Research / Scholarship posts
- September 28, 2010
- 08:00 AM
- 837 views
Virtual Therapy – Wave of the Future?
by Shaheen Lakhan in Brain Blogger
Depression is a mood disorder characterized by the absence of a positive effect, low mood, and various associated emotional, physical, cognitive, and behavioral symptoms. Associated symptoms include sadness, pessimism, loss of interest, changes in sleep, decreased appetite, and decreased motivation. New technology has allowed depression to now be treated by way of computer. European countries [...]... Read more »
DeRubeis, R., Siegle, G., & Hollon, S. (2008) Cognitive therapy versus medication for depression: treatment outcomes and neural mechanisms. Nature Reviews Neuroscience, 9(10), 788-796. DOI: 10.1038/nrn2345
Green, K., & Iverson, K. (2009) Computerized cognitive-behavioral therapy in a stepped care model of treatment. Professional Psychology: Research and Practice, 40(1), 96-103. DOI: 10.1037/a0012847
Marks IM, Cavanagh K, & Gega L. (2007) Computer-aided psychotherapy: revolution or bubble?. The British journal of psychiatry : the journal of mental science, 471-3. PMID: 18055948
Moussavi, S., Chatterji, S., Verdes, E., Tandon, A., Patel, V., & Ustun, B. (2007) Depression, chronic diseases, and decrements in health: results from the World Health Surveys. The Lancet, 370(9590), 851-858. DOI: 10.1016/S0140-6736(07)61415-9
Bates B, Choi JY, Duncan PW, Glasberg JJ, Graham GD, Katz RC, Lamberty K, Reker D, Zorowitz R, US Department of Defense.... (2005) Veterans Affairs/Department of Defense Clinical Practice Guideline for the Management of Adult Stroke Rehabilitation Care: executive summary. Stroke; a journal of cerebral circulation, 36(9), 2049-56. PMID: 16120847
- September 27, 2010
- 11:30 PM
- 592 views
Because publishing your paper is only half of the job
by Rogue in Into Oblivion
The title of this posting refers to the excellent article from David Dobbs I bookmarked very recently. I’d like to present you a very interesting initiative from French bioscience research program for high-school students called « Tous chercheurs ». The Community Page of the very last PLoS Biology is dedicated to this project and I find it really great. Because, indeed, publishing your science paper is only half of the job.... Read more »
Hammond, C., Karlin, D., & Thimonier, J. (2010) Creative Research Science Experiences for High School Students. PLoS Biology, 8(9). DOI: 10.1371/journal.pbio.1000447
- September 27, 2010
- 04:10 PM
- 612 views
Faculty, librarians and student research skills: are we on parallel paths?
by bjms1002 in the Undergraduate Science Librarian
One of the themes I’ve been writing a lot lately is that department faculty and librarians aren’t talking to each other as much as they should, especially in areas that they are both concerned about. One of the biggest areas we need to be talking more about concerns student’s library research skills (or information literacy [...]... Read more »
Davies-Vollum, Katherine Sian, & Greengrove, Cheryl. (2010) Developing a “Gateway” Course to Prepare Nontraditional Students for Success in Upper-Division Science Courses. Journal of College Science Teaching, 40(1), 28-33. info:/
- September 27, 2010
- 08:42 AM
- 1,311 views
News about the Integrated Microbial Genomes (IMG) resource
I’ve got a few news items regarding IMG, or Integrated Microbial Genomes, from the DOE Joint Genome Institute. The first item is that their Sept 2010 release occurred this week. IMG is now on version 3.2, has updated features and a bunch of new/revised genomes. I’ve begun updating our tutorial & will let you know when that is released. It’s not the craziest level of tool changes that I’ve seen from this group, but dang, they SURE don’t rest on their laurels! They are constantly changing and improving their interface and database.
If you are involved in microbial research and haven’t already checked out this powerful resource, I strongly suggest that you do. We’ve been training on this resource since 2006 and really believe in its value, which seems to increase with each of their releases. Mary & Trey presented an IMG workshop at NIH recently and it was surprising how many of their researchers were not aware of IMG. We hear that pretty often and it is too bad, it has so much to offer the microbial community and others as well.
