Click on links below to view/download indicated papers.
For Tuesday, May 30, 2017: student presentations
L13 Reading:
Go back and read any assigned papers that you may have missed earlier.
L13 Writing:
Identify and describe one good question that needs to be answered in order to allow the field to make progress. Explain why this one question is critical. Cite references. Note that this assignment will need to be delivered by email to the instructor on or before June 6, 2017.
For Tuesday, May 23, 2017: review
L12 Reading:
Go back and read any assigned papers that you may have missed earlier.
L12 Writing:
Prepare your presentation for L13.
For Tuesday, May 16, 2017: other prostheses, memory and proprioception.
L11 Reading:
berger-hampson-song-goonawardena-maramarelis-deadwyler-2011-j-neural-eng.pdf
hampson-gerhardt-marmarelis-song-opris-santos-berger-deadwyler-2012-j-neural-eng.pdf
hampson-song-opris-santos-shin-gerhardt-marmarelis-berger-deadwyler-2013-j-neural-eng.pdf
L11 Optional Reading:
Memory prostheses:
berger-ahuja-courellis-et-al-2005-ieee-embm.pdf
Somatosensory prostheses:
bensmaia-miller-2014-nature-rev-neurosci.pdf
tabot-dammann-berg-tenore-boback-vogelstein-bensmaia-2013-pnas-includes-correction.pdf
L11 Writing:
Write a review of the newest paper from the Berger memory prosthesis
project. This paper has a lot in common with their 2013 paper, so
should be a quick read.
deadwyler-hampson-song-opris-gerhardt-maramarelis-berger-2017-exp-neurol.pdf
Provide a very brief overview and then extract the data from Figure 4 and
replot them in a more understandable way. This might seem a silly
exercise, but is something you will need to do frequently with published
results. Concentrate only on the mean values; ignore standard error and
significance marks. Be reasonably accurate when extracting the data.
For Tuesday, May 9, 2017: patient selection and ethics.
L10 Reading:
For patient selection:
merabet-rizzo-pascual=leone-fernandez-2007-n-neural-eng.pdf
lane-huyck-troyk-schug-2012-disab-rehab.pdf
lane-nitsch-huyck-troyk-schug-2014-disability-rehab-assist-tech.pdf
anderson-warren-lee-2014-health-policy-technol.pdf
For ethics:
hansson-2005-j-med-methods.pdf
wolpe-2002-brain-cognition.pdf
hildt-2010-studies-ethics-law-technol.pdf
L10 Optional Reading:
ahuja-behrend-2013-prog-ret-eye-res.pdf
yanai-et-al-humayun-2003-trans-am-ophthalmol-soc.pdf
xia-peng-ren-2012-contemporary-clinical-trials.pdf
lane-huyck-troyk-2011-disab-rehab.pdf
lane-nitsch-scherer-2016-neurobionics-book.pdf
horthoff-1996-j-med-ethics.pdf
L10 Writing:
Using the Lane, et al., papers as a basis, critique the idea of including
subjects as so-called team members during early experimentation and later
clinical testing. Take a stand for or against the intimate inclusion of
subjects, and argue your stand either way.
For Tuesday, May 2, 2017: assessment techniques.
L9 Reading:
The first paper is a review of visual performance assessment written by
Dagnelie, and formed the basis of the lecture.
dagnelie-2008-annual-rev-bioeng.pdf
These other three papers should be read for measurement technique more
than results. Pay particular attention to any missing control conditions
or factors that would affect reproducibility.
