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.
This analysis explores the mirrored formats of scientific research and reality television from an interdisciplinary perspective. By dissecting the four “layers” of reality television and their contributions to authenticity or inauthenticity, it becomes clear that reality television is more pseudoscientific than anything. Textual analysis, in the form of the reality shows, is paired with scholarship on the material to present this argument.
An entire decade of films that emerged from the Hollywood system during the blockbuster era of the 1980s is often summed up as one marked by a “curious and disturbing phenomenon of children’s films conceived and marketed largely for adults — films that construct the adult spectator as a child, or, more precisely, as a childish adult, an adult who would like to be a child.” If it is possible, as film theorist Siegfried Kracauer proposed, that “in recording the visible world — whether current reality or an imaginary universe — films … provide clues to hidden mental processes,” what are we to deduce about the mental processes of the American public who would pay to sit in a movie theater and watch Raiders of the Lost Ark (1981) or Rambo: First Blood (1982) for multiple viewings? In addressing this questions it may be helpful to turn again to Krakauer, who reminds us that a box office “hit may cater only to one of many co-existing [mass] demands, and not even a very specific one,” and that even if one could draw conclusions about the “peculiar mentality of a nation” by analyzing the “pictorial and narrative motifs” of box office hits, this “by no means implies a fixed national character.” This is a key insight because it implies a diverse national character composed of mass demands that remain unmet by the “children’s films” produced for adults which remain emblematic of Hollywood during the 1980s. In this thesis, I argue that the mainstream Hollywood film Beverly Hills Cop contradicts this notion because it employs sophisticated strategies to work as resistance against the dominant American cultural ideologies of the mid-1980s. I briefly contextualize the film in its historical and cultural setting. Then, I analyze three narrative aspects of the film. First, I begin with the various interactions Eddie Murphy’s character Axel Foley has with several “gatekeepers” throughout the film. Next, I analyze a scene in which Foley is assaulted by Sgt. Taggart of the Beverly Hills Police Department. Finally, I analyze Foley’s relationships with the supporting characters Mikey and Jenny. Beverly Hills Cop is one of the most popular and successful American films of the 1980s. Its subversiveness suggests the possibility that a host of other popular films from the decade are similarly sophisticated. This points to the need for a reexamination of a decade of American cinema that has been cast as “children’s films conceived and marketed largely for adults.”
Influencer culture has, within the last few decades, evolved into a distinguishable subset of social media, as well as the entertainment and business worlds. This project seeks to highlight core aspects of what makes an influencer and what distinguishes the role from traditional celebrities through the experience and thoughts of Hannah Palmer, an influencer most popular on Instagram in the fashion and lifestyle market. Using her as a case study, this project seeks to analyze how Hannah exists in the culture and the unique approach to the culture that she takes. The core concepts Hannah interacts with, as most influencers do, include self-branding, parasocial relationships and communication, the concept of authenticity, the role of labor (both aspirational and invisible), and gender dynamics of the entertainment industry.
With a record-breaking number of anti-trans laws being proposed and passed in the several years, it is important to understand how news media are framing them. This study is a content analysis of news media representations of transgender people in sports in Arizona, with a focus on understanding how the news articles are constructed and what claims are being made within them. The purpose of this research is to investigate how the news media reflects and shapes the emerging debate about transgender inclusion in sports. The study uses a mixed-methods approach, combining quantitative and qualitative content analysis of news articles from major newspapers in Arizona. The results indicate that the majority of news articles were positive or neutral in nature regarding transgender inclusion in sports when reporting on the introduction of anti-trans bills in Arizona. This suggests that the media is not agreeing with the anti-trans legislation. The analysis also reveals the lack of transgender voices included in news articles related to anti-trans sports bans. This research highlights the need for responsible and accurate reporting in the media, particularly in shaping public opinion about policies related to transgender individuals in sports. It also emphasizes the importance of creating inclusive and supportive environments for transgender youth in sports.
I will argue that Fletcher as a queer female musician is less focused on physical beauty, but instead is more focused on inner beauty and the character of women instead. I will begin with defining beauty in its many forms and how this industry and market has grown in recent years through a review of the current literature in the applicable fields of study. The other side of this endeavor will be a review of selected song lyrics and an analysis of how they describe feminine beauty. This will demonstrate that queer women view and describe women differently- and in a more positive and humanizing manner.