The second item is that IMG has an annotation tool specifically designed for undergraduate education. Iddo Friedberg describes this as ‘Way cool’ in a recent tweet. The program/interface is named the “Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT)“, and is somewhat associated with the “Interpret a GEBA Genome for Education” project from JGI. “GEBA” stands for Genomic Encyclopedia of Bacteria and Archaea. Both efforts are aimed at encouraging undergraduate research in microbial genome annotation, which might lead to the ‘alternative science career’ as a biocurator!
You can read all about the tool in their PLoS Biology article “Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum“, or see a tour of the program/interface here. The tour makes the interface seem a bit clunky to me, but well thought out with lots of solutions to problems/issues often associated with undergraduate classes. The paper really provides a nice overview of the concept, collaborations, and initial outcomes of the 2008-2009 program.
Sign-ups are occurring for the 2011-2012 version of the program. The time frame is as follows:
Timeline to Participate:
1. Apply to be part of the 2011-2012 team by Monday, November 5, 2010 (download the application)
2. After acceptance, attend the workshop at the JGI (January 2011)
3. Implement in 2011-2012 academic year
as can be seen at the bottom of this page.
IMG-ACT Reference:
Ditty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z., Sanders-Lorenz, E., Axen, S., Kim, E., Johns, M., Scott, K., & Kerfeld, C. (2010). Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum PLoS Biology, 8 (8) DOI: 10.1371/journal.pbio.1000448
... Read more »
Ditty, J., Kvaal, C., Goodner, B., Freyermuth, S., Bailey, C., Britton, R., Gordon, S., Heinhorst, S., Reed, K., Xu, Z.... (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biology, 8(8). DOI: 10.1371/journal.pbio.1000448
- September 26, 2010
- 10:06 AM
- 765 views
Shadows on the wall: « Truth never triumphs, but its opponents eventually die »
by Rogue in Into Oblivion
Gregory Petsko wrote a small comment in the very last Genome Biology titled Shadows on the wall. A very angry but still contained one, nicely written and important to think about. Here is some of my thoughts about. Gregory Petsko discusses a question related to what people call « paradigms » and innovation. Paradigm is a word [...]... Read more »
Petsko GA. (2010) Shadows on the wall. Genome biology, 11(9), 136. PMID: 20863416
- September 26, 2010
- 07:28 AM
- 555 views
Big Pharma Explain How To Pick Cherries
by Neuroskeptic in Neuroskeptic
Here at Neuroskeptic, we see a lot of bad science. Maybe, over the years (all 2 of them) that I've been writing this blog, I've become a bit jaded. Maybe I'm less distressed by it than I used to be. Cynical, even.But this one really takes the biscuit. And then it takes the tin. And relieves itself in it: A New Population-Enrichment Strategy to Improve Efficiency of Placebo-Controlled Clinical Trials of Antidepressant Drugs.Don't worry - it's from a big pharmaceutical company (GlaxoSmithKline), so I don't have to worry about hurting feelings.It's is full to bursting with colourful graphs and pictures, but the basic idea is very simple. As in "simpleton".Suppose you're testing a new drug against placebo. You decide to do a multicentre trial, i.e. you enlist lots of doctors to give the drug, or placebo, to their patients. Each clinic or hospital which takes part is a "centre". Multicentre trials are popular because they're an easy way of quickly testing a drug on a large number of patients.Anyway, suppose that the results come in, and it turns out that the drug didn't work any better than placebo, which unfortunately is what happens rather often in modern trials of antidepressants. Oh dear. The drug's crap. That's the end of that chapter....or is it?!? say GSK. Maybe not. They have a clever trick. Look at the results from each centre individually. Placebo response rates will probably vary between centres: in some of them, the placebo people don't get better, in others, they get lots better.Now, suppose that you just chucked out all of the data from centres where the people on placebo got much better, on the grounds that there must be something weird going on in those ones. They reanalyzed the data from 1,837 patients given paroxetine or placebo, across 124 centres. In the dataset as a whole, paroxetine