Project description:Recent advances in computer hardware and software, particularly the availability of machine learning libraries, allow the introduction of data-based topics such as machine learning into the Biophysical curriculum for undergraduate and/or graduate levels. However, there are many practical challenges of teaching machine learning to advanced-level students in the biophysics majors, who often do not have a rich computational background. Aiming to overcome such challenges, we present an educational study, including the design of course topics, pedagogical tools, and assessments of student learning, to develop the new methodology to incorporate the basis of machine learning in an existing Biophysical elective course, and engage students in exercises to solve problems in an interdisciplinary field. In general, we observed that students had ample curiosity to learn and apply machine learning algorithms to predict molecular properties. Notably, feedback from the students suggests that care must be taken to ensure student preparations for understanding the data-driven concepts and fundamental coding aspects required for using machine learning algorithms. This work establishes a framework for future teaching approaches that unite machine learning and any existing course in the biophysical curriculum, while also pinpointing the critical challenges that educators and students will likely face.
Project description:We describe an update to an experiment demonstrating low-field NMR spectroscopy in the undergraduate physical chemistry laboratory. A Python-based data processing and analysis protocol is developed for this experiment. The Python language is used in fillable worksheets in the notebook software JupyterLab, providing an interactive means for students to work with the measured data step by step. The protocol teaches methods for the analysis of large data sets in science or engineering, a topic that is absent from traditional chemistry curricula. Python is among the most widely used modern tools for data analysis. In addition, its open-source nature reduces the barriers for adoption in an educational laboratory.
Project description:The purpose of this paper is to examine the impact of a province-wide physical education (PE) policy on secondary school students' moderate to vigorous physical activity (MVPA).Policy: In fall 2008, Manitoba expanded a policy requiring a PE credit for students in grades 11 and 12 for the first time in Canada. The PE curriculum requires grades 11 and 12 students to complete a minimum of 55 h (50% of course hours) of MVPA (e.g., ≥30 min/day of MVPA on ≥5 days a week) during a 5-month semester to achieve the course credit.A natural experimental study was designed using two sub-studies: 1) quasi-experimental controlled pre-post analysis of self-reported MVPA data obtained from census data in intervention and comparison [Prince Edward Island (PEI)] provinces in 2008 (n = 33,619 in Manitoba and n = 2258 in PEI) and 2012 (n = 41,169 in Manitoba and n = 4942 in PEI); and, 2) annual objectively measured MVPA in cohorts of secondary students in intervention (n = 447) and comparison (Alberta; n = 224) provinces over 4 years (2008 to 2012).In Study 1, two logistic regressions were conducted to model the odds that students accumulated: i) ≥30 min/day of MVPA, and ii) met Canada's national recommendation of ≥60 min/day of MVPA, in Manitoba versus PEI after adjusting for grade, sex, and BMI. In Study 2, a mixed effects model was used to assess students' minutes of MVPA per day per semester in Manitoba and Alberta, adjusting for age, sex, BMI, school location and school SES.In Study 1, no significant differences were observed in students achieving ≥30 (OR:1.13, 95% CI:0.92, 1.39) or ≥60 min/day of MVPA (OR:0.92, 95% CI: 0.78, 1.07) from baseline to follow-up between Manitoba and PEI. In Study 2, no significant policy effect on students' MVPA trajectories from baseline to last follow-up were observed between Manitoba and Alberta overall (-1.52, 95% CI:-3.47, 0.42), or by covariates.The Manitoba policy mandating PE in grades 11 and 12 had no effect on student MVPA overall or by key student or school characteristics. However, the effect of the PE policy may be underestimated due to the use of a nonrandomized research design and lack of data assessing the extent of policy implementation across schools. Nevertheless, findings can provide evidence about policy features that may improve the PE policy in Manitoba and inform future PE policies in other jurisdictions.
Project description:PurposeThis study aims to explore and compare Chinese university students' preferences for various physical activity motivation programs.Patients and methodsA cross-sectional study was conducted in China from February 25 to March 25, 2022. Participants anonymously completed an online questionnaire based on a DCE. A total of 1,358 university students participated in the survey. The conditional logit model (CLM), willingness to accept (WTA), and propensity score matching (PSM) were used to assess college students' preferences for different attributes and levels of physical activity incentive programs.ResultsRespondents identified the number of bonus, exercise time, and academic rewards as the three most significant attributes of the athletic incentive program. The importance of each attribute varied based on individual characteristics such as gender and BMI. In CLM, college students displayed a preference for a "¥4" bonus amount (OR: 2.04, 95% CI 1.95-2.13), "20 min" of exercise time (OR: 1.85, 95% CI 1.79-1.92), and "bonus points for comprehensive test scores" as academic rewards (OR: 1.33, 95% CI 1.28-1.37). According to the WTA results, college students were willing to accept the highest cost to obtain academic rewards tied to composite test scores.ConclusionThe number of bonus, exercise time, and academic rewards emerge as the three most crucial attributes of physical activity incentive programs. Furthermore, college students with different characteristics exhibit heterogeneity in their preferences for such programs. These findings can guide the development of programs and policies aimed at motivating college students to engage in physical activities.
