Multi-source ontology-based maize phenotype search engine

Title from PDF of title page (University of Missouri--Columbia, viewed on September 9, 2010).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Thesis advisor: Dr. Chi-Ren Shyu.M.S. University of Missouri--Columbia 2009.In the midst of this genomics era, major plant genome databases are collecting massive amounts of heterogeneous information, including sequence data, gene product information, as well as images and descriptions of mutant phenotypes. While basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of stored data, advanced search mechanisms that can take advantage of textual descriptions of various types of stored data are nonexistent. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing both of these issues, we have developed a unique search engine for the phenotypes in MaizeGDB. This advanced search mechanism exploits the content and structure of available domain ontologies for the purposes of query enrichment, with currently both the Plant Ontology and Gene Ontology being utilized. The search engine also has the flexibility to integrate various text description sources to aid the user in retrieving desired phenotype information. This framework can be generalized to any domain with a domain-specific ontology or to sets of text sources that are heterogeneous and interconnected.Includes bibliographical references

High-throughput analysis and advanced search for visually-observed phenotypes

Title from PDF of title page (University of Missouri--Columbia, viewed on May 13, 2013).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Dissertation advisor: Dr. Chi-Ren ShyuIncludes bibliographical references.Vita.Ph. D. University of Missouri--Columbia 2012."May 2012"The trend in many scientific disciplines today, especially in biology and genetics, is towards larger scale experiments in which a tremendous amount of data is generated. As imaging of data becomes increasingly more popular in experiments related to phenotypes, the ability to perform high-throughput big data analyses and to efficiently locate specific information within these data based on increasingly complicated and varying search criteria is of great importance to researchers. This research develops several methods for high-throughput phenotype analysis. This notably includes a registration algorithm called variable object pattern matching for mapping multiple indistinct and dynamic objects across images and detecting the presence of missing, extra, and merging objects. Research accomplishments resulted in a number of unique advanced search mechanisms including a retrieval engine that integrates multiple phenotype text sources and domain ontologies and a search method that retrieves objects based on temporal semantics and behavior. These search mechanisms represent the first of their kind in the phenotype community. While this computational framework is developed primarily for the plant community, it has potential applications in other domains including the medical field.Includes bibliographical references

Patient-derived acute myeloid leukemia (AML) bone marrow cells display distinct intracellular kinase phosphorylation patterns

Multiparametric analyses of phospho-protein activation in patients with acute myeloid leukemia (AML) offers a quantitative measure to monitor the activity of novel intracellular kinase (IK) inhibitors. As recent clinical investigation with FMS-like tyrosine-3 inhibitors demonstrated, targeting IK with selective inhibitors can have a modest clinical benefit. Because multiple IKs are active in patients with AML, multikinase inhibitors may provide the necessary inhibition profile to achieve a more sustained clinical benefit. We here describe a method of assessing the activation of several IKs by flow cytometry. In 40 different samples of patients with AML we observed hyper-activated phospho-proteins at baseline, which is modestly increased by adding stem cell factor to AML cells. Finally, AML cells had a significantly different phospho-protein profile compared with cells of the lymphocyte gate. In conclusion, our method offers a way to determine the activation status of multiple kinases in AML and hence is a reliable assay to evaluate the pharmacodynamic activity of novel multikinase inhibitors

Efficient organization of genetic data for easier statistical analysis [abstract]

Abstract only availableWhen biological experiments are run, specifically those examining genetics, huge amounts of data are produced. This data is hard to organize and even harder to analyze without organization. When faced with a vast amount of data, statistical patterns are hard to observe as associations between different types of data are nearly impossible to see. A relational database was designed to handle this problem. The database organizes data taken by large-scale, long-term genetic experiments into linked categories, and uses an interface system such that makes many approaches to analyze the data possible. The database is unique from other types of organization in that it can be readily applied to these different approaches, while also dealing with subject-specific phenotypic information. This information is often left out in other database structures concerning genetic experiments. To show an application of the database, the structure is being applied to a long-term Maize genetics experiment. Using PHP scripting to insert data taken in the field into a MySQL system, the database is being used to create a search engine for plant geneticists to use to get genotypical information from phenotypical observation. However, the structure is not limited to plant genetics nor search engines, but can be applied to a multitude of bioinformatic and statistical studies of experiment data

UMP, SCUN seal bilateral collaborations

Universiti Malaysia Pahang (UMP) fortified its international networking when it sealed a Memorandum of Understanding (MoU) with China’s South-Central University for Nationalities (SCUN) in Beijing, China, on June 1

"Freezing" the Tumor in a Known Position During Radiation Therapy In Regard to Boda-Heggemann et al

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Paradoxical lucidity: A potential paradigm shift for the neurobiology and treatment of severe dementias

Unexpected cognitive lucidity and communication in patients with severe dementias, especially around the time of death, have been observed and reported anecdotally. Here, we review what is known about this phenomenon, related phenomena that provide insight into potential mechanisms, ethical implications, and methodologic considerations for systematic investigation. We conclude that paradoxical lucidity, if systematically confirmed, challenges current assumptions and highlights the possibility of networkâ level return of cognitive function in cases of severe dementias, which can provide insight into both underlying neurobiology and future therapeutic possibilities.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/153062/1/alzjjalz201904002.pd

Replication of Norovirus in Cell Culture Reveals a Tropism for Dendritic Cells and Macrophages

Noroviruses are understudied because these important enteric pathogens have not been cultured to date. We found that the norovirus murine norovirus 1 (MNV-1) infects macrophage-like cells in vivo and replicates in cultured primary dendritic cells and macrophages. MNV-1 growth was inhibited by the interferon-αβ receptor and STAT-1, and was associated with extensive rearrangements of intracellular membranes. An amino acid substitution in the capsid protein of serially passaged MNV-1 was associated with virulence attenuation in vivo. This is the first report of replication of a norovirus in cell culture. The capacity of MNV-1 to replicate in a STAT-1-regulated fashion and the unexpected tropism of a norovirus for cells of the hematopoietic lineage provide important insights into norovirus biology

Low Energy Nuclear Reaction Aircraft- 2013 ARMD Seedling Fund Phase I Project

This report serves as the final written documentation for the Aeronautic Research Mission Directorate (ARMD) Seedling Fund's Low Energy Nuclear Reaction (LENR) Aircraft Phase I project. The findings presented include propulsion system concepts, synergistic missions, and aircraft concepts. LENR is a form of nuclear energy that potentially has over 4,000 times the energy density of chemical energy sources. It is not expected to have any harmful emissions or radiation which makes it extremely appealing. There is a lot of interest in LENR, but there are no proven theories. This report does not explore the feasibility of LENR. Instead, it assumes that a working system is available. A design space exploration shows that LENR can enable long range and high speed missions. Six propulsion concepts, six missions, and four aircraft concepts are presented. This report also includes discussion of several issues and concerns that were uncovered during the study and potential research areas to infuse LENR aircraft into NASA's aeronautics research