nau-bach-fisher-2013-trans-vis-sci-tech.pdf
thomspon-barnett-humayun-dagnelie-2003-iovs.pdf
dagnelie-et-al-2017-clinical-exp-ophthalmol.pdf
We'll be re-reading the following papers for technique (not results):
bourkiza-vurro-jeffries-pezaris-2013-plos-one.pdf
vurro-crowell-pezaris-2014-front-human-neurosci.pdf
stingl-bartz=schmidt-besch-et-al-zrenner-2013-proc-royal-soc-b.pdf
zhou-dorn-greenberg-et-al-2013-ieee-icmew.pdf
duret-brelen-lambert-gerard-delbeke-veraart-2006-restorative-neurol-neurosci.pdf
The following papers were mentioned in passing, and can be considered
optional:
Eccentric reading: sommerhalder-oueghlani-bagnoud-leonards-safran-pelizzone-2003-vis-research.pdf
Checkers: srivastava-troyk-dagnelie-2009-j-neural-eng.pdf
Navigation: cha-horch-normann-1992-annals-biomed-eng.pdf
Line following / door task: zhou-dorn-greenberg-et-al-2013-ieee-icmew.pdf
At the start of class, we went over the following two papers that
introduced the idea of magnetic stimulation instead of electrical
stimulation. As you read them, do not worry about the details
surrounding the electrical field modeling (they can be skipped).
Concentrate instead on the neural responses.
lee-fallegger-casse-fried-2016-sci-adv.pdf
bonmassar-lee-freeman-polasek-fried-gale-2012-nature-comm.pdf
L9 Writing:
Come up with a new way to map phosphenes for each of low (less than 20),
medium (20-100), and high (100-1000) density artificial
vision. Do not use any methods from the literature (e.g., pointing,
describing clock positions). Propose one method for each condition, or a
single method that covers all three. It will help tremendously to
imagine what the patient would perceive with an erroneous map, and how
the patient would interact with your proposed measurement system.
Consider that a given patient will be able to concentrate for 20-30
minutes at a time, and that their responses will be inherently variable
and only mostly truthful due to lapses in attention.
Assume any existing facility worldwide is at your disposal. Any device or apparatus you can imagine based on existing technology is OK, but no magical new technology (like, say, mind reading) is allowed. Invasive instruments beyond the implant itself are discouraged, but the implant can be augmented if it would help.
The length of your write-up should be about as long as a normal homework review.
For Tuesday, April 25, 2017: sensory substitution.
L8 Reading:
The papers this week are relatively easy reading, as they are mostly
high-level reviews of existing projects for sensory substitution methods
which end up being mostly low-grade, and so are called electronic travel aids.
dakopoulos-bourbakis-2010-ieee-tr-syst-man-cyber-c.pdf
merabet-et-al-2008-plos-one.pdf
ward-meijer-2010-conscious-cogn.pdf
clemons-bao-savarese-austin-sharma-2012-espa.pdf
velazquez-2010-wearable-and-autonomous-systems.pdf
bach=y=rita-kercel-2003-trends-cog-sci.pdf
L8 Optional Reading:
stiles-shimojo-2015-oxford-handbook-percept-org.pdf
ortiz-et-al-2011-plos-one.pdf
L8 Writing:
Write a mini-review of the Merabet, et al., 2008 paper.
Communicating with clarity (Tufte excerpts, Katzoff book):
Here is an excerpt from Edward Tufte's book that was discussed in the
first part of class.
tufte-1997-visual-and-statistical-thinking.pdf
And here are two additional PDFs from Tufte that are available, although purchase of the
hardcopy of The Visual Display of Quantitative Information is highly recommended.
tufte-2006-powerpoint.pdf
tufte-1974-data-analysis-for-politics-and-policy.pdf
And finally, here is a famous publication from Sam Katzoff, technical
writing guru at NASA, about writing technical reports that applies
quite well to writing scientific articles as well.
katzoff-1964-clarity-in-technical-writing.pdf
For Tuesday, April 4, 2017: cortical approach.
