Izabela Korwel » University

Searching in scientific literature

izabela — Fri, 22 Jan 2010 12:53:42 +0000

How do you perform your literature search? When you work on a project, and need to familiarize yourself/acknowledge all the previous papers, “to the best of your knowledge” all of them, reporting same or similar stuff, what do you do? I am working in the biomedical field. The first thing I so, I always go to [tag]SciFinder[/tag], put in a name of compound I need to look for, or the structure, or formulate phrase. What I particularly like about SciFinder is that it enables you to access full text articles with one mouse click, as long as your institution has a subscription to given journal or SciFinder has (there are some like that).
I am not really convinced to using Google Scholar. I guess it just is not “scientific” enough, as it is not a database… Maybe also the form how the results are displayed doesn’t particularly fit me. What I appreciate about it is the fact, that it is linked to my University library system, and checks availability of full text, and (I love it!) if it is not available, it is linked to Interlibrary Loan and after I log in- the order form is filled for me! I just need to click Submit. It can’t get easier than that. That’s why I would use it sometimes.
Now, the one thing I never use is PubMed. I tried. It is just beyond me to understand how to formulate question to get decent response and relevant hits, and how the results are displayed is completely useless for me, and hard to browse.
Anybody has different experience? Are you using another database or service?

Comic strips from the lab

izabela — Fri, 23 Oct 2009 00:07:16 +0000

I think the lab meeting was very successful today . The presenting student showed some strips from this web page, and now I am going through archive, having fun. “Addressing reviewers comments” is just hilarious. I think I am going to look through best 200 next, instead of trying to get anything useful done. After all, I just came back from vacation.

Webinar and membership app

izabela — Fri, 09 Oct 2009 19:22:07 +0000

Being a member of American Chemical Society, I decided to join also Society of Toxicology as well, it looks good on CV and they have good programs for carrier development.
However, the major reason was the fact, that they have a post-doc assembly, which is very active.
I recently part in SOT Webinar “From Postdoc to Faculty: Climbing the Ladder of Academia“. It was an eye opening event, and gave me some ideas where to start even thinking about my future carrier. And I am not even talking writing research statement and teaching philosophy, I am talking about independent scientific project! I was flirting with this thought, because I wanted to get some grant money to help with my salary, but it seems I need it to be even considered for the job. I never thought that if I changed a lab, I will need a project I can bring with me, not to compete with my old lab. Sound obvious? Yeah, sure, I just didn’t realize it.
After this Webinar, I wanted to join them on Facebook, to know when next events come, but was denied because I am not a member. I was upset for a while, but I thought about it more, considered the price, and the fact that I will attend the national meeting, and decided to apply.
And man, those guys are serious about their application. It is a really competitive process. You fill out all the information about your degrees and scientific work, and they consider you. I wish I signed earlier, I could add it to my “green card” application under “competitive professional organizations” . Well, of course I would have to get it done before their decision making, which happens only 3 times a year. Next time is in January. And, luckily, my boss is a full member, so I could use him as a “sponsor” and he was happy to write a recommendation letter for me.
Now, I will wait till sometimes next year, to see if I am good enough. I will keep you posted.

PCBs in Miami

izabela — Tue, 10 Jun 2008 21:23:03 +0000

As much as I love my job, sometimes I wonder how really important is what I do. Well, I am starting almost each scientific paper from “[tag]Polychlorinated biphenyls[/tag] are important environmental contaminants” or something of this sort. But are they really? To keep me going believing in it, I really need from time to time to read the articles like this about PCBs being found in whales or like that, featuring PCBs and other currently monitored pollutants in human blood, both published by [tag]National Geographic[/tag]. But in fact I never seen [tag]PCBs[/tag] being present in more “contemporary” literature before. Until today. I am currently “reading out” [tag]Edna Buchanan[/tag] crime stories, and here it is, on page 43 of “Suitable for framing”. They are talking about PCBs which were found in copier ink and are contaminating air in the office. Can be as well true! I guess it means that somebody, not just us scientist, not only knows, but also cares about those PCBs around them. And it reminds me as well about the interesting PCB-related web page somebody mentioned on last meeting. It was started by a parent who found out that PCBs may be present in caulk, and contaminate soil around schools, where children play. Really, when I think how little [tag]research translation[/tag] most of us, scientist do, I wonder where people really find all this information! I am sure they don’t read our scientific papers and journals, I don’t read them myself! I will print out and read articles related to my work, and that’s it. They are just plain boring. But that’s good that they do, and that’s good that I am working on something that matters. After all.

