8,985,726 results on '"ROBERT, A."'
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2. Smithsonian Science for North and South Carolina Classrooms: 'Improving Student Achievement across State Borders and State Standards'. Final Evaluation Report
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University of Memphis, Center for Research in Educational Policy (CREP), Smithsonian Institution (SI), Smithsonian Science Education Center (SSEC), Todd Zoblotsky, Robert McKinney, Carolyn Kaldon, Mojtaba Khajeloo, Yu Wu, and Ivysmeralys Morales
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The goal of Smithsonian Science for North and South Carolina Classrooms was to provide teachers with ongoing, differentiated professional development and research-based curricular materials to improve elementary student achievement in science, mathematics, and reading. This work used an inquiry-based science curriculum, Smithsonian Science for the Classroom, which is aligned with the Next Generation Science Standards (NGSS), and was implemented in Grades 3-5 within predominantly rural North and South Carolina school districts serving high-needs students. The Center for Research in Educational Policy (CREP) at the University of Memphis, a State of Tennessee Center of Excellence, was the independent third-party evaluator. CREP implemented a Randomized Controlled Trial (RCT) to collect and analyze data using a rigorous, mixed-methods approach, including quantitative analyses of student achievement data from the Stanford-10 and state assessments, and qualitative analyses of classroom observation data, as well as teacher feedback from professional development surveys, module logs, and focus groups. For this study, 36 schools (including one split cohort being treated as one school) in seven districts within North and South Carolina were randomly assigned to treatment and comparison groups. The study cohort, followed over three academic years (2020-21 through 2022-23), was composed of more than 1,600 third grade (2020-21) students in these schools. In the comparison condition, schools used their business-as-usual science curricula and teacher professional development and did not receive Smithsonian Science curricular materials or professional development. As the pretests for achievement outcomes, students took the Abbreviated Battery of the Stanford Achievement Test Series, Tenth Edition (Stanford-10) in Reading and Math in spring of 2021 (the cohort's third grade year). The main findings and posttests included the combined sample (i.e., both states combined) for (a) the Stanford-10 Science subtest, which was administered in the spring of 2023 (the cohort's fifth grade year), and (b) spring 2023 standardized state assessment scores in Reading and Math. Using a hierarchical linear model (HLM) with school as a random effect, the analysis of the effect of Smithsonian Science for the three main findings after several years of disruptions from the COVID-19 pandemic was (a) positive (g = 0.18) and statistically significant (p = 0.032) on the Stanford-10 science assessment and (b) positive for both Reading (g = 0.10) and Math (g = 0.16), meaning students in the treatment group performed better than the control group, but the effects were not statistically significant. Teachers were generally positive in terms of the professional development provided, and feedback on the module logs largely supported the effectiveness of the professional development and fidelity of implementation. Classroom observations further supported the effectiveness of the professional development and fidelity to inquiry-based practices in treatment classrooms (e.g., use of experiential hands-on learning and level of class time dedicated to inquiry-based science). With instructional time for science lagging other subject areas, and as learning recovery in reading and math after COVID-19 receive national attention, the results demonstrate that ongoing, differentiated, high-quality professional learning and high-quality instructional materials for science instruction can support student achievement in science, math, and reading.
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- 2024
3. An Abbreviated Form of the WISC-R: Is It Valid?
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Resnick, Robert J.
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The completed WISC-R's (Wechsler Intelligence Scale for Children-Revised) of 76 white urban children with academic problems (6 years, 0 months to 15 years, 9 months) were rescored utilizing the Satz and Mogel criteria for an abbreviated intelligence measure. Extremely high correlations for IQ's (.96 - .98) and subtests (.66 - .95) were found. However, when mean differences between complete WISC-R and the shortened form were examined, significant differences between administrations were found. Furthermore, one third of the subjects showed changes in intelligence classification levels when the abbreviated form was used. Thus, two of the three criteria previously suggested for a valid abbreviated intelligence test of: (1) high correlation between administration forms; (2) non significant t-tests between the abbreviated and standard form mean IQ; and (3) low percentage of IQ classification change with the administration of the short form were not met. It was concluded, however, that the abbreviated WISC-R may be appropriate when intelligence is a question relative to candidacy for therapy or as a non-critical, general indication of intelligence when IQ classification is not important and/or assessment time is limited. (Author/RC)
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- 2024
4. Relationships Between Teachers' Marks, Achievement Test Scores and Aptitude as a Function of Grade, Ethnicity and Sex.
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Texas Univ., Austin. Research and Development Center for Teacher Education., Borich, Gary D., and Peck, Robert F.
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Logical predictions about relationships between school aptitude and standardized achievement, aptitude and teachers' grades, and teachers' grades and standardized achievement can be made from the literature. These predictions are that (1) conventional school aptitude measures should predict standardized achievement test scores equally well for boys and girls but better for advantaged than disadvantaged children; (2) teachers' marks are more accurate for girls than for boys when judged against the sexes' standardized achievement test scores; are more accurate for middle-class than for disadvantaged children; and are least accurate for disadvantaged black males; and (3) teachers consistently give girls higher grades than boys but there are no important differences between boys' and girls' achievement when measured by standard achievement tests. The present study was conducted to test the strength of the relationships between pupil aptitude, standardized achievement and teachers' grades and to determine the percent of variance in grade point average accounted for by aptitude and standardized achievement in a representative sample of fifth- and ninth-grade Mexican-American, Black and Anglo students. (Author/RC)
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- 2024
5. Development and Standardization of Parallel Forms of the Curry-Geis Syllabication Skills Test [including Curry-Geis Syllabication Skills Test Form A and Form B)).
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Curry, Robert L. and Geis, Lynna
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Implicit in most of the recommendations for teaching reading is the inclusion of structural analysis as a part of the instructional program for developing skills in word recognition. This study focused on the development and standardization of a criterion referenced syllabication skills test designed to evaluate the individual proficiency of college students and inservice teachers. The 100-item test presents a word and four possible syllabications of that word from which the respondent must select one. Conclusions from the examination of the results of the data analysis obtained in the study were: (1) the test was valid and reliable for determining college students' abilities to apply syllabication skills; (2) parallel forms of the Syllabication Skills Test were developed and can be administered in approximately 40 minutes; (3) the arbitrary criterion level of 85 percent accuracy was logical in that the means of the tests were very similar to the established criterion level; and (4) judges in the field of reading considered the tests to be of educational value in the preparation of teachers. Copies of the Curry-Geis Syllabication Skills Test, Form A and Form B are included. (RC)
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- 2024
6. Nurses Improve Their Personal Communication.
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Miltz, Robert J.
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A three-day seminar for nurses was conducted to improve their ability to communicate effectively with other people. The method used in this seminar was microteaching. The basic ingredients of the microteaching concept are the communication techniques dimension, the teach-reteach dimension, and the immediate feedback dimension. Under the direction of a supervisor and working with others in the seminar, each participant demonstrated and spoke on the topic of her choice, with the aim of instructing the listeners. Each demonstration was recorded on video tape. The tape was viewed and analysed, followed by direct question and answer sessions and suggestions for improvement by the supervisor. The benefit of immediate feedback and reaction was apparent, and each participant developed more self-confidence as the seminar progressed. The concensus of opinion at the end of the session was that microteaching is a valuable tool not only for improving communication skills but also for improving teaching techniques. (JD)
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- 2024
7. Report of the Louisiana Statewide Planning for Physician Residency Program Committee.
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Louisiana Regional Medical Program, Baton Rouge., Louisiana State Office of Comprehensive Health Planning, Baton Rouge., and Sappenfield, Robert W.
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Preceding the body of the report, a brief review of the literature is provided to acquaint the reader with similarities and differences between national and local trends regarding the demographic characteristics of the physician population. The goal of the statewide residency study was to develop a strategy for the design and allocation of physician residencies consistent with statewide needs. A graphic model of the physician manpower production process was developed which enhanced understanding of the manpower problems facing Louisiana. Through the model, available data, and personal interviews with senior medical students and postgraduate trainees, data were compiled and analyzed regarding the need for physicians in Louisiana in 1982, where and how the number of physicians can be increased, the status of primary care treatment, likely sites for practicing physicians, and related concerns. The general conclusions point to several significant manpower production problems in Louisiana in its preparation for future needs for physician services. The study committee proposed several recommendations to meet the problem. (Appendixes contain supplementary tables and interview forms.) (AG)
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- 2024
8. Developing Job Sheets and Related Aids for Individualized Instruction in the Machine Shop.
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Tennessee Univ., Knoxville. Occupational Research and Development Coordinating Unit. and Shipp, Robert E.
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The document is divided according to the four different kinds of sheets presented. The first section contains assignment sheets on 28 machine shop topics and supplementary transparencies. Included in the information presented is the title of the sheet, the unit and occupation to which it applies, the objective, reference for information, directions, and a list of questions. The second section contains sheets on related information, usually dealing with tools or procedures for their use. Twenty-five topics are covered with title, unit, occupation, objective, references, an introduction, and information specified for each sheet. Operation sheets are in section 3; seven operations are included specifying title, unit, occupation, objective, introduction, reference, and procedure for each. The final section contains job sheets for 25 tools used in machine shop. In this section, the title, unit, occupation, objective, information, specifications, materials, tools and equipment, and procedures are outlined. A cross-index is provided, keyed to the job sheets, for relating the job, assignment, operation, and information sheets to each other. (AG)
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- 2024
9. Effective Retail Sales Techniques.
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Ohio State Univ., Columbus. Ohio Distributive Education Materials Lab. and Canei, Robert A.
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The manual is a 12-hour program for adults who are working or preparing to work as retail salespeople. It can also be used as a summarization manual for high school students. The manual consists of five sessions which take the individual from the human aspect of sales to the related sales technique. The sessions are entitled: employee and customer relations, approaches and presentations, objections and closing the sale, suggestion selling, and sales demonstrations. Each session provides an instructional outline, related methods, and appropriate handouts and transparency originals. The appendix lists keys of session evaluation, promotional devices, suggested films, case studies, and supplementary handouts and transparency masters. (NJ)
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- 2024
10. A Look at Metrics in Distributive Education.
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Ohio State Univ., Columbus. Ohio Distributive Education Materials Lab. and Canei, Robert A.
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The United States will convert to the metric system of measurement in the near future, and the distributive education programs in high school and at the adult level will have to train the needed personnel for business. The manual gives the basic conversion methods and instruction in teaching metrics. Metric programs conducted for business personnel would be the same as other distributive education programs, with the addition of promotion and publicity releases. The manual includes topical outlines and suggestions for the instructor in five sessions on program management, metric length, metric area, metric volume and capacity, and metric mass (weight). Transparencies testing materials, and student handouts accompany each section. Also included are supplementary materials, film summaries, promotional material, course evaluation sheets, and a list of material sources. (MF)
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- 2024
11. PRACTICAL NURSING IN ILLINOIS--A PROFILE.
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Illinois State Board of Vocational Education and Rehabilitation, Springfield., Illinois Univ., Urbana. Coll. of Education., and TOMLINSON, ROBERT M.
