Journal of Computer Science & Systems Biology

Tumor cell growth models involve high-dimensional parameter spaces that require computationally tractable methods to solve. To address a proposed tumor growth dynamics mathematical model, an instance of the particle swarm optimization method was implemented to speed up the search process in the multi-dimensional parameter space to find optimal parameter values that fit experimental data from mice cancel cells. The fitness function, which measures the difference between calculated results and experimental data, was minimized in the numerical simulation process. The results and search efficiency of the particle swarm optimization method were compared to those from other evolutional methods such as genetic algorithms.

Botulinum neurotoxins (BoNTs) are one of the potent toxins in nature but the toxicity is immediately eliminated by the harsh environment in the digestive tract because BoNTs are just a protein. However, BoNTs can get to synaptic junctions thanks to support of other proteins by aggregating with each other, combining with BoNTs and forming a large progenitor toxin complex (L-PTC). In order to explain how the complex formation enables the BoNTs to intrude into our body, we found that the three-dimensional structure of the L-PTC consists of an ovoid body with three legs and speculated important roles in the body and the legs. In the legs part, it is helpful for promoting absorption especially from the small intestine. Because experimental results showed that the legs are flexible and have specific binding sites of saccharides, the flexibilities may help the L-PTC to easily access the binding sites to the saccharides on the intestinal surface. However, such flexibilities have been only investigated by experimental methods. This means that we still have not objectively discussed what motions are generated from the shape of the L-PTC and how the structure is changed gradually. Therefore, we developed a new method integrating an analysis based on anisotropic network model and principal component analyses in order to measure the dynamics of the large-sized protein consisting of several subunits. The results showed that the L-PTC had characteristic motions which have large movements of the three legs. In addition, the flexible motions were appeared regardless of the theoretical models. Our application to measure the dynamics of the L- PTC suggested the importance of the flexibility which enables the L-PTC to break the epithelial barrier. We hope that the activity of the L-PTC is applied for developing a new oral drug delivery system.

Legged robots have a potential of being a walking machine on irregular ground. Eleven-bar linkages, Theo Jansen mechanism reproduces a smooth locomotion pattern as gait. Parallel motions have widely used in the heavy machinery and recently highlighted in a model of biological motions. The close-loop linkage simply provides a designed end-effector trajectory, whereas the trajectory is considered to be less modifiable due to the singularity problem. In the present study, the singularity on the modified Theo Jansen mechanism was addressed by introducing the parametric orbit as a new freedom point in the joint center, and analyzed its kinematics and dynamics by using multibody dynamics (MBD). The extendability of the mechanism in the viewpoint of flexibility in the gait trajectory was clearly demonstrated in the numerical simulation, providing new functional gait trajectories controlled by two control parameters that change the shape of the parametric oval in the joint center. In systematic determinant analyses of how broken trajectories were generated depending on four parameters, i.e., horizontal and vertical amplitudes and rotation angle of the joint center movement and its phase difference with the driving link, morpho-logical changes of generated trajectories in the phase-rotation-amplitude parameter space were revealed. Thus the extension capability of Theo Jansen mechanism was validated not only in smooth walking but also in jumping, climbing and running-like motions. In considering the ways of control, the present results indicated that there exists a inverse relationship between the rotation angle and the phase difference to significantly reduce the occurrence of the singularity and breakage failures of the mechanism, which is consistent with biological evidences of coupling oscillators that enables the nervous system to control the complex musculoskeletal system by using a few of simple parameters frequently represented by the phase and rotation in a torus state space.

Background: Gastroenterology (GI) fellows perform endoscopic procedures and are asked to record information regarding the procedure and their involvement. As no standard method for procedure logging exists and retrieval of data can be challenging, we have created a novel mobile device application (MDA) to accomplish this task. Objective: To determine if a novel MDA will allow for improved endoscopic procedure logging and data retrieval. Methods: A 19-item questionnaire was created to assess the current logging practice of GI fellows at our tertiary care academic medical center. Fellows then downloaded the MDA free-of-charge from the iTunes App store. After 8 weeks of MDA use, fellows were asked to complete the same questionnaire and the NASA task load index (TLX). The study was IRB approved. Results: 11 GI fellows were enrolled. Pre-MDA 7 maintained a paper log, 7 computer-based log, and 1 webbased log 83% of procedures completed were logged; 36.4% within 24 hr of procedure completion. Pre-MDA, fellows estimated their Polyp Detection Rate (PDR) to be 54.5% ± 18.8% and attending take-over rate (ATR) 39.25%. Post- MDA, 85.2% of procedures were logged (p=0.47); 54.5% within 24 hr (p=0.38). The MDA recorded PDR was 50% ± 31% (p=0.74) and ATR was 54% (p=0.19). TLX among MDA users demonstrated very low physical demand 8.6 [0, 21], low mental demand 18.3 [14, 25], low effort 27 [10, 60], and high success 84 [76, 100]. Conclusion: MDA procedure logging was efficient and successful. Data was easily retrieved and MDA use was quickly adopted. The MDA may be a useful tool for recording and retrieving procedure logs in a standard fashion.