L7 Reading:
Brindley and Lewin's classic work:
brindley-lewin-1968-j-physiol.pdf
Dobelle:
dobelle-2000-asaio.pdf
MIT:
schiller-slocum-kwak-kendall-tehovnik-2011-pnas.pdf
tehovnik-slocum-2013-neurosci-biobehav-rev.pdf
IIT / U. Chicago:
troyk-bak-berg-bradley-cogan-erickson-kufta-mccreery-schmidt-towle-2003-artificial-organs.pdf
bradley-troyk-berg-bak-cogan-erickson-kufta-masaro-mccreery-schmidt-towle-xu-2005-j-neurophsiol.pdf
L7 Optional Reading:
schiller-tehovnik-2008-perception.pdf
This is a controversial paper that goes into much detail, arguing that
cortical prostheses are the most compelling approach. It raised an
unusual amount of ire, resulting in the publication of two highly
critical responses by other researchers.
naumann-2012-search-for-paradise.pdf
This is a very long book. While it is worth reading the whole text, the
most relevant part for the course is Chapter 9. Read it over Easter break!
christie-ashmont-house-greger-2016-j-neural-eng.pdf
This is a nice review of retinal and especially cortical efforts, making
the argument that investigation with cortical surface microelectrodes should continue.
L7 Optional Video:
We saw the first few minutes of Blind Hope
during class. The whole video is about 45 minutes long. There is a lot
of overlap with Naumann's book, and reading it first can provide
significant insight when hearing Dobelle speak.
L7 Writing:
Write a mini-review of the Bradley, et al., 2005 paper. Read the entire
paper, but don't worry about the electrode details or histology. Concentrate your
analysis on Figures 9 and 10.
For Tuesday, March 28, 2017: retinal (iii), and optic nerve approaches.
L6 Reading:
Suprachoroidal approach (the last retinal project we'll discuss):
suaning-lovell-lehmann-2014-IEEE-biocas.pdf
matteucci-chen-tsai-dodds-dokos-morley-lovell-suaning-2013-iovs.pdf
Optic nerve approach:
veraart-raftopoulos-mortimer-delbeke-et-al-1998-brain-research.pdf
veraart-wanet=defalque-gerard-vanlierde-delbeke-2003-artificial-organs.pdf
duret-brelen-lambert-gerard-delbeke-veraart-2006-restorative-neurol-neurosci.pdf
sakaguchi-fujikando-ozawa-ustarizgonzalez-quiroz=mercado-2009-j-artif-organs.pdf
L6 Optional Reading:
brelen-potter-gersdorff-cosnard-veraart-delbeke-2006-j-neurosurg.pdf (shows implant)
sui-li-chai-we-zhou-sun-xu-li-ren-2009-implantable-neural-prostheses.pdf
(the Chinese project)
L6 Writing Assignment:
Review Duret, et al.'s 2006 paper (in the reading list above) where they have Patient 2 recognize objects. Concentrate your critique on Figures 5 and 6 where they discuss the time Patient 2 is actively using the prosthesis versus when they seem to be thinking.
For Tuesday, March 21, 2017: retinal (ii) approach.
L5 reading:
The Second Sight Argus-II retinal prosthesis:
da_cruz-dorn-et-al-greenberg-2016-ophthalmol.pdf
dorn-ahuja-caspi-da_cruz-dagnelie-sahel-greenberg-mcmahon-2013-jama-ophthalmol.pdf
The Alpha-IMS retinal prosthesis:
zrenner-2002-science.pdf
stingl-bartz=schmidt-besch-et-al-zrenner-2013-proc-royal-soc-b.pdf
stingl-bartz=schmidt-besch-et-al-zrenner-2015-vis-research.pdf
L5 optional reading:
This seems like a lot of reading, but much of the text is common among
all of the Argus II reports, making it easy to skim these optional articles.
stingl-et-al-2013-proc-r-soc-b-suppl.pdf
zhou-dorn-greenberg-et-al-2013-ieee-icmew.pdf
humayun-dorn-et-al-greenberg-2012-j-ophthamol.pdf
ahuja-dorn-caspi-mcmahon-dagnelie-da_cruz-stanga-humayun-greenberg-2011-br-j-ophthalmol.pdf
L5 writing:
Write up the 2013 study detailing the letter identification tasks used to
characterize the Argus II.
da_cruz-coley-et-al-greenberg-dagnelie-2013-br-j-ophthalmol.pdf
For Tuesday, March 14, 2017: retinal (i) approach.
