BME100 f2014:Group23 L6

BME 100 Fall 2014	Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help
OUR COMPANY Name: Cesar Marin Name: Brady Dennison Name: Kassandra Flores Name: Danielle Beach Name: Theodore Kyriacou Name: Joshua Kahn LAB 6 WRITE-UP Bayesian Statistics Overview of the Original Diagnosis System For testing the 68 patients each of the 34 teams of 6 students tested 2 patients. For each patient 3 DNA samples were taken to avoid any coincidental errors. Each team also had positive and negative controls, as well as different concentrations of the DNA sample in order to be able to analyze whether each patient sample was positive or negative. Three images of each concentration and each patient sample and positive and negative control samples were taken, so as to prevent error. In order to set up the fluorimeter a camera was leveled to each sample drop combined with SYBR green. These images were analyze for numerical values of green INTDEN using ImageJ, since green fluorescence determines the prescence of the disease. These numerical values allowd us to analyze the concentrations of the patient samples and compare them to the controls. If all 3 or 2/3 samples for each patient where determined to be positive (that means within the positive concentration range) then the teams concluded a positive result for that patient, and so with negative results. After analyzing each image, 8 patients received an inconclusive test result, while 30 patients received a positive test result, and 24 patients received a negative test result. Additionally, 3 groups did not complete the test analysis, so 6 patients did not receive any results. What Bayes Statistics Imply about This Diagnostic Approach Calculations 1 and 2 show that the system is not perfect, but still reliable for testing this disease. Both specificity and sensitivity calculations were close to 100%, and were at worst 23% from being perfectly accurate. As for human error there could be errors in concentrations in the drops for the fluorimeter. Another possible human error could be cross-contamination by using the same tips while transferring different samples. Another possible error, both human and machine, could be faulty INTDEN values from the ImageJ software. This could be due to wrong placement of ovals for the measurements. Calculations for 3 and 4 turned out to be very small, and below 50%; Therefore, these calculations show that calculating the development of the disease given a positive or negative test result is unreliable and inaccurate. Computer-Aided Design Name of device: PCRF- Polimerase Chain Reaction Fluorimeter TinkerCAD Our Design The new design is quite simple, it combines both the fluorimeter and the PCR machine into one, and the fluorimeter is improved for easy access and to make the overall process faster. The design includes an added structullowing four drops to be photographed simultaneously. In addition, a camera holder can be inserted into several locations along the wall to hold the camera steady for the photograph of the drop. It would be relatively cheap to include with the original PCR machine, especially since the entire design can be taken off and packaged separately. It is simple, and allows for the entire process to run smoothly and quicker than the original fluorimeter design. We used the TinkerCAD to design this extra portion that could be added onto the PCR machine, and the four layer contained inside the design. The new design is quite simple, it combines both the fluorimeter and the PCR machine into one, and the fluorimeter is improved for easy access and to make the overall process faster. The design includes an added structure on the side of the PCR machine, a box containing four structured layers. It is essentially the original fluorimeter except compressed onto four levels. Each level can be opened, and a slide with a drop can be inserted. On each end is an opening for the camera. The side can be lowered, immersing the four layers in darkness, and the camera can be moved up to each of the four openings, allowing four drops to be photographed simultaneously. In addition, a camera holder can be inserted into several locations along the wall to hold the camera steady for the photograph of the drop. It would be relatively cheap to include with the original PCR machine, especially since the entire design can be taken off and packaged separately. It is simple, and allows for the entire process to run smoothly and quicker than the original fluorimeter design. We used the TinkerCAD to design this extra portion that could be added onto the PCR machine, and the four layer contained inside the design. Design Description The new design is quite simple, it combines both the fluorimeter and the PCR machine into one, and the fluorimeter is improved for easy access and to make the overall process faster. The design includes an added structure on the side of the PCR machine, a box containing four structured layers. It is essentially the originfour layers in darkness, and the camera can be moved up to each of the four openings, allowing four drops to be photographed simultaneously. In addition, a camera holder can be inserted into several locations along the wall to hold the camera steady for the photograph of the drop. It would be relatively cheap to include with the original PCR machine, especially since the entire design can be taken off and packaged separately. It is simple, and allows for the entire process to run smoothly and quicker than the original fluorimeter design. We used the TinkerCAD to design these Feature 1: Consumables Kit The SYBR GREEN 1 Solution, buffer, Calf Thymus DNA, flourimeter slides, positive and negative samples, pipette tips, and plastic test tubes will be placed in a dark cold box. All components will be wrapped in bubble wrap as a precaution. Feature 2: Hardware - PCR Machine & Fluorimeter Consumables - Plastics, pipettor, and reagents (PCR mix, primers): Among the consumables, the pipette stood out the most in terms of a strength as a whole, utilizing a simple but effective method to prevent errors in testing or damage to the device. The micro pipette tip is equipped with a stopper on the base that serves to prevent any liquid from entering the pipette itself. Concerning weaknesses, the test tubes in particular weren't as suited to the situation. Specifically, they were difficult both to close and to handle due to their size, presenting issues with usage. The OpenPCR machine and software: The design of the machine in terms of materials was well thought out, with the wood exterior being durable, lightweight, and fairly resistant to any heat produced. Likewise, the software proved to be effective and offered no notable issues. The process, however, was time consuming and took much longer than it realistically should have. The Fluorimeter system (including slides,stand,etc.): The system worked exceptionally well, and the process ran smoothly with each procedure taking hardly any time at all. Additionally, the method was cheap and despite this, performed adequately. There were some difficulties, of course, consisting of issues with the camera setup where the stand had to be handled extremely carefully in order for the smartphone to not fall or lose focus of the slide. Along with this, light would often penetrate the exterior and risk altering the results.