how do you read PDFs?

July 28, 2010 at 8:59 am | | everyday science, help me, literature, open thread, software, stupid technology

I now have a longer commute, with at least 30 minutes of quality reading time. I don’t really want to carry my laptop everyday, so I’m seeking a better way to read journal articles. I’m not going to print them out, so don’t suggest reading them on paper. :)

[poll id=”3″]

Of course, cost is a factor, but I don’t want to go for the cheapest option if I end up never using it! My guess is that the Kindle DX is the best for reading PDFs, but loses on other fronts (e.g. large, expensive, limited, only grayscale). The iPad is a versatile color reader and I can sync with programs such as Papers or Mendeley (soon for the latter), but it is very expensive. Also, the screen isn’t as nice for reading print. The iPhone is way too small to read PDFs.

Man, I need to test-drive these devices for a month!

Other options?

Ubiquitous oxymoron in journal articles and the English vernacular

September 20, 2009 at 12:03 am | | help me, nerd

How many times have you heard someone refer to the “biggest bottleneck” in some process? I’d guess at least once a week if you’re an engineer. Now think about that for a moment.  Biggest bottleneck?  Exactly how much flow does a BIG bottleneck suppress? I didn’t have this epiphany until I typed “smallest bottleneck” in my dissertation.  But “biggest bottleneck” wins over “smallest bottleneck” by an 84:1 margin according to Google.  It is not rigorously an oxymoron, however, because there could literally be a series of bottlenecks and one could be the biggest (i.e., largest bore diameter), but the manner in which the term is commonly used suggests a contradictory role between the adjective and noun. I guess it’s like people saying “I could care less” when they mean “I couldn’t care less.” Am I crazy or does this bother anyone else?  “Accuracy above all else,” I say.


April 1, 2008 at 10:56 am | | blogs, help me

EDS is going to start charging readers of this blog. I hope that’s OK with everybody. You can use Paypal, credit card, or cash. But I’ll leave it up to y’all how much we charge.

All the proceeds (after we pay for site maintenance, travel expenses, and CEO compensation and bonuses) will go to the Virgle project.

hot gum!

October 17, 2007 at 4:36 pm | | help me, open thread, science and the public, science@home

Who wants to help me?

Here’s an email my PI received. First of all, it’s pretty cute that some high-school student is emailing professors at Stanford for some help. Secondly, it’s even cuter that the profs actually read the email!


My name is [redacted] and I’m a highschool student who is currently doing an Honors Chemistry project. My idea that I’m experimenting with is that I’m going to try to determine if there is a temperature change or a chemical change that affects the feeling of the mouth when gum is chewed. I was actually doing quite well with my ideas, but now I’m kind of stuck, so I was wondering if somebody in the chemistry department could e-mail me back or possibly help me.

My idea that I was going with is that I wanted to first start out and (using a mouth thermometer) get a starting temperature of a person’s mouth before chewing gum. Then, I wanted to pick a brand of gum in both mint and cinnamon flavors and seperately measure if there is an increasing or decreasing temperature change. My hypothesis is that there will not be a significant change at all, so that’s where the chemistry part comes in. I wanted to then somehow test saliva samples or something with the different chemicals of gum to determine which ingredient creates the “feeling” that the mouth is hot or cold. Except I really have no idea how to go about doing that.

Do you think someone could give me some ideas within the next day or so and let me know/point me in the right direction on how I should go about doing this experiment? That would be amazing, thank you!

My first thought was to look at two flavors of the same brand of gum, find the ingredients that are different, buy those (food-grade) chemicals, and taste them! But most gums just list “natural and artificial flavoring” in the ingredients, so that wouldn’t work. Separating the different ingredients in the gum is a possibility, but probably too difficult.

Another option is to guess the flavors the manufacturers used for cinnamon and mint (an educated guess, but doing some research about flavorings). I bet they use menthol for the mint. I don’t know what they use for the spicy cinnamon, but I know that capsaicin is the chemical that makes chili peppers taste “hot” (by interfering with the pain receptors in your mouth). You could use capsaicin and menthol on saliva samples and measure changes in the temperature or whatever. These would be good estimates of the chemicals they use as flavoring in gum.

Other thoughts? Would there be a very simple way of separating the flavor ingredient without a column or TLC plates? Maybe a paper towel? Or maybe the student could just dissolve the gum in warm water and use the solution of all the ingredients.

But I don’t know what they would measure in the saliva sample (gross!) that could relate to taste.

in cellulo?

July 30, 2007 at 10:27 am | | help me, literature, open thread

What do you call experiments done in a live cell? Some call it in vivo, but that seems to make more sense for in an entire organism (and some of the cellular work is done in single cells of more complex organisms, such as CHO cells). But it definitely should be differentiated from in vitro experiments, because you’re dealing with life!

How about in cellulo? Sounds sorta weird to me.

Is there an accepted term, even an archaic one? Does anyone have a preferred term?

UPDATE: Andrea in the comments suggest that the correct Latin for would be in cellulis.

any matlab gurus out there???

April 2, 2007 at 9:44 am | | everyday science, help me, software

I need some help with my Matlab m-file. Any geniuses know how to save a figure without the border?



  • The m-file produces an array of numbers: columns indicate the x- and rows the y-position of a pixel of intensity denoted by the number’s value
  • I make a figure and use the command pcolor
  • I turn the axis off
  • I save using the saveas command

Basically, I want the pcolor figure alone so I can import it into a different program and click on the image to move a stage to that location. Having a border means the stage will move to the wrong place. (I know this is a clunky solution to a scanning-stage program. Shut up. Stop making fun of me.)

Any thoughts? I’ve found that imwrite saves only the image array, but I don’t know how to use pcolor or shading 'interp' with imwrite.

To encourage random people to help me with my research, I’ll send an EDS magnet to the first person who tells me how to do this correctly—or at least points me in the right direction. I’ll update y’all as soon as I know.

[Update: Here’s a good image I created. See comments below.


I know, it’s flipped. But I can easily deal with that.

We have a winner, but I might send more magnets for more elegant solutions.]

50/50 Beamsplitter?

March 26, 2007 at 8:06 am | | everyday science, hardware, help me

I guess optics are harder to make in the infrared. You ask for a 50/50 beamsplitter for 3.5 to 6.5 microns and you get something like this. I guess it crosses 50% T a couple of times within the spectral window so I shouldn’t complain.

If anyone knows a good source for IR beamsplitters that have flat spectral responses and also don’t achieve their %Reflectance with multiple little reflections leading to strings of pulses separated in time by a few tens of femtoseconds let me know.

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