An Assessment of Engineering Students' Curricular and Co‐Curricular Experiences and Their Ethical Development

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95194/1/j.2168-9830.2012.tb00058.x.pd

Landscape of stimulation-responsive chromatin across diverse human immune cells.

A hallmark of the immune system is the interplay among specialized cell types transitioning between resting and stimulated states. The gene regulatory landscape of this dynamic system has not been fully characterized in human cells. Here we collected assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing data under resting and stimulated conditions for up to 32 immune cell populations. Stimulation caused widespread chromatin remodeling, including response elements shared between stimulated B and T cells. Furthermore, several autoimmune traits showed significant heritability in stimulation-responsive elements from distinct cell types, highlighting the importance of these cell states in autoimmunity. Allele-specific read mapping identified variants that alter chromatin accessibility in particular conditions, allowing us to observe evidence of function for a candidate causal variant that is undetected by existing large-scale studies in resting cells. Our results provide a resource of chromatin dynamics and highlight the need to characterize the effects of genetic variation in stimulated cells

Outcomes of engaging engineering undergraduates in co-curricular experiences

The effects of involvement in co-curricular experiences (i.e. internships, co-ops, service projects, and clubs and organizations) on student persistence in college is well documented in the education literature. What remains unclear are the specific ways that involvement influences the development of engineering undergraduate students. We found that when engineering students are involved in co-curricular experiences they exhibit greater leadership skills, are more thoughtful about their ethical decisions, and can articulate how involvement influences their ethical development. In this paper, we explore outcomes of participating in co-curricular experiences for engineering students at four undergraduate focused institutions.National Science FoundationPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86117/1/E3_ASEE_Cocurricular_2011.pd

We can’t get no satisfaction!: The relationship between students’ ethical reasoning and their satisfaction with engineering ethics education

Student satisfaction is a common metric for evaluating classes and other educational programs, and sometimes that satisfaction is seen as a proxy for effectiveness of those programs. For this paper, we examine student satisfaction within the context of engineering ethics education, examining the relationship between student satisfaction and ethical reasoning ability. As part of a national study of ethics education, we draw on survey data from 3,914 undergraduate engineering students, and results suggest that higher levels of ethical reasoning actually predict lower levels of satisfaction with ethics education. Further, the amount of ethics education and the methods through which it is taught also affect students’ levels of satisfaction.National Science FoundationPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86096/1/E3_ASEE_Satisfaction_2011.pd

Impact of Different Curricular Approaches to Ethics Education on Ethical Reasoning Ability

National Science FoundationPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/86116/1/E3_ASEE_Curricular_2011.pd

Systematics and evolution of predatory flower flies (Diptera Syrphidae) based on exon-capture sequencing

Flower flies (Diptera: Syrphidae) are one of the most species-rich dipteran families and provide important ecosystem services such as pollination, biological control of pests, recycling of organic matter and redistributions of essential nutrients. Flower fly adults generally feed on pollen and nectar, but their larval feeding habits are strikingly diverse. In the present study, high-throughput sequencing was used to capture and enrich phylogenetically and evolutionary informative exonic regions. With the help of the baitfisher software, we developed a new bait kit (SYRPHIDAE1.0) to target 1945 CDS regions belonging to 1312 orthologous genes. This new bait kit was successfully used to exon capture the targeted loci in 121 flower fly species across the different subfamilies of Syrphidae. We analysed different amino acid and nucleotide data sets (1302 loci and 154 loci) with maximum likelihood and multispecies coalescent models. Our analyses yielded highly supported similar topologies, although the degree of the SRH (global stationarity, reversibility and homogeneity) conditions varied greatly between amino acid and nucleotide data sets. The sisterhood of subfamilies Pipizinae and Syrphinae is supported in all our analyses, confirming a common origin of taxa feeding on soft-bodied arthropods. Based on our results, we define Syrphini stat.rev. to include the genera Toxomerus and Paragus. Our divergence estimate analyses with beast inferred the origin of the Syrphidae in the Lower Cretaceous (125.5-98.5 Ma) and the diversification of predatory flower flies around the K-Pg boundary (70.61-54.4 Ma), coinciding with the rise and diversification of their prey.Peer reviewe

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

A TESS Dress Rehearsal: Planetary Candidates and Variables from K2 Campaign 17

We produce light curves for all ∼34,000 targets observed with K2 in Campaign 17 (C17), identifying planet candidates, eclipsing binaries, and other periodic variables. The forward-facing direction of the C17 field means follow-up can begin immediately now that the campaign has concluded and interesting targets have been identified. The C17 field has a large overlap with C6, so this latest campaign also offers an infrequent opportunity to study a large number of targets already observed in a previous K2 campaign. The timing of the C17 data release, shortly before science operations begin with the Transiting Exoplanet Survey Satellite (TESS), also lets us exercise some of the tools and methods developed for identification and dissemination of planet candidates from TESS. We find excellent agreement between these results and those identified using only K2-based tools. Among our planet candidates are several planet candidates with sizes <4 R ⊕ and orbiting stars with Kp ≲ 10 (indicating good RV targets of the sort TESS hopes to find) and a Jupiter-sized single-transit event around a star already hosting a 6 day planet candidate

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe