Using the Gene Ontology to Annotate Biomedical Journal Articles

We are creating a gold-standard corpus of manually annotated full-text biomedical journal articles toward natural-language-processing applications. Central to this is our use of entire ontologies of the Open Biomedical Ontologies initiative as well as other terminologies as term sources, in contrast to most other such annotation projects, which have used small, ad hoc schemas. In addition to the standard difficulties in such annotation projects, each of the terminologies we have used has idiosyncrasies and ambiguities that present further challenges to consistent, high-quality annotation of these articles. In this paper we present and discuss the most salient of these with regard to the Gene Ontology that we have encountered and addressed in our annotation guidelines and training. The utility of these guidelines can be seen in the high and still-increasing interannotator-agreement statistics that we continually monitor.
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A Hackney 4th of July

Illustrated script of a performed walk between Hoxton Hall, Hoxton Street, to the Building Exploratory at Orsman Road (via The Regent's Canal), Hackney on the 4th of July, 2009, 2-4p

The Ingestion of 39 or 64 g·h-1 of Carbohydrate is Equally Effective at Improving Endurance Exercise Performance in Cyclists

In an investigator-blind, randomized cross-over design, male cyclists (mean± SD) age 34.0 (± 10.2) years, body mass 74.6 (±7.9) kg, stature 178.3 (±8.0) cm, peak power output (PPO) 393 (±36) W, and VO2max 62 (±9) ml·kg-1·min(-1) training for more than 6 hr/wk for more than 3y (n = 20) completed four experimental trials. Each trial consisted of a 2-hr constant load ride at 95% of lactate threshold (185 ± 25 W) then a work-matched time trial task (~30 min at 70% of PPO). Three commercially available carbohydrate (CHO) beverages, plus a control (water), were administered during the 2-hr ride providing 0, 20, 39, or 64 g·hr-1 of CHO at a fluid intake rate of 1L·hr(-1). Performance was assessed by time to complete the time trial task, mean power output sustained, and pacing strategy used. Mean task completion time (min:sec ± SD) for 39 g·hr(-1) (34:19.5 ± 03:07.1, p = .006) and 64 g·hr(-1) (34:11.3 ± 03:08.5 p = .004) of CHO were significantly faster than control (37:01.9 ± 05:35.0). The mean percentage improvement from control was -6.1% (95% CI: -11.3 to -1.0) and -6.5% (95% CI: -11.7 to -1.4) in the 39 and 64 g·hr(-1) trials respectively. The 20 g·hr(-1) (35:17.6 ± 04:16.3) treatment did not reach statistical significance compared with control (p = .126) despite a mean improvement of -3.7% (95% CI -8.8-1.5%). No further differences between CHO trials were reported. No interaction between CHO dose and pacing strategy occurred. 39 and 64 g·hr-1 of CHO were similarly effective at improving endurance cycling performance compared with a 0 g·hr(-1) control in our trained cyclists

Survey of Accounting Principals in Generally Accepted Accounting Principals and Financial Statement Analysis

For my senior research thesis I decided that I would do research on various case studies that are in the field of accounting. Accounting is my major here at the University of Mississippi and I wanted to do research on a topic that is relevant to my major. I was provide a series of cases about all different subject in the accounting world. These topic were given to me by my instructor and I was to fo through each case thoroughly and answer all the questions. If I didn’t know the answer to the question or needed more insight on the subject I would use my intermediate Accounting book for more insights. Through the various case studies, I was able to go into more depth than my traditional accounting classes. The case studies also provided me with a real world application of accounting. These cases simulate real world accounting issues and I was able to apply my knowledge in real life situations. I am very thankful for doing this thesis. I have learn more about accounting through the case studies and has helped me in my classes. The cases have also helped me in the business world as well. During several of my internships, I have used the knowledge and experiences while doing this thesis and applied them to my job. I conclude that this thesis has helped me I ways that I didn’t realize going into the thesis

Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling

<p>Abstract</p> <p>Background</p> <p>The use of computational methods for predicting protein interaction networks will continue to grow with the number of fully sequenced genomes available. The Co-Conservation method, also known as the Phylogenetic profiles method, is a well-established computational tool for predicting functional relationships between proteins.</p> <p>Results</p> <p>Here, we examined how various aspects of this method affect the accuracy and topology of protein interaction networks. We have shown that the choice of reference genome influences the number of predictions involving proteins of previously unknown function, the accuracy of predicted interactions, and the topology of predicted interaction networks. We show that while such results are relatively insensitive to the <it>E</it>-value threshold used in defining homologs, predicted interactions are influenced by the similarity metric that is employed. We show that differences in predicted protein interactions are biologically meaningful, where judicious selection of reference genomes, or use of a new scoring scheme that explicitly considers reference genome relatedness, produces known protein interactions as well as predicted protein interactions involving coordinated biological processes that are not accessible using currently available databases.</p> <p>Conclusion</p> <p>These studies should prove valuable for future studies seeking to further improve phylogenetic profiling methodologies as well for efforts to efficiently employ such methods to develop new biological insights.</p