Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide promising ways for addressing key scientific questions.
Results
We develop a set of computational methods and open source tools for identifying co-expressed embryonic domains and the associated genes simultaneously. To map the expression patterns of many genes into the same coordinate space and account for the embryonic shape variations, we develop a mesh generation method to deform a meshed generic ellipse to each individual embryo. We then develop a co-clustering formulation to cluster the genes and the mesh elements, thereby identifying co-expressed embryonic domains and the associated genes simultaneously. Experimental results indicate that the gene and mesh co-clusters can be correlated to key developmental events during the stages of embryogenesis we study. The open source software tool has been made available at http://compbio.cs.odu.edu/fly/.
Conclusions
Our mesh generation and machine learning methods and tools improve upon the flexibility, ease-of-use and accuracy of existing methods.
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Fruit fly embryogenesis is one of the best understood animal development systems, and the spatiotemporal gene expression dynamics in this process are captured by digital images. Analysis of these high-throughput images will provide novel insights into the functions, interactions, and networks of animal genes governing development. To facilitate comparative analysis, web-based interfaces have been developed to conduct image retrieval based on body part keywords and images. Currently, the keyword annotation of spatiotemporal gene expression patterns is conducted manually. However, this manual practice does not scale with the continuously expanding collection of images. In addition, existing image retrieval systems based on the expression patterns may be made more accurate using keywords.
Results
In this article, we adapt advanced data mining and computer vision techniques to address the key challenges in annotating and retrieving fruit fly gene expression pattern images. To boost the performance of image annotation and retrieval, we propose representations integrating spatial information and sparse features, overcoming the limitations of prior schemes.
Conclusions
We perform systematic experimental studies to evaluate the proposed schemes in comparison with current methods. Experimental results indicate that the integration of spatial information and sparse features lead to consistent performance improvement in image annotation, while for the task of retrieval, sparse features alone yields better results.
Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment on the pace of biological discovery. It is thus imperative to design an automated system for efficient image annotation and comparison.
Results
We present a computational framework to perform anatomical keywords annotation for Drosophila gene expression images. The spatial sparse coding approach is used to represent local patches of images in comparison with the well-known bag-of-words (BoW) method. Three pooling functions including max pooling, average pooling and Sqrt (square root of mean squared statistics) pooling are employed to transform the sparse codes to image features. Based on the constructed features, we develop both an image-level scheme and a group-level scheme to tackle the key challenges in annotating Drosophila gene expression pattern images automatically. To deal with the imbalanced data distribution inherent in image annotation tasks, the undersampling method is applied together with majority vote. Results on Drosophila embryonic expression pattern images verify the efficacy of our approach.
Conclusion
In our experiment, the three pooling functions perform comparably well in feature dimension reduction. The undersampling with majority vote is shown to be effective in tackling the problem of imbalanced data. Moreover, combining sparse coding and image-level scheme leads to consistent performance improvement in keywords annotation.
The right to cast a meaningful vote, equal in value to other votes, is a fundamental tenet US elections. Despite the 1964 Supreme Court decision formally establishing the one person, one vote principle as a legal requirement of elections, our democracy consistently falls short of it. With mechanisms including the winner-take-all format in the Electoral College, disproportioned geographic allocation of senators, extreme partisan gerrymandering in the House of Representatives, and first-past-the-post elections, many voters experience severe vote dilution. <br/><br/>In order to legitimize our democratic structures, American elections should be reformed so every person’s vote has equal weight, ensuring that the election outcomes reflect the will of the people. Altering the current election structure to include more proportional structures including rank choice voting and population-based representation, will result in a democracy more compatible with the one person, one vote principle.
An in depth look at the rhetoric behind the campus carry debate at the University of Texas at Austin. This thesis researched and examined primary sources from The Daily Texan and The Austin-American Statesman attempting to analyze what was at stake for both sides of the argument and what the most effective rhetorical tool was.