Project description:We have investigated intrachain contact dynamics in unfolded cytochrome cb562 by monitoring heme quenching of excited ruthenium photosensitizers covalently bound to residues along the polypeptide. Intrachain diffusion for chemically denatured proteins proceeds on the microsecond time scale with an upper limit of 0.1 μs. The rate constants exhibit a power-law dependence on the number of peptide bonds between the heme and Ru complex. The power-law exponent of -1.5 is consistent with theoretical models for freely jointed Gaussian chains, but its magnitude is smaller than that reported for several synthetic polypeptides. Contact formation within a stable loop was examined in a His63-heme ligated form of the protein under denaturing conditions. Loop formation accelerated contact kinetics for the Ru66 labeling site, owing to reduction in the length of the peptide separating redox sites. For other labeling sites within the stable loop, quenching rates were modestly reduced compared to the open chain polymer.
Project description:Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Förster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model protein; comparison of conformational stabilities ( ΔGH2O∘) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. In addition, the determination of intraprotein distances based upon the FRET pair Trp-59 and the heme group for unfolded states of cytochrome c highlights the evolution of the protein structure under unfolding conditions. Analysis and discussion of these results provide opportunities to gain in-depth understanding of models for protein folding while enhancing students' skills with optical techniques. Collectively, the combination of optical spectroscopy, rigorous quantitative analysis, and a focus on biophysics illustrates the significance of fundamental research at the growing intersection of chemistry, biology, and physics.
Project description:Evidence of school-based physical activity (PA) on academic performance in children and adolescents was inconsistent, especially in high school students who face a high academic burden. In this study, we tested the efficacy of a strengthened physical education (PE) program on academic outcomes in Shanghai. A quasi-experimental design was conducted to investigate the effect of strengthened PE on academic scores by calculating the grade-cohort difference before and after the intervention. PE curriculum switched from traditional short duration (40 minutes) general fitness training to long duration (90 minutes) specialized sports (e.g., football, aerobics). A total of 460 high school students (236 pre-intervention and 224 post-intervention) were enrolled in grade 10 and followed for two and three semesters. The academic outcome was assessed by district-standardized test scores. A difference-in-difference approach was employed. After two semesters, the standardized Chinese language scores and English language scores for the post intervention group were increased by 0.61 SD (95% confidence interval (CI): 0.44, 0.78, p < 0.001) and 0.28 SD (95% CI: 0.09, 0.47, p = 0.01). However, the standardized math scores for the post intervention group were decreased in girls. After three semesters, standardized Chinese language scores for the post intervention group were increased by 0.27 SD (95% CI: 0.06, 0.48, p = 0.01). Math scores and English language scores decreased by 0.18 SD (95% CI: -0.36, -0.01, p = 0.04) and 0.23 SD (95% CI: -0.38, -0.09, p = 0.00), respectively. A school-based physical education program had mixed effects on academic scores in high school students.
Project description:We present a laboratory experiment that introduces high school chemistry students to microfluidics while teaching fundamental properties of acid-base chemistry. The procedure enables students to create microfluidic systems using nonspecialized equipment that is available in high school classrooms and reagents that are safe, inexpensive, and commercially available. The experiment is designed to ignite creativity and confidence about experimental design in a high school chemistry class. This experiment requires a computer program (e.g., PowerPoint), Shrinky Dink film, a readily available silicone polymer, weak acids, bases, and a colorimetric pH indicator. Over the span of five 45-min class periods, teams of students design and prepare devices in which two different pH solutions mix in a predictable way to create five different pH solutions. Initial device designs are instructive but rarely optimal. During two additional half-class periods, students have the opportunity to use their initial observations to redesign their microfluidic systems to optimize the outcome. The experiment exposes students to cutting-edge science and the design process, and solidifies introductory chemistry concepts including laminar flow, neutralization of weak acids-bases, and polymers.
Project description:A perspective on the development of mechanistic carbene chemistry is presented. The author will point out questions that have been answered, and a next generation of questions will be proposed.
Project description:The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence-structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by 'hidden' conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.