barely outperformed placebo. However, in the centres where people on placebo only improved a little, the drug was much better than placebo!Well, of course it was. Imagine that the drug has no effect. Some people just get better and others don't. Let's assume that each person randomly gets between 0 and 25 better, with an equal chance of any outcome. Half are on drug and half are on placebo, but it makes no difference.Let's further assume that there are 50 centres, with 20 people per centre (1000 people total). I knocked up a "simulation" of this in Excel (it took 10 minutes). Here's what you get:The blue dots show, for each imaginary centre, drug improvement vs. placebo improvement. There's no correlation (it's random), and, on average, there is no difference: both average out at 12 points. The drug doesn't work.The red dots show the "Treatment Effect" i.e. [drug improvement - placebo improvement]. The average is 0 - because the drug doesn't work. But there's a strong negative correlation between Treatment Effect and the placebo improvement - in centres where people improved lots on placebo, the drug worked worse.This is exactly what Glaxo show in Figure 1a (see above). They write:The analysis of the surface response indicated the predominant role of center specific placebo response as compared with the dose strength in determining the Treatment Effect of paroxetine.But of course they correlate. You're correlating placebo improvement with itself: the "Treatment Effect" is a function of the placebo improvement. It's classic regression to the mean.Of course if you chuck out the centres where people on placebo do well (the grey box in my picture), the drug seems to work pretty nicely. But this is cheating. It is cherry-picking. It is completely unscientific.The authors note that this could be a source of bias, but say that it wouldn't be one if it was planned out in advance: "in order to overcome the bias risk, the enrichment strategy should be accounted for and pre-planned in the study protocol." This is like saying that if you announce, before playing chess, that you are going to cheat, it's not cheating.To be fair to the authors, assuming the drug does work, this method would improve your chances of correctly detecting the effect. Centres with very high placebo responses quite possibly are junk. Assuming the drug works.But if we're assuming the drug works, why are we bothering to do a trial? The whole point of a trial is to discover something we don't know. The authors justify their approach by suggesting that it would be useful for drug companies who want to do a "proof-of-concept" trial to find out whether an experimental drug might work under the most favourable conditions, i.e. whether they should bother continuing to research it.They say that such trials "are inherently exploratory in their conception, aimed at signal detection, open to innovation..." - in other words, that they're not meant to be as rigorous as late-stage trials.Fair enough. But this method is not even suitable for proof-of-concept, because it would (as I have shown above in my 10 minute simulation) increase your chance of finding an "effect" from a drug that doesn't work.Whatever the truth is, this method will give the same result, so it's not useful evidence. It's like saying "Heads I win, tails you lose". You've set it up so that I lose - the coin toss doesn't us anything.All of the author's results are based on trials in which the drug "should have worked": they do not appear to have simulated what would happen if they used this method on trials where it didn't work, as I just did. So I'm doing Pharma a big favour by writing this post, because if they adopt this approach, they're more likely to waste money on drugs that don't work.They should be paying me for this stuff.Merlo-Pich E, Alexander RC, Fava M, & Gomeni R (2010). A New Population-Enrichment Strategy to Improve Efficiency of Placebo-Controlled Clinical Trials o... Read more »
Merlo-Pich E, Alexander RC, Fava M, & Gomeni R. (2010) A New Population-Enrichment Strategy to Improve Efficiency of Placebo-Controlled Clinical Trials of Antidepressant Drugs. Clinical pharmacology and therapeutics. PMID: 20861834
- September 25, 2010
- 02:48 PM
- 514 views
It's not what you publish, it's where you publish it
by Hadas Shema in Information Culture