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THIS DOCUMENT, THE FIRST OF FIVE PLANNED REPORTS, PRESENTS THE HISTORY AND BACKGROUND OF PRACTICAL NURSING, WITH PARTICULAR REFERENCE TO ILLINOIS. IT DESCRIBES THE BETTER LICENSING PROCEDURES AND STANDARDS THAT HAVE COME WITH THE INCREASED RECOGNITION OF THE VALUE OF THE OCCUPATION TO THE MEDICAL PROFESSION. THE REPORT ALSO DESCRIBES A 1600-HOUR CURRICULUM, INCLUDING THEORY AND PRACTICE, SUGGESTED BY THE ILLINOIS DEPARTMENT OF REGISTRATION AND EDUCATION IN 1965. TABLES GIVE DATA ON THE PRESENT BACKGROUND OF THE NURSES (BY EDUCATION AND EXPERIENCE), ON THEIR CHARACTERISTICS (MOST NOTABLY, DEVOTION TO THEIR CAREERS AND STABILITY IN THE LABOR MARKET), ON PRESENT EMPLOYMENT IN ILLINOIS AND ADJACENT AREAS, AND ON THE NEED FOR ADDITIONAL RECRUITMENT AND TRAINING TO FILL CURRENT AND FUTURE NEEDS. (HH)
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- 2024
12. CRISPR/Cas9 Gene Targeting plus Nanopore DNA Sequencing with the Plasmid pBR322 in the Classroom
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Röbbe Wünschiers, Robert Maximilian Leidenfrost, Hauke Holtorf, Bernd Dittrich, Thomas Dürr, and Jürgen Braun
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Both nanopore-based DNA sequencing and CRISPR/Cas-based gene editing represent groundbreaking innovations in molecular biology and genomics, offering unprecedented insights into and tools for working with genetic information. For students, reading, editing, and even writing DNA will be part of their everyday life. We have developed a laboratory procedure that includes (i) the biosynthesis of a guide RNA for, (ii) targeting Cas9 to specifically linearize the pBR322 plasmid, and (iii) the identification of the cutting site through nanopore DNA sequencing. The protocol is intentionally kept simple and requires neither living organisms nor biosafety laboratories. We divided the experimental procedures into separate activities to facilitate customization. Assuming access to a well-equipped molecular biology laboratory, an initial investment of approximately $2,700 is necessary. The material costs for each experiment group amount to around $130. Furthermore, we have developed a freely accessible website (https://dnalesen.hs-mittweida.de) for sequence read analysis and visualization, lowering the required computational skills to a minimum. For those with strong computational skills, we provide instructions for terminal-based data processing. With the presented activities, we aim to provide a hands-on experiment that engages students in modern molecular genetics and motivates them to discuss potential implications. The complete experiment can be accomplished within half a day and has been successfully implemented by us at high schools, in teacher training, and at universities. Our tip is to combine CRISPR/Cas gene targeting with nanopore-based DNA sequencing. As a tool, we provide a website that facilitates sequence data analysis and visualization.
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- 2024
13. Online Student Engagement in the Turkish Context: A Prisma-Based Systematic Review
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Handan Atun, Dincer Cinar, Elif Sengun Oztas, Yasemin Gulbahar, Sa’ad Laws, Alan S. Weber, Robert Bianchi, and Khawla Kittaneh
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The ability to interact or engage with the instructor, other students, and the content i.e., to experience online student engagement, is one main difference between traditional and digital media employed in teaching and learning processes. As literature on this topic in the Turkish context has proliferated, to date, virtually no systematic reviews of this research have been carried out in order to identify potential gaps in the literature. To address this issue, this study investigated previously conducted research in chronological order on student engagement at the post-secondary level in the Turkish context using a PRISMA-based systematic review screening process. The results show that online engagement research and practices have clearly increased and diversified over time. Specifically, online engagement research in the Turkish context has tended to focus on computer science students studying in online-only, LMS-supported environments where their behavioral engagement has been investigated quantitatively. Considering these findings, this systematic review suggests that future studies in the Turkish context should examine other fields besides computer science education, focus more on collaborative tools and the social dimension of engagement, use more qualitative methods, and investigate blended environments as well as online-only.
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- 2024
14. Higher Pay Won't Solve Teachers' Problems: We've Made Teaching 'Too Hard for Mere Mortals.' Statement to the U.S. Committee on Health, Education, Labor & Pensions on 'The Immediate and Long-Term Challenges Facing Public School Teachers: Low Pay, Teacher Shortages, and Underfunded Public Schools'
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American Enterprise Institute (AEI) and Robert Pondiscio
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The author's statement to the U.S. Senate Committee on Health, Education, Labor & Pensions on the challenges faced by America's classroom teachers focuses on a few of the factors that lead to teacher frustration and burnout that higher pay, however well-intended, does not change. They include, but are not limited to, poor teacher preparation, deteriorating classroom conditions--specifically classroom disorder and disruption--shoddy curriculum, and increasingly the expectation that they will not just teach reading, math, or their subject areas effectively, but also play a quasi-therapeutic role in response to students' behavioral and mental health needs. We are asking teachers to do too many things to do any of them well at any salary.
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- 2024
15. Evaluating the Longer Term Impact of Early College High Schools on Workforce Outcomes
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American Institutes for Research (AIR), Mengli Song, Kristina Zeiser, Kyle Neering, Robert Schwarzhaupt, and Sara Mitchell
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This report describes results from the Long-Term Impact of Early College High Schools Study--funded by the Institute of Education Sciences (IES) (#R305A210017)--which aimed to explore the long-term impacts of early college (EC) high schools on students' academic outcomes (e.g., college enrollment, degree attainment) and workforce, financial, and later life outcomes after schooling. In this report--the second follow-up report on our initial EC impact study--we focus specifically on key questions about workforce, financial, and other life outcomes: What were the impacts of ECs on workforce, financial, and other life outcomes in the 12th to 14th years after expected high school graduation? Did the impacts of ECs vary by participant characteristics? This report describes findings which build on a previous EC impact study, which was a multisite student-level randomized controlled trial with randomization based on admission lotteries. The analyses in this report focus on individuals who originally participated in 17 admission lotteries conducted by seven ECs for three cohorts of students, and examined outcomes after formal schooling. Key takeaways include the following: (1) Participants who were admitted to an EC, regardless of whether they attended the EC, did not experience a significant effect on any of the workforce, financial, and other life outcomes measured with survey data 12 to 14 years after expected high school graduation; and (2) EC impacts on workforce, financial, and other life outcomes measured 12 to 14 years after expected high school graduation did not differ significantly by individuals' race/ethnicity, low-income status, or prior achievement. While our initial impact study and first follow-up study found that attending an EC had effects on secondary and postsecondary enrollment, and completion for participants with different background characteristics, we found that attending an EC had no impact on any of the workforce, financial, and other life outcomes that we analyzed 12 to 14 years after participants' expected high school graduation. Future studies could consider examining workforce, financial, and other life outcomes in years before the 12th to 14th year after expected high school graduation using administrative data sources (e.g., IRS or unemployment insurance records). Further research may also examine if other factors, such as EC students' college major or labor market opportunities, influence the impact of ECs on longer-term outcomes.
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- 2024
16. How to Build a Quantum Supercomputer: Scaling Challenges and Opportunities
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Mohseni, Masoud, Scherer, Artur, Johnson, K. Grace, Wertheim, Oded, Otten, Matthew, Aadit, Navid Anjum, Bresniker, Kirk M., Camsari, Kerem Y., Chapman, Barbara, Chatterjee, Soumitra, Dagnew, Gebremedhin A., Esposito, Aniello, Fahim, Farah, Fiorentino, Marco, Khalid, Abdullah, Kong, Xiangzhou, Kulchytskyy, Bohdan, Li, Ruoyu, Lott, P. Aaron, Markov, Igor L., McDermott, Robert F., Pedretti, Giacomo, Gajjar, Archit, Silva, Allyson, Sorebo, John, Spentzouris, Panagiotis, Steiner, Ziv, Torosov, Boyan, Venturelli, Davide, Visser, Robert J., Webb, Zak, Zhan, Xin, Cohen, Yonatan, Ronagh, Pooya, Ho, Alan, Beausoleil, Raymond G., and Martinis, John M.
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Quantum Physics - Abstract
In the span of four decades, quantum computation has evolved from an intellectual curiosity to a potentially realizable technology. Today, small-scale demonstrations have become possible for quantum algorithmic primitives on hundreds of physical qubits and proof-of-principle error-correction on a single logical qubit. Nevertheless, despite significant progress and excitement, the path toward a full-stack scalable technology is largely unknown. There are significant outstanding quantum hardware, fabrication, software architecture, and algorithmic challenges that are either unresolved or overlooked. These issues could seriously undermine the arrival of utility-scale quantum computers for the foreseeable future. Here, we provide a comprehensive review of these scaling challenges. We show how the road to scaling could be paved by adopting existing semiconductor technology to build much higher-quality qubits, employing system engineering approaches, and performing distributed quantum computation within heterogeneous high-performance computing infrastructures. These opportunities for research and development could unlock certain promising applications, in particular, efficient quantum simulation/learning of quantum data generated by natural or engineered quantum systems. To estimate the true cost of such promises, we provide a detailed resource and sensitivity analysis for classically hard quantum chemistry calculations on surface-code error-corrected quantum computers given current, target, and desired hardware specifications based on superconducting qubits, accounting for a realistic distribution of errors. Furthermore, we argue that, to tackle industry-scale classical optimization and machine learning problems in a cost-effective manner, distributed quantum-assisted probabilistic computing with custom-designed accelerators should be considered as a complementary path toward scalability., Comment: 50 pages, 42 figures
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- 2024
17. Construction of an invertible mapping to boundary conforming coordinates for arbitrarily shaped toroidal domains
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Babin, Robert, Hindenlang, Florian, Maj, Omar, and Köberl, Robert
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Physics - Plasma Physics ,Mathematical Physics - Abstract
Boundary conforming coordinates are commonly used in plasma physics to describe the geometry of toroidal domains, for example, in three-dimensional magnetohydrodynamic equilibrium solvers. The magnetohydrodynamic equilibrium configuration can be approximated with an inverse map, defining nested surfaces of constant magnetic flux. For equilibrium solvers that solve for this inverse map iteratively, the initial guess for the inverse map must be well defined and invertible. Even if magnetic islands are to be included in the representation, boundary conforming coordinates can still be useful, for example to parametrize the interface surfaces in multi-region, relaxed magnetohydrodynamics. Given a fixed boundary shape, finding a valid boundary conforming mapping can be challenging, especially for the non-convex boundaries from recent developments in stellarator optimization. In this work, we propose a new algorithm to construct such a mapping, by solving two Dirichlet-Laplace problems via a boundary integral method. We can prove that the generated harmonic map is always smooth and has a smooth inverse. Furthermore, we can find a discrete approximation of the mapping that preserves this property.
