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Background A variety of protocols exist for producing whole genome run-on transcription datasets. However, little is known about how differences between these protocols affect the signal within the resulting libraries. Results Using run-on transcription datasets generated from the same biological system, we show that a variety of GRO- and PRO-seq preparation methods leave identifiable signatures within each library. Specifically we show that the library preparation method results in differences in quality control metrics, as well as differences in the signal distribution at the 5 ′ end of transcribed regions. These shifts lead to disparities in eRNA identification, but do not impact analyses aimed at inferring the key regulators involved in changes to transcription. Conclusions Run-on sequencing protocol variations result in technical signatures that can be used to identify both the enrichment and library preparation method of a particular data set. These technical signatures are batch effects that limit detailed comparisons of pausing ratios and eRNAs identified across protocols. However, these batch effects have only limited impact on our ability to infer which regulators underlie the observed transcriptional changes. 

Abstract Design researchers have long sought to understand the mechanisms that support creative idea development. However, one of the key challenges faced by the design community is how to effectively measure the nebulous construct of creativity. The social science and engineering communities have adopted two vastly different approaches to solving this problem, both of which have been deployed throughout engineering design research. The goal of this paper was to compare and contrast these two approaches using design ratings of nearly 1000 engineering design ideas. The results of this study identify that while these two methods provide similar ratings of idea quality, there was a statistically significant negative relationship between these methods for ratings of idea novelty. In addition, the results show discrepancies in the reliability and consistency of global ratings of creativity. The results of this study guide the deployment of idea ratings in engineering design research and evidence. 

Design researchers have long sought to understand the mechanisms that support creative idea development. However, one of the key challenges faced by the design community is how to effectively measure the nebulous construct of creativity. The social science and engineering communities have adopted two vastly different approaches to solving this problem, both of which have been deployed throughout engineering design research. The goal of this paper was to compare and contrast these two approaches using design ratings of nearly 1000 engineering design ideas paired with a qualitative study with expert raters. The results of this study identify that while these two methods provide similar ratings of idea quality, there was a statistically significant negative relationship between these methods for ratings of idea novelty. Qualitative analysis of recordings from expert raters’ think aloud concept mapping points to potential sources of disagreement. In addition, the results show that while quasi-expert and expert raters provided similar ratings of design novelty, there was not significant agreement between these groups for ratings of design quality. The results of this study provide guidance for the deployment of idea ratings in engineering design research and evidence for the development and potential modification of engineering design creativity metrics. 

Abstract Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (Tamias canipes, Tamias cinereicollis, Tamias dorsalis, T. quadrivittatus, Tamias rufus, and Tamias umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population-genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group. [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.] 

Abstract Product dissection is a popular educational tool in engineering design due to its ability to help students understand a product, provide inspiration for new design ideas, and aid in product redesign. While prior research has investigated how dissecting a product before idea generation impacts the creative output of the ideation session, these studies failed to look at the types of ideas generated before dissection or how the type of product dissected impacts this. Thus, the goal of the current study was to examine how product dissection impacts the solution space explored by students. Fifty-five undergraduate engineering students participated in the experiment; 40 participants virtually dissected a product, while the remaining 15 completed a personality test. The results of the study highlight that students explored new types of ideas during the second ideation session for all conditions and at all levels, with students having the biggest increase in embodiment variety when they dissected analogically far products. Overall, there were no differences in design variety between students in the dissection condition and the incubation condition. This study highlights how incubation can impact design variety and calls for further investigation of the interaction between product dissection and incubation. 

Design variety metrics measure how much a design space is explored. We propose that a generalized class of entropy measures based on Sharma-Mittal entropy offers advantages over existing methods to measure design variety. We show that an exemplar metric from Sharma-Mittal entropy, which we call the Herfindahl–Hirschman Index for Design (HHID) has the following desirable advantages over existing metrics: (a) More Accuracy: It better aligns with human ratings compared to existing and commonly used tree-based metrics for two new datasets; (b) Higher Sensitivity: It has higher sensitivity compared to existing methods when distinguishing between the variety of sets; (c) Allows Efficient Optimization: It is a submodular function, which enables us to optimize design variety using a polynomial-time greedy algorithm; and (d) Generalizes to Multiple Measures: The parametric nature of this metric allows us to fit the metric to better represent variety for new domains. The paper also contributes a procedure for comparing metrics used to measure variety via constructing ground truth datasets from pairwise comparisons. Overall, our results shed light on some qualities that good design variety metrics should possess and the non-trivial challenges associated with collecting the data needed to measure those qualities. 

Abstract Product dissection has the ability to create an engaging and active learning environment for engineering students. The purpose of this paper was to further investigate students’ perceptions on product dissection in the classroom. This paper was developed to provide an examination of the usefulness of product dissection for idea generation and how product dissection modules might aid in students’ understanding of the module. The findings of this paper conclude that students felt that the product dissection module was useful, valuable, and enjoyable and that students had a positive sentiment towards the designed aspects of the dissection module. Through the use of content analysis, areas for improvement in these modules are identified. 

The purpose of product dissection is to teach students how a product works and provide them with inspiration for new ideas. However, little is known about how variations in dissection activities impact creative outcomes or engineering self-efficacy (ESE) and creative self-efficacies (CSE). This is important since the goal of engineering education is to produce capable and creative engineers. The current study was, thus, developed to address this research gap through a factorial experiment. The results showed that idea development was not impacted by dissection conditions but that ESE and CSE were increased through these activities. The results also showed that higher levels of CSE and ESE had alternate effects on novel idea development indicating they are at odds in engineering education.