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.
Soccer is bar none, the most popular sport in the entire world. It is played, followed, and loved by virtually every single country on Earth. Despite this massive support for the sport which houses some of the world’s biggest names in the world, its shortcomings when dealing with issues of racial injustice and incidents of racist behavior have become more pronounced in recent years. Although this open discussion regarding racism within the sport has recently begun to sprout, its roots can be tied back to decades ago while continuing to the present day, with players, referees, coaches, fans, commentators, and more all involved on both sides of the issue. <br/> We found this topic to be most prevalent in today’s society after witnessing multiple shameful racist incidents that have occurred to some of the world’s biggest players throughout European football in 2019, as well as the recent ongoing fight for racial reform and increased awareness regarding racial injustice in the United States. By doing comprehensive research and analysis on such incidents that have occurred throughout the years we hope to raise more awareness regarding this subject that has plagued the beautiful game. In addition, we hope to offer ways to remedy the problem one step at a time, all while answering the tough, but necessary questions regarding what specifically should be done in the sport, that others have been afraid to talk about for far too long. Specifically, we wanted to mainly highlight the experience of black players, with a further discussion on other minority groups, in English and Italian football as these two leagues have been a part of the largest debate between how club traditions, player-fan interactions, league policies, and staff management have all affected the way we view the game as the endemic of racism within the sport is exacerbated.
My project examined the different types of parenting information parents and caregivers use. And how useful, accurate, accessible, and likely to use these types of parenting information are. I also examined these differences across SES to see if there were any variances.
Flora Vita is a digital platform that connects families to outdoor excursions, programmed activities and local events, encouraging the familial ecosystem to flourish within Arizona's vast environment. We curate unique opportunities that allow families to cultivate internal relationships with one another and form relationships with local like-minded families in pursuit of a healthy lifestyle.
Graduating from college is an important time of life transitions and career development for undergraduates and their future. Future self-identification, the connection between an individual’s current and future self, can negatively predict depression and utilize self-control as a mechanism to achieve later academic goals. Investigating an individual’s future self- identification, depression scores, and behavioral outcomes in the face of the COVID-19 pandemic can help optimize college graduate success in an uncertain world. The present study aimed to (1) determine if earlier future self-identification moderated the changes between later outcomes (e.g., depression, perceived alcohol consumption, and academic and career goals) from pre-COVID-19 to during COVID-19, (2) investigate if psychological resources (e.g., self-control and emotion regulation) had any intermediary effects between earlier future self-identification and later depression and behavioral outcomes during the pandemic, and (3) test for any moderation effects of future self-identification on the relationship between available psychological resources before COVID-19 and during COVID-19. The present research demonstrated that students with greater earlier future self-identification were less likely to change their academic and career goals and were less likely to experience symptoms of depression during the pandemic. Additionally, self-control was demonstrated as an intermediary factor between earlier future self-identification and later academic and career goal changes. These findings may help college graduates develop resilience in other stressful situations.
Within the pediatric hospitalization experience, fear and anxiety are two emotions commonly felt by children of all ages. Hospitalized children can greatly benefit from interventions designed to help them cope with these emotions throughout their medical experiences. This study draws on each of our clinical experiences as volunteers at Phoenix Children’s Hospital, and uses a qualitative analysis of three semi-structured interviews with currently employed Child Life Specialists to understand and analyze the use of medical play, a form of play intervention with a medical theme or medical equipment. We explore the goals and benefits of medical play for hospitalized pediatric patients, the process of using medical play as an intervention, including the activity design process, the assessments and adjustments made throughout the child’s hospitalization, and the considerations and limitations to implementing medical play activities. Ultimately, we found that the element of fun that defines play can be channeled into medical play activities implemented by skilled Child Life Specialists, who are experts in their field, in clinical settings to promote several different and beneficial goals, including pediatric patient coping.
Waste pickers are the victims of harsh economic and social factors that have hurt many developing countries and billions of people around the world. Due to the rise of industrialization since the 19th century, waste and disposable resources have been discarded around the world to provide more resources, products, and services to wealthy countries. This has put developing countries in a precarious position where people have had very few economic opportunities besides taking on the role of waste pickers, who not only face physical health consequences due to the work they do but also face exclusion from society due to the negative views of waste pickers. Many people view waste pickers as scavengers and people who survive off of doing dirty work, which creates tensions between waste pickers and others in society. This even leads to many countries outlawing waste picking and has led to the brutal treatment of waste pickers throughout the world and has even led to thousands of waste pickers being killed by anti-waste picker groups and law enforcement organizations in many countries. <br/> Waste pickers are often at the bottom of supply-chains as they take resources that have been used and discarded, and provide them to recyclers, waste management organizations, and others who are able to turn these resources into usable materials again. Waste pickers do not have many opportunities to rise above the situation they are in as waste picking has become the only option for many people who need to provide for themselves and their families. They are not compensated very well for the work they do, which also contributes to the situation where waste pickers are forced into a position of severe health risks, backlash from society and governments, not being able to seek better opportunities due to a lack of earning potential, and not being connected with end-users. Now is the time to create new business models that solve these large problems in our global society and create a sustainable way to ensure that waste pickers are treated properly around the world.
This study tested the effect of status threat on ingroup identification and examined identity concealability and stereotype endorsement as moderators of the relationship. Participants included a visible identity group (Asian men) and a concealable identity group (gay men). Participants were randomized into either a status threat condition, in which they read a vignette that reminded them of a negative stereotype about the target group and discussed positive stereotypes of the group as well, or a control condition that discussed positive stereotypes only. Participants then responded to a measure of ingroup identification and a measure of stereotype endorsement. A significant main effect of status threat on ingroup identification was found, such that participants in the status threat condition showed lower ingroup identification. The interaction of condition and concealability was not significant. The interaction of condition and stereotype endorsement was marginally significant, such that the main effect shows up stronger for those lower on stereotype endorsement. The main effect is interpreted as a potential protective strategy for self-esteem. The stereotype threat interaction is interpreted as a difference in the way that those who do and do not endorse the stereotype view the legitimacy of the status threat.