Imperfect labels (SISSI), a new method for training object detection models with noisy and missing annotations in a semi-supervised fashion. Our network learns from noisy labels generated with simple image processing algorithms, which are iteratively corrected during self-training. Due to the nature of missing bounding boxes in the pseudo labels, which would negatively affect the training, we propose to train on dynamically generated synthetic-like images using seamless cloning. Our method successfully provides an adaptive early learning correction technique for object detection. The combination of early learning correction that has been applied in classification and semantic segmentation before and synthetic-like image generation proves to be more effective than the usual semi-supervised approach by > 15% AP and > 20% AR across three different readers. Our code is available at https://github.com/marwankefah/SISSI., Comment: To appear at MICCAI 2022 Workshop on Domain Adaptation and Representation Transfer (DART)
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- 2022
43. Transcriptomic profiles of multiple organ dysfunction syndrome phenotypes in pediatric critical influenza.
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Novak, Tanya, Crawford, Jeremy, Hahn, Georg, Hall, Mark, Thair, Simone, Newhams, Margaret, Chou, Janet, Mourani, Peter, Tarquinio, Keiko, Markovitz, Barry, Loftis, Laura, Weiss, Scott, Higgerson, Renee, Schwarz, Adam, Pinto, Neethi, Thomas, Neal, Gedeit, Rainer, Sanders, Ronald, Mahapatra, Sidharth, Coates, Bria, Kurachek, Stephen, Shein, Steven, Lange, Christoph, Thomas, Paul, Randolph, Adrienne, Ackerman, Kate, Tellez, David, Mcquillen, Patrick, and Cvijanovich, Natalie
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MODS ,critical care ,influenza ,neutrophil degranulation ,neutrophil transcripts ,organ failure ,pediatric intensive care ,sepsis ,Humans ,Multiple Organ Failure ,Influenza ,Human ,Transcriptome ,Phenotype ,Hospitalization ,Bacterial Infections - Abstract
BACKGROUND: Influenza virus is responsible for a large global burden of disease, especially in children. Multiple Organ Dysfunction Syndrome (MODS) is a life-threatening and fatal complication of severe influenza infection. METHODS: We measured RNA expression of 469 biologically plausible candidate genes in children admitted to North American pediatric intensive care units with severe influenza virus infection with and without MODS. Whole blood samples from 191 influenza-infected children (median age 6.4 years, IQR: 2.2, 11) were collected a median of 27 hours following admission; for 45 children a second blood sample was collected approximately seven days later. Extracted RNA was hybridized to NanoString mRNA probes, counts normalized, and analyzed using linear models controlling for age and bacterial co-infections (FDR q
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- 2023
44. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome
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Parry, Erin M, Leshchiner, Ignaty, Guièze, Romain, Johnson, Connor, Tausch, Eugen, Parikh, Sameer A, Lemvigh, Camilla, Broséus, Julien, Hergalant, Sébastien, Messer, Conor, Utro, Filippo, Levovitz, Chaya, Rhrissorrakrai, Kahn, Li, Liang, Rosebrock, Daniel, Yin, Shanye, Deng, Stephanie, Slowik, Kara, Jacobs, Raquel, Huang, Teddy, Li, Shuqiang, Fell, Geoff, Redd, Robert, Lin, Ziao, Knisbacher, Binyamin A, Livitz, Dimitri, Schneider, Christof, Ruthen, Neil, Elagina, Liudmila, Taylor-Weiner, Amaro, Persaud, Bria, Martinez, Aina, Fernandes, Stacey M, Purroy, Noelia, Anandappa, Annabelle J, Ma, Jialin, Hess, Julian, Rassenti, Laura Z, Kipps, Thomas J, Jain, Nitin, Wierda, William, Cymbalista, Florence, Feugier, Pierre, Kay, Neil E, Livak, Kenneth J, Danysh, Brian P, Stewart, Chip, Neuberg, Donna, Davids, Matthew S, Brown, Jennifer R, Parida, Laxmi, Stilgenbauer, Stephan, Getz, Gad, and Wu, Catherine J
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Cancer ,Rare Diseases ,Lymphoma ,Genetics ,Hematology ,Human Genome ,Humans ,Leukemia ,Lymphocytic ,Chronic ,B-Cell ,Lymphoma ,Large B-Cell ,Diffuse ,Serine-Arginine Splicing Factors ,Medical and Health Sciences ,Immunology - Abstract
Richter syndrome (RS) arising from chronic lymphocytic leukemia (CLL) exemplifies an aggressive malignancy that develops from an indolent neoplasm. To decipher the genetics underlying this transformation, we computationally deconvoluted admixtures of CLL and RS cells from 52 patients with RS, evaluating paired CLL-RS whole-exome sequencing data. We discovered RS-specific somatic driver mutations (including IRF2BP2, SRSF1, B2M, DNMT3A and CCND3), recurrent copy-number alterations beyond del(9p21)(CDKN2A/B), whole-genome duplication and chromothripsis, which were confirmed in 45 independent RS cases and in an external set of RS whole genomes. Through unsupervised clustering, clonally related RS was largely distinct from diffuse large B cell lymphoma. We distinguished pathways that were dysregulated in RS versus CLL, and detected clonal evolution of transformation at single-cell resolution, identifying intermediate cell states. Our study defines distinct molecular subtypes of RS and highlights cell-free DNA analysis as a potential tool for early diagnosis and monitoring.