Americans today face an age of information overload. With the evolution of Media 3.0, the internet, and the rise of Media 3.5—i.e., social media—relatively new communication technologies present pressing challenges for the First Amendment in American society. Twentieth century law defined freedom of expression, but in an information-limited world. By contrast, the twenty-first century is seeing the emergence of a world that is overloaded with information, largely shaped by an “unintentional press”—social media. Americans today rely on just a small concentration of private technology powerhouses exercising both economic and social influence over American society. This raises questions about censorship, access, and misinformation. While the First Amendment protects speech from government censorship only, First Amendment ideology is largely ingrained across American culture, including on social media. Technological advances arguably have made entry into the marketplace of ideas—a fundamental First Amendment doctrine—more accessible, but also more problematic for the average American, increasing his/her potential exposure to misinformation. <br/><br/>This thesis uses political and judicial frameworks to evaluate modern misinformation trends, social media platforms and current misinformation efforts, against the background of two misinformation accelerants in 2020, the COVID-19 pandemic and U.S. presidential election. Throughout history, times of hardship and intense fear have contributed to the shaping of First Amendment jurisprudence. Thus, this thesis looks at how fear can intensify the spread of misinformation and influence free speech values. Extensive research was conducted to provide the historical context behind relevant modern literature. This thesis then concludes with three solutions to misinformation that are supported by critical American free speech theory.
Partisan politics has created an increasingly polarized political climate in the United States. Despite the divisive political climate, women’s representation in politics has also increased drastically over the years. I began this project to see if there is a partisan rivalry between women in politics or a sense of shared “womanhood.” This thesis explores the role political parties play for women in office by examining how they vote on bills, what type of bills they propose, and whether or not they work collaboratively with their female counterparts at the Arizona State Legislature. My main goals for this project are to see how strong or weak political parties are in shaping political behavior at the Arizona State Legislature and to determine if there is a sense of “womanhood” despite different political affiliations. I also explore the role party affiliation plays within women legislators at the Arizona State Legislature.
In an effort to address the lack of literature in on-campus active travel, this study aims to investigate the following primary questions:<br/>• What are the modes that students use to travel on campus?<br/>• What are the motivations that underlie the mode choice of students on campus?<br/>My first stage of research involved a series of qualitative investigations. I held one-on-one virtual interviews with students in which I asked them questions about the mode they use and why they feel that their chosen mode works best for them. These interviews served two functions. First, they provided me with insight into the various motivations underlying student mode choice. Second, they provided me with an indication of what explanatory variables should be included in a model of mode choice on campus.<br/>The first half of the research project informed a quantitative survey that was released via the Honors Digest to attract student respondents. Data was gathered on travel behavior as well as relevant explanatory variables.<br/>My analysis involved developing a logit model to predict student mode choice on campus and presenting the model estimation in conjunction with a discussion of student travel motivations based on the qualitative interviews. I use this information to make a recommendation on how campus infrastructure could be modified to better support the needs of the student population.
This research analyzes lesbian, gay, bisexual, transgender, and queer/ questioning (LGBTQ) students’ experiences with sex education in Arizona. This research is a grey literature review of Arizona’s previous state policies, current state sex education curricula law, and legislative proposals within the past few years. Analysis focuses on changes after the repeal of the “no promo homo” law in 2019. Through defining the differences between abstinence only and comprehensive sex education (CSE), this will provide a framework to better understand approaches to sex education. As of now, Arizona stresses abstinence-based education. Delving into LGBTQ students’ general experiences in schools provides a foundation to better understand why these students especially benefit from CSE. Since LGBTQ students are disproportionately affected by bullying and are at increased sexual health risks, it is important to address misperceptions surrounding the LGBTQ community. The purpose of this research is to push for more LGBTQ inclusive sex education curricula in Arizona.
This podcast highlights the voices of organizers and activists across the nation. Representatives from various organizations and individual activists provide their experiences in working within reproductive health activist spaces. By listening to their stories and expertise, the hope is for listeners to center Reproductive Justice as a point of view. The goal is to encourage the audience to join an organization, support their local organizations, or at the very least, learn about resources provided to them by local and national organizations.