ASU Scholarship Showcase

Background: Aspects of the food environment such as the availability of different types of food stores have recently emerged as key modifiable factors that may contribute to the increased prevalence of obesity. Given that many of these studies have derived their results based on secondary datasets and the relationship of food stores with individual weight outcomes has been reported to vary by store type, it is important to understand the extent to which often-used secondary data correctly classify food stores. We evaluated the classification bias of food stores in Dun & Bradstreet (D&B) and InfoUSA commercial business lists.

Methods: We performed a full census in 274 randomly selected census tracts in the Chicago metropolitan area and collected detailed store attributes inside stores for classification. Store attributes were compared by classification match status and store type. Systematic classification bias by census tract characteristics was assessed in multivariate regression.

Results: D&B had a higher classification match rate than InfoUSA for supermarkets and grocery stores, while InfoUSA was higher for convenience stores. Both lists were more likely to correctly classify large supermarkets, grocery stores, and convenience stores with more cash registers and different types of service counters (supermarkets and grocery stores only). The likelihood of a correct classification match for supermarkets and grocery stores did not vary systemically by tract characteristics whereas convenience stores were more likely to be misclassified in predominately Black tracts.

Conclusion: Researches can rely on classification of food stores in commercial datasets for supermarkets and grocery stores whereas classifications for convenience and specialty food stores are subject to some systematic bias by neighborhood racial/ethnic composition.

Background: The field of cancer genomics has rapidly adopted next-generation sequencing (NGS) in order to study and characterize malignant tumors with unprecedented resolution. In particular for cancer, one is often trying to identify somatic mutations--changes specific to a tumor and not within an individual's germline. However, false positive and false negative detections often result from lack of sufficient variant evidence, contamination of the biopsy by stromal tissue, sequencing errors, and the erroneous classification of germline variation as tumor-specific.

Results: We have developed a generalized Bayesian analysis framework for matched tumor/normal samples with the purpose of identifying tumor-specific alterations such as single nucleotide mutations, small insertions/deletions, and structural variation. We describe our methodology, and discuss its application to other types of paired-tissue analysis such as the detection of loss of heterozygosity as well as allelic imbalance. We also demonstrate the high level of sensitivity and specificity in discovering simulated somatic mutations, for various combinations of a) genomic coverage and b) emulated heterogeneity.

Conclusion: We present a Java-based implementation of our methods named Seurat, which is made available for free academic use. We have demonstrated and reported on the discovery of different types of somatic change by applying Seurat to an experimentally-derived cancer dataset using our methods; and have discussed considerations and practices regarding the accurate detection of somatic events in cancer genomes. Seurat is available at https://sites.google.com/site/seuratsomatic.

The Writing Pal (W-Pal) is an intelligent tutoring system (ITS) designed to provide students with explicit writing strategy instruction and practice. W-Pal includes a suite of educational games developed to increase writing engagement and provide opportunities to practice writing strategies. In this study, first (L1) (n = 26) and second (L2) language (n = 16) students interacted with W-Pal over eight sessions. We collected students’ daily self- reports of engagement, motivation, and perceptions of performance, as well as their reported game attitudes (difficulty, helpfulness for learning, and enjoyment). Results indicated that, for all students, interactions with W-Pal led to increases in writing performance and more positive attitudes towards the system (engagement, motivation, and perceived performance). For L1 students, game difficulty was a significant predictor of boredom; however, for the L2 students, game enjoyment predicted both their motivation and perceived writing improvement. Notably, the L2 students’ game ratings accounted for more variance in these daily reports than did the ratings of L1 students. This study suggests that L1 and L2 students experience similar benefits offered by game-based strategy practice in an ITS. Further, the link between game attitudes and overall daily perceptions of training may be stronger for L2 students than L1 students.

Background: Opioid peptides, including dynorphin A, besides their analgesic action in the nervous system, exert a broad spectrum of effects on cells of the immune system, including leukocyte migration, degranulation and cytokine production. The mechanisms whereby opioid peptides induce leukocyte responses are poorly understood. The integrin Mac-1 (alpha(M)beta(2), CD11b/CD18) is a multiligand receptor which mediates numerous reactions of neutrophils and monocyte/macrophages during the immune-inflammatory response. Our recent elucidation of the ligand recognition specificity of Mac-1 suggested that dynorphin A and dynorphin B contain Mac-1 recognition motifs and can potentially interact with this receptor.

