Computer evaluation of network dynamics models with application to cell cycle control in budding yeast

Cellular processes are governed by complex networks of interacting genes and proteins. Theoretical molecular biologists attempt to describe these processes via mathematical models by writing biochemical reaction equations. Modellers are building increasingly larger and complex mathematical models to describe these cellular processes, making model evaluation a time consuming and difficult task. The authors describe an automatable process for model evaluation and a software system that implements this process. The software is adaptable to many types of models and is freely available along with all needed data files. The cell cycle control system for budding yeast is known in fine detail and constrained by more than 100 phenotypic observations in mutant strains. As an example, the authors apply their process to a model of cell cycle control in budding yeast containing dozens of regulatory equations and explaining nearly all of the known mutant phenotypes.

Evaluation of an autotutorial-simulator program for instruction of hollow organ closure

Forty students were randomly assigned into two study groups (traditional, T; and simulator, S) of 20 students each for a core operative practice laboratory. Students were randomly paired and their group assignment and identity remained anonymous to the evaluators throughout the study. Questionnaires were distributed to students to evaluate prior surgical experience and obtain learning resource use information. Before the evaluation sessions, both groups were given identical learning resource opportunities except students in Group S received hollow organ simulators and practice materials for gastrotomy closure. All students were forewarned that surgical instruction would not be available during the evaluation sessions. In the first live animal evaluation session, all student pairs were videotaped after which stomachs were harvested for gross evaluation of the surgical site. Group T performed an additional gastrotomy for video and gross evaluation 2 weeks later. Questionnaire, and gross and video evaluation results were compared statistically between groups and sessions. The hollow organ model did not suitably simulate live stomach tissue; the material was more fragile and stiff and suture cut-out was a problem even with appropriate suture tension and technique. The model was effective for teaching needle placement, instrument usage, creating proper tissue inversion, and methods to minimize instrument handling of tissue during gastrotomy closure. Prior practice with models did not boost student confidence during their live gastrotomy session. The autotutorials (ATs) were well received by students but did not sufficiently address how to manage mucosal eversion, suture tension, and bleeding encountered during live gastrotomy. AT viewing time positively correlated with mean total video score for Group T during both sessions. None of the students had prior experience performing hollow organ closure and no significant difference in experience level was evident between groups. Mean closure time was not significantly different between groups for session one (Group T, mean, 31.5 minutes, range, 18.4 to 53.4; Group S, mean, 28.2 minutes, range, 16.8 to 36), but was significantly reduced for session two (Group T, mean, 21.3 minutes, range, 13.9 to 31). This AT/simulator program does not significantly influence students' overall gastrotomy closure technique; gross and video evaluation scores were not significantly different between groups. Without instructor supervision, an additional gastrotomy experience did not improve surgical technique appreciably for Group T; however, these students performed the second procedure with more confidence and speed.(ABSTRACT TRUNCATED AT 400 WORDS)

Evaluation of video tape and a simulator for instruction of basic surgical skills

Twenty first-year veterinary students with no prior participatory experience in surgery were randomly paired and assigned into two study groups. Ten students (group V) viewed a hemostatic technique video tape until they thought they could competently perform and assist in performing a hand-tied ligature on a blood vessel in a live animal. Ten students (group VS) wer also given a simulator for technique practice. Paired students were video recorded and blindly evaluated on their ability to perform and assist proper ligation of a bleeding vessel. Inexpensive hemostasis models were very helpful for teaching students essential surgeon and assistant skills involved in hand-tied ligature placement. Students who practiced with simulators performed significantly better as surgeon and assistant, and in total psychomotor skill evaluation, then students watching the video only. Students using simulators performed ligation with significantly more accuracy and tended to be more expeditious at this task. Further training is needed for students to acquire skills necessary for efficient bleeding vessel exposure and isolation.

A model for the analysis of neighbor finding in pointer-based quadtrees

A natural byproduct of the tree-like nature of the quadtree is that many basic image processing operations can be implemented as tree traversals which differ in the nature of the computation that is performed at each node. Some of these computations involve the inspection of a node's adjacent neighbors (termed neighbor finding). A new model is developed for images represented by quadtrees, and it is used to analyze various neighbor-finding techniques. The model's predicted costs for neighbor finding correlate very closely with empirical results and it is superior to the model that was used previously.