Last post I mentioned the Matthew Effect, or "The rich get richer." In Bibliometrics, it means that the more you're cited and/or the more you publish, the more you'll continue to get cited/publish. When applied to journals, that means that papers published in high-impact journals get cited more often. As a result, the IF of the journals remains high, and so on. In short, a positive feedback loop. However, there's always a question of quality. Perhaps the papers published in high-impact journals are, indeed, better? Lariviere and Gingras (2010) tried to solve the problem by using duplicates: the same paper published twice, in a high IF journal and in a low IF journal. In order to find those papers, they searched the WoS database, comparing papers according to their names, first authors and the number of cited references. Out of 4,918 pairs of papers identified they ended up using 4,532. The publication year of the pairs was either identical of in the one year range in about 80% of the papers. They compared the average numbers of citations and average of relative citations for disciplines with more than 30 duplicates. The biggest Matthew Effect was found in the clinical medicine (21.46 for high IF, 12.08 for low IF) and Biomedical Research. (19.77 and 8.15). Significant differences were also found for Chemistry, Engineering and Technology, Physics and Social Sciences. However, there weren’t significant differences for Biology, Earth and Space, Health (Social Sciences), Math and Psychology. Personally, I wonder if part of the effect can be accounted for the pay walls: libraries tend to buy more subscriptions to high-impact journals, so the chances of getting access to a paper in one of those journals is higher. Speaking of the Matthew Effect, John Wilbanks, vice president of science at Creative Commons, just published a short article in Seed Magazine about the subject. He points out that in 1968 (the year Merton named the “Matthew Effect”) “the average age of a biomedical researcher in the US receiving his or her first significant funding was 35 or younger.” Today, it’s almost 42 for NIH grants. That means that fewer young, talented scientists get opportunities for independent research, while the already established scientists get even more funding. Wilbanks recommends that we “start rethinking the way we reward and fund science and assess researchers using more than just citations.” All I can say, Mr. Wilbanks, is that Bibliometricans are working on it…P.S. Of course, as soon as I finished this post I ran into this post in The Scholarly Kitchen about the very same paper. Oh, well.Lariviere, V. & Gingras, Y. (2010). The impact factor’s Matthew effect: a natural experiment in bibliometrics Journal of the American Society for Information Science and Technology, 2 (61), 424-427 : 10.1002/asi.21232... Read more »
V. Lariviere, & Y. Gingras. (2010) The impact factor’s Matthew effect: a natural experiment in bibliometrics. Journal of the American Society for Information Science and Technology, 2(61), 424-427. info:/10.1002/asi.21232
- September 24, 2010
- 08:00 AM
- 1,278 views
RAS, Low-Carb Diets and NEAT
by Arya M. Sharma in Dr. Sharma's Obesity Notes
This morning, on the last day of the 2010 EASD in Stockholm, I co-chaired the Michael Berger debate on whether or not blocking the renin-angiotensin system is the be all and end all of organ protection. The debaters were Bo Feld-Rasmussen from the University of Copenhagen and Andrea Natali form the University of Pisa, Italy.
As is [...]... Read more »
Shai I, Schwarzfuchs D, Henkin Y, Shahar DR, Witkow S, Greenberg I, Golan R, Fraser D, Bolotin A, Vardi H.... (2008) Weight loss with a low-carbohydrate, Mediterranean, or low-fat diet. The New England journal of medicine, 359(3), 229-41. PMID: 18635428
- September 24, 2010
- 07:39 AM
- 1,246 views
Alcohol Consumption affects Morphological Complexity
by Sean Roberts in A Replicated Typo 2.0
Recent research suggests that language adapts to the balance between declarative and procedural memory users. Since alcohol consumption affects procedural but not declarative memory (Smith & Smith, 2003), we might expect to see communities that have a high alcohol consumption using less complex morphology...... Read more »
Smith C, & Smith D. (2003) Ingestion of ethanol just prior to sleep onset impairs memory for procedural but not declarative tasks. Sleep, 26(2), 185-91. PMID: 12683478
- September 23, 2010
- 11:58 PM
- 688 views
Gelatinous zoop!