Talk at the conference

izabela — Fri, 16 May 2008 15:32:04 +0000

Next week, it is a big day in my scientific carrier. I am going to give a [tag]talk[/tag] at the [tag]international conference[/tag]. I am very exited. I find it as a great chance to kind of force people to notice my research . It just seems to be more direct interaction than [tag]poster[/tag], at which people may stop or may not, depending on how interesting graphical explanation of your results you prepare. The problem is that my research is rather inter-disciplinary. It is too biological for chemists to notice, and too chemical for biologist to care.
At the same time, I am stressed like hell. Not only my boss already twice removed some slides from my posters, making me to invent my story from the very beginning. Also, telling the presentation is one thing, answering all the questions people may ask is another. They can ask me about anything they like, most probably- anything they are experts in. Which not necessarily is something connected to my research…
Anyway, I know a lot of people preparing for a presentation like that would prepare slides in Power Point, then sit down and write their whole presentation. And then I guess try to learn it by heart?
I don’t do that. I prepare slides, thinking how I am going to talk about them. And then I just run the [tag]presentation[/tag] and just talk about them. It seem like harder way of doing that. But at least, I will find myself in front of 150 people in big room and if I freeze, I won’t need to remind myself what the heck was the first word of the first sentence of my introduction to my talk….
My boss already gave me one the advice I really like. Focus on your plot- explain axis and what is presented on the plot, and the story will come to you…
Anyway, I wonder how many people really write the presentation down, and how many prefer to go live?

On Open access publishing

izabela — Thu, 01 May 2008 17:35:42 +0000

The big issue this year is the new [tag]NIH[/tag] policy requiring to provide the copy of accepted manuscript resulting from NIH sponsored grant to [tag]open access[/tag] repository in biological sciences database PubMed. As much as I was always thrilled by open access publishing, I am starting to seriously rethink this opinion. New policy requires that every manuscript accepted after April 7, 2007, describing research financed by NIH, needs to be submitted to [tag]PubMed[/tag]. You have some options though. You may send the “dirty manuscript”- your file as of the day the manuscript was accepted – or, in some cases – the final published paper (after proofing, journal style re-wording etc.).

The “case” depends on the journal in which final manuscript is published, or really what copyrights you retained when submitting. The article, depending on your choice of way to submit it, may appear in PubMed right away, or after 6 or 12 months. It may be exactly the same file as published paper, or it may differ quite considerably (but not in the scientific content!).

Of course, the publishers of non-open-access journals worry about their profits, and it looks that they have the basis for that. Some, like American Chemical Society, suggest that you pay $1000 (per manuscript!) to retain the right to open access distribution of that article, and thus it may be published on PubMed (or your own web page for that matter) right away. Seems to be a bit costly to me. As somebody commented today, it is a week or two worth of supplies, not a spare change really.

Now, in the beginning the whole open access was invented as the way to provide to everybody – be it the US taxpayers or whole scientific community even in poor countries – non limited access to all the results, papers and ideas. The question is, if it is not going to block or at least seriously limit the possibility for the scientists in poorer countries to publish in popular, and thus probably expensive journals? They currently have an option, because only NIH requires posting papers, and if you don’t want to buy open access, you don’t have to. The questions is, if paying large amounts of money to have your paper published (which to some extent is already present as per page fee in some journals, but not in many) is not the direction in which the open access movement is going? And this is my impression it may be the case.