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- 2024
18. MuCol Milestone Report No. 5: Preliminary Parameters
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Accettura, Carlotta, Adrian, Simon, Agarwal, Rohit, Ahdida, Claudia, Aimé, Chiara, Aksoy, Avni, Alberghi, Gian Luigi, Alden, Siobhan, Alfonso, Luca, Amapane, Nicola, Amorim, David, Andreetto, Paolo, Anulli, Fabio, Appleby, Rob, Apresyan, Artur, Asadi, Pouya, Mahmoud, Mohammed Attia, Auchmann, Bernhard, Back, John, Badea, Anthony, Bae, Kyu Jung, Bahng, E. J., Balconi, Lorenzo, Balli, Fabrice, Bandiera, Laura, Barbagallo, Carmelo, Barlow, Roger, Bartoli, Camilla, Bartosik, Nazar, Barzi, Emanuela, Batsch, Fabian, Bauce, Matteo, Begel, Michael, Berg, J. Scott, Bersani, Andrea, Bertarelli, Alessandro, Bertinelli, Francesco, Bertolin, Alessandro, Bhat, Pushpalatha, Bianchi, Clarissa, Bianco, Michele, Bishop, William, Black, Kevin, Boattini, Fulvio, Bogacz, Alex, Bonesini, Maurizio, Bordini, Bernardo, de Sousa, Patricia Borges, Bottaro, Salvatore, Bottura, Luca, Boyd, Steven, Breschi, Marco, Broggi, Francesco, Brunoldi, Matteo, Buffat, Xavier, Buonincontri, Laura, Burrows, Philip Nicholas, Burt, Graeme Campbell, Buttazzo, Dario, Caiffi, Barbara, Calatroni, Sergio, Calviani, Marco, Calzaferri, Simone, Calzolari, Daniele, Cantone, Claudio, Capdevilla, Rodolfo, Carli, Christian, Carrelli, Carlo, Casaburo, Fausto, Casarsa, Massimo, Castelli, Luca, Catanesi, Maria Gabriella, Cavallucci, Lorenzo, Cavoto, Gianluca, Celiberto, Francesco Giovanni, Celona, Luigi, Cemmi, Alessia, Ceravolo, Sergio, Cerri, Alessandro, Cerutti, Francesco, Cesarini, Gianmario, Cesarotti, Cari, Chancé, Antoine, Charitonidis, Nikolaos, Chiesa, Mauro, Chiggiato, Paolo, Ciccarella, Vittoria Ludovica, Puviani, Pietro Cioli, Colaleo, Anna, Colao, Francesco, Collamati, Francesco, Costa, Marco, Craig, Nathaniel, Curtin, David, Damerau, Heiko, Da Molin, Giacomo, D'Angelo, Laura, Dasu, Sridhara, de Blas, Jorge, De Curtis, Stefania, De Gersem, Herbert, Delahaye, Jean-Pierre, Del Moro, Tommaso, Denisov, Dmitri, Denizli, Haluk, Dermisek, Radovan, Valdor, Paula Desiré, Desponds, Charlotte, Di Luzio, Luca, Di Meco, Elisa, Diociaiuti, Eleonora, Di Petrillo, Karri Folan, Di Sarcina, Ilaria, Dorigo, Tommaso, Dreimanis, Karlis, Pree, Tristan du, Yildiz, Hatice Duran, Edgecock, Thomas, Fabbri, Siara, Fabbrichesi, Marco, Farinon, Stefania, Ferrand, Guillaume, Somoza, Jose Antonio Ferreira, Fieg, Max, Filthaut, Frank, Fox, Patrick, Franceschini, Roberto, Ximenes, Rui Franqueira, Gallinaro, Michele, Garcia-Sciveres, Maurice, Garcia-Tabares, Luis, Gargiulo, Ruben, Garion, Cedric, Garzelli, Maria Vittoria, Gast, Marco, Generoso, Lisa, Gerber, Cecilia E., Giambastiani, Luca, Gianelle, Alessio, Gianfelice-Wendt, Eliana, Gibson, Stephen, Gilardoni, Simone, Giove, Dario Augusto, Giovinco, Valentina, Giraldin, Carlo, Glioti, Alfredo, Gorzawski, Arkadiusz, Greco, Mario, Grojean, Christophe, Grudiev, Alexej, Gschwendtner, Edda, Gueli, Emanuele, Guilhaudin, Nicolas, Han, Chengcheng, Han, Tao, Hauptman, John Michael, Herndon, Matthew, Hillier, Adrian D, Hillman, Micah, Holmes, Tova Ray, Homiller, Samuel, Jana, Sudip, Jindariani, Sergo, Johannesson, Sofia, Johnson, Benjamin, Jones, Owain Rhodri, Jurj, Paul-Bogdan, Kahn, Yonatan, Kamath, Rohan, Kario, Anna, Karpov, Ivan, Kelliher, David, Kilian, Wolfgang, Kitano, Ryuichiro, Kling, Felix, Kolehmainen, Antti, Kong, K. C., Kosse, Jaap, Krintiras, Georgios, Krizka, Karol, Kumar, Nilanjana, Kvikne, Erik, Kyle, Robert, Laface, Emanuele, Lane, Kenneth, Latina, Andrea, Lechner, Anton, Lee, Junghyun, Lee, Lawrence, Lee, Seh Wook, Lefevre, Thibaut, Leonardi, Emanuele, Lerner, Giuseppe, Li, Peiran, Li, Qiang, Li, Tong, Li, Wei, Lindroos, Mats, Lipton, Ronald, Liu, Da, Liu, Miaoyuan, Liu, Zhen, Voti, Roberto Li, Lombardi, Alessandra, Lomte, Shivani, Long, Kenneth, Longo, Luigi, Lorenzo, José, Losito, Roberto, Low, Ian, Lu, Xianguo, Lucchesi, Donatella, Luo, Tianhuan, Lupato, Anna, Ma, Yang, Machida, Shinji, Madlener, Thomas, Magaletti, Lorenzo, Maggi, Marcello, Durand, Helene Mainaud, Maltoni, Fabio, Manczak, Jerzy Mikolaj, Mandurrino, Marco, Marchand, Claude, Mariani, Francesco, Marin, Stefano, Mariotto, Samuele, Martin-Haugh, Stewart, Masullo, Maria Rosaria, Mauro, Giorgio Sebastiano, Mazzolari, Andrea, Mękała, Krzysztof, Mele, Barbara, Meloni, Federico, Meng, Xiangwei, Mentink, Matthias, Métral, Elias, Miceli, Rebecca, Milas, Natalia, Mohammadi, Abdollah, Moll, Dominik, Montella, Alessandro, Morandin, Mauro, Morrone, Marco, Mulder, Tim, Musenich, Riccardo, Nardecchia, Marco, Nardi, Federico, Nenna, Felice, Neuffer, David, Newbold, David, Novelli, Daniel, Olvegård, Maja, Onel, Yasar, Orestano, Domizia, Osborne, John, Otten, Simon, Torres, Yohan Mauricio Oviedo, Paesani, Daniele, Griso, Simone Pagan, Pagani, Davide, Pal, Kincso, Palmer, Mark, Pampaloni, Alessandra, Panci, Paolo, Pani, Priscilla, Papaphilippou, Yannis, Paparella, Rocco, Paradisi, Paride, Passeri, Antonio, Pasternak, Jaroslaw, Pastrone, Nadia, Pellecchia, Antonello, Piccinini, Fulvio, Piekarz, Henryk, Pieloni, Tatiana, Plouin, Juliette, Portone, Alfredo, Potamianos, Karolos, Potdevin, Joséphine, Prestemon, Soren, Puig, Teresa, Qiang, Ji, Quettier, Lionel, Rabemananjara, Tanjona Radonirina, Radicioni, Emilio, Radogna, Raffaella, Rago, Ilaria Carmela, Ratkus, Andris, Resseguie, Elodie, Reuter, Juergen, Ribani, Pier Luigi, Riccardi, Cristina, Ricciardi, Stefania, Robens, Tania, Robert, Youri, Rogers, Chris, Rojo, Juan, Romagnoni, Marco, Ronald, Kevin, Rosser, Benjamin, Rossi, Carlo, Rossi, Lucio, Rozanov, Leo, Ruhdorfer, Maximilian, Ruiz, Richard, Saini, Saurabh, Sala, Filippo, Salierno, Claudia, Salmi, Tiina, Salvini, Paola, Salvioni, Ennio, Sammut, Nicholas, Santini, Carlo, Saputi, Alessandro, Sarra, Ivano, Scarantino, Giuseppe, Schneider-Muntau, Hans, Schulte, Daniel, Scifo, Jessica, Sen, Tanaji, Senatore, Carmine, Senol, Abdulkadir, Sertore, Daniele, Sestini, Lorenzo, Rêgo, Ricardo César Silva, Simone, Federica Maria, Skoufaris, Kyriacos, Sorbello, Gino, Sorbi, Massimo, Sorti, Stefano, Soubirou, Lisa, Spataro, David, Queiroz, Farinaldo S., Stamerra, Anna, Stapnes, Steinar, Stark, Giordon, Statera, Marco, Stechauner, Bernd Michael, Su, Shufang, Su, Wei, Sun, Xiaohu, Sytov, Alexei, Tang, Jian, Tang, Jingyu, Taylor, Rebecca, Kate, Herman Ten, Testoni, Pietro, Thiele, Leonard Sebastian, Garcia, Rogelio Tomas, Topp-Mugglestone, Max, Torims, Toms, Torre, Riccardo, Tortora, Luca, Tortora, Ludovico, Trifinopoulos, Sokratis, Udongwo, Sosoho-Abasi, Vai, Ilaria, Valente, Riccardo Umberto, van Rienen, Ursula, Van Weelderen, Rob, Vanwelde, Marion, Velev, Gueorgui, Venditti, Rosamaria, Vendrasco, Adam, Verna, Adriano, Vernassa, Gianluca, Verweij, Arjan, Verwilligen, Piet, Villamizar, Yoxara, Vittorio, Ludovico, Vitulo, Paolo, Vojskovic, Isabella, Wang, Dayong, Wang, Lian-Tao, Wang, Xing, Wendt, Manfred, Widorski, Markus, Wozniak, Mariusz, Wu, Yongcheng, Wulzer, Andrea, Xie, Keping, Yang, Yifeng, Yap, Yee Chinn, Yonehara, Katsuya, Yoo, Hwi Dong, You, Zhengyun, Zanetti, Marco, Zaza, Angela, Zhang, Liang, Zhu, Ruihu, Zlobin, Alexander, Zuliani, Davide, and Zurita, José Francisco
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Physics - Accelerator Physics - Abstract
This document is comprised of a collection of updated preliminary parameters for the key parts of the muon collider. The updated preliminary parameters follow on from the October 2023 Tentative Parameters Report. Particular attention has been given to regions of the facility that are believed to hold greater technical uncertainty in their design and that have a strong impact on the cost and power consumption of the facility. The data is collected from a collaborative spreadsheet and transferred to overleaf.