by John Carroll in Chronicles of Zostera
There is an interesting blog over on discovermagazine.com about the way sea walnuts (or ctenophores, or Mnemiopsis leidyi) feed (in addition to a cool video, which is posted below). Apparently, these organisms use their cilia to create almost undetectable currents, and they are then capable of catching unsuspecting prey with great efficiency. Due to their incredible ability to feed stealthily and efficiently, they have been particularly devastating invaders in European water bodies. When these comb jellies showed up in the Black Sea, they contributed to a food web collapse by consuming many of the fish larvae that would typically serve as the base of the food chain. In fact, gelatinous zooplankton are often considered productivity dead-ends; they consume productivity in the forms of other plankton, however, they offer little food value to other species. So the productivity is not transferred to other trophic levels, and food webs collapse. This is also becoming a problem in human impacted systems. This blog made me remember some research some colleagues at the School of Marine and Atmospheric Science conducted. PhD student Marianne McNamara, under the tutelage of Darcy Lonsdale, investigated the impact of high abundances of ctenophores on larval bivalve mortality. In their article "Shifting abundance of the ctenophore Mnemiopsis leidyi and the implications for larval bivalve mortality," published earlier this year in Marine Biology, McNamara et al investigated how ctenophore abundance has changed, their digestion rates, and finally, their ability to control bivalve larvae. The data from this article is of particular importance for the hard clam restoration and management effort in Great South Bay, NY (their field sites), since the comb jellies may exert a strong predation pressure on hard clam larvae.They conducted field surveys to investigate the abundance of ctenophores and other zooplankton. They enumerated and took volumetric measurements of the comb jellies, then looked at their gut contents. Finally, they conducted lab feeding experiments, and then used equations to calculate their ability to control bivalve larvae.McNamara et al found high densities of ctenophores in the early summer, and larger ctenophores in the late summer, and when compared to the literature, densities were considerably higher than in previous decades. This is of particular importance, since bivalve veligers made up approximately 63% of the ctenophores' gut contents, indicating this is a particularly valuable food source for the jellies. In addition, using their equations from densities and feeding rates, they predicted that at peak abundances, the ctenophores could consume over 94% of the bivalve veligers in Great South Bay. This is a particularly alarming figure. In addition, the peak abundances of ctenophores occurs earlier in the year (early summer) now than it did decades ago (in the fall), putting peak abundances of comb jellies in the water column at the same time as the bivalve larvae. Clearly, this study illustrates the potential ecosystem impacts of increasing gelatinous zooplankton. While they have already been shown to be particularly harmful as invaders, it is now apparent that they can have impacts where they are native as well. It is likely that increasing human impacts leading to pelagic dominated production will lead to more ctenophores in coastal systems, which can prevent benthos from reestablishing in these areas. This might be the case in Great South Bay, where the hard clam populations are struggling to recover despite the Nature Conservancy's efforts at replenishing them. Now I don't know about their high end estimates, as one could imagine if ctenophores were capable of consuming essentially all of the bivalve veligers, then veligers and comb jellies wouldn't be collected together in plankton tows. However, it is clear that ctenophores can possibly have a major impact on a local ecosystem.McNamara, M., Lonsdale, D., & Cerrato, R. (2009). Shifting abundance of the ctenophore Mnemiopsis leidyi and the implications for larval bivalve mortality Marine Biology, 157 (2), 401-412 DOI: 10.1007/s00227-009-1327-6... Read more »
McNamara, M., Lonsdale, D., & Cerrato, R. (2009) Shifting abundance of the ctenophore Mnemiopsis leidyi and the implications for larval bivalve mortality. Marine Biology, 157(2), 401-412. DOI: 10.1007/s00227-009-1327-6
- September 23, 2010
- 10:29 PM
- 675 views
A Taste For Trash
by Journal Watch Online in Journal Watch Online
The Glaucous Gull ain’t no gourmet—and that could be bad news for endangered Alaskan birds. A taste for human garbage may fueling an increase in the population of the Arctic’s largest gull, which is also a voracious predator. The trash-based food chain could end up imperiling more than a dozen species, concludes a new study. […] Read More »... Read more »
Weiser, E., & Powell, A. (2010) Does Garbage in the Diet Improve Reproductive Output of Glaucous Gulls?. The Condor, 112(3), 530-538. DOI: 10.1525/cond.2010.100020
- September 23, 2010
- 01:56 PM
