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.
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.
In 2002, after applying for government assistance in the state of Washington, Lydia Fairchild was told that her two children were not a genetic match with her and that therefore, biologically, she could not be their mother. Researchers later determined that the genetic mismatch was due to chimerism, a condition in which two genetically distinct cell lines are present in one body. The state accused Fairchild of fraud and filed a lawsuit against her. Following evidence from another case of chimerism documented in The New England Journal of Medicine in a woman named Karen Keegan, Fairchild was able to secure legal counsel and establish evidence of her biological maternity. A cervical swab eventually revealed Fairchild’s second distinct cell line, showing that she had not genetically matched her children because she was a chimera. Fairchild’s case was one of the first public accounts of chimerism and has been used as an example in subsequent discussions about the validity and reliability of DNA evidence in legal proceedings within the United States.
In December 2011, the Stillbirth Collaborative Research Network, or SCRN, published the article “Causes of Death Among Stillbirths” in The Journal of the American Medical Association. The authors of the article investigate the causes of stillbirth and possible reasons for the racial, ethnic, and geographic disparities in stillbirth rates. According to the Centers for Disease Control and Prevention, or CDC, stillbirth is the death of a fetus at twenty or more weeks during pregnancy. “Causes of Death Among Stillbirths” explores the common causes of stillbirth in different racial and ethnic groups, and provides a framework for future research into medical interventions to help reduce racial and ethnic stillbirth disparity.
In 2007, Françoise Baylis and Jason Scott Robert published “Part-Human Chimeras: Worrying the Facts, Probing the Ethics” in The American Journal of Bioethics. Within their article, hereafter “Part-Human Chimeras,” the authors offer corrections on “Thinking About the Human Neuron Mouse,” a report published in The American Journal of Bioethics in 2007 by Henry Greely, Mildred K. Cho, Linda F. Hogle, and Debra M. Satz, which discussed the debate on the ethics of creating part-human chimeras. Chimeras are organisms that contain two or more genetically distinct cell lines. Both publications discuss chimeras with DNA from different species, specifically in response to studies in which scientists injected human brain cells into mice. “Part-Human Chimeras,” contributes to a chain of ethical and scientific discussion that occurred in the mid-2000s on whether people should be able to conduct research on chimeras, especially in embryos.
In April 1994, Elizabeth Raymond, Sven Cnattingius, and John Kiely published “Effects of Maternal Age, Parity, and Smoking on the Risk of Stillbirth” in the British Journal of Obstetrics and Gynecology, now known as BJOG: An International Journal of Obstetrics and Gynecology. The article examines how advanced maternal age, defined as delivery at thirty-five years old or older, cigarette smoking, and nulliparity, or the state of never having given birth, can negatively impact pregnancy. At the time of publication, according to Raymond and colleagues, stillbirths comprised over half of all perinatal, or close to birth, deaths and more than one-third of total fetal and infant deaths in Europe and North America. In the article, Raymond and her coauthors demonstrate how certain risk factors may increase the risk of stillbirth at different stages of pregnancy, which helped set a foundation for future research in interventions to prevent stillbirth.
In 2006, bioethicist Jason Scott Robert published “The Science and Ethics of Making Part-Human Animals in Stem Cell Biology” in The FASEB Journal. There, he reviews the scientific and ethical justifications and restrictions on creating part-human animals. Robert describes part-human animals, otherwise known as chimeras, as those resulting from the intentional combination of human and nonhuman cells, tissues, or organs at any stage of development. He specifically criticizes restrictions against creating part-human animals made by the National Academy of Sciences, or NAS, in 2005, arguing that while they ensure that such research is morally justifiable, they might limit scientists from conducting useful science using part-human animals or entities. Robert challenges the moral rationales behind prohibiting chimera research, arguing that they may impede scientists from conducting research that could have important benefits to biology and medicine, and suggests how to balance the conflicting moral and scientific needs of such science.
Scientist Franz Max Albert Kramer worked as a psychiatrist in Poland and the Netherlands in the early twentieth century and is known for his contributions to research on psychological conditions that experts call hyperkinetic syndromes. Children with hyperkinetic syndromes display inattention, overactivity, and impulsivity. Along with scientist Hans Pollnow, Kramer defined a specific kind of hyperkinetic syndrome based on an initial case study of seventeen children, initially known as Kramer-Pollnow Syndrome. In 1980, the third edition of the Diagnostic and Statistical Manual of Mental Disorders, or DSM-III, renamed Kramer-Pollnow syndrome to be attention deficit disorder, or ADD. A later revision, in 1987, renamed it attention deficit hyperactivity disorder, or ADHD. Kramer advanced child psychiatry research by laying the groundwork for further research on and understanding of what experts call, as of 2021, ADHD.