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- 2024
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19. VIEWER: an extensible visual analytics framework for enhancing mental healthcare
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Wang, Tao, Codling, David, Msosa, Yamiko, Broadbent, Matthew, Kornblum, Daisy, Polling, Catherine, Searle, Thomas, Delaney-Pope, Claire, Arroyo, Barbara, MacLellan, Stuart, Keddie, Zoe, Docherty, Mary, Roberts, Angus, Stewart, Robert, Dobson, Richard, and Harland, Robert
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Computer Science - Human-Computer Interaction ,Computer Science - Software Engineering - Abstract
Objective: To design and implement VIEWER, a versatile toolkit for visual analytics of clinical data, and to systematically evaluate its effectiveness across various clinical applications while gathering feedback for iterative improvements. Materials and Methods: VIEWER is an open-source and extensible toolkit that employs distributed natural language processing and interactive visualisation techniques to facilitate the rapid design, development, and deployment of clinical information retrieval, analysis, and visualisation at the point of care. Through an iterative and collaborative participatory design approach, VIEWER was designed and implemented in a large mental health institution, where its clinical utility and effectiveness were assessed using both quantitative and qualitative methods. Results: VIEWER provides interactive, problem-focused, and comprehensive views of longitudinal patient data from a combination of structured clinical data and unstructured clinical notes. Despite a relatively short adoption period and users' initial unfamiliarity, VIEWER significantly improved performance and task completion speed compared to the standard clinical information system. Users and stakeholders reported high satisfaction and expressed strong interest in incorporating VIEWER into their daily practice. Discussion: VIEWER provides a cost-effective enhancement to the functionalities of standard clinical information systems, with evaluation offering valuable feedback for future improvements. Conclusion: VIEWER was developed to improve data accessibility and representation across various aspects of healthcare delivery, including population health management and patient monitoring. The deployment of VIEWER highlights the benefits of collaborative refinement in optimizing health informatics solutions for enhanced patient care.
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- 2024
20. Precision Adaptive Hormone Control for Personalized Metastatic Prostate Cancer Treatment
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Phan, Trung V., Li, Shengkai, Howe, Benjamin, Amend, Sarah R., Pienta, Kenneth J., Brown, Joel S., Gatenby, Robert A., Frangakis, Constantine, Austin, Robert H., and Keverkidis, Ioannis G.
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Quantitative Biology - Quantitative Methods ,Nonlinear Sciences - Adaptation and Self-Organizing Systems ,Physics - Biological Physics - Abstract
With the oncologist acting as the ``game leader'', we employ a Stackelberg game-theoretic model involving multiple populations to study prostate cancer. We refine the drug dosing schedule using an empirical Bayes feed-forward analysis, based on clinical data that reflects each patient's prostate-specific drug response. Our methodology aims for a quantitative grasp of the parameter landscape of this adaptive multi-population model, focusing on arresting the growth of drug-resistant prostate cancer by promoting competition across drug-sensitive cancer cell populations. Our findings indicate that not only is it is feasible to considerably extend cancer suppression duration through careful optimization, but even transform metastatic prostate cancer into a chronic condition instead of an acute one for most patients, with supporting clinical and analytical evidence.
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- 2024
21. Radial Evolution of ICME-Associated Particle Acceleration Observed by Solar Orbiter and ACE
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Walker, Malik H., Allen, Robert C., Li, Gang, Ho, George C., Mason, Glenn M., Rodriguez-Pacheco, Javier, Wimmer-Schweingruber, Robert F., and Kouloumvakos, Athanasios
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Astrophysics - Solar and Stellar Astrophysics ,Physics - Space Physics - Abstract
On 2022 March 10, a coronal mass ejection (CME) erupted from the Sun, resulting in Solar Orbiter observations at 0.45 au of both dispersive solar energetic particles arriving prior to the interplanetary CME (ICME) and locally accelerated particles near the ICME-associated shock structure as it passed the spacecraft on 2022 March 11. This shock was later detected on 2022 March 14 by the Advanced Composition Explorer (ACE), which was radially aligned with Solar Orbiter, at 1 au. Ion composition data from both spacecraft -- via the Solar Orbiter Energetic Particle Detector/ Suprathermal Ion Spectrograph (EPD/SIS) and the Ultra Low Energy Isotope Spectrometer (ULEIS) on ACE -- allows for in-depth analysis of the radial evolution of species-dependent ICME shock-associated acceleration processes for this event. We present a study of the ion spectra observed at 0.45 and 1 au during both the gradual solar energetic particle (SEP) and energetic storm particle (ESP) phases of the event. We find that the shapes of the spectra seen at each spacecraft have significant differences that were likely caused by varying shock geometry: Solar Orbiter spectra tend to lack spectral breaks, and the higher energy portions of the ACE spectra have comparable average flux to the Solar Orbiter spectra. Through an analysis of rigidity effects on the spectral breaks observed by ACE, we conclude that the 1 au observations were largely influenced by a suprathermal pool of $\mathrm{He}^{+}$ ions that were enhanced due to propagation along a stream interaction region (SIR) that was interacting with the ICME at times of observation., Comment: 15 pages, 7 figures, submitted to A&A
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- 2024
22. Angular Divergent Component of Motion: A step towards planning Spatial DCM Objectives for Legged Robots
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Herron, Connor W., Schuller, Robert, Beiter, Benjamin C., Griffin, Robert J., Leonessa, Alexander, and Englsberger, Johannes
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Computer Science - Robotics ,Electrical Engineering and Systems Science - Systems and Control - Abstract
In this work, the Divergent Component of Motion (DCM) method is expanded to include angular coordinates for the first time. This work introduces the idea of spatial DCM, which adds an angular objective to the existing linear DCM theory. To incorporate the angular component into the framework, a discussion is provided on extending beyond the linear motion of the Linear Inverted Pendulum model (LIPM) towards the Single Rigid Body model (SRBM) for DCM. This work presents the angular DCM theory for a 1D rotation, simplifying the SRBM rotational dynamics to a flywheel to satisfy necessary linearity constraints. The 1D angular DCM is mathematically identical to the linear DCM and defined as an angle which is ahead of the current body rotation based on the angular velocity. This theory is combined into a 3D linear and 1D angular DCM framework, with discussion on the feasibility of simultaneously achieving both sets of objectives. A simulation in MATLAB and hardware results on the TORO humanoid are presented to validate the framework's performance.
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- 2024
23. Universal Workflow Language and Software Enables Geometric Learning and FAIR Scientific Protocol Reporting
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Epps, Robert W., Volk, Amanda A., White, Robert R., Tirawat, Robert, Bramante, Rosemary C., and Berry, Joseph J.
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Computer Science - Digital Libraries ,Physics - Physics and Society - Abstract
The modern technological landscape has trended towards increased precision and greater digitization of information. However, the methods used to record and communicate scientific procedures have remained largely unchanged over the last century. Written text as the primary means for communicating scientific protocols poses notable limitations in human and machine information transfer. In this work, we present the Universal Workflow Language (UWL) and the open-source Universal Workflow Language interface (UWLi). UWL is a graph-based data architecture that can capture arbitrary scientific procedures through workflow representation of protocol steps and embedded procedure metadata. It is machine readable, discipline agnostic, and compatible with FAIR reporting standards. UWLi is an accompanying software package for building and manipulating UWL files into tabular and plain text representations in a controlled, detailed, and multilingual format. UWL transcription of protocols from three high-impact publications resulted in the identification of substantial deficiencies in the detail of the reported procedures. UWL transcription of these publications identified seventeen procedural ambiguities and thirty missing parameters for every one hundred words in published procedures. In addition to preventing and identifying procedural omission, UWL files were found to be compatible with geometric learning techniques for representing scientific protocols. In a surrogate function designed to represent an arbitrary multi-step experimental process, graph transformer networks were able to predict outcomes in approximately 6,000 fewer experiments than equivalent linear models. Implementation of UWL and UWLi into the scientific reporting process will result in higher reproducibility between both experimentalists and machines, thus proving an avenue to more effective modeling and control of complex systems., Comment: 17 pages, 5 figures
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- 2024
24. Global Issues in Local Contexts: Japanese University EFL Learners' Reactions to the Development of Relevant and Engaging SDGS Materials
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Robert Sheridan and Kathryn M. Tanaka
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With the growing importance of the United Nations' SDGs, many EFL textbooks addressing the goals have been developed. However, these textbooks generally discuss the applicability of the SDGs in Global South countries, and for university students in Japan, this has resulted in "SDG burnout," as they study the topic but often fail to find meaningful connections to the materials. This article builds on previous research into the efficacy of culturally familiar materials, and it takes SDG education in a new direction through the creation of materials in dialogue with social justice issues. Four lessons were created by the researchers, and as part of the post-reading assignment, learners had the autonomy to choose between culturally familiar or unfamiliar activities related to either the news or popular culture. A 6-point Likert scale was used to gauge student interest, which indicated that the inclusion of social justice issues may positively affect interest. A series of binomial tests revealed that learners preferred culturally familiar activities and activities related to the news. These findings provide important implications for teaching the SDGs as they suggest learners might be most receptive to culturally familiar materials that are based on the news and connected to issues of social justice.
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- 2024
25. Strengthening School Connectedness to Increase Student Success. Overview Brief #29: Student Mental Health and Well-Being
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Annenberg Institute for School Reform at Brown University, Results for America, American Institutes for Research (AIR), Johns Hopkins University, Everyone Graduates Center, EdResearch for Action, Robert Balfanz, Angela Jerabek, Krystal Payne, and Jenny Scala
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The EdResearch for Action "Overview Series" summarizes the research on key topics to provide K-12 education decision makers and advocates with an evidence base to ground discussions about how to best serve students. This overview brief discusses the central question: What is the evidence on strategies to build a sense of school connectedness and engagement among all students? Key insights are arranged in the following sections: (1) breaking down the issue; (2) evidence-based practices; and (3) practices to avoid. [The BARR Center and Network for College Success are additional collaborators for this report.]
