User talk:Andy Maloney/Surface passivation effects on kinesin and microtubules

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If you do not have an account with Open Wet Ware, you can obtain one from here. I would like to have people format their questions and comments in the following manner:
 * 1) Make a subheading with your name by typing in the following to the wiki:
 * 2) * ===Your Name=== This subheading will be your area where you can post new comments to or, update any comments that you may have previously posted.
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 * 4) * ~: The output of this looks like: Andy Maloney 12:29, 7 February 2011 (EST):.

If you are unfamiliar with how to use media wiki markup, please take a look at the following formatting article. If for some reason you are not willing to join the wiki, you can email me by following the link below.


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As much as I would like to keep my dissertation completely open and in the media wiki format, I will have to at some point format it to the guidelines dictated by my university. This will necessitate putting a final "snap shot" of the dissertation in a book format of which, all comments will have their own special appendix in each chapter.

Thanks for looking at my open dissertation!

Cesar A. Rodriguez-Rosario

 * Cesar's Lab Page.


 * 1) You might want to change the voice of the dissertation. I like it like this, colloquial an honest. But it might get you in trouble later down the line with the university. For example, things 'like I became obsessed with ...' or 'I thought he was out of his mind' are true, but might jump out at your dissertation committee. So, think how to stay honest to the trial-and-error and informal collaborations that are natural for science, while making sure the language is acceptable for your committee. Don't give them any easy shots at you!
 * 2) * Andy Maloney 15:31, 19 March 2011 (EDT): Personally, this is how I feel. I seriously do not care one iota in making the language of my dissertation more pompous. This is outright ridiculous and I feel that it is archaic to speak in a language that is designed to be difficult. However, not being ignorant with my language is a the right way to go and I completely agree with what you have said. Retaining the feel of a conversation without making asinine remarks is the way I'd like to keep things and the iteration from the rough draft to the first (the one right now as of this writing) removes the more flamboyant remarks I made.


 * 1) You might want to either relable your plot axis or expand the caption. For example, "Graph showing speed values after temperature stabilization. ". Speed of what? It is in the text, but needs to be on the plots also.
 * 2) * Andy Maloney 15:31, 19 March 2011 (EDT): Good points. I've reworked the figure captions.

Steve
Steve Koch 15:14, 6 April 2011 (EDT): The navigation links are currently for Chapter 2, not Chapter 3 never mind
 * Suggest changing to "Biophysical observations of motility". This is because there are tons of other ways of studying--biochemically, cryo-EM, x-ray crystallography.  In terms of motility, a 3rd important way is via fluorescence microscopy and observation of dye-labeled motors.  Find a couple refs for that and add to your sentence.
 * Andy Maloney 17:53, 6 April 2011 (EDT): I have no clue what you are asking me to do with this one.
 * Steve Koch 23:11, 6 April 2011 (EDT): I am saying as you have it written now, you say, "these are the ways to study the system." But there are a zillion ways to study the system.  If you say there are a few ways to observe kinesin / microtubule translocation or motion or movement, then it's much more accurate.  But even then, optical tweezers and gliding assays aren't the only way.  You can also observe kinesin and / or cargo moving on microtubules via fluorescence.  Either by labeling the kinesin with dye (like Vale and others) or GFP or a dyed bead.  Plus you can do this in vitro or intra cellular too.
 * Andy Maloney 16:23, 7 April 2011 (EDT): Got it.
 * "movie looses" -> loses
 * Andy Maloney 17:53, 6 April 2011 (EDT): Thanks. It's been changed
 * Long term: worried about Instructables post going behind a pay wall. Low priority, but finding a way to archive those pages would be nice.  FriendFeed for suggestions?
 * Andy Maloney 17:53, 6 April 2011 (EDT): That won't happen. The post is public domain and if Instructables did put up a pay wall they would be violating copyright law if it remained on their servers. While Instructables likes to bludgeon visitors with advertisements, their mentality is still firmly planted in the maker community which likes to disseminate information and not put a wall around it.
 * Can you define or link to definition of mise en place? I can guess it means my own place.  should it always be italicized?
 * Andy Maloney 17:53, 6 April 2011 (EDT): Done. Linked to the Wikipedia article. I guess it doesn't need to be italicized.
 * typo: (Hunt 1994). showed
 * Andy Maloney 17:53, 6 April 2011 (EDT): Done.
 * typo: "total of 15 time"
 * Andy Maloney 17:53, 6 April 2011 (EDT): Done.
 * "thanks to Larry Herskowitz"-> "written by" (cite Larry's dissertation)
 * Andy Maloney 17:53, 6 April 2011 (EDT): Done.
 * "The software did not track" -> "Microtubules successfully tracked for fewer than 100 consective images were discarded."
 * Andy Maloney 17:53, 6 April 2011 (EDT): Changed.
 * "analysis program again written by" -> "analysis program written by Larry Herskowtiz and Steve Koch" (cite Larry's dissertation)
 * Andy Maloney 17:53, 6 April 2011 (EDT): Done.
 * "transient" -> transverse or "Brownian motion transverse to the motility direction"
 * Andy Maloney 17:53, 6 April 2011 (EDT): Done.
 * Important The discussion of Figure 8 in the text and the caption is going to confuse people, due to the fact that the figure shows speed versus time. It's important to convey that we smooth the x,y time series data and then calculate the speed.  Figure 8 shows the speed from smoothed or unsmoothed data, but there's currently a risk that someone would think we smoothed the speed data, which would produce a different answer.  Let me try by revising Figure 8 caption:
 * Figure 8: Data analysis. Blue markers are the speed values from unsmoothed X and Y positions of the microtubule end. The black curve shows the speed values calculated after smoothing the position data using a Gaussian window with a width of 2 seconds. The red curve shows the speed data after removing the first and last 5 second time periods and is the data that is then analyzed by the KDE algorithm.
 * Andy Maloney 17:53, 6 April 2011 (EDT): Switched to your description.
 * Note: You use "data" as a singular, which is fine with me. Most people still like to say "data" is always plural, but I really don't care.  "data" can be short for "data set" which would then be singular.  Just letting you know in case you care.
 * Andy Maloney 17:53, 6 April 2011 (EDT): Ha! Where? I can change it to datum if you want me to.
 * I am thinking it would be good to retain a short "acknowledgements" section in each chapter to thank Haiqing and Gabe for the kinesin and also to acknowledge the funding sources. Basically, just repeat the acknowledgements from the paper we submitted to PLoS ONE.  I am thinking this, even though you do acknowledge in the chapter on acknowledgements, because on the web, people are likely to only read one chapter at a time.
 * Andy Maloney 17:53, 6 April 2011 (EDT): Good call. Done.
 * "green fire blue LUT using a custom..." -> "...written by Larry Herskowitz and Andy Maloney."?
 * Compile this as EXE and post it somewhere? (it wouldn't work without NI Vision license, though)
 * Andy Maloney 17:53, 6 April 2011 (EDT): Did it already and it is now on the server as an exe. The software files are referenced with a link to them on the server.
 * Figure 13:
 * "upside down"-> "down-pointing" maybe is more clear.
 * Andy Maloney 17:53, 6 April 2011 (EDT): Yes it is.
 * "error bars are the SEM for each region.." this is misleading, try -> "each data point is the mean for three ROIs from separate samples at the corresponding assay time point. error bars are the SEM of those three measurements."
 * Andy Maloney 17:53, 6 April 2011 (EDT): Changed the wording.