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  • June 29, 2012
  • 02:35 AM
  • 815 views

Impact Factor Boxing 2012

by Duncan Hull in O'Really?

In the world of abused performance metrics, the impact factor is the undisputed heavyweight champion of the (publishing) world.

And it’s been an eventful year in the ring scientific publishing too. A new journal called PeerJ launched with a radical new publish ’til you perish business model [1]. There’s another new journal on the way too in the shape of eLifeSciences - with it’s own significant differences from current publishing models. Then there was the Finch report on Open Access. And if that wasn’t enough fun, there’s been the Altmetrics movement gathering pace [2], alongside a hint that the impact factor may be losing its grip on the supposed “title” [3].
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  • June 28, 2012
  • 06:03 AM
  • 680 views

CFS: Oral Histories of Comics Scholarship

by Ernesto Priego in The Comics Grid. Journal of Comics Scholarship

“Oral Histories of Comics Scholarship” hopes to crowdsource digital surrogates of analogue audio recordings or digital recordings that the comics scholarship community might have in their personal collections.... Read more »

  • June 27, 2012
  • 07:20 AM
  • 330 views

Herkent u deze melodie? [Dutch]

by Henkjan Honing in Music Matters

Je zit in je auto en draait wat aan de knop van de radio. Je hoort al snel of bepaalde muziek je bevalt of niet. Je herkent een stem, een liedje of zelfs de uitvoering ervan. Iedereen doet het, iedereen kan het. En vaak ook nog eens razendsnel: sneller dan een noot gemiddeld klinkt.Als u gevraagd zou worden om naar een reeks muziekfragmenten van 0,2 seconde te luisteren, zal blijken dat u met gemak aan kan geven welk fragment klassiek, jazz, R&B of pop is (zie luistertest). Een snippertje geluid geeft ons toegang tot de herinnering aan eerder gehoorde muziek, ook al hebben we deze serie noten nog nooit eerder gehoord. Die herinnering kan heel specifiek zijn: aan een liedje van Björk, bijvoorbeeld. Maar ze kan ook heel algemeen zijn: we herkennen een bepaald genre: klassiek, country, jazz. De nuances in klankkleur, karakteristiek voor een liedje of een heel genre, zitten kennelijk op een abstracte manier in ons geheugen opgeslagen. Daarom is de draaiknop (of tiptoets) van de autoradio zo’n succesvolle interface geworden…Vandaag verschenen er verschillende items in de media n.a.v. van een stukje in Volkskrant over de oorwurm en de hype rond Song Pop, een app die gebruik maakt van het hierboven beschreven muzikale talent dat we allemaal delen: het razendsnel herkennen van muziek.Over oorwurm: Volkskrant, NOS op 3 Over Song Pop App: Editie NL   Gjerdingen, Robert O., & Perrott, D. (2008). Scanning the Dial: The Rapid Recognition of Music Genres Journal of New Music Research, 37 (2), 93-100 DOI: 10.1080/09298210802479268... Read more »

Gjerdingen, Robert O., & Perrott, D. (2008) Scanning the Dial: The Rapid Recognition of Music Genres. Journal of New Music Research, 37(2), 93-100. DOI: 10.1080/09298210802479268  

  • June 25, 2012
  • 09:11 AM
  • 348 views

Why does a well-tuned modern piano not sound out-of tune?