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- 2024
26. Let's Get Practical! Two Frameworks to Improve Practices of Open Education
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Robert Schuwer and Ben Janssen
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In our Open Educational Resources (OER) advocacy work, we have encountered various challenges considering formulating a vision and policy on Open Education and implementing these visions and policies. Among these issues are a lack of proper definitions and terminology and lack of support for formulating and implementing a vision and policies for Open Education. To tackle these issues, two frameworks are proposed. One framework addresses the categorisation and definition of learning materials (including OER) within an educational ecosystem, emphasising the importance of distinguishing various types of resources. The other framework is meant to support defining a vision on Open Education in a specific context, bridging instrumental characteristics with value-driven goals. Several use cases are described to illustrate practical use of these frameworks. Both frameworks should provide clarity and practical guidance for stakeholders, from governments to individual educators, navigating the complexities of OER adoption and Open Education.
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- 2024
27. Deconstructing a Geology Field Trip to Reconstruct around a Pedagogical Framework: A Case Study on the Integration of Cognitive Learning Theories and Learning Progressions
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Erin P. Argyilan, Kristin T. Huysken, and Robert Votaw
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Field-based education is an integral component of undergraduate geoscience curricula and provides educational and social benefits associated with enhanced learning. But field excursions can too often end up as simple show-and-tell events and fall short of implementing effective teaching practices and achieving desired student learning gains. Moreover, logistical and economic pressures tend to discourage or create obstacles for the inclusion of field-based activities in undergraduate geoscience programs, especially in commuter-based colleges and universities. This case study shares how a one-day field trip offered at a commuter-based undergraduate campus of Indiana University was deconstructed to identify content-specific learning outcomes, and then reconstructed to a unit-based learning progression. The site-specific geologic content focused on describing and correlating outcrops of Paleozoic sedimentary strata in the Starved Rock area of Illinois. Shifting from a single-day field trip to a multi-session learning progression focused on instructional scaffolding and emphasized formative assessments that integrate cognitive learning theories including retrieval practice, elaboration, spaced practice and dual coding. Common practices of field geologists such as creating sketches of outcrops (dual-coding) were purposefully integrated as meaningful activities with opportunities for peer mentoring and reflection. Restructuring to a three-week unit included pre- and post-trip assessments to enable instructors to identify and address knowledge gaps and facilitate self-driven learning opportunities for students.
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- 2024
28. Understanding the Child Care and Early Education Workforce: The Need for More and Better Data. BASE Knowledge Review Series. OPRE Report 2023-190
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Administration for Children and Families (DHHS), Office of Planning, Research and Evaluation (OPRE), MDRC, MEF Associates, Chapin Hall at the University of Chicago, Emily R. Wiegand, Robert M. Goerge, Victor Porcelli, and Cynthia Miller
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High-quality, stable child care and early education (CCEE) can have lasting, positive impacts on children. However, the challenges of recruiting, strengthening, and retaining the CCEE workforce are well documented. CCEE educators typically have low levels of formal education and compensation; limited opportunities for education, training, and professional development; inconsistent working conditions; and high levels of stress and burnout. Additionally, the CCEE sector is well known for high turnover rates, which can strain remaining educators and decrease the quality of care they offer. Turnover can also lead to diminishing returns on an organization's professional development investments. The COVID-19 pandemic has exacerbated these issues. The Building and Sustaining the Child Care and Early Education Workforce (BASE) project conducted an environmental scan and a literature review to identify and document existing knowledge about the CCEE workforce and strategies to strengthen it. One of the main themes identified from this effort was a need for more and better data on the workforce dynamics of CCEE educators. In particular, data are needed on who enters, advances in, stays in, and exits different roles, settings, and types of CCEE care or leaves the field altogether--as well as when, how, and why they do. This information is important for understanding workforce dynamics and informing the development, evaluation, and improvement of strategies that effectively build and sustain a qualified and stable CCEE workforce. For this reason, the BASE project team conducted a data scan to summarize the landscape of existing data sources that may address these gaps and identify areas where future data collection may be most useful. This brief summarizes the findings from the data scan.
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- 2024
29. Climate, food and humans predict communities of mammals in the United States
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Kays, Roland, Snider, Matthew H., Hess, George, Cove, Michael V., Jensen, Alex, Shamon, Hila, McShea, William J., Rooney, Brigit, Allen, Maximilian L., Pekins, Charles E., Wilmers, Christopher C., Pendergast, Mary E., Green, Austin M., Suraci, Justin, Leslie, Matthew S., Nasrallah, Sophie, Farkas, Dan, Jordan, Mark, Grigione, Melissa, LaScaleia, Michael C., Davis, Miranda L., Hansen, Chris, Millspaugh, Josh, Lewis, Jesse S., Havrda, Michael, Long, Robert, Remine, Kathryn R., Jaspers, Kodi J., Lafferty, Diana J. R., Hubbard, Tru, Studds, Colin E., Barthelmess, Erika L., Andy, Katherine, Romero, Andrea, O'Neill, Brian J., Hawkins, Melissa T. R., Lombardi, Jason V., Sergeyev, Maksim, Fisher-Reid, M. Caitlin, Rentz, Michael S., Nagy, Christopher, Davenport, Jon M., Rega-Brodsky, Christine C., Appel, Cara L., Lesmeister, Damon B., Giery, Sean T., Whittier, Christopher A., Alston, Jesse M., Sutherland, Chris, Rota, Christopher, Murphy, Thomas, Lee, Thomas E., Mortelliti, Alessio, Bergman, Dylan L., Compton, Justin A., Gerber, Brian D., Burr, Jess, Rezendes, Kylie, DeGregorio, Brett A., Wehr, Nathaniel H., Benson, John F., O’Mara, M. Teague, Jachowski, David S., Gray, Morgan, Beyer, Dean E., Belant, Jerrold L., Horan, Robert V., Lonsinger, Robert C., Kuhn, Kellie M., Hasstedt, Steven C. M., Zimova, Marketa, Moore, Sophie M., Herrera, Daniel J., Fritts, Sarah, Edelman, Andrew J., Flaherty, Elizabeth A., Petroelje, Tyler R., Neiswenter, Sean A., Risch, Derek R., Iannarilli, Fabiola, van der Merwe, Marius, Maher, Sean P., Farris, Zach J., Webb, Stephen L., Mason, David S., Lashley, Marcus A., Wilson, Andrew M., Vanek, John P., Wehr, Samuel R., Conner, L. Mike, Beasley, James C., Bontrager, Helen L., Baruzzi, Carolina, Ellis-Felege, Susan N., Proctor, Mike D., Schipper, Jan, Weiss, Katherine C. B., Darracq, Andrea K., Barr, Evan G., Alexander, Peter D., Şekercioğlu, Çağan H., Bogan, Daniel A., Schalk, Christopher M., Fantle-Lepczyk, Jean E., Lepczyk, Christopher A., LaPoint, Scott, Whipple, Laura S., Rowe, Helen Ivy, Mullen, Kayleigh, Bird, Tori, Zorn, Adam, Brandt, LaRoy, Lathrop, Richard G., McCain, Craig, Crupi, Anthony P., Clark, James, and Parsons, Arielle
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- 2024
30. The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation.
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Kosch, Tiffany, Torres-Sánchez, María, Liedtke, H, Summers, Kyle, Yun, Maximina, Crawford, Andrew, Maddock, Simon, Ahammed, Md, Araújo, Victor, Bertola, Lorenzo, Bucciarelli, Gary, Carné, Albert, Carneiro, Céline, Chan, Kin, Chen, Ying, Crottini, Angelica, da Silva, Jessica, Denton, Robert, Dittrich, Carolin, Espregueira Themudo, Gonçalo, Farquharson, Katherine, Forsdick, Natalie, Gilbert, Edward, Che, Jing, Katzenback, Barbara, Kotharambath, Ramachandran, Levis, Nicholas, Márquez, Roberto, Mazepa, Glib, Mulder, Kevin, Müller, Hendrik, OConnell, Mary, Orozco-terWengel, Pablo, Palomar, Gemma, Petzold, Alice, Pfennig, David, Pfennig, Karin, Reichert, Michael, Robert, Jacques, Scherz, Mark, Siu-Ting, Karen, Snead, Anthony, Stöck, Matthias, Stuckert, Adam, Stynoski, Jennifer, Tarvin, Rebecca, and Wollenberg Valero, Katharina
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Amphibians ,Biodiversity conservation ,Comparative genomics ,Genomics ,Lissamphibia ,Metagenomics ,Phylogenomics ,Population genomics ,Taxonomy ,Transcriptomics ,Animals ,Amphibians ,Genomics ,Conservation of Natural Resources ,Genome - Abstract
Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium ) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to leap to the next level.
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- 2024
31. Beat-AML 2024 ELN-refined risk stratification for older adults with newly diagnosed AML given lower-intensity therapy.
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Hoff, Fieke, Blum, William, Huang, Ying, Welkie, Rina, Swords, Ronan, Traer, Elie, Stein, Eytan, Lin, Tara, Archer, Kellie, Patel, Prapti, Collins, Robert, Baer, Maria, Duong, Vu, Arellano, Martha, Stock, Wendy, Odenike, Olatoyosi, Redner, Robert, Kovacsovics, Tibor, Deininger, Michael, Zeidner, Joshua, Olin, Rebecca, Smith, Catherine, Foran, James, Schiller, Gary, Curran, Emily, Koenig, Kristin, Heerema, Nyla, Chen, Timothy, Martycz, Molly, Stefanos, Mona, Marcus, Sonja, Rosenberg, Leonard, Druker, Brian, Levine, Ross, Burd, Amy, Yocum, Ashley, Borate, Uma, Mims, Alice, Byrd, John, and Madanat, Yazan
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Humans ,Leukemia ,Myeloid ,Acute ,Aged ,Female ,Male ,Middle Aged ,Aged ,80 and over ,Prognosis ,Risk Assessment ,Mutation ,Antineoplastic Combined Chemotherapy Protocols - Abstract
Although the 2022 European LeukemiaNet (ELN) acute myeloid leukemia (AML) risk classification reliably predicts outcomes in younger patients treated with intensive chemotherapy, it is unclear whether it applies to adults ≥60 years treated with lower-intensity treatment (LIT). We aimed to test the prognostic impact of ELN risk in patients with newly diagnosed (ND) AML aged ≥60 years given LIT and to further refine risk stratification for these patients. A total of 595 patients were included: 11% had favorable-, 11% intermediate-, and 78% had adverse-risk AML. ELN risk was prognostic for overall survival (OS) (P < .001) but did not stratify favorable- from intermediate-risk (P = .71). Within adverse-risk AML, the impact of additional molecular abnormalities was further evaluated. Multivariable analysis was performed on a training set (n = 316) and identified IDH2 mutation as an independent favorable prognostic factor, and KRAS, MLL2, and TP53 mutations as unfavorable (P < .05). A mutation score was calculated for each combination of these mutations, assigning adverse-risk patients to 2 risk groups: -1 to 0 points (Beat-AML intermediate) vs 1+ points (Beat-AML adverse). In the final refined risk classification, ELN favorable- and intermediate-risk were combined into a newly defined Beat-AML favorable-risk group, in addition to mutation scoring within the ELN adverse-risk group. This approach redefines risk for older patients with ND AML and proposes refined Beat-AML risk groups with improved discrimination for OS (2-year OS, 48% vs 33% vs 11%, respectively; P < .001), providing patients and providers additional information for treatment decision-making.
