ASU Scholarship Showcase

This study dealt with emotional responses elicited by certain products, which helped to understand the attributes of the product leading to emotional responses. Emotional Design is a way of design that is using emotions generated by people as reference and measurement. Making good use of emotional design could let the user discover resonance in the interaction between user and product, which could help the product to be more attractive to users. This research proposes to apply qualitative research method to uncover the secrets of emotional bonds between users and products This study also offered an useful tool to examine the strength and weakness of a certain product from perspective of emotion, and the insights could help designers to refine the product to become emotional attractive, thus create better user experience and bigger opportunity for the product on the market in the future.

High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.

Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies.

The image of “Shostakovich” and the relationships surrounding it in the West during the Cold War can be viewed from several angles. Selected Cold War encounters between the United States and the Soviet Union involving Shostakovich’s music—especially the 1959 New York Philharmonic tour to the USSR—offer insight into three perspectives on Shostakovich symphonies in the Cold War: (1) the direct, (2) the implicit, and (3) the micro/intimate. This heuristic hones our understanding of the various types of relationships cultivated with music during the Cold War, while also widening the discussion of Shostakovich’s symbolic presentation during the conflict.

An urban forest assessment is essential for developing a baseline from which to measure changes and trends. The most precise way to assess urban forests is to measure and record every tree on a site, but although this may work well for relatively small populations (e.g., street trees, small parks), it is prohibitively expensive for large tree populations. Thus, random sampling offers a cost-effective way to assess urban forest structure and the associated ecosystem services for large-scale assessments. The methodology applied to assess ecosystem services in this study can also be used to assess the ecosystem services provided by vacant land in other urban contexts and improve urban forest policies, planning, and the management of vacant land. The study’s findings support the inclusion of trees on vacant land and contribute to a new vision of vacant land as a valuable ecological resource by demonstrating how green infrastructure can be used to enhance ecosystem health and promote a better quality of life for city residents.

Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays.

Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot.

Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA.

Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.

Communicating climate risks is crucial when engaging the public to support climate action planning and addressing climate justice. How does evidence-based communication influence local residents’ risk perception and potential behavior change in support of climate planning? Built upon our previous study of Climate Justice maps illustrating high scores of both social and ecological vulnerability in Michigan’s Huron River watershed, USA, a quasi-experiment was conducted to examine the effects of Climate Justice mapping intervention on residents’ perceptions and preparedness for climate change associated hazards in Michigan. Two groups were compared: residents in Climate Justice areas with high social and ecological vulnerability scores in the watershed (n=76) and residents in comparison areas in Michigan (n=69). Measurements for risk perception include perceived exposure, sensitivity, and adaptability to hazards. Results indicate that risk information has a significant effect on perceived sensitivity and level of preparedness for future climate extremes among participants living in Climate Justice areas. Findings highlight the value of integrating scientific risk assessment information in risk communication to align calculated and perceived risks. This study suggests effective risk communication can influence local support of climate action plans and implementation of strategies that address climate justice and achieve social sustainability in local communities.

Sera from patients with ovarian cancer contain autoantibodies (AAb) to tumor-derived proteins that are potential biomarkers for early detection. To detect AAb, we probed high-density programmable protein microarrays (NAPPA) expressing 5177 candidate tumor antigens with sera from patients with serous ovarian cancer (n = 34 cases/30 controls) and measured bound IgG. Of these, 741 antigens were selected and probed with an independent set of ovarian cancer sera (n = 60 cases/60 controls). Twelve potential autoantigens were identified with sensitivities ranging from 13 to 22% at >93% specificity. These were retested using a Luminex bead array using 60 cases and 60 controls, with sensitivities ranging from 0 to 31.7% at 95% specificity. Three AAb (p53, PTPRA, and PTGFR) had area under the curve (AUC) levels >60% (p < 0.01), with the partial AUC (SPAUC) over 5 times greater than for a nondiscriminating test (p < 0.01). Using a panel of the top three AAb (p53, PTPRA, and PTGFR), if at least two AAb were positive, then the sensitivity was 23.3% at 98.3% specificity. AAb to at least one of these top three antigens were also detected in 7/20 sera (35%) of patients with low CA 125 levels and 0/15 controls. AAb to p53, PTPRA, and PTGFR are potential biomarkers for the early detection of ovarian cancer.

To address the need to study frozen clinical specimens using next-generation RNA, DNA, chromatin immunoprecipitation (ChIP) sequencing and protein analyses, we developed a biobank work flow to prospectively collect biospecimens from patients with renal cell carcinoma (RCC). We describe our standard operating procedures and work flow to annotate pathologic results and clinical outcomes. We report quality control outcomes and nucleic acid yields of our RCC submissions (N=16) to The Cancer Genome Atlas (TCGA) project, as well as newer discovery platforms, by describing mass spectrometry analysis of albumin oxidation in plasma and 6 ChIP sequencing libraries generated from nephrectomy specimens after histone H3 lysine 36 trimethylation (H3K36me3) immunoprecipitation. From June 1, 2010, through January 1, 2013, we enrolled 328 patients with RCC. Our mean (SD) TCGA RNA integrity numbers (RINs) were 8.1 (0.8) for papillary RCC, with a 12.5% overall rate of sample disqualification for RIN <7. Banked plasma had significantly less albumin oxidation (by mass spectrometry analysis) than plasma kept at 25°C (P<.001). For ChIP sequencing, the FastQC score for average read quality was at least 30 for 91% to 95% of paired-end reads. In parallel, we analyzed frozen tissue by RNA sequencing; after genome alignment, only 0.2% to 0.4% of total reads failed the default quality check steps of Bowtie2, which was comparable to the disqualification ratio (0.1%) of the 786-O RCC cell line that was prepared under optimal RNA isolation conditions. The overall correlation coefficients for gene expression between Mayo Clinic vs TCGA tissues ranged from 0.75 to 0.82. These data support the generation of high-quality nucleic acids for genomic analyses from banked RCC. Importantly, the protocol does not interfere with routine clinical care. Collections over defined time points during disease treatment further enhance collaborative efforts to integrate genomic information with outcomes.

This study reviews scholarly papers and case studies on urban vacant land to gain a stronger understanding of its public value in terms of the ecological and social benefits it can bring. This literature review offers a conceptual overview of the potential benefits of vacant land with the goal of addressing gaps in knowledge about vacant land and to provide suggestions to planners and designers on how vacant properties can be integrated with other green infrastructure in cities. There are many opportunities to redevelop vacant land to enhance its ecological and social value, and many design professionals and scholars are becoming interested in finding new ways to exploit this potential, especially with regard to planning and design. A better appreciation of the public value of urban vacant land is vital for any effort to identify alternative strategies to optimize the way these spaces are utilized for both short-term and long-term uses to support urban regeneration and renewal. This study will help planners and designers to understand and plan for urban vacant land, leading to better utilization of these spaces and opening up alternative creative approaches to envisioning space and landscape design in our urban environments.