Matching Items (81)
Description
Background
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.
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.
ContributorsZhang, Wenlu (Author) / Feng, Daming (Author) / Li, Rongjian (Author) / Chernikov, Andrey (Author) / Chrisochoides, Nikos (Author) / Osgood, Christopher (Author) / Konikoff, Charlotte (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ji, Shuiwang (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2013-12-28
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval
Description
Background
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.
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.
ContributorsYuan, Lei (Author) / Woodard, Alexander (Author) / Ji, Shuiwang (Author) / Jiang, Yuan (Author) / Zhou, Zhi-Hua (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / Ira A. Fulton School of Engineering (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor)
Created2012-05-23
Description
Background
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.
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.
ContributorsSun, Qian (Author) / Muckatira, Sherin (Author) / Yuan, Lei (Author) / Ji, Shuiwang (Author) / Newfeld, Stuart (Author) / Kumar, Sudhir (Author) / Ye, Jieping (Author) / Biodesign Institute (Contributor) / Center for Evolution and Medicine (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Ira A. Fulton School of Engineering (Contributor)
Created2013-12-03
Description
The purpose of this study is to better understand factors that may contribute to the changes in physical activity from high school to college. Using questions based on the social cognitive theory, intra and interpersonal factors that affect being and/or remaining physically active, as well as those that can help encourage students to participate in the future will be identified, hopefully generating a positive domino effect for future generations when they transition from high school to college. 20 minute zoom interviews were conducted with participants and responses were analyzed and placed into one of three categories: social, personal, or behavioral. Overall, we found that physical activity by students in college was performed as an intentional health-related activity, whereas physical activity by those same students in high school was performed for enjoyment and social purposes. So, this means we must change the stigma about physical activity as people become older, and adults must rediscover why they participated in physical activity when they were younger. Relating more to another theory rather than social cognitive theory, self-determination theory, supports that adults must find personal motivation and enjoyment in physical activity again in order to increase participation.
ContributorsKupitz, Kendall (Author) / Montalvo, Alicia (Thesis director) / Holzapfel, Simon (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)
Created2023-05
Description
Why aren’t people with disabilities readily accepted into all aspects of the community and society? What are we missing out on?
Even though inclusion is a civil right, people with disabilities are commonly discriminated against and excluded in all different aspects of society. We as a community are not affording individuals with disabilities the opportunity to feel that they fully belong and have a purpose. Everyone deserves a chance to be understood and included, no matter the misconceptions or circumstances. The inclusion of people with disabilities affects all people. When we, as a community, readily accept and include individuals with disabilities, we all learn to value people’s differences and learn to see what each person has to offer.
For my creative project, I conducted a 4-week virtual speakers series on disability and inclusion. Over the course of four weeks in September 2022 I hosted a virtual speakers series with a new speaker each week focusing on different topics. Topics discussed included self-advocacy, research on inclusion and early childhood development, inclusive sports, and IEP advocacy and inclusive education.
My goal within this project and for society as a whole is for people with disabilities to be accepted and included without having to fight for it. People are afraid of what they don't know. If people with disabilities were more commonly included in the community, the fear would dissipate. People with disabilities would just be teammates, peers, and fellow employees. It would be a natural authentic everyday occurrence. I hope that society can work together to treat everyone the way they deserve to be treated.
ContributorsMaestretti, Tegan (Author) / Holzapfel, Simon (Thesis director) / Puruhito, Krista (Committee member) / Barrett, The Honors College (Contributor) / College of Health Solutions (Contributor)
Created2022-12
Description
The genetic disorder Down syndrome (DS), clinically known as Trisomy 21, is characterized by the presence of either a part or full extra copy of chromosome 21. When compared with children of typical development, children with DS consistently score lower on gross motor skill tasks. Balance specifically is one of the hardest skills for individuals with DS (especially
children) to acquire, and neglecting to train balance early on can predispose individuals with DS to further movement instabilities, injuries, social struggles from activity limitations, and an overall lack of independence. One of the more unique forms of physical activity that requires a large amount of both static and dynamic balance is ballet. Dance-specific therapy has been shown to improve gross motor control functioning and specifically balance in a variety of populations with neuromuscular condions, but the research around ballet-specific therapy for those with DS is lacking. The purpose of this pilot study was to further investigate the effects of ballet-specific training on balance ability and general motor functioning in young students with DS as measured by the Four Square Step Test (FSST), Pediatric Balance Scale (PBS), and the gross and fine motor domains of the Vineland Adaptive Behavior Scale lll (VABS lll). It was hypothesized that participation in the 6-week summer cohort of Ballet Arizona’s Adaptive Dance Program would lead to improved scores on the PBS and VABS lll and decreased test times in the FSST. Improvements were observed for all measures for both participants (sample size n=2), except for P1's FSST, which increased in post-testing by 2.25s. Due to the study design, no conclusive statements can be made about whether the ballet program was responsible for the improvements observed in post-testing. More rigorous research with larger sample sizes (>30) is warranted to more fully understand the impact of an adapted ballet program on the balance ability of young individuals with DS. However, the program is still recommended for young individuals with DS because of the benefits it provides outside of motor skill development.