by Henkjan Honing in Music Matters

Karlheinz Stockhausen is listening."Neue Musik ist anstrengend", wrote Die Zeit some time ago: "Der seit Pythagoras’ Zeiten unternommene Versuch, angenehme musikalische Klänge auf ganzzahlige Frequenzverhältnisse der Töne zurückzuführen, ist schon mathematisch zum Scheitern verurteilt. Außereuropäische Kulturen beweisen schließlich, dass unsere westliche Tonskala genauso wenig naturgegeben ist wie eine auf Dur und Moll beruhende Harmonik: Die indonesische Gamelan-Musik und Indiens Raga-Skalen klingen für europäische Ohren schräg."The definition of music as “sound” wrongly suggests that music, like all natural phenomena, adheres to the laws of nature. In this case, the laws would be the acoustical patterns of sound such as the (harmonic) relationships in the structure of the dominant tones, which determine the timbre. This is an idea that has preoccupied primarily the mathematically oriented music scientists, from Pythagoras to Hermann von Helmholtz. The first, and oldest, of these scientists, Pythagoras, observed, for example, that “beautiful” consonant intervals consist of simple frequency relationships (such as 2:3 or 3:4). Several centuries later, Galileo Galilei wrote that complex frequency relationships only “tormented” the eardrum. But, for all their wisdom, Pythagoras, Galilei, and like-minded thinkers got it wrong. In music, the “beautiful,” so-called “whole-number” frequency relationships rarely occur—in fact, only when a composer dictates them. The composer often even has to have special instruments built to achieve them, as American composer Harry Partch did in the twentieth century. Contemporary pianos are tuned in such a way that the sounds produced only approximate all those beautiful “natural” relationships. The tones of the instrument do not have simple whole number ratios, as in 2:3 or 3:4. Instead, they are tuned so that every octave is divided into twelve equal parts (a compromise to facilitate changes of key). The tones exist, therefore, not as whole number ratios of each other, but as multiples of 12√2 (1:1.05946).According to Galilei, each and every one of these frequency relationships are “a torment” to the ear. But modern listeners experience them very differently. They don’t particularly care how an instrument is tuned, otherwise many a concertgoer would walk out of a piano recital because the piano sounded out of tune. It seems that our ears adapt quickly to “dissonant” frequencies. One might even conclude that whether a piano is “in tune” or “out of tune” is entirely irrelevant to our appreciation of music. [fragment from Honing, 2011.]Julia Kursell (2011). Kräftespiel. Zur Dissymmetrie von Schall und Wahrnehmung. Zeitschrift für Medienwissenschaft, 2 (1), 24-40 DOI: 10.4472_zfmw.2010.0003Honing, H. (2012). Een vertelling. In S. van der Maas, C. Hulshof, & P. Oldenhave (Eds.), Liber Plurum Vocum voor Rokus de Groot (pp. 150-154). Amsterdam: Universiteit van Amsterdam (ISBN 978-90-818488-0-0).Whalley, Ian. (2006). William A. Sethares: Tuning, Timbre, Spectrum, Scale (Second Edition). Computer Music Journal, 30 (2) DOI: 10.1162/comj.2006.30.2.92... Read more »

Julia Kursell. (2011) Kräftespiel. Zeitschrift für Medienwissenschaft, 2(1), 24-40. DOI: 10.4472_zfmw.2010.0003  

  • June 24, 2012
  • 07:57 PM
  • 695 views

Understanding the Journal Impact Factor – Part Two

by Hadas Shema in Information Culture

Despite its many faults (see part I), the Journal Impact Factor (JIF) is considered an influential index to a journal’s quality, and publishing in high-impact journals is essential to a researcher’s academic career. Reminder: to calculate, for example, the 2010 JIF for a journal - JIF= (2010 citations to 2009+2008 articles)/(no. of “citable” articles published in [...]









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  • June 24, 2012
  • 06:01 PM
  • 1,193 views

