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SEquence Evaluation throughk-mer Representation (SEEKR) is a method of sequence comparison that uses sequence substrings calledk-mers to quantify the nonlinear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimateP-values that ascribe statistical significance to SEEKR-derived similarities, as well as visualize different aspects ofk-mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that containXIST-like sequence features, and we demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains. We also highlight ways in which SEEKR can be applied to augment studies of lncRNA conservation, and we outline the best practice of visualizing RNA-seq read density to evaluate support for lncRNA annotations before their in-depth study in cell types of interest. 

Purpose We designed a science and engineering curricular program that includes design features that promote student interest and motivation and examined teacher and students’ views on meaningfulness, motivation, and interest. Design/methodology/approach The research approach consisted of mixed methods including content analyses and descriptive statistics. Findings The curricular program successfully included all four of the US National Academies of Sciences’ design features for promoting interest and motivation through scientific investigation and engineering design. During interviews, teachers and students expressed evidence of design features associated with interest and motivation. After experiencing the program, more than 60% of all students scored high on all four science and engineering meaningfulness and interest survey items. Originality A curricular program that extends science learning through the engineered design of solutions is an innovative approach to foster both conceptual knowledge development and interest and motivation in science and engineering. 

Abstract BackgroundAnimal movement is a key ecological process that is tightly coupled to local environmental conditions. While agriculture, urbanisation, and transportation infrastructure are critical to human socio-economic improvement, these have spurred substantial changes in animal movement across the globe with potential impacts on fitness and survival. Notably, however, human disturbance can have differential effects across species, and responses to human activities are thus largely taxa and context specific. As human disturbance is only expected to worsen over the next decade it is critical to better understand how species respond to human disturbance in order to develop effective, case-specific conservation strategies. MethodsHere, we use an extensive telemetry dataset collected over 22 years to fill a critical knowledge gap in the movement ecology of lowland tapirs (Tapirus terrestris) across areas of varying human disturbance within three biomes in southern Brazil: the Pantanal, Cerrado, and Atlantic Forest. ResultsFrom these data we found that the mean home range size across all monitored tapirs was 8.31 km²(95% CI 6.53–10.42), with no evidence that home range sizes differed between sexes nor age groups. Interestingly, although the Atlantic Forest, Cerrado, and Pantanal vary substantially in habitat composition, levels of human disturbance, and tapir population densities, we found that lowland tapir movement behaviour and space use were consistent across all three biomes. Human disturbance also had no detectable effect on lowland tapir movement. Lowland tapirs living in the most altered habitats we monitored exhibited movement behaviour that was comparable to that of tapirs living in a near pristine environment. ConclusionsContrary to our expectations, although we observed individual variability in lowland tapir space use and movement, human impacts on the landscape also had no measurable effect on their movement. Lowland tapir movement behaviour thus appears to exhibit very little phenotypic plasticity in response to human disturbance. Crucially, the lack of any detectable response to anthropogenic disturbance suggests that human modified habitats risk being ecological traps for tapirs and this information should be factored into conservation actions and species management aimed towards protecting lowland tapir populations.