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 study was designed to learn what students call various forms of cannabis. A survey was created with questions designed to understand students' knowledge of types of cannabis, methods of use, and potency. An introduction and methods section of the research paper is included.
Appearance ideals are standards of beauty imposed by a culture or society, that are unrealistic and impossible to achieve. Research documents the existence of three appearance ideals, thin, muscular and hourglass ideals. The thin ideal is the pursuit of a very thin and low body weight. The muscular ideal is the pursuit of a toned and fit body. The hourglass ideal is the pursuit of a shapely body with bigger breasts and hips/buttocks than waist. These ideals are associated with disordered eating. However, no current study has examined the prevalence of all three ideals, or how the combination of ideals relates to dietary restraint, one example of a disordered eating behavior. This study was conducted on 505 undergraduate women at Arizona State University, who were completing research credit for a psychology course. The women participated in an online survey that assessed their demographics, each ideal, and dietary restraint. Results show that all combinations of ideals exist. Specifically, 41.5% of the sample endorse high levels of all three ideals, while 12.5% report thin and muscular ideals, 9.5% report thin and hourglass ideals, 9.9% report hourglass and muscular ideals, 8.4% report low levels of all three ideals, 6.4% report muscular ideal only, 6.4% report hourglass ideal only, and 5.6% report thin ideal only. Endorsing more than one ideal significantly associated with dietary restraint. Findings fulfill an important gap in the literature, suggest future directions for research, and have important clinical implications.
The present study examined Mexican American females’ perspectives on childbearing and marriage and the role of cultural influences on their perspectives given high rates of pregnancy and early marriage among Mexican and Mexican American females in the U.S. and worldwide. Participants were ten Mexican American females between 20 and 22 years of age who participated in qualitative interviews about their perspectives on marriage and childbearing and how their Mexican cultural background, including their upbringing, family members, peers, and the media influenced their perspectives. Findings highlight that there is indeed a connection between Mexican culture and perspectives on marriage and childbearing amongst participants, and participants particularly noted the role of female family members, stereotypes, and educational pursuits in shaping their perspectives.
The coronavirus pandemic has proven to be a challenging time for the Hispanic community, facing impacts on stress and depression symptoms at disproportionate rates. The current study examined the associations between socioeconomic COVID stressors and depression symptoms; and coping styles, including problem-focused and emotion-focused coping, and depression symptoms amongst Mexican heritage parents. Coping styles were also examined as a moderator of the association between socioeconomic COVID stressors and depression symptoms
Appearance-related peer victimization has been shown to have strong social, health, and economic consequences on victims. Low body satisfaction has also been associated with higher appearance-related peer victimization prevalence. Preadolescent children are particularly vulnerable to the exposure and effects of appearance-related peer victimization. Research shows gender minorities have been particularly at risk for peer victimization. More studies are needed to adequately capture the appearance-related peer victimization experiences of gender minorities within this vulnerable age group. The current study aimed to explore the prevalence rate of appearance-related peer victimization and associated variables across gender certain and uncertain preadolescents residing in the United States. 5354 children between the ages of 8 and 13 participated in this cross-sectional study. Gender groups were categorized as certain (children reported identifying as boy or girl) and uncertain (children reported being unsure of their gender or other). The sample was racially and ethnically diverse. A two-tailed independent samples t-test was performed for each variable to examine mean differences across gender certain and uncertain groups. Key findings revealed significant mean differences in appearance-related peer victimization [t(139) = 3.21, p < .001, d =.36], body satisfaction [t(211) = 6.32, p <.001, d = .55], body esteem [ t(5352) = 10.77, p = <.001, d = .71], and self-esteem [t(231) = 9.25, p = <.001, d = .73] such that gender uncertain children reported higher mean levels of appearance-related peer victimization; gender uncertain children also reported lower levels of body satisfaction, body esteem, and self-esteem. A correlational analysis indicated that as peer victimization frequency increased all children reported lower body satisfaction, body esteem, and general self-esteem. Body satisfaction and general self-esteem were more strongly positively correlated among gender uncertain children versus gender certain children. However, gender certain children reported stronger positive associations between body esteem and general self-esteem in comparison with gender uncertain children. Gender uncertain children report higher rates of appearance-related peer victimization and lower body satisfaction. Additional studies are needed to replicate and expand research on the appearance-related peer victimization experiences of preadolescent gender minority children and the related effects to body satisfaction.