In defense of pink microscopes

by TheCellularScale in The Cellular Scale

I know I am late to the party here, as the "Science is a girl thing" video (embedded below) came out Friday and has already been ripped to shreds by many a blog. But I just couldn't stop thinking about it, so here's my opinion on that video and pinkifying science in general.Hello Kitty Microscope I am reminded of a quote from Pres. Obama's initial campaign.  He said (something like) "We need to shatter the blasphemy that says a black child with a book is acting white."  It is equally true that "we need to shatter the blasphemy that says a woman in science is acting masculine." Sometimes women in science dress down and wear less make up on purpose because they are worried that they won't be taken seriously if they look 'girlie' or even 'attractive'. Or specifically, "If I look like I took a long time doing my hair, nails, and make up, people might think I am not spending time doing science." It is just as sexist to think that a woman wearing heels in the lab is less capable or less dedicated to science as it is to think that women shouldn't be in a lab in the first place. What a woman wears to the lab (within lab safety guidelines anyway) has NOTHING to do with how good she is at science or with how seriously she takes her work.  NOTHING.  The woman who wears heels and makeup, the woman who wears the same sweatpants 3 days in a row, and the woman who wears a t-shirt with jeans should all be taken equally seriously as scientists and judged on their work and not their appearance.  Being 'masculine' does not help you be a better scientist and for crissake women, do not brag about having a 'masculine brain'. You are not helping inspire young girls to success when you attribute your intelligence and ability to being like a man. I fully support feminine scientists and pink science equipment. There is no reason that a microscope shouldn't be pink and there is no reason that a girl shouldn't be able to have her own Computer Engineer Barbie if she wants one.  Computational Neuroscientist BarbieThe message that you can both care about shoes and be a successful working scientist is important. It helps shatter the stereotype that scientific women are or should be masculine. Recently a study by Betz and Sekaquaptewa (2012) investigated the influence of overtly feminine cues (such as pink clothes, makeup, etc) on middle-school girls' interest in math as a future career. They had the students read an magazine-style interview with a feminine woman (pictured as wearing make up and pink and described as liking fashion magazines), and a neutral woman (pictured with dark clothes and glasses and described as liking reading). The finding that has been the focus of this paper's blog coverage is that for the girls that did not label math or science as their favorite subject, the feminine cues significantly reduced their self-reported interest in math as a career. They attribute this to the girls thinking that the feminine women are 'too good' and thus being discouraged because they don't see themselves as ever reaching those heights. While this is an interesting hypothesis, a closer look at the study is merited.  First of all, there is not un-gendered control study. Might a similar effect might show up for middle school boys when shown either a muscular, athletic man who likes football or a neutral man who isn't particularly muscular, wears glasses and likes reading? This could be a general 'attractivity' thing where kids are intimidated by role models who 'have it all' or 'are too good'. Maybe it's not really a gender issue. Secondly, what hasn't been discussed much is that 54% of the girls initially listed math or science as their favorite subject! And for those girls, the femininity of the woman in the article had no statistically significant effects on their interest in science and math.  54% ! more than half of the girls in this study reported science, math, or both as their FAVORITE subject! and while there were no significant effects, there was a trend (p=0.19) toward the femininity of the role model increasing these girls' report of how 'attainable' both her femininity and scientific success might be. Betz and Sekaquaptewa, 2012 Figure 3This graph shows the "self-reported likelihood of attaining role model femininity and STEM (science, tech, engineering, and math) success" If anything the feminine role model slightly increased the attainability of these characteristics for girls who already like science (not significant, p=0.19).    Regardless, I think the conclusion that feminine-looking science is bad for girls is not on sound footing. And again, I defend pink microscopes. If you have already seen the It's a girl thing video, you might be now expecting me to support it.  But don't worry, I think it is as idiotic and every other scientist on the planet does.  Far from showing feminine scientists, it is showing a scientist (the man) and separate from that a bunch of giggly girls dropping things. NOT HELPFUL. The only part I liked was the girl looking like she was concentrating and writing equations on the clear board. She looked feminine and pretty and she was 'doing' science.  If these girls had been actually doing science through the entire video (sitting at microscopes like the guy did, for example), I might actually have liked it.The thing that is wrong with this video is not that these girls are wearing heels (though short skirts do violate lab safety codes), or that they look feminine or pretty. That's all fine. The problem is that they are not doing science, they are giggling and blowing kisses. If your goal is to combine femininity and prettiness with science, you have to COMBINE them, not present them as two completely separate things.In conclusion, I'll leave you with one of the best comments so far: Cartomancer on Pharyngula suggests some equally stereotypical and offensive videos to promote diversity in science: "67. cartomancer says: 22 June 2012 at 10:41 amI want to see what they’d come up with to get more LGBT people and ethnic minorities into science. “Science: it’s a gay thing!” featuring Abercrombie and Fitch models, bare-chested apart from an open lab coat, playing with unfeasibly suggestive phallic test tubes. Cut to discotheque-esque laser equipment and the word “science” with the C as a big rainbow.Or how about “Science: it’s a black thing!” – grinding hip-hop beats acco... Read more »