- 745 views
Reflections on the WEIRD Evolution of Human Psychology
by Eric Michael Johnson in The Primate Diaries
The latest stop in the #PDEx tour is being hosted by PLoS Blogs:What happens if researchers inadvertently fall prey to confirmation bias at a societal level?Addressing this question Canadian psychologists Joseph Henrich, Steven J. Heine and Ara Norenzayan at the University of British Columbia (where I am also located) recently published a paper in the journal Behavioral Brain Sciences. Their research documents how most of the studies that psychologists claim show human universals are really just extrapolations from a single social group, the cultural equivalent of the psychopaths in my example. As The New York Times wrote in their review:According to the study, 68 percent of research subjects in a sample of hundreds of studies in leading psychology journals came from the United States, and 96 percent from Western industrialized nations. Of the American subjects, 67 percent were undergraduates studying psychology — making a randomly selected American undergraduate 4,000 times likelier to be a subject than a random non-Westerner.The subpopulation that Henrich and colleagues found to be overrepresented are entirely WEIRD (Western, Educated, Industrialized, Rich, and Democratic) societies. While it’s bad enough that WEIRD American undergraduates are serving as our model for human behavior, what their paper goes on to document should be of concern to all behavioral and cognitive researchers (particularly those whose work focuses on human evolutionary explanations). Henrich, J., Heine, S., & Norenzayan, A. (2010). The weirdest people in the world? Behavioral and Brain Sciences, 33 (2-3), 61-83 DOI: 10.1017/S0140525X0999152XRead the rest of the post here and stay tuned for the next entry in The Primate Diaries in Exile tour.... Read more »
Henrich, J., Heine, S., & Norenzayan, A. (2010) The weirdest people in the world?. Behavioral and Brain Sciences, 33(2-3), 61-83. DOI: 10.1017/S0140525X0999152X
- September 23, 2010
- 01:56 PM
- 601 views
Reflections on the WEIRD Evolution of Human Psychology
by Eric Michael Johnson in The Primate Diaries in Exile
The latest stop in the #PDEx tour is being hosted by PLoS Blogs:What happens if researchers inadvertently fall prey to confirmation bias at a societal level?Addressing this question Canadian psychologists Joseph Henrich, Steven J. Heine and Ara Norenzayan at the University of British Columbia (where I am also located) recently published a paper in the journal Behavioral Brain Sciences. Their research documents how most of the studies that psychologists claim show human universals are really just extrapolations from a single social group, the cultural equivalent of the psychopaths in my example. As The New York Times wrote in their review:According to the study, 68 percent of research subjects in a sample of hundreds of studies in leading psychology journals came from the United States, and 96 percent from Western industrialized nations. Of the American subjects, 67 percent were undergraduates studying psychology — making a randomly selected American undergraduate 4,000 times likelier to be a subject than a random non-Westerner.The subpopulation that Henrich and colleagues found to be overrepresented are entirely WEIRD (Western, Educated, Industrialized, Rich, and Democratic) societies. While it’s bad enough that WEIRD American undergraduates are serving as our model for human behavior, what their paper goes on to document should be of concern to all behavioral and cognitive researchers (particularly those whose work focuses on human evolutionary explanations). Henrich, J., Heine, S., & Norenzayan, A. (2010). The weirdest people in the world? Behavioral and Brain Sciences, 33 (2-3), 61-83 DOI: 10.1017/S0140525X0999152XRead the rest of the post here and stay tuned for the next entry in The Primate Diaries in Exile tour.... Read more »
Henrich, J., Heine, S., & Norenzayan, A. (2010) The weirdest people in the world?. Behavioral and Brain Sciences, 33(2-3), 61-83. DOI: 10.1017/S0140525X0999152X
- September 23, 2010
- 11:55 AM
- 625 views
Dangerous dependence on virtual water deepens
by Maria José Viñas in GeoSpace
The rate of global groundwater depletion has been on the rise, warning of a potential disaster for an increasingly globalized agricultural system says Marc Bierkens of Utrecht University in Utrecht, the Netherlands.
In an upcoming study, Bierkens and his colleagues find that not only is global groundwater extraction outstripping its natural recharge rate, this disparity has [...]... Read more »
Paolo D’Odorico, Francesco Laio, and Luca Ridolfi. (2010) Does globalization of water reduce societal resilience to drought?. Geophysical Research Letters. info:/10.1029/2010GL043167
Marc.F.P. Bierkens et al. (2010) A worldwide view of groundwater depletion. Geophysical Research Letters. info:/10.1029/2010GL044571
- September 22, 2010
- 11:24 AM
- 341 views
Renewed Muck, Stuck
by Journal Watch Online in Journal Watch Online