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- 2024
32. AI-based automation of enrollment criteria and endpoint assessment in clinical trials in liver diseases
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Iyer, Janani S, Juyal, Dinkar, Le, Quang, Shanis, Zahil, Pokkalla, Harsha, Pouryahya, Maryam, Pedawi, Aryan, Stanford-Moore, S Adam, Biddle-Snead, Charles, Carrasco-Zevallos, Oscar, Lin, Mary, Egger, Robert, Hoffman, Sara, Elliott, Hunter, Leidal, Kenneth, Myers, Robert P, Chung, Chuhan, Billin, Andrew N, Watkins, Timothy R, Patterson, Scott D, Resnick, Murray, Wack, Katy, Glickman, Jon, Burt, Alastair D, Loomba, Rohit, Sanyal, Arun J, Glass, Ben, Montalto, Michael C, Taylor-Weiner, Amaro, Wapinski, Ilan, and Beck, Andrew H
- Subjects
Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Trials and Supportive Activities ,Clinical Research ,6.1 Pharmaceuticals ,Oral and gastrointestinal ,Humans ,Artificial Intelligence ,Clinical Trials as Topic ,Non-alcoholic Fatty Liver Disease ,Liver Cirrhosis ,Patient Selection ,Endpoint Determination ,Female ,Retrospective Studies ,Male ,Automation ,Liver Diseases ,Reproducibility of Results ,Medical and Health Sciences ,Immunology ,Biomedical and clinical sciences ,Health sciences - Abstract
Clinical trials in metabolic dysfunction-associated steatohepatitis (MASH, formerly known as nonalcoholic steatohepatitis) require histologic scoring for assessment of inclusion criteria and endpoints. However, variability in interpretation has impacted clinical trial outcomes. We developed an artificial intelligence-based measurement (AIM) tool for scoring MASH histology (AIM-MASH). AIM-MASH predictions for MASH Clinical Research Network necroinflammation grades and fibrosis stages were reproducible (κ = 1) and aligned with expert pathologist consensus scores (κ = 0.62-0.74). The AIM-MASH versus consensus agreements were comparable to average pathologists for MASH Clinical Research Network scores (82% versus 81%) and fibrosis (97% versus 96%). Continuous scores produced by AIM-MASH for key histological features of MASH correlated with mean pathologist scores and noninvasive biomarkers and strongly predicted progression-free survival in patients with stage 3 (P
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- 2024
33. The pace of life for forest trees.
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Bialic-Murphy, Lalasia, McElderry, Robert M, Esquivel-Muelbert, Adriane, van den Hoogen, Johan, Zuidema, Pieter A, Phillips, Oliver L, de Oliveira, Edmar Almeida, Loayza, Patricia Alvarez, Alvarez-Davila, Esteban, Alves, Luciana F, Maia, Vinícius Andrade, Vieira, Simone Aparecida, Arantes da Silva, Lidiany Carolina, Araujo-Murakami, Alejandro, Arets, Eric, Astigarraga, Julen, Baccaro, Fabrício, Baker, Timothy, Banki, Olaf, Barroso, Jorcely, Blanc, Lilian, Bonal, Damien, Bongers, Frans, Bordin, Kauane Maiara, Brienen, Roel, de Medeiros, Marcelo Brilhante, Camargo, José Luís, Araújo, Felipe Carvalho, Castilho, Carolina V, Castro, Wendeson, Moscoso, Victor Chama, Comiskey, James, Costa, Flávia, Müller, Sandra Cristina, de Almeida, Everton Cristo, Lôla da Costa, Antonio Carlos, de Andrade Kamimura, Vitor, de Oliveira, Fernanda, Del Aguila Pasquel, Jhon, Derroire, Géraldine, Dexter, Kyle, Di Fiore, Anthony, Duchesne, Louis, Emílio, Thaise, Farrapo, Camila Laís, Fauset, Sophie, Draper, Federick C, Feldpausch, Ted R, Ramos, Rafael Flora, Martins, Valeria Forni, Simon, Marcelo Fragomeni, Reis, Miguel Gama, Manzatto, Angelo Gilberto, Herault, Bruno, Herrera, Rafael, Coronado, Eurídice Honorio, Howe, Robert, Huamantupa-Chuquimaco, Isau, Huasco, Walter Huaraca, Zanini, Katia Janaina, Joly, Carlos, Killeen, Timothy, Klipel, Joice, Laurance, Susan G, Laurance, William F, Fontes, Marco Aurélio Leite, Oviedo, Wilmar Lopez, Magnusson, William E, Dos Santos, Rubens Manoel, Peña, Jose Luis Marcelo, de Abreu, Karla Maria Pedra, Marimon, Beatriz, Junior, Ben Hur Marimon, Melgaço, Karina, Melo Cruz, Omar Aurelio, Mendoza, Casimiro, Monteagudo-Mendoza, Abel, Morandi, Paulo S, Gianasi, Fernanda Moreira, Nascimento, Henrique, Nascimento, Marcelo, Neill, David, Palacios, Walter, Camacho, Nadir C Pallqui, Pardo, Guido, Pennington, R Toby, Peñuela-Mora, Maria Cristina, Pitman, Nigel CA, Poorter, Lourens, Cruz, Adriana Prieto, Ramírez-Angulo, Hirma, Reis, Simone Matias, Correa, Zorayda Restrepo, Rodriguez, Carlos Reynel, Lleras, Agustín Rudas, Santos, Flavio AM, Bergamin, Rodrigo Scarton, Schietti, Juliana, Schwartz, Gustavo, and Serrano, Julio
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Trees ,Carbon ,Temperature ,Longevity ,Carbon Cycle ,Forests ,Life History Traits ,General Science & Technology - Abstract
Tree growth and longevity trade-offs fundamentally shape the terrestrial carbon balance. Yet, we lack a unified understanding of how such trade-offs vary across the world's forests. By mapping life history traits for a wide range of species across the Americas, we reveal considerable variation in life expectancies from 10 centimeters in diameter (ranging from 1.3 to 3195 years) and show that the pace of life for trees can be accurately classified into four demographic functional types. We found emergent patterns in the strength of trade-offs between growth and longevity across a temperature gradient. Furthermore, we show that the diversity of life history traits varies predictably across forest biomes, giving rise to a positive relationship between trait diversity and productivity. Our pan-latitudinal assessment provides new insights into the demographic mechanisms that govern the carbon turnover rate across forest biomes.
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- 2024
34. Foam fractionation studies of recombinant human apolipoprotein A-I
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Lethcoe, Kyle, Fox, Colin A, Hafiane, Anouar, Kiss, Robert S, Liu, Jianfang, Ren, Gang, and Ryan, Robert O
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Biochemistry and Cell Biology ,Biological Sciences ,Biotechnology ,Atherosclerosis ,Apolipoprotein AI ,Bioreactor ,Foam fractionation ,Nanodisc ,Nanodisk ,Reconstituted high-density lipoprotein ,Other Biological Sciences ,Chemical Engineering ,Biochemistry & Molecular Biology ,Biophysics ,Biochemistry and cell biology - Abstract
Apolipoprotein A-I (apoA-I), the primary protein component of plasma high-density lipoproteins (HDL), is comprised of two structural regions, an N-terminal amphipathic α-helix bundle domain (residues 1-184) and a hydrophobic C-terminal domain (residues 185-243). When a recombinant fusion protein construct [bacterial pelB leader sequence - human apoA-I (1-243)] was expressed in Escherichia coli shaker flask cultures, apoA-I was recovered in the cell lysate. By contrast, when the C-terminal domain was deleted from the construct, large amounts of the truncated protein, apoA-I (1-184), were recovered in the culture medium. Consequently, following pelB leader sequence cleavage in the E. coli periplasmic space, apoA-I (1-184) was secreted from the bacteria. When the pelB-apoA-I (1-184) fusion construct was expressed in a 5 L bioreactor, substantial foam production (~30 L) occurred. Upon foam collection and collapse into a liquid foamate, SDS-PAGE revealed that apoA-I (1-184) was the sole major protein present. Incubation of apoA-I (1-184) with phospholipid vesicles yielded reconstituted HDL (rHDL) particles that were similar in size and cholesterol efflux capacity to those generated with full-length apoA-I. Mass spectrometry analysis confirmed that pelB leader sequence cleavage occurred and that foam fractionation did not result in unwanted protein modifications. The facile nature and scalability of bioreactor-based apolipoprotein foam fractionation provide a novel means to generate a versatile rHDL scaffold protein.
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- 2024
35. Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.
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Steindorff, Andrei, Aguilar-Pontes, Maria, Robinson, Aaron, Andreopoulos, Bill, LaButti, Kurt, Kuo, Alan, Mondo, Stephen, Riley, Robert, Otillar, Robert, Haridas, Sajeet, Lipzen, Anna, Grimwood, Jane, Schmutz, Jeremy, Clum, Alicia, Reid, Ian, Moisan, Marie-Claude, Butler, Gregory, Nguyen, Thi, Dewar, Ken, Conant, Gavin, Drula, Elodie, Henrissat, Bernard, Hansel, Colleen, Singer, Steven, Hutchinson, Miriam, de Vries, Ronald, Natvig, Donald, Powell, Amy, Tsang, Adrian, and Grigoriev, Igor
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Genome ,Fungal ,Evolution ,Molecular ,Genomics ,Phylogeny ,Fungi ,Adaptation ,Physiological ,Fungal Proteins - Abstract
Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.