Reading and writing assignments will be drawn from the following papers.
Yet another review of retinal implants:
chuang-margo-greenberg-2014-br-j-ophthalmol.pdf
The Rizzo-Wyatt (MEEI / MIT) retinal prosthesis effort:
rizzo-wyatt-loewenstein-kelly-shire-2003a-invest-ophth-vis-sci.pdf
rizzo-wyatt-loewenstein-kelly-shire-2003b-invest-ophth-vis-sci.pdf
rizzo-wyatt-loewenstein-kelly-shire-2003c-invest-ophth-vis-sci.pdf
The Palanker (Stanford) retinal prosthesis effort:
boinagrov-pangratz=fueher-goetz-palanker-2014-j-neural-eng.pdf
lorach-goetz-smith-lei-mandel-kamins-mathieson-huie-harris-sher-palanker-2015-nat-med.pdf
mathieson-loudin-goetz-huie-wang-kamins-glambos-smith-harris-sher-palanker-2012-nat-photonics.pdf
L4 reading:
Chuang, Margo, Greenberg (note that this is NOT the same Greenberg as in the Argus-II project)
Rizzo, et al. (a)
Rizzo, et al. (b)
Mathieson, et al.
L4 optional reading:
Boinagrov, et al.
Rizzo, et al. (c)
L4 writing:
Review Lorach, et al., figures 3, 4, and 6.
For Tuesday, March 7, 2017: thalamic approach.
No writing assignment. Reading as follows.
L3 reading:
pezaris-reid-2007-pnas.pdf
pezaris-reid-2009-IEEE-TRBME-preprint.pdf
bourkiza-vurro-jeffries-pezaris-2013-plos-one.pdf
L3 optional reading:
vurro-crowell-pezaris-2014-front-human-neurosci.pdf
killian-vurro-keith-kyada-pezaris-2016-sci-rep.pdf
killian-vurro-keith-kyada-pezaris-2016-sci-rep-supplementary.pdf
For Tuesday, February 28, 2017: causes of blindness, electrical approaches to visual prosthetics.
L2.1 reading:
Vision 2020. Despite being a very large document, it is a quick read. Read through page 8; after that is optional.
Also
read Thylefors,
et al., 1995 on the demographics of blindness, and
Mader, George,
2006 on war-time trauma.
Optional reading:
Jackson, 1996 on landmine blindness,
Theylefors, 1992 on the demographics of ocular trauma, and
Bell, Mino, 2015 on employment outcomes of the blind.
L2.2 reading:
Read Goetz, Palanker, 2016 for an excellent overview of electrical approaches to visual prosthetics.
L2.2 writing:
Read Pezaris,
Eskandar, 2009, and dissect it
completely. Find all of the flaws. Tear it to pieces. Do not hold back
just because it was written by the lecturer.
For Tuesday, February 21, 2017: the early visual system, structure of the retina, and coordinate transformations in the visual system.
Read Hubel, "Eye Brain Vision", 1995 . This is a long, fascinating book by one of the founders of the field of Neurobiology, the late Nobel laureate David H. Hubel. You should skim it to familiarize yourself with background material on the early visual system, concentrating on Chapters 3 and 4. In addition to the PDF linked above, used copies of this out-of-print text are readily available (see, for example, bookfinder.com).
Read the review paper Andersen, Snyder, Li, Stricanne, 1993 on coordinate transformations first, and then the experimental report Andersen, Bracewell, et al, 1990 that contains one component of the review. The written assignment will be drawn on these two papers that introduce the idea of gain fields as a representational mechanism for adapting the center-surround response field to a coordinate system that includes other non-retinal position (eye-in-head, head-on-body, body-in-space) inputs.
For the writing assignment: read the entire second paper (Andersen, Bracewell, et al, 1990), but in your review concentrate on Figures 4 and 6; don't worry about the details in the second half of the paper where they talk about the different kinds of planar fits (Figures 7 and onward; but do look at Figure 14 for a putative model). See the Homework section of the main course page for specific instructions on the mini-review format.
