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1. Choosing your own adventure: Engaging the new learning society through integrative curriculum design

   https://doi.org/10.29007/567f  

   Ryder, Elizabeth; Ruiz, Carolina; Weaver, Shari; Gegear, Robert (February 2020, EPiC Series in Education Science)

   In our increasingly data-driven society, it is critical for high school students to learn to integrate computational thinking with other disciplines in solving real world problems. To address this need for the life sciences in particular, we have developed the Bio-CS Bridge, a modular computational system coupled with curriculum integrating biology and computer science. Our transdisciplinary team comprises university and high school faculty and students with expertise in biology, computer science, and education. Our approach engages students and teachers in scientific practices using biological data that they can collect themselves, and computational tools that they help to design and implement, to address the real-world problem of pollinator decline. Our modular approach to high school curriculum design provides teachers with the educational flexibility to address national and statewide biology and computer science standards for a wide range of learner types. We are using a teacher- leader model to disseminate the Bio-CS Bridge, whose components will be freely available online. 

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2. Providing tailored reflection instructions in collaborative learning using large language models

   https://doi.org/10.1111/bjet.13548  

   Naik, Atharva; Yin, Jessica_Ruhan; Kamath, Anusha; Ma, Qianou; Wu, Sherry_Tongshuang; Murray, R_Charles; Bogart, Christopher; Sakr, Majd; Rose, Carolyn_P (December 2024, British Journal of Educational Technology)

   AbstractThe relative effectiveness of reflection either through student generation of contrasting cases or through provided contrasting cases is not well‐established for adult learners. This paper presents a classroom study to investigate this comparison in a college level Computer Science (CS) course where groups of students worked collaboratively to design database access strategies. Forty‐four teams were randomly assigned to three reflection conditions ([GEN] directive to generate a contrasting case to the student solution and evaluate their trade‐offs in light of the principle, [CONT] directive to compare the student solution with a provided contrasting case and evaluate their trade‐offs in light of a principle, and [NSI] a control condition with a non‐specific directive for reflection evaluating the student solution in light of a principle). In the CONT condition, as an illustration of the use of LLMs to exemplify knowledge transformation beyond knowledge construction in the generation of an automated contribution to a collaborative learning discussion, an LLM generated a contrasting case to a group's solution to exemplify application of an alternative problem solving strategy in a way that highlighted the contrast by keeping many concrete details the same as those the group had most recently collaboratively constructed. While there was no main effect of condition on learning based on a content test, low‐pretest student learned more from CONT than GEN, with NSI not distinguishable from the other two, while high‐pretest students learned marginally more from the GEN condition than the CONT condition, with NSI not distinguishable from the other two. Practitioner notesWhat is already known about this topicReflection during or even in place of computer programming is beneficial for learning of principles for advanced computer science when the principles are new to students.Generation of contrasting cases and comparing contrasting cases have both been demonstrated to be effective as opportunities to learn from reflection in some contexts, though questions remain about ideal applicability conditions for adult learners.Intelligent conversational agents can be used effectively to deliver stimuli for reflection during collaborative learning, though room for improvement remains, which provides an opportunity to demonstrate the potential positive contribution of large language models (LLMs).What this paper addsThe study contributes new knowledge related to the differences in applicability conditions between generation of contrasting cases and comparison across provided contrasting cases for adult learning.The paper presents an application of LLMs as a tool to provide contrasting cases tailored to the details of actual student solutions.The study provides evidence from a classroom intervention study for positive impact on student learning of an LLM‐enabled intervention.Implications for practice and/or policyAdvanced computer science curricula should make substantial room for reflection alongside problem solving.Instructors should provide reflection opportunities for students tailored to their level of prior knowledge.Instructors would benefit from training to use LLMs as tools for providing effective contrasting cases, especially for low‐prior‐knowledge students. 

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3. CRISPR‐Cas9 Genome Editing in the Moss Physcomitrium (Formerly Physcomitrella ) patens

   https://doi.org/10.1002/cpz1.725  

   Wu, Shu‐Zon; Ryken, Samantha E.; Bezanilla, Magdalena (April 2023, Current Protocols)

   Abstract Until recently, precise genome editing has been limited to a few organisms. The ability of Cas9 to generate double stranded DNA breaks at specific genomic sites has greatly expanded molecular toolkits in many organisms and cell types. Before CRISPR‐Cas9 mediated genome editing,P. patenswas unique among plants in its ability to integrate DNA via homologous recombination. However, selection for homologous recombination events was required to obtain edited plants, limiting the types of editing that were possible. Now with CRISPR‐Cas9, molecular manipulations inP. patenshave greatly expanded. This protocol describes a method to generate a variety of different genome edits. The protocol describes a streamlined method to generate the Cas9/sgRNA expression constructs, design homology templates, transform, and quickly genotype plants. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Constructing the Cas9/sgRNA transient expression vector Alternate Protocol 1: Shortcut to generating single and pooled Cas9/sgRNA expression vectors Basic Protocol 2: Designing the oligonucleotide‐based homology‐directed repair (HDR) template Alternate Protocol 2: Designing the plasmid‐based HDR template Basic Protocol 3: Inducing genome editing by transforming CRISPR vector intoP. patensprotoplasts Basic Protocol 4: Identifying edited plants. 