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- 2024
36. Long COVID Illness: Disparities in Understanding and Receipt of Care in Emergency Department Populations
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Rodriguez, Robert M, Reyes, Karen, Kumar, Vijaya Arun, Chinnock, Brian, Eucker, Stephanie A, Rising, Kristin L, Rafique, Zubaid, Gottlieb, Michael, Nichol, Graham, Morse, Dana, Molina, Melanie, Arreguin, Mireya I, Shughart, Lindsey, Conn, Christopher, Eckstrand, Svea, Mesbah, Heba, Chakraborty, Lauren, and Welch, Robert D
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Biomedical and Clinical Sciences ,Clinical Sciences ,Infectious Diseases ,Clinical Research ,Minority Health ,Coronaviruses ,Health Services ,Emerging Infectious Diseases ,Health Disparities ,Emergency Care ,Good Health and Well Being ,Emergency & Critical Care Medicine ,Clinical sciences - Abstract
Study objectiveMost long coronavirus disease (long COVID) studies rely on traditional surveillance methods that miss underserved populations who use emergency departments (EDs) as their primary health care source. In medically underserved ED populations, we sought to determine (1) whether there are gaps in awareness and self-declared understanding about long COVID illness, and (2) the prevalence, impact on school/work attendance, and receipt of care for long COVID symptoms.MethodsThis study was a cross-sectional, convenience sample survey study of adult patients at 11 geographically representative US EDs from December 2022 to October 2023. Awareness and self-declared understanding about long COVID illness were measured. Prevalence, impact on school/work attendance, and receipt of care for long COVID symptoms were also assessed.ResultsOf 1,618 eligible patients, 1455 (89.9%) agreed to participate, including 33.4% African Americans and 30.9% Latino/a. Of the patients, 17.1% lacked primary care. In total, 33.2% had persistent COVID-19 symptoms lasting >1 month, and 20.3% had symptoms >3 months. Moreover, 49.8% with long COVID symptoms missed work/school because of symptoms; 30.3% of all participants and 33.5% of participants who had long COVID symptoms had prior awareness and self-declared understanding of long COVID. Characteristics associated with poor understanding of long COVID were African American race (adjusted odds ratio [aOR] 3.68, 95% confidence interval [CI] 2.66 to 5.09) and Latino/a ethnicity (aOR 3.16, 95% CI 2.15 to 4.64). Participants lacking primary care were less likely to have received long COVID care (24.6% versus 51.2%; difference 26.6%; 95% CI 13.7% to 36.9%).ConclusionsDespite high prevalence and impact on school/work attendance of long COVID symptoms, most of this ED population had limited awareness and self-declared understanding of long COVID, and many had not received care. EDs should consider the development of protocols for diagnosis, education, and treatment of long COVID illness.
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- 2024
37. Protocol for producing hyperpolarized 13C-bicarbonate for clinical MRI of extracellular pH in aggressive tumors
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Mu, Changhua, Liu, Xiaoxi, Riselli, Andrew, Slater, James, Escobar, Evelyn, Dang, Duy, Drapeau, Scott, Santos, Romelyn Delos, Andosca, Stacy, Nguyen, Hao, Larson, Peder EZ, Bok, Robert, Vigneron, Daniel B, Kurhanewicz, John, Wilson, David M, and Flavell, Robert R
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Physical Sciences ,Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Biomedical Imaging ,Cancer ,Biotechnology and bioengineering ,Chemistry ,Clinical Protocol ,Health Sciences ,Metabolism ,Molecular/Chemical Probes - Abstract
Tumor acidosis is one of the hallmarks indicating the initiation and progression of various cancers. Here, we present a protocol for preparing a hyperpolarized (HP) 13C-bicarbonate tissue pH MRI imaging contrast agent to detect aggressive tumors. We describe the steps for the formulation and polarization of a precursor molecule 13C-glycerol carbonate (13C-GLC), the post-dissolution reaction, and converting HP 13C-GLC to an injectable HP 13C-bicarbonate solution. We then detail procedures for MRI data acquisition to generate tumor pH maps for assessing tumor aggressiveness. For complete details on the use and execution of this protocol, please refer to Mu et al.1.
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- 2024
38. PDS 70b Shows Stellar-like Carbon-to-Oxygen Ratio
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Hsu, Chih-Chun, Wang, Jason J., Blake, Geoffrey A., Xuan, Jerry W., Zhang, Yapeng, Ruffio, Jean-Baptiste, Horstman, Katelyn, Cronin, Julianne, Sappey, Ben, Xin, Yinzi, Finnerty, Luke, Echeverri, Daniel, Mawet, Dimitri, Jovanovic, Nemanja, Ó, Clarissa R. Do, Baker, Ashley, Bartos, Randall, Calvin, Benjamin, Cetre, Sylvain, Delorme, Jacques-Robert, Doppmann, Gregory W., Fitzgerald, Michael P., Liberman, Joshua, López, Ronald A., Morris, Evan, Pezzato-Rovner, Jacklyn, Schofield, Tobias, Skemer, Andrew, Wallace, J. Kent, and Wang, Ji
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
The $\sim$5 Myr PDS 70 is the only known system with protoplanets residing in the cavity of the circumstellar disk from which they formed, ideal for studying exoplanet formation and evolution within its natal environment. Here we report the first spin constraint and C/O measurement of PDS 70b from Keck/KPIC high-resolution spectroscopy. We detected CO (3.8 $\sigma$) and H$_2$O (3.5 $\sigma$) molecules in the PDS 70b atmosphere via cross-correlation, with a combined CO and H$_2$O template detection significance of 4.2 $\sigma$. Our forward model fits, using BT-Settl model grids, provide an upper limit for the spin-rate of PDS 70b ($<$29 km s$^{-1}$). The atmospheric retrievals constrain the PDS 70b C/O ratio to ${0.28}^{+0.20}_{-0.12}$ ($<$0.63 under 95$\%$ confidence level) and a metallicity [C/H] of ${-0.2}^{+0.8}_{-0.5}$ dex, consistent with that of its host star. The following scenarios can explain our measured C/O of PDS 70b in contrast with that of the gas-rich outer disk (for which C/O $\gtrsim$ 1). First, the bulk composition of PDS 70b might be dominated by dust+ice aggregates rather than disk gas. Another possible explanation is that the disk became carbon-enriched $\textit{after}$ PDS 70b was formed, as predicted in models of disk chemical evolution and as observed in both very low mass star and older disk systems with $\textit{JWST}$/MIRI. Because PDS 70b continues to accrete and its chemical evolution is not yet complete, more sophisticated modeling of the planet and the disk, and higher quality observations of PDS 70b (and possibly PDS 70c), are necessary to validate these scenarios., Comment: Accepted to ApJ Letters; 15 pages, 3 figures
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- 2024
39. Dimension-independent rates for structured neural density estimation
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Vandermeulen, Robert A., Tai, Wai Ming, and Aragam, Bryon
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Statistics - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,Mathematics - Statistics Theory ,62G05, 62G07, 62A09, 62M05, 62M40, 60J10, 60J20 ,G.3 ,I.5.1 ,I.4.10 ,I.4.m - Abstract
We show that deep neural networks achieve dimension-independent rates of convergence for learning structured densities such as those arising in image, audio, video, and text applications. More precisely, we demonstrate that neural networks with a simple $L^2$-minimizing loss achieve a rate of $n^{-1/(4+r)}$ in nonparametric density estimation when the underlying density is Markov to a graph whose maximum clique size is at most $r$, and we provide evidence that in the aforementioned applications, this size is typically constant, i.e., $r=O(1)$. We then establish that the optimal rate in $L^1$ is $n^{-1/(2+r)}$ which, compared to the standard nonparametric rate of $n^{-1/(2+d)}$, reveals that the effective dimension of such problems is the size of the largest clique in the Markov random field. These rates are independent of the data's ambient dimension, making them applicable to realistic models of image, sound, video, and text data. Our results provide a novel justification for deep learning's ability to circumvent the curse of dimensionality, demonstrating dimension-independent convergence rates in these contexts.
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- 2024
40. Potential habitability of present-day Mars subsurface for terrestrial-like methanogens
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Butturini, Andrea, Benaiges-Fernandez, Robert, Fors, Octavi, and Garcia-Castellanos, Daniel
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Astrophysics - Earth and Planetary Astrophysics - Abstract
The intense debate about the presence of methane in the Martian atmosphere has stimulated the study of methanogens adapted to terrestrial habitats that mimic Martian environments. We examinate the environmental conditions, energy sources and ecology of terrestrial methanogens thriving in deep crystalline fractures, sub-sea hypersaline lakes and subglacial water bodies considered as analogs of a hypothetical habitable Martian subsurface. We combine this information with recent data on the distribution of buried water or ice and radiogenic elements on Mars and with models of the subsurface thermal regime of this planet to identify a 4.3-8.8 km-deep regolith habitat at the mid-latitude location of Acidalia Planitia, that might fit the requirements for hosting putative Martian methanogens analogous to the methanogenic families Methanosarcinaceae and Methanomicrobiaceae., Comment: 75 pages, 6 Figures, 3 Tables, Submitted to AstroBiology
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- 2024
41. Spectral domain likelihoods for Bayesian inference in time-varying parameter models
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Gustafsson, Oskar, Villani, Mattias, and Kohn, Robert
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Statistics - Methodology - Abstract
Inference for locally stationary processes is often based on some local Whittle-type approximation of the likelihood function defined in the frequency domain. The main reasons for using such a likelihood approximation is that i) it has substantially lower computational cost and better scalability to long time series compared to the time domain likelihood, particularly when used for Bayesian inference via Markov Chain Monte Carlo (MCMC), ii) convenience when the model itself is specified in the frequency domain, and iii) it provides access to bootstrap and subsampling MCMC which exploits the asymptotic independence of Fourier transformed data. Most of the existing literature compares the asymptotic performance of the maximum likelihood estimator (MLE) from such frequency domain likelihood approximation with the exact time domain MLE. Our article uses three simulation studies to assess the finite-sample accuracy of several frequency domain likelihood functions when used to approximate the posterior distribution in time-varying parameter models. The methods are illustrated on an application to egg price data.
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- 2024
42. A Phase-Space Electronic Hamiltonian for Molecules in a Static Magnetic Field II: Quantum Chemistry Calculations with Gauge Invariant Atomic Orbitals
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Bhati, Mansi, Tao, Zhen, Bian, Xuezhi, Rawlinson, Jonathan, Littlejohn, Robert, and Subotnik, Joseph E.
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Physics - Chemical Physics - Abstract
In a companion paper, we have developed a phase-space electronic structure theory of molecules in magnetic fields, whereby the electronic energy levels arise from diagonalizing a phase-space Hamiltonian $\hat H_{PS}(\bf{X},\bf{\Pi})$ that depends parametrically on nuclear position and momentum. The resulting eigenvalues are translationally invariant; moreover, if the magnetic field is in the $z-$direction, then the eigenvalues are also invariant to rotations around the $z-$direction. However, like all Hamiltonians in a magnetic field, the theory has a gauge degree of freedom (corresponding to the position of the magnetic origin in the vector potential), and requires either $(i)$ formally, a complete set of electronic states or $(ii)$ in practice, gauge invariant atomic orbitals (GIAOs) in order to realize such translational and rotational invariance. Here we describe how to implement a phase-space electronic Hamiltonian using GIAOs within a practical electronic structure package (in our case, Q-Chem). We further show that novel phenomena can be observed with finite $\bf{B}-$fields, including minimum energy structures with $\bf{\Pi}_{min} \ne 0$, indicating non-zero electronic motion in the ground-state., Comment: Added reference to paper I
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- 2024
43. A Phase-Space Electronic Hamiltonian for Molecules in a Static Magnetic Field I: Conservation of Total Pseudomomentum and Angular Momentum
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Bhati, Mansi, Tao, Zhen, Bian, Xuezhi, Rawlinson, Jonathan, Littlejohn, Robert, and Subotnik, Joseph E.