  • June 20, 2012
  • 05:00 PM
  • 601 views

New Research: Do organic animal operations encourage management decisions that negatively impact animal welfare?

by Austin Bouck in Animal Science Review

Few agricultural debates come close to generating the same passionate and heated responses that organic farming seems to elicit. The discussion surpasses the interests of producers with conflicting ideologies to be hotly debated by assertive consumers as well; people who highlight the paradox created by their interest in the safe and responsible production of their food, while avoiding all involvement in its creation. The originally proposed Organic Foods Production Act of 1990 received nearly 300,000 comments on the proposed requirements, more than any other piece of legislation in history (Vos, 2000). Clearly this indicated that the role organic farming played in food production was extremely important to U.S. citizens then, and continues to be a relevant topic as organic operations have grown by 40-50% every five years since 1992 (USDA, 2010)...... Read more »

Vonne Lund, & Bo Algers. (2003) Research on animal health and welfare in organic farming—a literature review. Livestock Production Science, 80(1-2), 55-68. info:/10.1016/S0301-6226(02)00321-4

  • June 20, 2012
  • 07:58 AM
  • 660 views

Was Pythagoras wrong?

by Henkjan Honing in Music Matters

The definition of music as “sound” wrongly suggests that music, like all natural phenomena, adheres to the laws of nature. In this case, the laws would be the acoustical patterns of sound such as the (harmonic) relationships in the structure of the dominant tones, which determine the timbre. This is an idea that has preoccupied primarily the mathematically oriented music scientists, from Pythagoras to Hermann von Helmholtz. But, for all their wisdom, Pythagoras, Galilei, and like-minded thinkers got it wrong. ... Read more »

Julia Kursell. (2011) Kräftespiel. Zeitschrift für Medienwissenschaft, 2(1), 24-40. DOI: 10.4472_zfmw.2010.0003  

  • June 10, 2012
  • 09:07 AM
  • 308 views

Does #exergame experience impact movement quantity and quality? (study)

by Stephen Yang in ExerGame Lab

I often wonder if previous experience in playing an #exergame impacts the overall experience and success of game play. Levac et al. also wanted to know whether motivation to succeed at the game...

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  • June 9, 2012
  • 04:44 AM
  • 632 views

