Student Performance on the BDSI for Basic Data Structures

A Concept Inventory (CI) is an assessment to measure student conceptual understanding of a particular topic. This article presents the results of a CI for basic data structures (BDSI) that has been previously shown to have strong evidence for validity. The goal of this work is to help researchers or instructors who administer the BDSI in their own courses to better understand their results. In support of this goal, we discuss our findings for each question of the CI using data gathered from 1,963 students across seven institutions.

Does an Urban Wilderness Promote Gentrification? A Case Study from Knoxville, Tennessee, USA

The Knoxville Urban Wilderness (KUW) is a successful example of a growing global movement to utilize vacant urban land as many cities “de-urbanize”. A key question is whether this particular kind of green space promotes social inequality via green gentrification. Our analysis shows how the KUW has affected nearby home prices. Socioeconomic data including income, educational attainment, and race is also presented to explore the possibility of gentrification in South Knoxville. Our findings do not support strong evidence of gentrification, which implies that lower-income households are benefiting from advances in environmental amenities. Other households in specific areas are benefiting from both increases in home values and from expansions of the KUW. These are encouraging results for urban planning efforts that seek to utilize large areas of vacant urban land while also having positive social and economic impacts.

3R Blackboard: A platform for animal and organ sharing

Since the embedding of the principles of the 3Rs (Replacement, Reduction and Refinement) in national and international regulations on the use of animals, scientists have been challenged to find ways to reduce the number of animals in their research. Here, we present a digital platform, called ‘3R Backboard’, linked to a laboratory animal management system, which facilitates sharing of surplus biological materials from animals (e.g. tissues, organs and cells) to other research teams. Based on information provided, such as genotype, age and sex, other animal workers were able to indicate their interest in collecting specific tissues and to communicate with the person providing the animals. A short pilot study of this approach conducted in a limited academic environment presented strong evidence of its effectiveness and resulted in a notable reduction of the number of mice used. In addition, the use of 3R Blackboard led to resource saving, knowledge exchange and even establishment of new collaboration.

The Effect of Concealed-Carry and Handgun Restrictions on Gun-Related Deaths: Evidence from the Sullivan Act of 1911

The 1911 NY State Sullivan Act (SA) outlawed carrying concealable firearms without a licence, established strict licencing rules, and regulated the sale and possession of handguns. We analyse the effects of the SA using historical data on mortality rates, pistol permits, and citations for illegal carrying. Our analysis of pistol permits and citations reveal clear initial effects of the SA on gun-related behaviours. Using synthetic control and difference-in-differences methodologies, our main analyses show no effects on overall homicide rates, evidence of a reduction in overall suicide rates, and strong evidence of a large and sustained decrease in gun-related suicide rates.

Single step estimation of ARMA roots for non-fundamental nonstationary fractional models

We propose a single step estimator for the autoregressive and moving-average roots (without imposing causality or invertibility restrictions) of a nonstationary Fractional ARMA process. These estimators employ an efficient tapering procedure, which allows for a long memory component in the process, but avoid estimating the nonstationarity component, which can be stochastic and/or deterministic. After selecting automatically the order of the model, we robustly estimate the AR and MA roots for trading volume for the thirty stocks in the Dow Jones Industrial Average Index in the last decade. Two empirical results are found. First, there is strong evidence that stock market trading volume exhibits non-fundamentalness. Second, non-causality is more common than non-invertibility.

Structural basis of ion - substrate coupling in the Na+-dependent dicarboxylate transporter VcINDY

The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen induced-fit mechanism. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's induced-fit mechanism is a result of the sodium-dependent formation of the substrate binding site.