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- 2023
45. Coping Style Moderates the Relationship between Community Violence and Depressive Symptoms in Urban Adolescents
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Gresham, Bria Leigh, Orihuela, Catheryn A., and Mrug, Sylvie
- Abstract
Community violence exposure is associated with increased depressive symptoms in adolescents. This study examined whether coping style moderates this relationship over time. Eighty-four low-income, urban adolescents (M[subscript age] = 13.36, 50% female, 95% African American) participated in two waves of a longitudinal study. Youth reported on their community violence exposure and coping style at Wave 1, and their depressive symptoms at Waves 1 and 2 (17 months apart). Problem-focused coping attenuated the effect of community violence exposure on depressive symptoms ([beta] = -0.47, p < 0.05), whereas avoidant coping amplified the effect of community violence on depressive symptoms ([beta] = 0.63, p < 0.05). Adolescents exposed to community violence are at an increased risk of developing depressive symptoms if they use low levels of problem-focused coping or high levels of avoidant coping. Interventions targeting coping strategies may improve psychological adjustment of urban youth exposed to community violence.
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- 2023
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46. Proper usage of Scherrer's and Guinier's formulas in X-ray analysis of size distribution in systems of monocrystalline CeO2 nanoparticles
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Valério, Adriana, Trindade, Fabiane J., Penacchio, Rafaela F. S., Ramos, Bria C., Damasceno, Sérgio, Estradiote, Maurício B., Rodella, Cristiane B., Ferlauto, André S., Kycia, Stefan W., and Morelhão, Sérgio L.
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Condensed Matter - Materials Science - Abstract
Small-angle X-ray scattering (SAXS) and X-ray diffraction (XRD) techniques are widely used as analytical tools in the optimization and control of nanomaterial synthesis processes. In crystalline nanoparticle systems with size distribution, the discrepant size values determined by using SAXS and XRD still lacks a well-established description in quantitative terms. To address fundamental questions, the isolated effect of size distribution is investigated by SAXS and XRD simulation in polydisperse systems of virtual nanoparticles. It quantitatively answered a few questions, among which the most accessible and reliable size values and what they stand for regarding the size distribution parameters. When a finite size distribution is introduced, the two techniques produce differing results even in perfectly crystalline nanoparticles. Once understood, the deviation in resulting size values can, in principle, resolve two parameters size distributions of crystalline nanoparticles. To demonstrate data analysis procedures in light of this understanding, XRD and SAXS experiments were carried out on a series of powder samples of cubic ceria nanoparticles. Besides changes in the size distribution related to the synthesis parameters, proper comparison of XRD and SAXS results revealed particle-particle interaction effects underneath the SAXS intensity curves. It paves the way for accurate and reliable methodologies to assess size, size dispersion, and degree of crystallinity in synthesized nanoparticles., Comment: 24 pages (16 of main text and 8 of appendix), 18 figures
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- 2022
47. Leptin-mediated meta-inflammation may provide survival benefit in patients receiving maintenance immunotherapy for extensive-stage small cell lung cancer (ES-SCLC)
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Vita, Emanuele, Stefani, Alessio, Piro, Geny, Mastrantoni, Luca, Cintoni, Marco, Cicchetti, Giuseppe, Sparagna, Ileana, Monaca, Federico, Horn, Guido, Russo, Jacopo, Barone, Diletta, Di Salvatore, Mariantonietta, Trisolini, Rocco, Lococo, Filippo, Mazzarella, Ciro, Cancellieri, Alessandra, Carbone, Carmine, Larici, Anna Rita, Mele, Maria Cristina, Pilotto, Sara, Milella, Michele, Tortora, Giampaolo, and Bria, Emilio
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- 2023
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48. Prior vaccination promotes early activation of memory T cells and enhances immune responses during SARS-CoV-2 breakthrough infection
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Painter, Mark M., Johnston, Timothy S., Lundgreen, Kendall A., Santos, Jefferson J. S., Qin, Juliana S., Goel, Rishi R., Apostolidis, Sokratis A., Mathew, Divij, Fulmer, Bria, Williams, Justine C., McKeague, Michelle L., Pattekar, Ajinkya, Goode, Ahmad, Nasta, Sean, Baxter, Amy E., Giles, Josephine R., Skelly, Ashwin N., Felley, Laura E., McLaughlin, Maura, Weaver, Joellen, Kuthuru, Oliva, Dougherty, Jeanette, Adamski, Sharon, Long, Sherea, Kee, Macy, Clendenin, Cynthia, da Silva Antunes, Ricardo, Grifoni, Alba, Weiskopf, Daniela, Sette, Alessandro, Huang, Alexander C., Rader, Daniel J., Hensley, Scott E., Bates, Paul, Greenplate, Allison R., and Wherry, E. John
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- 2023
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49. The Language of Compassion: Hospital Chaplains’ Compassion Capacity Reduces Patient Depression via Other-Oriented, Inclusive Language
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Mascaro, Jennifer S., Palmer, Patricia K., Willson, Madison, Ash, Marcia J., Florian, Marianne P., Srivastava, Meha, Sharma, Anuja, Jarrell, Bria, Walker, Elizabeth Reisinger, Kaplan, Deanna M., Palitsky, Roman, Cole, Steven P., Grant, George H., and Raison, Charles L.