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Physics - Chemical Physics - Abstract
We develop a phase-space electronic structure theory of molecules in magnetic fields. For a system of electrons in a magnetic field with vector potential $\bf{A}(\hat{\bf{r}})$, the usual Born-Oppenheimer Hamiltonian is the sum of the nuclear kinetic energy and the electronic Hamiltonian, $\frac{(\bf{P} - q\bf{A}(\bf{X}) )^2}{2M} + \hat{H}_{e}(\bf{X})$ (where $q$ is a nuclear charge). To include the effects of coupled nuclear-electron motion in the presence of magnetic field, we propose that the proper phase-space electronic structure Hamiltonian will be of the form $\frac{(\bf{P} - q^{\textit{eff}}\bf{A}(\bf{X}) - e\hat{\bf{\Gamma}})^2}{2M} + \hat{H}_{e}(\bf{X})$. Here, $q^{\textit{eff}}$ represents the {\em screened} nuclear charges and the $\hat{\bf{\Gamma}}$ term captures the local pseudomomentum of the electrons. This form reproduces exactly the energy levels for a hydrogen atom in a magnetic field; moreover, single-surface dynamics along the eigenstates is guaranteed to conserve both the total pseudomomentum as well as the total angular momentum in the direction of the magnetic field. This Hamiltonian form can be immediately implemented within modern electronic structure packages (where the electronic orbitals will now depend on nuclear position ($\bf{X}$) and nuclear momentum ($\bf{P}$)). One can expect to find novel beyond Born-Oppenheimer magnetic field effects for strong enough fields and/or nonadiabatic systems., Comment: Added reference to paper II
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- 2024
44. First Calculations of Starspot Spectra based on 3D Radiative Magnetohydrodynamics Simulations
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Smitha, H. N., Shapiro, Alexander I., Witzke, Veronika, Kostogryz, Nadiia M., Unruh, Yvonne C., Bhatia, Tanayveer S., Cameron, Robert, Seager, Sara, and Solanki, Sami K.
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Astrophysics - Solar and Stellar Astrophysics ,Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Astrophysics of Galaxies ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Accurate calculations of starspot spectra are essential for multiple applications in astronomy. The current standard is to represent starspot spectra by spectra of stars that are cooler than the quiet star regions. This implies approximating a starspot as a non-magnetic 1D structure in radiative-convective equilibrium, parametrizing convective energy transport by mixing length theory. It is the inhibition of convection by the starspot magnetic field that is emulated by using a lower spot temperature relative to the quiet stellar regions. Here, we take a different approach avoiding the approximate treatment of convection and instead self-consistently accounting for the interaction between matter, radiation, and the magnetic field. We simulate spots on G2V, K0V, M0V stars with the 3D radiative magnetohydrodynamics code MURaM and calculate spectra ($R \approx 500$ from 250~nm to 6000~nm) using ray-by-ray radiative transfer with the MPS-ATLAS code. We find that the 1D models fail to return accurate umbral and penumbral spectra on K0V and M0V stars where convective and radiative transfer of energy is simultaneously important over a broad range of atmospheric heights rendering mixing length theory inaccurate. However, 1D models work well for G2V stars, where both radiation and convection significantly contribute to energy transfer only in a narrow region near the stellar surface. Quantitatively, the 1D approximation leads to errors longward of 500 nm of about 50\% for both umbral and penumbral flux contrast relative to quiet star regions on M0V stars, and less than 2\% (for umbrae) and 10\% (for penumbrae) for G2V stars., Comment: Accepted for publication in the Astrophysical Journal Letters
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- 2024
45. Determining the Quark Mass with the Gradient Flow
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Takaura, Hiromasa, Harlander, Robert, and Lange, Fabian
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High Energy Physics - Lattice - Abstract
We propose a new method to determine the quark mass by using bilinear operators of the flowed quark field defined within the gradient-flow formalism. This method enables the quark mass determination through a comparison of perturbative calculations with lattice data. The gauge-invariant nature of the observable should allow clear control over perturbative errors. At the same time, the gradient flow suppresses the noise in the lattice measurements of the observable, which simply consists of one-point functions. Concerning the perturbative input in this framework, we study the mass dependence of the flowed quark condensate $\langle \bar{\chi}(t,x) \chi(t,x) \rangle$ at the two-loop level. For this purpose, we develop a novel approach for expanding massive gradient-flow integrals in the limit of small and large $(m^2t)$. We also present a fully numerical result which includes the full mass dependence., Comment: 8 pages, 1 figure. Proceedings of the 41st International Symposium on Lattice Field Theory (LATTICE2024), 28 July - 3 August, 2024 Liverpool, UK
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- 2024
46. Quantum Algorithm for Vibronic Dynamics: Case Study on Singlet Fission Solar Cell Design
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Motlagh, Danial, Lang, Robert A., Campos-Gonzalez-Angulo, Jorge A., Zeng, Tao, Aspuru-Guzik, Alan, and Arrazola, Juan Miguel
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Quantum Physics - Abstract
Vibronic interactions between nuclear motion and electronic states are critical for the accurate modeling of photochemistry. However, accurate simulations of fully quantum non-adiabatic dynamics are often prohibitively expensive for classical methods beyond small systems. In this work, we present a quantum algorithm based on product formulas for simulating time evolution under a general vibronic Hamiltonian in real space, capable of handling an arbitrary number of electronic states and vibrational modes. We develop the first trotterization scheme for vibronic Hamiltonians beyond two electronic states and introduce an array of optimization techniques for the exponentiation of each fragment in the product formula, resulting in a remarkably low cost of implementation. To demonstrate practical relevance, we outline a proof-of-principle integration of our algorithm into a materials discovery pipeline for designing more efficient singlet fission-based organic solar cells. Based on commutator bounds, we estimate that a $100$ femtosecond evolution using a second-order Trotter product formula of a $4$-state model of an anthracene-fullerene interface requires $117$ qubits and $1.5 \times 10^7$ Toffoli gates in a reduced dimensionality of $11$ modes. In its full dimensionality of $246$ modes, it requires $1065$ qubits and $2.7 \times 10^9$ Toffoli gates.
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- 2024
47. Do Observations Prefer Thawing Quintessence?
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Payeur, Guillaume, McDonough, Evan, and Brandenberger, Robert
- Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics ,General Relativity and Quantum Cosmology ,High Energy Physics - Phenomenology ,High Energy Physics - Theory - Abstract
In light of recent observations, we study evidence for thawing quintessence over a cosmological constant as dark energy, with emphasis on the effect of the choice of priors. Working with a parametrization for the equation of state parameter motivated by the theory, we find a preference for thawing quintessence compared to a bare cosmological constant {\it only} if we use priors which are heavily informed by the data itself. If we extend the priors to physically better motivated ranges, the evidence for thawing quintessence disappears., Comment: 12 pages, 8 figures
- Published
- 2024
48. Principles of Visual Tokens for Efficient Video Understanding
- Author
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Hao, Xinyue, Li, Gen, Gowda, Shreyank N, Fisher, Robert B, Huang, Jonathan, Arnab, Anurag, and Sevilla-Lara, Laura
- Subjects
Computer Science - Computer Vision and Pattern Recognition - Abstract
Video understanding has made huge strides in recent years, relying largely on the power of the transformer architecture. As this architecture is notoriously expensive and video is highly redundant, research into improving efficiency has become particularly relevant. This has led to many creative solutions, including token merging and token selection. While most methods succeed in reducing the cost of the model and maintaining accuracy, an interesting pattern arises: most methods do not outperform the random sampling baseline. In this paper we take a closer look at this phenomenon and make several observations. First, we develop an oracle for the value of tokens which exposes a clear Pareto distribution where most tokens have remarkably low value, and just a few carry most of the perceptual information. Second, we analyze why this oracle is extremely hard to learn, as it does not consistently coincide with visual cues. Third, we observe that easy videos need fewer tokens to maintain accuracy. We build on these and further insights to propose a lightweight video model we call LITE that can select a small number of tokens effectively, outperforming state-of-the-art and existing baselines across datasets (Kinetics400 and Something-Something-V2) in the challenging trade-off of computation (GFLOPs) vs accuracy.
- Published
- 2024
49. Ensuring Safety and Trust: Analyzing the Risks of Large Language Models in Medicine
- Author
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Yang, Yifan, Jin, Qiao, Leaman, Robert, Liu, Xiaoyu, Xiong, Guangzhi, Sarfo-Gyamfi, Maame, Gong, Changlin, Ferrière-Steinert, Santiago, Wilbur, W. John, Li, Xiaojun, Yuan, Jiaxin, An, Bang, Castro, Kelvin S., Álvarez, Francisco Erramuspe, Stockle, Matías, Zhang, Aidong, Huang, Furong, and Lu, Zhiyong
- Subjects
Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Computers and Society - Abstract
The remarkable capabilities of Large Language Models (LLMs) make them increasingly compelling for adoption in real-world healthcare applications. However, the risks associated with using LLMs in medical applications have not been systematically characterized. We propose using five key principles for safe and trustworthy medical AI: Truthfulness, Resilience, Fairness, Robustness, and Privacy, along with ten specific aspects. Under this comprehensive framework, we introduce a novel MedGuard benchmark with 1,000 expert-verified questions. Our evaluation of 11 commonly used LLMs shows that the current language models, regardless of their safety alignment mechanisms, generally perform poorly on most of our benchmarks, particularly when compared to the high performance of human physicians. Despite recent reports indicate that advanced LLMs like ChatGPT can match or even exceed human performance in various medical tasks, this study underscores a significant safety gap, highlighting the crucial need for human oversight and the implementation of AI safety guardrails.
- Published
- 2024
50. Making molecules by mergoassociation: the role of center-of-mass motion
- Author
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Bird, Robert C. and Hutson, Jeremy M.
- Subjects
Physics - Atomic Physics ,Physics - Chemical Physics ,Quantum Physics - Abstract
In mergoassociation, two atoms in separate optical traps are combined to form a molecule when the traps are merged. Previous theoretical treatments have considered only the relative motion of the atoms, neglecting coupling to the motion of the center of mass. We develop a theoretical method to include the coupling to center-of-mass motion and consider its consequences for experiments for both weak and strong coupling. We consider the example of RbCs and then extend the treatment to other systems where mergoassociation may be effective, namely RbSr, RbYb and CsYb. We consider the role of the coupling when the traps are anisotropic and the potential use of moveable traps to construct quantum logic gates.
- Published
- 2024
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