Christopher M. Frenz

Primary Virtual and in vitro Bioassay Screening of Natural Inhibitors from Flavonoids against COX-2

Abstract In this study, we reported the screening of 9 compounds of flavonoids from the ZINC and PubChem databases (containing 2 092 flavonoids) using the iGEMDOCK software tool against the COX-2 3D protein structures. Each compound was also evaluated by an in vitro bioassay testing the inhibition of COX-2. Centaureidin and luteolin were found to be the potential inhibitors of COX-2 as demonstrated by IC 50 : 45 and 36.6 μmol·L −1 , respectively. In addition, structure activity relationships and other important factors of the flavonoids binding to the active site of COX-2 were discussed, which is expected for further rational drug design.

Improving elevator call time responsiveness via an artificial neural network control mechanism

Elevator traffic comprises the movement of individuals from the floor from which they called the elevator to their destination floor. This project seeks to improve elevator call time responsiveness by utilizing the concept that traffic flows generally form definable patterns that can be used to predict future traffic flow behaviors. A feed-forward neural network-based control algorithm has been developed that can approximate elevator call patterns by learning to associate time of day with specific call locations. This algorithm was tested against fuzzy patterns of elevator calls in which the randomly generated calls were biased towards certain floors at certain times of day. When the average neural network controlled call times of 10 such fuzzy sets were compared to the typical scenario of the elevator returning to the first floor after each call, a 42% improvement in elevator call time responsiveness was observed. It is thereby suggested that a machine learning enabled-elevator control system could result in increased user satisfaction by reducing wait times by helping to ensure that the elevator is at the most likely place the elevator will be called from prior to an individual even pushing the call button. The utility of such an algorithm is likely further enhanced, however, by the fact that having the elevator in the most likely call location can also lead to significant energy savings in that the elevator will need to travel less to pick up prospective passengers.

Engineering Nature's Nanotech

In this paper, the author discussed the possibilities and the advantages of natural nanotechnology over synthethic materials. Proteins for example, as natures nanomachines is easily accessible and does not require fabrication. nanotechnology is set to open up numerous doors for the future, some of which we will likely not even be able to foresee today. As we begin to venture forth into this new nanoscale world, however, perhaps we should also take the time to appreciate and study the diversity of the nanotechnologies that already exist within and all around us.

Possibilities and limitations of computer simulation

Computer simulations are becoming an increasingly powerful tool that scientists and engineers can employ to aid in solving challenging problems. A further consideration when planning or implementing computer simulations is to take into account the computational resources available and the length of time those resources will remain available. Simulations can be utilized to guide researchers in the proper direction and to investigate phenomena that are currently beyond our capacity to investigate using empirical means, but they should not be utilized as a replacement for empirical methods

Automated extraction of health resource URLs from biomedical abstracts

The World Wide Web has grown to become one of the most pervasive and comprehensive information repositories available today and many compare the knowledge contained within it to a modern day library of Alexandria. Yet, despite its vastness, one of the downsides to using Web-based information sources is that the information contained in most Web pages has never been reviewed for accuracy or quality and thus it is often considered unsuitable for application where accuracy is of critical importance. While sites of questionable quality clearly should be avoided, one cannot deny the utility and advantages of Web based resources, and thus a methodology has been developed to identify expert vetted health-related Web resources. The resultant computer software searches for biomedical abstracts via Pubmed that pertain to a health topic of interest and via regular expression based pattern matching extracts all of the URLs that appear in the article abstracts. Given that articles that appear in Pubmed typically endure peer-review processes it can be assumed that all of the resources referenced by these articles have a reasonable level of quality, since they are being cited by experts. Thus the program is able to compile a list of quality Web resources pertaining to health topics. This system has successfully been used to create a list of Influenza related Web resources as a means of illustrating its utility.

Mining the Web for C\C++ code with perl

The Web represents one of the largest repositories of information ever compiled by mankind and as such search techniques are essential to navigating its depths and returning pertinent information. Typically the search techniques employed in search engines such as Google entail the use of keywords in which Web pages containing the specified keywords are sought out and then ranked using an algorithm such as PageRank. While keywords are suitable for many search tasks, certain types of data cannot be readily searched using keywords alone. Regular expression based pattern matching allows for enhanced search capability in that it allows for a textual pattern to be specified and matching to be performed against the pattern. Regular expressions have been developed that allow for the identification of common C\C++ code structures such a loops, conditionals and functions. These regular expressions are then integrated into a Perl program that performs a keyword based search of the Yahoo Search engine and used to extract any code elements that match those patterns. Thus an algorithm or programming technique can be specified with keywords, the Yahoo search used to identify Web pages pertinent to those keywords, and the regular expressions used to identify and extract any C\C++ code found in the resultant Web pages. Application of this technique would likely be of great benefit towards creating specialized search capabilities for software developers.

The Application of Regular Expression-Based Pattern Matching to Profiling the Developmental Factors that Contribute to the Development of the Inner Ear

The biomedical literature has always played a critical role in the development of hypotheses to test, experimental design, and the analysis of study results. Yet, the ever-expanding body of biomedical literature is starting to present new challenges, in which locating pertinent literature from among the millions of published research articles is often a challenging task. A regular expression-based pattern matching method has been developed to profile the various gene and protein factors that may play a role in various tissues contained within an organism. This methodology has been demonstrated through the profiling of the various factors that are involved in the development of the inner ear, and is shown to be both effective and accurate.