full transcript

From the Ted Talk by Joe DeRisi: Solving medical mysteries

Unscramble the Blue Letters

So, we built out the chip. We made a chip that has every known virus ever discovered on it. Why not? Every plant vruis, every icsnet virus, every marine virus. Everything that we could get out of GenBank — that is, the notanial repository of scnueeqes. Now we're using this chip. And what are we using it for? Well, first of all, when you have a big chip like this, you need a little bit more informatics, so we designed the system to do automatic diagnosis. And the idea is that we simply have virtual patterns, because we're never going to get samples of every virus — it would be vtairlluy iiospbsmle. But we can get virtual patterns, and compare them to our observed result — which is a very complex mixture — and come up with some sort of score of how likely it is this is a rhinovirus or something. And this is what this looks like. If, for example, you used a cell ctuurle that's cinalrlohcy infected with papilloma, you get a little computer readout here, and our aoltghirm says it's probably papilloma type 18. And that is, in fact, what these particular cell cultures are chronically infected with.

Open Cloze

So, we built out the chip. We made a chip that has every known virus ever discovered on it. Why not? Every plant _____, every ______ virus, every marine virus. Everything that we could get out of GenBank — that is, the ________ repository of _________. Now we're using this chip. And what are we using it for? Well, first of all, when you have a big chip like this, you need a little bit more informatics, so we designed the system to do automatic diagnosis. And the idea is that we simply have virtual patterns, because we're never going to get samples of every virus — it would be _________ __________. But we can get virtual patterns, and compare them to our observed result — which is a very complex mixture — and come up with some sort of score of how likely it is this is a rhinovirus or something. And this is what this looks like. If, for example, you used a cell _______ that's ___________ infected with papilloma, you get a little computer readout here, and our _________ says it's probably papilloma type 18. And that is, in fact, what these particular cell cultures are chronically infected with.

Solution

  1. impossible
  2. insect
  3. virtually
  4. algorithm
  5. culture
  6. chronically
  7. virus
  8. sequences
  9. national

Original Text

So, we built out the chip. We made a chip that has every known virus ever discovered on it. Why not? Every plant virus, every insect virus, every marine virus. Everything that we could get out of GenBank — that is, the national repository of sequences. Now we're using this chip. And what are we using it for? Well, first of all, when you have a big chip like this, you need a little bit more informatics, so we designed the system to do automatic diagnosis. And the idea is that we simply have virtual patterns, because we're never going to get samples of every virus — it would be virtually impossible. But we can get virtual patterns, and compare them to our observed result — which is a very complex mixture — and come up with some sort of score of how likely it is this is a rhinovirus or something. And this is what this looks like. If, for example, you used a cell culture that's chronically infected with papilloma, you get a little computer readout here, and our algorithm says it's probably papilloma type 18. And that is, in fact, what these particular cell cultures are chronically infected with.

Frequently Occurring Word Combinations

ngrams of length 2

collocation frequency
tissue culture 5
culture cells 4
prostate cancer 3
antiviral defense 3
single diagnostic 2
common cold 2
small windows 2
virus shares 2
making dna 2
dna chips 2
printing dna 2
herpes virus 2
genetic material 2
respiratory syncytial 2
syncytial virus 2
positive control 2
experimentally inoculate 2
inoculate people 2
chronically infected 2
case report 2
open lung 2
lung biopsy 2

ngrams of length 3

collocation frequency
tissue culture cells 4
making dna chips 2
respiratory syncytial virus 2
experimentally inoculate people 2
open lung biopsy 2

Important Words

  1. algorithm
  2. automatic
  3. big
  4. bit
  5. built
  6. cell
  7. chip
  8. chronically
  9. compare
  10. complex
  11. computer
  12. culture
  13. cultures
  14. designed
  15. diagnosis
  16. discovered
  17. fact
  18. genbank
  19. idea
  20. impossible
  21. infected
  22. informatics
  23. insect
  24. marine
  25. mixture
  26. national
  27. observed
  28. papilloma
  29. patterns
  30. plant
  31. readout
  32. repository
  33. result
  34. rhinovirus
  35. samples
  36. score
  37. sequences
  38. simply
  39. sort
  40. system
  41. type
  42. virtual
  43. virtually
  44. virus