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post biodesign phd oral defense 04-12-2014d1734
2014-08-29
post biodesign phd oral defense 04-12-2014d1734 defense was held 4-11-14 pass/fail form partially filled "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\04-21-2014d2130\Kurt Whittemore Report for Dissertation Defense.pdf" pass/fail form fully filled 04-21-2014d2130 "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\04-21-2014d2130\4-21-14\Kurt Whittemore Report for Dissertation Defense.pdf" -confirmation that the college received my form --https://mail.google.com/mail/u/0/?ui=2&shva=1#search/confirmation/1457ce1a80f57a23 (04-22-2014d1030) audio recording of presentation "C:\Users\kurtw_000\Documents\kurt\storage\DR\Audio 2014\04-12-2014d1446\PhD oral defense 14-04-11-15-24-45.wav" Video recording of phd oral defense --video from Mengjiao (there's some breaks in the video and a change of format, but this video should give a general idea of the event) ---videos and images found here: "C:\Users\kurtw_000\Documents\kurt\storage\videos\2014\04-27-2014d1418\Records for Kurt Whittemore's Defense--2014.04.11" ---small video for viewing and sharing: "C:\Users\kurtw_000\Documents\kurt\storage\videos\2014\04-27-2014d1418\Records for Kurt Whittemore's Defense--2014.04.11\videos\Spring 2014 Oral Defense feature phone small.mp4" --video from Biodesign IT (restrictions on video) ---http://biodesignreplay.vidyo.asu.edu/replay/showRecordingExternal.html?key=hPPRZnl8Od51R0G ---https://mail.google.com/mail/u/0/?ui=2&shva=1#label/Career/145532e945ce0861 ---this video seems to have some restrictions about copying and sharing -[notes from Dr. Johnston on dissertation document 04-13-2014d1634] notes from audio recording { questions after presentation start at 1 01 50 Diego you didn't check if there was an immune response against the antigens you found me the screen was testing an immune response but I didn't use alternative methods Diego why would entropy change as people get older me affinities and antibody repertoire changes with age Diego difference between complexity and randomness. careful with terms Neal a completely non random thesis world be bad if it were all as (letter as). order of letters matters. what if all the binding events on the array are not independent. how could you determine interconnectedness of binding events me statistician zipf and power law distribution of letters and words. . .maybe complex mathematics could find interdependence of features on array Bradley asked about lab dreams project animation. me progressing slowly Krishna were the identified tumor antigens previously associated with cancer me yes with the myc mad max and others Krishna did you look at function. were they house keeping genes Me yes. also house keeping genes are related to cancer in other studies sai asked if bacteria are the best for making mammalian proteins me may not always be the best but most practical public audience questions ended at 1 11 08 exam part with committee starts at 1 19 08 Phil what further experiments could you do to relate entropy measure to health I talked about sera from athletes and non athletes Phil how would you decide number of groups and class sizes me standard deviation, power, the test Phil what about infectious and chronic disease groups me expect low entropy for infection and high for chronic valiery better explanation of idea behind this question about lymphoma and vaccine me both lots of antibodies against few targets Stephen you could have followed up and looked up numbers for antibodies in blood after vaccine or infection Kathy comment about be cell cancers me dog lsa is a b cell cancer Bert interested in normal and cancer mouse. what was the system strain etc me fvbn neu t mice tumor at 33 weeks. thus one had tumor at 33.1 weeks. could detect peptides increasing 8 weeks before. maybe immune system battling tumor discussion about response to her2 Stephen give therapy at peak immunosignature doesn't look chaotic Bert entropy of entropy (over time) Stephen tiger has more samples Bert trying to understand monoclonal entropy slide Kathy comment about avidity Stephen he thinks avidity is independent of specific binding. many high affinity antibodies have a more rigid structure which could help explain result.when they bind they bind tight and don't bind much else. previous experiment in our lab showed that antibody diluted into sera bound just as well Stephen practical idea for work. quantify antibody specificity for antibody companies. people are worried about cross reactivity. I thought this was a really good idea. Phil that would be cheaper than proto arrays Bert idea of looking at hiv people and comparing those that develop broadly neutralizing antibodies Phil if you were given a lot of money how would you redo the experiment. he asked what was the hardest part me I answered wrong by saying I would screen a lot more (committee didn't like this answer). then I said I would screen the spot with highest p value which was decreasing with tumor sera Stephen why didn't you have shen and Felicia try to vaccinate mice with the clones you found? me everyone was so busy Kathy is it necessary to include other measures other than entropy me yes I got better performance in my own tests Kathy maybe include goodness of fit of one distribution to the other. . . and peptide sequence information. counts of all peptides with a similar sequence. Kathy maybe some of the measures could be thrown out Kathy how did you rank entropy me four different experiments and p value between disease and normal Kathy did you select certain features before calculating abstat me no Stephen why not just do ages with scatter plot me I did but it didn't work well they were interested in the r2 of the scatter plot as well as the ages. I told them the old ones were all in 50s and 60s Stephen what are requirements for system for monitoring me needs to be cheap Stephen joke. this is so useful. you can tell people how old they are exam section ends at 2 01 39 Stephen rhinopest has also been eradicated if you have a pointer just point don't wave didn't make it add clear that I was taking about preventative vaccines didn't explain that I needed sera from someone with a tumor and someone without presentation too fast Bart thought entropy explanation was clear Kathy you can make an exception for champagne just once thesis so imaginative and unique with new and interesting ideas. I felt like I'm an art student haha Stephen you didn't finish everything you started got laser pointer as a gift from cim } -[other gifts 05-05-2014d0830]
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