Nobody said it was going to be easy – and they were right. A landmark effort to restore a huge swath of Florida’s wetlands isn’t bringing native plants back to some areas, a new study finds. And to add insult to injury, an invasive exotic shrub appears to be gaining ground due to the restoration. […] Read More »... Read more »
Toth, L. (2010) Unrealized Expectations for Restoration of a Floodplain Plant Community. Restoration Ecology. DOI: 10.1111/j.1526-100X.2010.00731.x
- September 22, 2010
- 09:58 AM
- 636 views
The citation game
by Hadas Shema in Information Culture
Although "Publish or perish" is more catchy, I believe it should be "Get cited or perish". Why? Because many people (without naming names, we're talking about your promotion committee)also rely on citation data when deciding a scientist's future.While citations often correlate with other measurements of scientific influence (awards, research grants, etc.) citations are hardly objective, and depend on more factors than someone finding your work useful.Time-dependent factors: Recent publications are more likely to get cited than older ones.The Matthew effect: "The rich get richer and the poor get poorer." The name was given by Merton (1968) who based it upon the Gospel of Matthew: "For to all those who have, more will be given, and they will have an abundance; but from those who have nothing, even what they have will be taken away."—Matthew 25:29, New Revised Standard Version.What it means is that the more cited a paper is, the more it will continue to get cited. Works for famous scientists as well. Field-dependent factors: Your chances for citing go up when you work in a bigger field with more publications and vice-versa.Journal-dependent factors: Getting published in a high-factor journal doesn't necessarily mean your paper is the best thing since sliced bread, but it means more people are likely to think so. Also, the first paper in a journal usually gets cited more often (I wonder if that's still relevant, given how wide-spread electronic access is these days).Paper-dependent factors: The frequency of citations for the paper correlates positively with the number of co-authors and the length of the reference list. Cite more, get cited more. Longer papers get cited more often than shorter ones, simply because they have more content.Author/reader dependent factors: Developing a good social network with colleagues can get you cited more often. Availability of publication: Do people have access to your paper? Open Access papers get cited more often (given that many universities' policy regarding paid subscriptions is "NOT", that's hardly surprising). Technical problems: Errors in the citing of your paper may prevent the citing from counting when a paper's references list is analysed. Another important rule is to pick one form of your name and stick to it (if you're John Smith, don't start being John K. Smith all of a sudden). Above all, write a good paper (it can't hurt). An important note: most of the material in this post is from Bornmann and Daniel's excellent review (2008). Bornmann, L., & Daniel, H. (2008). What do citation counts measure? A review of studies on citing behavior Journal of Documentation, 64 (1), 45-80 DOI: 10.1108/00220410810844150Eysenbach, G. (2006). Citation Advantage of Open Access Articles PLoS Biology, 4 (5) DOI: 10.1371/journal.pbio.0040157... Read more »
Bornmann, L., & Daniel, H. (2008) What do citation counts measure? A review of studies on citing behavior. Journal of Documentation, 64(1), 45-80. DOI: 10.1108/00220410810844150
Eysenbach, G. (2006) Citation Advantage of Open Access Articles. PLoS Biology, 4(5). DOI: 10.1371/journal.pbio.0040157
- September 22, 2010
- 08:00 AM
- 901 views
Shock Therapy – A Thing of the Past or the Only Way Out?
by Shaheen Lakhan in Brain Blogger
When most people think of electroconvulsive therapy (ECT), the first thing that comes to mind may be a scene in the 1975 film “One flew over the Cuckoo’s nest,” where Jack Nicholson undergoes the treatment, in a way more akin to torture than medical care. There are people holding him down, he is not under [...]... Read more »
Breggin, P. (2007) ECT Damages the Brain: Disturbing News for Patients and Shock Doctors Alike. Ethical Human Psychology and Psychiatry, 9(2), 83-86. DOI: 10.1891/152315007782021196
Coentre R, Barrocas D, Chendo I, Abreu M, Levy P, Maltez J, & Figueira ML. (2009) [Electroconvulsive therapy: myths and evidences]. Acta medica portuguesa, 22(3), 275-80. PMID: 19686628
- September 21, 2010
- 04:01 PM
- 845 views
How to handle the paper glut
by Rogue in Into Oblivion
In a Letter to Science, Donald Siegel and Philippe Baveye discuss what they call « the paper glut » we face and address suggestions to improve the reviewing system. « Publish or perrish » has become a real fashion of doing research and has somehow replaced the desire to share knowledge. The authors recall that the amount of schlarly [...]... Read more »
Siegel D, & Baveye P. (2010) Battling the paper glut. Science (New York, N.Y.), 329(5998), 1466. PMID: 20847251
- September 20, 2010
- 06:00 AM
- 938 views
What is "contextualizing" patient care?