On scientific review

izabela — Wed, 26 Mar 2008 18:54:05 +0000

If you are a scientist, from time to time you hear a discussion about Open Access or Impact Factors… You for sure have your opinion on those “hot topics”. Now, is anybody ever thinking about how unfair the [tag]peer review[/tag] procedure is? The reviewer always knows who wrote the paper he is reviewing, and I am sure quite often people who should do not refuse. Isn’t reviewing somebody’s paper the best way to get to them? And you will never know, because the reviewer remains anonymous. I am leaving alone the fact how often reviewers know little about the subject and ask really….. trivial questions.
Now, there are two possible ways to change the peer review process. My favorite would be to make it double blind- reviewer doesn’t know whose paper he is reviewing and the author doesn’t know who reviewed his manuscript. Sounds fair to me. But recently discussing it with my husband, he came up with another idea- the double-open peer review. Scientists prepare manuscript and simply put it out to the open discussion by everybody who cares. Of course if you ever read all the comments to news stories on any news web page, you realize that the discussion to be constructive needs to be somehow moderated. Moderated, not censored! I cannot think of simply making that type of open review happen, but I like the idea.

Power calculations in R

izabela — Tue, 28 Aug 2007 15:01:11 +0000

My first huge disappointment with R. My boss wanted me to do simple [tag]power calculations[/tag] to see how adding 2 animals to one of groups will improve statistical power. Yeah, I know, you are not supposed to do “retrospective power calculations”. Tell it to people providing lab animals, they always give you couple more just in case something happened to one or two you have. So, sometimes we have to do just that. Well, not in R.
There is this nice and simple [tag]power.t.test[/tag] function, with
n= for number of subjects in a group
delta = for difference between groups
sd= for standard deviation
sig.level= for desired alpha
power= for power, obviously
All you need to do is to define all but one and the remaining is calculated. Great, but how about if your groups are of unequal sizes? There is always Google? Not this time.
There is nice package [tag]pwr[/tag], if you happen to work on proportions and can use beauty of binomial distribution. That’s it.
Solution? I opened SAS and did what I needed in 1 min.
[tag]Proc power[/tag] works like power.t.test, but you can do calculations with different sd’s in groups, different group sizes and different experimental design. Wonder, when R catches up…

Dunnett all-to-control test in R

izabela — Wed, 22 Aug 2007 17:24:14 +0000

OK, it is going to be a first of series of blog entries on my struggle with [tag]R project[/tag]. I consider myself an amateur in statistics and in R, so they are going to be without any theoretical background and discussions of the math underneath the stuff I am going to write about, so any comments are welcome.

Anyway, my task was to run [tag]Dunnett test[/tag] on set of data from some animal study. If it was my experiment, I would run one-way ANOVA and maybe happily discover some other relationships significant and were unable to make sense out of it in the paper. This time, not my project, and I was told Dunnett is all they need.

OK, thanks God for Google, I found nice article in R News from December 2002, where the stuff was quite well explained, read my data into R, one line of code:
simint (variable1~group, conf.level=0.95, alternative=’two.sided’

got my results and….disturbing:

Warning message:
‘simint.default’ is deprecated.
Use ‘glht’ instead.
See help(“Deprecated”) and help(“multcomp-deprecated”).
Great! In plain English, I just wasted my time discovering something that maybe next time I need to run same test won’t be there any more.

OK, count down from 150, and start looking for [tag]glht[/tag].

Of course, something I just minutes ago did in one line, now requires no less then three:

model <- aov(variable1~group)
results <- glht(model, linefc=mcp(group='Dunnett'), alternative='t' )
summary(results)

Maybe it is better though, as I got all significance levels at once.

Dry ice

izabela — Tue, 15 May 2007 17:59:11 +0000

Have you ever bought dry ice at Wal-Mart paying with business credit card? You have no idea what you are missing. I had to do it 3 time during past week. It seems unbelievable, but each time I faced different set of obstacles. Now looking back, I think my first time was most successful, as the cashier had no idea how to do that and the manager was rather polite. Although it took her 15 minutes and 3 trips to office to find the right key. Yesterday, I couldn’t convince cashier (different one, unfortunately) that dry ice is not the same as regular ice and I cannot pick it up on my way out. Not only because the ice is in locked container….. Today, although I insisted I need to fill up provided box, I got two larger pieces in Wal-Mart disposable bag…. Couldn’t fit the stuff in my styrofoam box to drive back to lab.

I think the quotient of cashier’s intelligence and the product price needs to be constant. Next time I will add the 3 miles to see how it works in Hy-Vee.