For background on the non-uniform resolution of visual representation as it originates in the eye, read Curcio, Sloan, Kalina, Hendrickson, 1990 for the topography of photoreceptors in the human eye, and Curcio, Allen, 1990 for the topography of human retinal ganglion cells (the output of the retina, the axons of which form the optic nerve). Randall Munroe's XKCD comic on visual acuity can be found at https://xkcd.com/1080/large.
Full list of papers (in alphabetical order)
ahuja-behrend-2013-prog-ret-eye-res.pdf
ahuja-dorn-caspi-mcmahon-dagnelie-da_cruz-stanga-humayun-greenberg-2011-br-j-ophthalmol.pdf
andersen-bracewell-barash-gnadt-fogassi-1990-j-neurosci.pdf
andersen-snyder-li-stricanne-1993-curr-op-neurobiol.pdf
bach=y=rita-kercel-2003-trends-cog-sci.pdf
bell-mino-2015-j-blindness-innov-research.pdf
bensmaia-miller-2014-nature-rev-neurosci.pdf
berger-ahuja-courellis-et-al-2005-ieee-embm.pdf
berger-hampson-song-goonawardena-maramarelis-deadwyler-2011-j-neural-eng.pdf
boinagrov-pangratz=fueher-goetz-palanker-2014-j-neural-eng.pdf
bonmassar-lee-freeman-polasek-fried-gale-2012-nature-comm.pdf
bourkiza-vurro-jeffries-pezaris-2013-plos-one.pdf
bradley-troyk-berg-bak-cogan-erickson-kufta-masaro-mccreery-schmidt-towle-xu-2005-j-neurophsiol.pdf
brelen-potter-gersdorff-cosnard-veraart-delbeke-2006-j-neurosurg.pdf
brindley-lewin-1968-j-physiol.pdf
chuang-margo-greenberg-2014-br-j-ophthalmol.pdf
curcio-allen-1990-j-comp-neurol.pdf
curcio-sloan-kalina-hendrickson-1990-j-comp-neurol.pdf
da_cruz-coley-dorn-merlini-filley-christpher-chen-wuyyuru-sahel-stanga-humayun-greenberg-dagnelie-2013-br-j-ophthalmol.pdf
da_cruz-dorn-et-al-greenberg-2016-ophthalmol.pdf
dagnelie-2008-annual-rev-bioeng.pdf
dagnelie-et-al-2017-clinical-exp-ophthalmol.pdf
dakopoulos-bourbakis-2010-ieee-tr-syst-man-cyber-c.pdf
deadwyler-hampson-song-opris-gerhardt-maramarelis-berger-2017-exp-neurol.pdf
dorn-ahuja-caspi-da_cruz-dagnelie-sahel-greenberg-mcmahon-2013-jama-ophthalmol.pdf
duret-brelen-lambert-gerard-delbeke-veraart-2006-restorative-neurol-neurosci.pdf
glannon-2014-front-sys-neurosci.pdf
goetz-palanker-2016-rep-prog-phys.pdf
hampson-gerhardt-marmarelis-song-opris-santos-berger-deadwyler-2012-j-neural-eng.pdf
hampson-song-opris-santos-shin-gerhardt-marmarelis-berger-deadwyler-2013-j-neural-eng.pdf
hildt-2010-studies-ethics-law-technol.pdf
ho-humayun-et-al-greenberg-2015-j-ophthalmol.pdf
hubel-eye-brain-vision-slides.pdf
humayun-dorn-et-al-greenberg-2012-j-ophthamol.pdf
jackson-1996-eye.pdf
killian-vurro-keith-kyada-pezaris-2016-sci-rep-supplementary.pdf
killian-vurro-keith-kyada-pezaris-2016-sci-rep.pdf