The rise of grasslands is linked to atmospheric CO2 decline in the late Palaeogene

Grasslands are predicted to experience a major biodiversity change by the year 2100. A better understanding of how grasslands have responded to past environmental changes will help predict the outcome of current and future environmental changes. Here, we explore the relationship between past atmospheric CO2 and temperature fluctuations and the shifts in diversification rate of Poaceae (grasses) and Asteraceae (daisies), two exceptionally species-rich grassland families (~11,000 and ~23,000 species, respectively). To this end, we develop a Bayesian approach that simultaneously estimates diversification rates through time from time-calibrated phylogenies and correlations between environmental variables and diversification rates. Additionally, we present a statistical approach that incorporates the information of the distribution of missing species in the phylogeny. We find strong evidence supporting a simultaneous increase in diversification rates for grasses and daisies after the most significant reduction of atmospheric CO2 in the Cenozoic (~34 Mya). The fluctuations of paleo-temperatures, however, appear not to have had a significant relationship with the diversification of these grassland families. Overall, our results shed new light on our understanding of the origin of grasslands in the context of past environmental changes.

Evidence of sodium limitation in ants and termites in a Neotropical savanna

Nutritional ecology of ropical ecosystems like Neotropical savannas, which are of high conservation concern, is understudied. Sodium is essential for heterotrophs but availability often falls short relative to plant consumer requirements. Savanna plant consumers like ants and termites should be sodium-limited due to high temperatures, nutrient-poor soils, and lack of oceanic sodium deposition. We tested the hypothesis that Neotropical savanna ants and termites are sodium-limited. Termites were tested by supplementing 0.25 m2 plots with H2O (control), 0.1%, 0.5%, or 1.0% NaCl and measuring termite presence and artificial substrate mass loss after 1 week. Ants were tested by collecting ants that recruited to H2O (control), 0.1%, 0.5%, and 1.0% NaCl and 1.0%, 10%, and 20% sugar baits on paired diurnal–nocturnal transects. Termites were 16 times more likely to occur on 1% NaCl than H2O plots and wood-feeding termites were most frequent. However, the decomposition rate did not differ among treatments. Ant bait use increased with increasing NaCl concentration and 1% NaCl usage was similar to sugar bait usage. Ants were 3.7 times more active nocturnally than diurnally, but contrary to predictions bait type (water, sugar or NaCl) usage did not differ between day and night. Together, these results provide strong evidence of sodium limitation in Neotropical savannas.

On optimal cloaking-by-mapping transformations

A central ingredient of cloaking-by-mapping is the diffeomorphisn which transforms an annulus with a small hole into an annulus with a finite size hole, while being the identity on the outer boundary of the annulus. The resulting meta-material is anisotropic, which makes it difficult to manufacture. The problem of minimizing anisotropy among radial transformations has been studied in [4]. In this work, as in [4], we formulate the problem of minimizing anisotropy as an energy minimization problem. Our main goal is to provide strong evidence for the conjecture that for cloaks with circular boundaries, non-radial transformations do not lead to lower degree of anisotropy. In the final section, we consider cloaks with non-circular boundaries and show that in this case, non-radial cloaks may be advantageous, when it comes to minimizing anisotropy.

Function and constraint in enhancers with multiple evolutionary origins

Motivation: Thousands of human gene regulatory enhancers are composed of sequences with multiple evolutionary origins. These evolutionarily "complex" enhancers consist of older "core" sequences and younger "derived" sequences. However, the functional relationship between the sequences of different evolutionary origins within complex enhancers is poorly understood. Results: We evaluated the function, selective pressures, and sequence variation across core and derived components of human complex enhancers. We find that both components are older than expected from the genomic background, and cores are enriched for derived sequences of similar evolutionary ages. Both components show strong evidence of biochemical activity in massively parallel report assays (MPRAs). However, core and derived sequences have distinct transcription factor (TF) binding preferences that are largely stable across evolutionary origins. Given these signatures of function, both core and derived sequences have substantial evidence of purifying selection. Nonetheless, derived sequences exhibit weaker purifying selection than adjacent cores. Derived sequences also tolerate more common genetic variation and are enriched compared to cores for eQTL associated with gene expression variability in human populations. Conclusions: Both core and derived sequences have strong evidence of gene regulatory function, but derived sequences have distinct constraint profiles, TF binding preferences, and tolerance to variation compared with cores. We propose that the step-wise integration of younger derived and older core sequences has generated regulatory substrates with robust activity and the potential for functional variation. Our analyses demonstrate that synthesizing study of enhancer evolution and function can aid interpretation of regulatory sequence activity and functional variation across human populations.