Interpreting Assessments of Student Learning in the Introductory Physics Classroom and Laboratory

Assessment is the primary means of feedback between students and instructors. However, to effectively use assessment, the ability to interpret collected information is essential. We present insights into three unique, important avenues of assessment in the physics classroom and laboratory. First, we examine students’ performance on conceptual surveys. The goal of this research project is to better utilize the information collected by instructors when they administer the Force Concept Inventory (FCI) to students as a pre-test and post-test of their conceptual understanding of Newtonian mechanics. We find that ambiguities in the use of the normalized gain, g, may influence comparisons among individual classes. Therefore, we propose using stratagrams, graphical summaries of the fraction of students who exhibit “Newtonian thinking,” as a clearer, more informative method of both assessing a single class and comparing performance among classes. Next, we examine students’ expressions of confusion when they initially encounter new material. The goal of this research project is to better understand what such confusion actually conveys to instructors about students’ performance and engagement. We investigate the relationship between students’ self-assessment of their confusion over material and their performance, confidence in reasoning, pre-course self-efficacy and several other measurable characteristics of engagement. We find that students’ expressions of confusion are negatively related to initial performance, confidence and self-efficacy, but positively related to final performance when all factors are considered together. Finally, we examine students’ exhibition of scientific reasoning abilities in the instructional laboratory. The goal of this research project is to explore two inquiry-based curricula, each of which proposes a different degree of scaffolding. Students engage in sequences of these laboratory activities during one semester of an introductory physics course. We find that students who participate in the less scaffolded activities exhibit marginally stronger scientific reasoning abilities in distinct exercises throughout the semester, but exhibit no differences in the final, common exercises. Overall, we find that, although students demonstrate some enhanced scientific reasoning skills, they fail to exhibit or retain even some of the most strongly emphasized skills.Physic

Paving the Way for a Car Free Day in Stellenbosch, South Africa

Social inequality affects transportation in Stellenbosch, including high usage of personal vehicles by predominantly White drivers who cause road congestion and parking shortages. Working with faculty from the Department of Logistics at Stellenbosch University, our goal was to investigate considerations for a Car Free Day in Stellenbosch to mitigate congestion issues. We developed a plan by interviewing experts and stakeholders and observing traffic. The Car Free Day involves Park and Rides for driving commuters, local business engagement, and options for sustainable transportation. Our findings revealed concerns with commute disruption and a racialized disparity with public transportation awareness and use, especially around minibus-taxis

Evolution of the Bovine TLR Gene Family and Member Associations with Mycobacterium avium Subspecies paratuberculosis Infection

Members of the Toll-like receptor (TLR) gene family occupy key roles in the mammalian innate immune system by functioning as sentries for the detection of invading pathogens, thereafter provoking host innate immune responses. We utilized a custom next-generation sequencing approach and allele-specific genotyping assays to detect and validate 280 biallelic variants across all 10 bovine TLR genes, including 71 nonsynonymous single nucleotide polymorphisms (SNPs) and one putative nonsense SNP. Bayesian haplotype reconstructions and median joining networks revealed haplotype sharing between Bos taurus taurus and Bos taurus indicus breeds at every locus, and specialized beef and dairy breeds could not be differentiated despite an average polymorphism density of 1 marker/158 bp. Collectively, 160 tagSNPs and two tag insertion-deletion mutations (indels) were sufficient to predict 100% of the variation at 280 variable sites for both Bos subspecies and their hybrids, whereas 118 tagSNPs and 1 tagIndel predictively captured 100% of the variation at 235 variable sites for B. t. taurus. Polyphen and SIFT analyses of amino acid (AA) replacements encoded by bovine TLR SNPs indicated that up to 32% of the AA substitutions were expected to impact protein function. Classical and newly developed tests of diversity provide strong support for balancing selection operating on TLR3 and TLR8, and purifying selection acting on TLR10. An investigation of the persistence and continuity of linkage disequilibrium (r2≥0.50) between adjacent variable sites also supported the presence of selection acting on TLR3 and TLR8. A case-control study employing validated variants from bovine TLR genes recognizing bacterial ligands revealed six SNPs potentially eliciting small effects on susceptibility to Mycobacterium avium spp paratuberculosis infection in dairy cattle. The results of this study will broadly impact domestic cattle research by providing the necessary foundation to explore several avenues of bovine translational genomics, and the potential for marker-assisted vaccination