kiral-kornek-osullivan-greene-savage-mccarthy-grayden-burkitt-2014-j-neural-eng.pdf
lane-huyck-troyk-2011-disab-rehab.pdf
lane-huyck-troyk-schug-2012-disab-rehab.pdf
lane-nitsch-huyck-troyk-schug-2014-disability-rehab-assist-tech.pdf
lee-fallegger-casse-fried-2016-sci-adv.pdf
lorach-goetz-smith-lei-mandel-kamins-mathieson-huie-harris-sher-palanker-2015-nat-med.pdf
luo-zhong-clemo-da_cruz-2016-am-j-ophthalmol.pdf
mathieson-loudin-goetz-huie-wang-kamins-glambos-smith-harris-sher-palanker-2012-nat-photonics.pdf
matteucci-chen-tsai-dodds-dokos-morley-lovell-suaning-2013-iovs.pdf
merabet-et-al-2008-plos-one.pdf
merabet-rizzo-pascual=leone-fernandez-2007-n-neural-eng.pdf
nau-bach-fisher-2013-trans-vis-sci-tech.pdf
naumann-2012-search-for-paradise.pdf
pezaris-eskandar-2009-neurosurgical-focus.pdf
pezaris-reid-2007-pnas.pdf
pezaris-reid-2009-IEEE-TRBME-preprint.pdf
rizzo-belting-cinelli-allegrini-genovesi=ebert-barca-di_bartolo-2014-am-j-ophthalmol.pdf
rizzo-wyatt-loewenstein-kelly-shire-2003a-invest-ophth-vis-sci.pdf
rizzo-wyatt-loewenstein-kelly-shire-2003b-invest-ophth-vis-sci.pdf
rizzo-wyatt-loewenstein-kelly-shire-2003c-invest-ophth-vis-sci.pdf
sakaguchi-fujikando-ozawa-ustarizgonzalez-quiroz=mercado-2009-j-artif-organs.pdf
schiller-tehovnik-2008-perception.pdf
stiles-shimojo-2015-oxford-handbook-percept-org.pdf
stingl-bartz=schmidt-besch-et-al-zrenner-2013-proc-royal-soc-b.pdf
stingl-bartz=schmidt-besch-et-al-zrenner-2015-vis-research.pdf
stingl-et-al-2013-proc-r-soc-b-suppl.pdf
stronks-dagnelie-2013-expert-reviews.pdf
suaning-lovell-lehmann-2014-IEEE-biocas.pdf
sui-li-chai-we-zhou-sun-xu-li-ren-2009-implantable-neural-prostheses.pdf
tabot-dammann-berg-tenore-boback-vogelstein-bensmaia-2013-pnas-includes-correction.pdf
tehovnik-slocum-2013-neurosci-biobehav-rev.pdf
thomspon-barnett-humayun-dagnelie-2003-iovs.pdf
thylefors-1992-aus-nz-j-opthalmol.pdf
thylefors-negrel-pararajasegaram-dadzie-1995-bull-who.pdf
troyk-bredeson-cogan-et-al-bak-2014-ieee-embs.pdf
velazquez-2010-wearable-and-autonomous-systems-not-sure-this-is-worthwhile.pdf
veraart-raftopoulos-mortimer-delbeke-et-al-1998-brain-research.pdf
vision-2020-who.pdf
vurro-crowell-pezaris-2014-front-human-neurosci.pdf
ward-meijer-2010-conscious-cogn.pdf
weitz-et-al-weiland-2015-sci-transl-med.pdf
yanai-et-al-2003-trans-am-ophthalmol-soc.pdf
yanai-lakhanpal-weiland-mahadevappa-van_boemel-fujii-greenberg-caffey-de_Juan-humayun-2003-trans-am-ophthalmol-soc.pdf
zhou-dorn-greenberg-et-al-2013-ieee-icmew.pdf
zrenner-2002-science.pdf
zrenner-bruckmann-greppmaier-hoertdoerfer-kernstock-sliesoraityte-stingl-wilhelm-2011-arvo-abstract.pdf