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4. A sensitive fluorescent assay for measuring carbon‐phosphorus lyase activity in aquatic systems

   https://doi.org/10.1002/lom3.10418  

   Granzow, Benjamin N.; Sosa, Oscar A.; Gonnelli, Margherita; Santinelli, Chiara; Karl, David M.; Repeta, Daniel J. (January 2021, Limnology and Oceanography: Methods)

   Abstract In the oligotrophic ocean where inorganic phosphate (P_i) concentrations are low, microorganisms supplement their nutrient requirements with phosphorus (P) extracted from dissolved organic matter (DOM). Most P in DOM is bound as phosphate esters, which are hydrolyzed by phosphoesterases to P_i. However, a large fraction of DOM‐P occurs as phosphonates, reduced organophosphorus compounds with a CP bond that do not yield P_ithrough simple ester hydrolysis alone. Phosphonates require an additional step that cleaves the CP bond and oxidizes P(III) to P(V) to yield P_i. Most phosphonates are metabolized by the C‐P lyase pathway, which cleaves CP bonds and oxidizes phosphonates to P_i, enabling microbial assimilation. While the activity of common phosphoesterases such as alkaline phosphatase and phosphodiesterase can be measured by a fluorescent assay, a comparable method to assess C‐P lyase activity (CLA) in natural water samples does not exist. To address this, we synthesized a dansyl‐labeled phosphonate compound, and measured its hydrolysis by C‐P lyase using high performance liquid chromatography. We found that laboratory cultures of marine bacteria expressing the C‐P lyase pathway are able to hydrolyze the dansyl phosphonate, while bacteria expressing other phosphonate degradation pathways do not. Finally, we performed several field tests of the assay to measure water column profiles of CLA at Sta. ALOHA in the North Pacific Subtropical Gyre. Activity was elevated near the deep chlorophyll maximum suggesting high levels of phosphonate degradation in that region. 

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5. Peak and Per-Step Tibial Bone Stress During Walking and Running in Female and Male Recreational Runners

   https://doi.org/10.1177/03635465211014854  

   Meardon, Stacey A.; Derrick, Timothy R.; Willson, John D.; Baggaley, Michael; Steinbaker, C. Ryan; Marshall, Margaret; Willy, Richard W. (June 2021, The American Journal of Sports Medicine)

   Background:Athletes, especially female athletes, experience high rates of tibial bone stress injuries (BSIs). Knowledge of tibial loads during walking and running is needed to understand injury mechanisms and design safe running progression programs. Purpose:To examine tibial loads as a function of gait speed in male and female runners. Study Design:Controlled laboratory study. Methods:Kinematic and kinetic data were collected on 40 recreational runners (20 female, 20 male) during 4 instrumented gait speed conditions on a treadmill (walk, preferred run, slow run, fast run). Musculoskeletal modeling, using participant-specific magnetic resonance imaging and motion data, was used to estimate tibial stress. Peak tibial stress and stress-time impulse were analyzed using 2-factor multivariate analyses of variance (speed*sex) and post hoc comparisons (α = .05). Bone geometry and tibial forces and moments were examined. Results:Peak compression was influenced by speed ( P < .001); increasing speed generally increased tibial compression in both sexes. Women displayed greater increases in peak tension ( P = .001) and shear ( P < .001) than men when transitioning from walking to running. Further, women displayed greater peak tibial stress overall ( P < .001). Compressive and tensile stress-time impulse varied by speed ( P < .001) and sex ( P = .006); impulse was lower during running than walking and greater in women. A shear stress-time impulse interaction ( P < .001) indicated that women displayed greater impulse relative to men when changing from a walk to a run. Compared with men, women displayed smaller tibiae ( P < .001) and disproportionately lower tibial forces ( P≤ .001-.035). Conclusion:Peak tibial stress increased with gait speed, with a 2-fold increase in running relative to walking. Women displayed greater tibial stress than men and greater increases in stress when shifting from walking to running. Sex differences appear to be the result of smaller bone geometry in women and tibial forces that were not proportionately lower, given the womens’ smaller stature and lower mass relative to men. Clinical Relevance:These results may inform interventions to regulate running-related training loads and highlight a need to increase bone strength in women. Lower relative bone strength in women may contribute to a sex bias in tibial BSIs, and female runners may benefit from a slower progression when initiating a running program. 

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