Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer.

Genome-wide fragmentation patterns in cell-free DNA (cfDNA) in plasma are strongly influenced by cellular origin due to variation in chromatin accessibility across cell types. Such differences between healthy and cancer cells provide the opportunity for development of novel cancer diagnostics. Here, we investigated whether analysis of cfDNA fragment end positions and their surrounding DNA sequences reveals the presence of tumor-derived DNA in blood. We performed genome-wide analysis of cfDNA from 521 samples and analyzed sequencing data from an additional 2147 samples, including healthy individuals and patients with 11 different cancer types. We developed a metric based on genome-wide differences in fragment positioning, weighted by fragment length and GC content [information-weighted fraction of aberrant fragments (iwFAF)]. We observed that iwFAF strongly correlated with tumor fraction, was higher for DNA fragments carrying somatic mutations, and was higher within genomic regions affected by copy number amplifications. We also calculated sample-level means of nucleotide frequencies observed at genomic positions spanning fragment ends. Using a combination of iwFAF and nine nucleotide frequencies from three positions surrounding fragment ends, we developed a machine learning model to differentiate healthy individuals from patients with cancer. We observed an area under the receiver operative characteristic curve (AUC) of 0.91 for detection of cancer at any stage and an AUC of 0.87 for detection of stage I cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, demonstrating that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring.

Analysis of recurrently protected genomic regions in cell-free DNA found in urine.

Cell-free DNA (cfDNA) in urine is a promising analyte for noninvasive diagnostics. However, urine cfDNA is highly fragmented. Whether characteristics of these fragments reflect underlying genomic architecture is unknown. Here, we characterized fragmentation patterns in urine cfDNA using whole-genome sequencing. Size distribution of urine cfDNA fragments showed multiple strong peaks between 40 and 120 base pairs (bp) with a modal size of 81- and sharp 10-bp periodicity, suggesting transient protection from complete degradation. These properties were robust to preanalytical perturbations, such as at-home collection and delay in processing. Genome-wide sequencing coverage of urine cfDNA fragments revealed recurrently protected regions (RPRs) conserved across individuals, with partial overlap with nucleosome positioning maps inferred from plasma cfDNA. The ends of cfDNA fragments clustered upstream and downstream of RPRs, and nucleotide frequencies of fragment ends indicated enzymatic digestion of urine cfDNA. Compared to plasma, fragmentation patterns in urine cfDNA showed greater correlation with gene expression and chromatin accessibility in epithelial cells of the urinary tract. We determined that tumor-derived urine cfDNA exhibits a higher frequency of aberrant fragments that end within RPRs. By comparing the fraction of aberrant fragments and nucleotide frequencies of fragment ends, we identified urine samples from cancer patients with an area under the curve of 0.89. Our results revealed nonrandom genomic positioning of urine cfDNA fragments and suggested that analysis of fragmentation patterns across recurrently protected genomic loci may serve as a cancer diagnostic.

Call on me! Undergraduates' perceptions of voluntarily asking and answering questions in front of large-enrollment science classes.

Allowing students to voluntarily ask and answer questions in front of the whole class are common teaching practices used in college science courses. However, few studies have examined college science students' perceptions of these practices, the extent to which students choose to engage in these practices, and what discourages students from participating. In this study, we surveyed 417 undergraduates at a research-intensive institution about their experiences asking and answering questions in large-enrollment college science courses. Specifically, students answered questions about to what extent they perceive voluntarily asking and answering questions in large-enrollment science courses is helpful to them and why. They also answered questions about to what extent they engage in asking and answering questions in large-enrollment college science courses and what factors could discourage them from participating. Using binary logistic regression, we examined whether there were differences among students of different demographic groups regarding their opinions about asking and answering questions. We found that overwhelmingly students reported that other students voluntarily asking and answering instructor questions is helpful to them. Notably, compared to continuing generation students, first-generation students were more likely to perceive other students asking questions to be helpful. Despite perceiving asking and answering questions to be helpful, over half of students reported that they never ask or answer questions in large-enrollment college science courses during a semester, and women were more likely than men to report never asking questions. We identified fear of negative evaluation, or students' sense of dread associated with being unfavorably evaluated, as a primary factor influencing their decision to answer instructor questions. This work adds to a growing body of literature on student participation in large-enrollment college science courses and begins to uncover underlying factors influencing student participation.

To be funny or not to be funny: Gender differences in student perceptions of instructor humor in college science courses.

For over 50 years instructor humor has been recognized as a way to positively impact student cognitive and affective learning. However, no study has explored humor exclusively in the context of college science courses, which have the reputation of being difficult and boring. The majority of studies that explore humor have assumed that students perceive instructor humor to be funny, yet students likely perceive some instructor humor as unfunny or offensive. Further, evidence suggests that women perceive certain subjects to be more offensive than men, yet we do not know what impact this may have on the experience of women in the classroom. To address these gaps in the literature, we surveyed students across 25 different college science courses about their perceptions of instructor humor in college science classes, which yielded 1637 student responses. Open-coding methods were used to analyze student responses to a question about why students appreciate humor. Multinomial regression was used to identify whether there are gender differences in the extent to which funny, unfunny, and offensive humor influenced student attention to course content, instructor relatability, and student sense of belonging. Logistic regression was used to examine gender differences in what subjects students find funny and offensive when joked about by college science instructors. Nearly 99% of students reported that they appreciate instructor humor and reported that it positively changes the classroom atmosphere, improves student experiences during class, and enhances the student-instructor relationship. We found that funny humor tends to increase student attention to course content, instructor relatability, and student sense of belonging. Conversely, offensive humor tends to decrease instructor relatability and student sense of belonging. Lastly, we identified subjects that males were more likely to find funny and females were more likely to find offensive if a college science instructor were to joke about them.

A Course-Embedded Comparison of Instructor-Generated Videos of Either an Instructor Alone or an Instructor and a Student.

Instructor-generated videos have become a popular way to engage students with material before a class, yet this is a relatively unexplored area of research. There is support for the use of videos in which instructors tutor students, but few studies have been conducted within the context of a classroom. In this study, conducted in a large-enrollment college physiology course, we used a randomized crossover design to compare the impact of two types of instructor-generated videos that students watched as part of their preclass assignments. We compared videos featuring only an instructor (instructor-only videos) with videos featuring an instructor tutoring a student (instructor-tutee videos). We analyzed student survey responses and weekly physiology quiz scores and found that students preferred, enjoyed, and valued the instructor-only videos significantly more than the instructor-tutee videos. In contrast to prior literature, students with a grade point average (GPA) below the median (3.49) performed significantly better on physiology quizzes after watching instructor-only videos compared with instructor-tutee videos. Students with a GPA at or above the median performed equivalently on physiology quizzes after watching instructor-only or instructor-tutee videos. We present this study as an example of bringing cognitive science studies into the context of a real physiology classroom.