Predictive control and optimization of bioprocesses for recombinant T-PA protein production by mammalian cells

Genetically engineered mammalian cells produce a large array of recombinant proteins for research, diagnostic and therapeutic applications. The relatively low cellular production rates in mammalian cells require intensification of the production methods to raise product concentrations and volumetric productivity. Recombinant human tissue plasminogen activator (t-PA) produced in Chinese Hamster Ovary (CHO) cells served as the basis for this investigation. Multiple model adaptive protocols were applied to control the extracellular environment with the goal of fed-batch and perfusion process optimization of protein titers and productivity. Fed-batch and perfusion bioreactors in various forms are widely used to produce recombinant proteins and monoclonal antibodies for therapeutic and diagnostic use. Better control of the cellular environment can lead to higher volumetric productivity, ensure product consistency and optimize medium utilization. The objective was to manipulate and control substrate concentrations in fed-batch and perfusion bioprocesses using predictive modeling and control. The goal of the predictive controller was to minimize future deviations from the set point concentration, by structuring the controller output. The appropriate structure for the future manipulated variable was specified using the selected model of uptake rate estimates. When there was a deviation from the set point value, the flow rates were adjusted to drive the process close to the set point value in a defined first order manner. The shape of the first order process response depended on the magnitude of the deviation from the set point value. With daily sampling, a feed rate profile (8 flow rates per day) was specified to control the bioprocess. The predictive control protocols have demonstrated glucose variation of less than 0.4 mM in transient conditions, and less than 0.2 mM in pseudo-steady-state conditions. The non-linear controller allows for rapid changes in set point concentrations (6 to 9 h) or a reference trajectory to be followed. Set point changes and reference trajectories were simulated and tested with real process data. Modeling error and measurement bias was simulated to have the greatest potential effect during exponential growth. With good model estimation of the process, predictive control was able to maintain the process at the set point with a level of variability approaching that of the glucose assay. Fed-batch operation for the production of t-PA using Chinese Hamster Ovary (CHO) cells was optimized using serial and parallel experimentation. The isotonic concentrate efficacy was improved to obtain 2- to 2.5-fold increases in integrated viable cell days versus batch. With a low glucose inoculum train, the viability index was increased up to 4.5-fold. Hydrolysates were substituted for the amino acid portion of the concentrate with no significant change in fed-batch results. The concentrate addition rate was based on a constant 4 pmol/cell-day glucose uptake rate that maintained relatively constant glucose concentrations (approximately 3 mM). Increased viable cell indices did not lead to concomitant increases in t-PA concentrations compared to batch. The fed-batch concentrate was tested in hybridoma culture, where a four-fold increase in viable cell index yielded a four-fold increase in antibody concentration. Instead, there appeared to be an extracellular t-PA concentration maximum at 30-35 mg/L. The half-life of t-PA decreased from 42 to 14 days with decreasing cell viability (> 90% to ~ 70%), but this was not sufficient to explain the apparent t-PA threshold. Analysis of both the total and t-PA mRNA levels in dose response experiments revealed no response to extracellular t-PA concentrations. Instead, increasing intracellular t-PA levels revealed a secretory pathway limitation. A new reactor configuration used an acoustic filter to retain the cells in the reactor and an ultrafiltration module to strip the t-PA from the clarified medium and returned the permeate back to the reactor. By adding this harvesting step, the t-PA fed-batch production was increased over 2-fold, up to a yield of80mg/L. Perfusion cultures of CHO cells producing t-PA were performed using an acoustic filter to retain cells in the bioreactor as spent medium was removed. A robust off-line glucose analysis and predictive control protocol was developed that maintained the process within approximately 0.5 mM of the glucose set point without the need for a more fallible on-line sensor. Earlier onset of perfusion with a ramping glucose set point (1 to 2 mM/day) resulted in improved growth and consistency in the perfusion culture start-up. A medium formulation with elevated levels of glutamine resulted in significant increases in glutamine consumption and ammonium production, along with reductions in consumption rates of glucose and several amino acids. In contrast, elevated levels of glucose had no significant impact on the cellular metabolism. Amino acid analysis of the initial batch and early perfusion culture resulted in an improved medium formulation which resulted in increased medium residence times and increased t-PA concentrations. Glucose depletion was used as an indicator of the extent of overall medium utilization, to map acceptable ranges of operation and the edge of failure. Peak t-PA concentrations of over 90 mg/L were obtained by controlling at a glucose depletion of approximately 25 mM, but were not sustainable for more than 3 days. A consistent t-PA concentration of 40 mg/L was obtained at a glucose depletion of 22.5 mM. The variability in the t-PA concentrations increased gradually with increasing glucose depletion up to approximately 23 mM, then increased 3-fold between a glucose depletion of 23 and 25 mM.Applied Science, Faculty ofChemical and Biological Engineering, Department ofGraduat