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- 2023
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50. Progress toward a universal biomedical data translator
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Fecho, Karamarie, Thessen, Anne E, Baranzini, Sergio E, Bizon, Chris, Hadlock, Jennifer J, Huang, Sui, Roper, Ryan T, Southall, Noel, Ta, Casey, Watkins, Paul B, Williams, Mark D, Xu, Hao, Byrd, William, Dančík, Vlado, Duby, Marc P, Dumontier, Michel, Glusman, Gustavo, Harris, Nomi L, Hinderer, Eugene W, Hyde, Greg, Johs, Adam, Su, Andrew I, Qin, Guangrong, Zhu, Qian, Dougherty, Jennifer, Huang, Conrad, Magis, Andrew, Smith, Brett, Celebi, Remzi, Chen, Zhehuan, Azevedo, Ricardo De Miranda, Emonet, Vincent, Lee, Jay, Weng, Chunhua, Yilmaz, Arif, Kim, Keum Joo, Santos, Eugene, Tonstad, Lucas, Veenhuis, Luke, Yakaboski, Chase, Acevedo, Liliana, Carrell, Steven, Deutsch, Eric, Glen, Amy, Hoffman, Andrew, Koslicki, David, Kvarfordt, Lindsey, Liu, Zheng, Liu, Shaopeng, Ma, Chunyu, Mendoza, Luis, Muluka, Arun Teja, Womack, Finn, Wood, Erica, Roach, Jared, Goel, Prateek, Weber, Rosina, Williams, Andrew, Gormley, Joseph, Zisk, Tom, Hanspers, Kristina, Hoatlin, Maureen, Pico, Alexander, Riutta, Anders, Callaghan, Jackson, Xu, Colleen, Ahalt, Stanley C, Balhoff, Jim, Edwards, Stephen, Haaland, Perry, Knowles, Michael, Krishnamurthy, Ashok, Mandal, Meisha, Peden, David B, Pfaff, Emily, Schurman, Shepherd, Shrivastava, Shalki, Yi, Hong, Reilly, Jason, Kanwar, Richa, Cox, Steven, Vaidya, Gaurav, Wang, Max, Alkanaq, Ahmed, Costanzo, Maria, Koesterer, Ryan, Flannick, Jason, Burtt, Noel, Kluge, Alexandria, Rubin, Irit, Strasser, Michael Michi, Chung, Lawrence, Kang, Jimin, Mantilla, Michelle, Muller, Sandrine, Persaud, Bria, Wei, Qi, Baumgartner, Andrew, Dai, Cheng, and Duvvuri, Venkata
- Subjects
Pharmacology and Pharmaceutical Sciences ,Biomedical and Clinical Sciences ,Cardiovascular Medicine and Haematology ,Biomedical Data Translator Consortium ,Cardiorespiratory Medicine and Haematology ,Oncology and Carcinogenesis ,Other Medical and Health Sciences ,General Clinical Medicine ,Cardiovascular medicine and haematology ,Pharmacology and pharmaceutical sciences - Abstract
Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well-being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline-specific differences in terminology and representation. To address these challenges, the Biomedical Data Translator Consortium has developed and tested a pilot knowledge graph-based "Translator" system capable of integrating existing biomedical data sets and "translating" those data into insights intended to augment human reasoning and accelerate translational science. Having demonstrated feasibility of the Translator system, the Translator program has since moved into development, and the Translator Consortium has made significant progress in the research, design, and implementation of an operational system. Herein, we describe the current system's architecture, performance, and quality of results. We apply Translator to several real-world use cases developed in collaboration with subject-matter experts. Finally, we discuss the scientific and technical features of Translator and compare those features to other state-of-the-art, biomedical graph-based question-answering systems.
- Published
- 2022
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