by Michelle Lin in Academic Life In Emergency Medicine
Medicine is as much about Science as it is about Art. This is no better illustrated than an educational intervention study about "contextualizing" patient care, published in JAMA. What is contextualization?It is the "process of identifying individual patient circumstances (their context) and, if necessary, modifying the plan of care to accommodate those circumstances". In other words, this is care beyond the evidence-based guidelines, beyond standardized quality measures, and beyond the checklists.What if the patient hasn't been able to afford the more expensive blood pressure medications they've been prescribed by their primary care physician? What if your patient is marginally housed with poor access to food? What if your patient gets confused easily when reading pill bottles?What if your patient has no access to care?These are real concerns in the Emergency Department setting. In contrast, contextualized patient care really isn't taught in any formal fashion in medical school or residency. It's learned on the job.Study questionCan a 4-hour educational course on contextualizing patient care improve a 4th year medical student's ability to detect and act on contextual "red flags" in standardized patient exams?Study methodologyStudents at 2 sites were quasi-randomized into the control (no educational course) versus study group (received educational course). Students from both groups participated in an end-of-rotation session where they each assessed 4 standardized patients. There were 4 patient cases: 43 y/o man with recent persistent asthma symptoms despite being prescribed a low dose of a high-cost, brand-name, inhaled glucocorticoid47 y/o woman presenting for preop assessment of hip replacement reports mild hypertension and being overweight59 y/o man with diabetes presents with 2 presyncopal episodes after previous physician increased insulin dosage72 y/o man with unexplained weight lossEach case had 4 variants:Baseline caseHad a contextual red flagHad a biomedical red flagHad both a contextual and biomedical red flagFor instance, in the case of the 59 y/o diabetic man with presyncopal symptoms:Contextual red flag: Confuses dosages and says "It's hard for me to keep numbers straight".Biomedical red flag: "I felt some pounding in my chest when it happened."Baseline error: No adjustment of insulin dosing or discussion of dietary change to prevent hypoglycmemiaContextual error: No discussion of obstacles to self-care in patient with cognitive disabilities which impair his ability to administer his own insulin. He had recently left a community where he had assistance.Biomedical error: No EKG, Holter monitor, or stress test ordered in patient with symptoms of arrhythmia.ResultsStudents in the intervention group (90%) were more likely to probe for contextual issues in the standardized patient encounters than the control group students (62%). The intervention students were also more likely to develop appropriately revised treatment plans for patients with contextual issues (69%) compared to the control group students (22%). As expected there was no difference between the two groups in the rate of probing and treatment plan development for patients with biomedial issues. LimitationAs with many prospective educational studies, there was a large attrition rate. Of the 189 of who consented to participate, only 124 remained to participate in the standardized patient encounters at the end of the 4 weeks. The authors appropriately conducted a sensitivity analysis to determine the worst-case scenario, which assumed that the students in the intervention group did NOT benefit from the educational intervention. Even with this scenario, recalculations still demonstrated statistically significant benefit from the intervention:Probing contextual red flag: Control (60%), Intervention (82%)Planning contextually-appropriate treatment: Control (22%), Intervention (55%)ConclusionThis study demonstrates that teaching contextualized patient care is possible and that a 4-hour course is effective in changing student behavior. Schwartz A, Weiner SJ, Harris IB, & Binns-Calvey A (2010). An educational intervention for contextualizing patient care and medical students' abilities to probe for contextual issues in simulated patients. JAMA : the journal of the American Medical Association, 304 (11), 1191-7 PMID: 20841532.... Read more »
Schwartz A, Weiner SJ, Harris IB, & Binns-Calvey A. (2010) An educational intervention for contextualizing patient care and medical students' abilities to probe for contextual issues in simulated patients. JAMA : the journal of the American Medical Association, 304(11), 1191-7. PMID: 20841532
- September 18, 2010
- 10:26 PM
- 972 views
Why do we still publish research (via) papers?
by Daniel Mietchen in Research Cycle Research
Mind the bugs in the system: papers. Photo: Jenn Forman Orth When I lost a WiFi connection recently, I was left with the usual error message, which led me to look more attentively at the URL than I am used … Continue reading →... Read more »
Origgi, G. (2010) Epistemic Vigilance and Epistemic Responsibility in the Liquid World of Scientific Publications. Social Epistemology, 24(3), 149-159. DOI: 10.1080/02691728.2010.499179
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