Results: In this study, we have synthesized the peptide library spanning the sequence of dynorphin AB, containing dynorphin A and B, and showed that the peptides bound recombinant alpha I-M-domain, the ligand binding region of Mac-1. In addition, immobilized dynorphins A and B supported adhesion of the Mac-1-expressing cells. In binding to dynorphins A and B, Mac-1 cooperated with cell surface proteoglycans since both anti-Mac-1 function-blocking reagents and heparin were required to block adhesion. Further focusing on dynorphin A, we showed that its interaction with the alpha I-M-domain was activation independent as both the alpha 7 helix-truncated (active conformation) and helix-extended (nonactive conformation) alpha I-M-domains efficiently bound dynorphin A. Dynorphin A induced a potent migratory response of Mac-1-expressing, but not Mac-1-deficient leukocytes, and enhanced Mac-1-mediated phagocytosis of latex beads by murine IC-21 macrophages.

Conclusions: Together, the results identify dynorphins A and B as novel ligands for Mac-1 and suggest a role for the Dynorphin A-Mac-1 interactions in the induction of nonopiod receptor-dependent effects in leukocytes.

While expert groups often make recommendations on a range of non-controversial as well as controversial issues, little is known about how the level of expert consensus-the level of expert agreement-influences perceptions of the recommendations. This research illustrates that for non-controversial issues expert groups that exhibit high levels of agreement are more persuasive than expert groups that exhibit low levels of agreement. This effect is mediated by the perceived entitativity-the perceived cohesiveness or unification of the group-of the expert group. But for controversial issues, this effect is moderated by the perceivers' implicit assumptions about the group composition. When perceivers are provided no information about a group supporting the Affordable Care Act-a highly controversial piece of U.S. legislation that is divided by political party throughout the country-higher levels of agreement are less persuasive than lower levels of agreement because participants assume there were more democrats and fewer republicans in the group. But when explicitly told that the group was half republicans and half democrats, higher levels of agreement are more persuasive.

The broad recognition specificity exhibited by integrin α_Mβ₂ (Mac-1, CD11b/CD18) has allowed this adhesion receptor to play innumerable roles in leukocyte biology, yet we know little about how and why α_Mβ₂ binds its multiple ligands. Within α_Mβ₂, the α_MI-domain is responsible for integrin’s multiligand binding properties. To identify its recognition motif, we screened peptide libraries spanning sequences of many known protein ligands for α_MI-domain binding and also selected the α_M I-domain recognition sequences by phage display. Analyses of >1400 binding and nonbinding peptides derived from peptide libraries showed that a key feature of the α_MI-domain recognition motif is a small core consisting of basic amino acids flanked by hydrophobic residues. Furthermore, the peptides selected by phage display conformed to a similar pattern. Identification of the recognition motif allowed the construction of an algorithm that reliably predicts the α_MI-domain binding sites in the α_Mβ₂ ligands. The recognition specificity of the α_MI-domain resembles that of some chaperones, which allows it to bind segments exposed in unfolded proteins. The disclosure of the α_Mβ₂ binding preferences allowed the prediction that cationic host defense peptides, which are strikingly enriched in the α_MI-domain recognition motifs, represent a new class of α_Mβ₂ ligands. This prediction has been tested by examining the interaction of α_Mβ₂ with the human cathelicidin peptide LL-37. LL-37 induced a potent α_Mβ₂-dependent cell migratory response and caused activation of α_Mβ₂ on neutrophils. The newly revealed recognition specificity of α_Mβ₂ toward unfolded protein segments and cationic proteins and peptides suggests that α_Mβ₂ may serve as a previously proposed “alarmin” receptor with important roles in innate host defense.

The aim of this article was to study sound source localization by cochlear implant (CI) listeners with low-frequency (LF) acoustic hearing in both the operated ear and in the contralateral ear. Eight CI listeners had symmetrical LF acoustic hearing and 4 had asymmetrical LF acoustic hearing. The effects of two variables were assessed: (i) the symmetry of the LF thresholds in the two ears and (ii) the presence/absence of bilateral acoustic amplification. Stimuli consisted of low-pass, high-pass, and wideband noise bursts presented in the frontal horizontal plane. Localization accuracy was 23° of error for the symmetrical listeners and 76° of error for the asymmetrical listeners. The presence of a unilateral CI used in conjunction with bilateral LF acoustic hearing does not impair sound source localization accuracy, but amplification for acoustic hearing can be detrimental to sound source localization accuracy.