Making sense of confusion : Relating performance, confidence, and self-efficacy to expressions of confusion in an introductory physics class

Although confusion is generally perceived to be negative, educators dating as far back as Socrates, who asked students to question assumptions and wrestle with ideas, have challenged this notion. Can confusion be productive? How should instructors interpret student expressions of confusion? During two semesters of introductory physics that involved Just-in-Time Teaching (JiTT) and research-based reading materials, we evaluated performance on reading assignments while simultaneously measuring students’ self-assessment of their confusion over the preclass reading material (N = 137; Nfall = 106, Nspring = 88). We examined the relationship between confusion and correctness, confidence in reasoning, and (in the spring) precourse self-efficacy.We find that student expressions of confusion before coming to class are negatively related to correctness on preclass content-related questions, confidence in reasoning on those questions, and selfefficacy, but weakly positively related to final grade when controlling for these factors (β = 0.23, p = 0.03)

Making sense of confusion : Relating performance, confidence, and self-efficacy to expressions of confusion in an introductory physics class

Although confusion is generally perceived to be negative, educators dating as far back as Socrates, who asked students to question assumptions and wrestle with ideas, have challenged this notion. Can confusion be productive? How should instructors interpret student expressions of confusion? During two semesters of introductory physics that involved Just-in-Time Teaching (JiTT) and research-based reading materials, we evaluated performance on reading assignments while simultaneously measuring students’ self-assessment of their confusion over the preclass reading material (N = 137; Nfall = 106, Nspring = 88). We examined the relationship between confusion and correctness, confidence in reasoning, and (in the spring) precourse self-efficacy.We find that student expressions of confusion before coming to class are negatively related to correctness on preclass content-related questions, confidence in reasoning on those questions, and selfefficacy, but weakly positively related to final grade when controlling for these factors (β = 0.23, p = 0.03)

Small Non-coding RNA Expression and Vertebrate Anoxia Tolerance

Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus, the most anoxiatolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance. The epaulette shark (Hemiscyllium ocellatum), crucian carp (Carassius carassius), western painted turtle (Chrysemys picta bellii), and leopard frog (Rana pipiens) were exposed to anoxia and recovery, and small ncRNAs were sequenced from the brain (one of the most anoxia-sensitive tissues) prior to, during, and following exposure to anoxia. Results: Small ncRNA profiles were broadly conserved among species under normoxic conditions, and these expression patterns were largely conserved during exposure to anoxia. In contrast, differentially expressed genes are mostly unique to each species, suggesting that each species may have evolved distinct small ncRNA expression patterns in response to anoxia. Mitochondria-derived small ncRNAs (mitosRNAs) which have a robust response to anoxia in A. limnaeus embryos, were identified in the other anoxia tolerant vertebrates here but did not display a similarly robust response to anoxia. Conclusion: These findings support an overall stabilization of the small ncRNA transcriptome during exposure to anoxic insults, but also suggest that multiple small ncRNA expression pathways may support anoxia tolerance, as no conserved small ncRNA response was identified among the anoxia-tolerant vertebrates studied. This may reflect divergent strategies to achieve the same endpoint: anoxia tolerance. However, it may also indicate that there are multiple cellular pathways that can trigger the same cellular and physiological survival processes, including hypometabolism

Teaching and physics education research: bridging the gap.

Physics faculty, experts in evidence-based research, often rely on anecdotal experience to guide their teaching practices. Adoption of research-based instructional strategies is surprisingly low, despite the large body of physics education research (PER) and strong dissemination effort of PER researchers and innovators. Evidence-based PER has validated specific non-traditional teaching practices, but many faculty raise valuable concerns toward their applicability. We address these concerns and identify future studies required to overcome the gap between research and practice