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Browsing by Subject "modelling"

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  • Grazhdankin, Evgeni (2018)
    We have developed a software for homology modelling by satisfaction of distance restraints using MODELLER back-end. The protocols used extend exploration of distance restraints and conformational space. We drive the models in optimization cycle towards better structures as assessed by the used metrics on DOPE score, retrospective distance restraint realization and others. Hydrogen bond networks are optimized for their size and connectivity density. The performance of the method is evaluated for its ability to reconstruct GPCR structures and an extracellular loop 2. The software is written in object-oriented Python (v.2.7) and supports easy extension with additional modules. We built a relational PostgreSQL database for the restraints to allow for data-driven machine and deep learning applications. An important part of the work was the visualization of the distance restraints with custom PyMOL scripts for three-dimensional viewing. Additionally, we automatically generate a plethora of diagnostic plots for assessing the performance of the modelling protocols. The software utilizes parallelism and is computationally practical with compute requirements on an order of magnitude lower than those typically seen in molecular dynamics simulations. The main challenges left to be solved is the evaluation of restraint goodness, assigning secondary structures, restraint interconditioning, and water and ligand placement.
  • Kallio, Varpu (2014)
    The purpose of this study is to evaluate patients' quality of life and healthcare use before and after bariatric surgery and produce new, clinical data-based information on the cost-effectiveness of bariatric surgery. Healthcare resources are limited and expenditures have grown from year to year. Therefore it is important to make cost-effectiveness evaluations so that financial resources could be allocated properly. The research population consists of patients who have undergone gastric bypass or sleeve gastrectomy in the Hospital District of Helsinki and Uusimaa, during the years 2007-2009. The study population consists of 147 gastric bypass patients and 79 sleeve gastrectomy patients. In this study the decision analytic model, used in the Finohta study "Sairaalloisen lihavuuden leikkaushoito" was updated using actual, up-to-date information. The analysis was done using a decision tree and a Markov model with a time horizon of 10 years. The cost data in this study was based on actual data for the first two years after surgery. A forecast model was used to predict the costs for the years 3-10 after surgery. Patients' quality of life scores were based on real data for the years 1 (the year of operation) to 4. Quality of life scores for the other years were predicted. In the literature review section, international studies on the cost-effectiveness of bariatric surgery and its impacts on drug therapy were evaluated. The studies showed that the use of medicines, which were used to treat obesity-related diseases were lower in the surgery group. However, drugs used to treat vitamin deficiencies, depression and gastrointestinal diseases were higher in the surgery group. Most studies found that surgery is the most cost-effective way to treat morbid obesity. This study confirms the role of the bariatric surgery in the treatment of morbid obesity in Finland. Even though the healthcare costs were increased in the first two years after the operation, the conclusions of the Finohta study didn't change. The bariatric surgery is cheaper and more effective than ordinary treatment and the most cost-effective way to treat morbid obesity. The mean costs were 30 309 € for the gastric bypass, 31 838 € for the sleeve gastectomy and 36 482 € for ordinary treatment. The mean numbers of quality-adjusted life-years were 6.919 for the gastric bypass, 6.920 for the sleeve gastrectomy and 6.661 for ordinary treatment. However, there is demand for more information for the long-term effects, benefits and risks of the surgery. How much the surgery will actually save money, will be hopefully clarified in the long-term follow-up study, which should also include an actual control group.