ContributorsMitrovic, Jelena (Author) / Peterson, Daniel (Thesis director) / Holzapfel, Simon (Committee member) / Barrett, The Honors College (Contributor) / College of Health Solutions (Contributor)
Created2022-12
Description
The purpose of this study, originally, was to contribute to the completion of a meta-analysis conducted by Mara Wierstra from the University of Virginia. Wierstra had requested individual participant data from two separate studies conducted in our lab: "Acute bouts of assisted cycling improves cognitive and upper extremity movement functions in adolescents with Down syndrome" and "Assisted Cycling Therapy (ACT) improves inhibition in adolescents with autism spectrum disorder." From the data requested, the participants were required to complete three separate tests (i.e., Tower of London, Trail Making Task and the Stroop Test). After compiling the data and sending it to her, we decided to conduct a small meta-analysis of our own, drawing connecting conclusions from the data from the two studies. We concluded that observationally our data suggest an advantage for ACT over voluntary cycling and no cycling across two separate populations (i.e., Autism Spectrum Disorder and Down syndrome), and across different measures of executive function (i.e., Stroop Test, Trail Making Test, and Tower of London). The data suggest that the ACT interventions may promote the upregulation of neurotropic factors leading to neurogenesis in the prefrontal cortex of the brain.
ContributorsParker, Cade Joseph (Author) / Ringenbach, Shannon (Thesis director) / Holzapfel, Simon (Committee member) / School of Nutrition and Health Promotion (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The Walter Cronkite School of Journalism and Mass Communications stands as a "gold standard" of journalism education throughout the country. In my time at the school though, I found that some aspects in the whole of the curriculum were missing. I as well as several other friends became interested in production and the technical side of things. This seemed to be the direction we wanted to go and soon realized this played a crucial part in journalism. Although there is a studio production class and a studio production track through the immersive Cronkite News program, there is not much in between. This inspired me to take a look deeper into production skills and their place within a journalism education. The project is split into three main sections that dive into the ideas of teaching production skills and technical skills to journalism students and whether or not it is valuable. The first part is the background of the project and why this project came to be. The background section explores the inspiration for the project. The project continues with a look at job statistics and where the industry currently sits. This continues into the final section that contains personal stories and interviews with professionals in the field. This is a critical section to back up claims made through research and evaluation. There is a lot of personal experience and non-traditional research done through this project, but the assertions and conclusions made are clear. Through job statistics, personal stories, and interviews with professionals, this project examines how production could be taught in a traditional journalism program. These stories show that a journalism curriculum may not be the best place to teach production in depth, but that it still is an incredibly important part of the journalism world as a whole.
ContributorsHardy, Joseph Michael (Author) / Jacoby, Jim (Thesis director) / McJannet, Rob (Committee member) / College of Public Service and Community Solutions (Contributor) / Walter Cronkite School of Journalism and Mass Communication (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The Chinese tourism market has become the largest tourism market in the world and continues to show promise in its future development. Global destinations such as Southeast Asia, France and now Australia have begun to see a major boom in Chinese tourists within the past decade due to less restrictive travel policies, a growing economy and higher disposable income rates within urban centers in China. Australia has become the top destination among Chinese citizens that wish to travel due to its coastal and beach attractions, unique wildlife, and general welcoming attitude toward Chinese citizens. As the market continues to grow, the characteristics and demographics change as well. The Chinese government did not allow for international travel until the early 1990s. During this time, package tours offered by government-regulated travel agencies were the prominent method of travel planning with travelers over the age of 35 making up the majority of travelers. However, in the past decade there has been a shift from group travel toward independent travel due to higher income and more independence among young adults. There remains a stigma against Chinese tourists due to behavioral and cultural challenges Chinese tourists face when traveling abroad, but as Chinese travelers begin to travel in smaller groups and have greater exposure to international cultures, these negative stereotypes will start to disappear. This paper focuses on the impact the Chinese tourism market has on Cairns, Australia. Cairns is characterized by its backpacking culture, easy access to environmental attractions and a high number of annual travelers from Asia and China specifically. The paper uses qualitative research and compiles information from news sources, government documents and statistical data regarding Chinese outbound tourism and its impacts on Australian tourism. There is also a case study composed of personal observations of a nature park in North Queensland which uses specific marketing and attraction coordination to appeal to Chinese tourists. This case study analyzes the tactics used by local destinations that cater to group travel over independent travel and points out the benefits of this type of specialized tourism. The research concludes by arguing the trend toward independent travel is beneficial to the Cairns tourism industry rather than harmful as long as the industry recognizes the new trends in Chinese tourism and does not focus on the previous trends of group travel when appealing to Chinese tourists. Instead, the industry should continue to focus on the backpacking culture and work toward catering to the demands of millennial travelers.
ContributorsRochon, Jacob Henri (Author) / Goodman, Rebekka (Thesis director) / McWilliams, Claire (Committee member) / College of Public Service and Community Solutions (Contributor) / School of Politics and Global Studies (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Lower extremity function is vital for activities of daily living especially in stroke survivors. An innovative way to improve lower extremity function may be Assisted Cycle Therapy. This is among the first studies to examine ACT in stroke survivors. Twenty-three participants post-stroke performed ACT, VC and NC and pre and post measures of lower extremity function were conducted with the Lower Extremity Motor Coordination Test (LEMOCOT). The results showed that the non-paretic lower extremity improved its function after ACT, but not after VC or NC. Lower extremity function in the paretic leg improved after ACT and VC, but not after NC. These results suggest that ACT resulted in increased production of BDNF in the motor cortex which resulted in improvements in global motor function.
ContributorsSzeto, Monica (Author) / Ringenbach, Shannon (Thesis director) / Holzapfel, Simon (Committee member) / Barrett, The Honors College (Contributor)
Created2016-12