Teaching Neuroanatomy With A Showercap

by Neuroskeptic in Neuroskeptic

Learning the names and locations of the different parts of the brain is a task that has brought grief to generations of students.I myself didn't know my caudate from my cingulate cortex all through my undergraduate studies and the first year of my doctorate. I only cracked it after spending a couple of days in the library, surrounded by a stack of anatomy textbooks, copying diagrams and coloring them in over and over until I could do it from memory.Now a group of Australian physiologists say there's a better way - Showercap Mindmap: a spatial activity for learning physiology terminology and locationBasically, undergraduate students were split into groups of 3 or 4 and each team was given a pack:The Showercap Mindmap packs included a clear, unmarked plastic shower cap, a whiteboard marker, and 15 sticky, color-coded labels. Lobe labels were blue (occipital, temporal, parietal, and frontal). Specialist areas were green (the corpus callosum, Broca’s area, and Wernicke’s area). Labels relating to information processing were yellow (hearing; heat; pain and temperature; and interpretation and integration of information). Cortex labels were orange (motor, association, somatosensory, auditory, and visual).One student on each team wore the cap and the others had 10 minutes to attach the labels to the correct parts of their head, corresponding to the different brain areas, with the help of a neuroanatomy textbook.This strikes me as a fantastic idea, and something that could actually make learning neuroanatomy fun, or at least a bit more involving than it usually is. The authors of the paper say that students using the method learned more effectively than those using a more conventional approach. Even the cap-wearers benefited. They couldn't see the labels being placed, but they could feel them.Vanags T, Budimlic M, Herbert E, Montgomery MM, and Vickers T (2012). Showercap Mindmap: a spatial activity for learning physiology terminology and location. Advances in physiology education, 36 (2), 125-30 PMID: 22665427... Read more »

Vanags T, Budimlic M, Herbert E, Montgomery MM, & Vickers T. (2012) Showercap Mindmap: a spatial activity for learning physiology terminology and location. Advances in physiology education, 36(2), 125-30. PMID: 22665427  

  • June 6, 2012
  • 10:03 AM
  • 291 views

Wordt popmuziek steeds treuriger? [Dutch]

by Henkjan Honing in Music Matters

Socioloog Christian von Scheve (Freie Universität Berlin) en muziek-psycholoog Glenn Schellenberg (University of Toronto) analyseerden zo’n duizend liedjes die tussen 1965 en 2009 in de Amerikaanse hitlijsten stonden. Daarbij vergeleken ze onder meer toonsoorten en tempo’s.De onderzoekers concludeerden dat er nu meer liedjes in de hitlijsten verschijnen die in mineur worden geschreven dan in de jaren zestig. Van mineurnummers is bekend dat ze een gevoel van verdriet opwekken. Derhalve stellen de onderzoekers dat nummers in de hitlijsten steeds treuriger worden (bron: Nu.nl).Maar hoe ‘mineur’ klikken popsongs in mineur eigenlijk? Denk bijvoorbeeld aan Everybody van de Backstreet Boys of Love Game van Lady Gaga… [Item op Radio 2] Schellenberg, E., & von Scheve, C. (2012). Emotional Cues in American Popular Music: Five Decades of the Top 40. Psychology of Aesthetics, Creativity, and the Arts DOI: 10.1037/a0028024... Read more »

Schellenberg, E., & von Scheve, C. (2012) Emotional Cues in American Popular Music: Five Decades of the Top 40. Psychology of Aesthetics, Creativity, and the Arts. DOI: 10.1037/a0028024  

  • June 6, 2012
  • 07:12 AM
  • 628 views

How can I stop…… stammering?

by Stuart Farrimond in Dr Stu's Science Blog

London 1940 was a grey place. In June, smog and grey skies made way for sunshine. Not that there was any summer cheer. Homes were in a perpetual gloom because of blacked-out windows. Food was scarce and kitchen broth was the family staple meal. And then the Germans were approaching. Against this backdrop, the new … Continue reading »... Read more »

Büchel, C., & Sommer, M. (2004) What Causes Stuttering?. PLoS Biology, 2(2). DOI: 10.1371/journal.pbio.0020046  

Carl Herder, Courtney Howard, Chad Nye, & Martine Vanryckeghem. (2006) Effectiveness of Behavioral Stuttering Treatment: A Systematic Review and Meta-Analysis. CONTEMPORARY ISSUES IN COMMUNICATION SCIENCE AND DISORDERS, 33(`), 61-73. info:/

Prins, D., & Ingham, R. (2008) Evidence-Based Treatment and Stuttering--Historical Perspective. Journal of Speech, Language, and Hearing Research, 52(1), 254-263. DOI: 10.1044/1092-4388(2008/07-0111)  

  • June 5, 2012
  • 08:49 PM
  • 462 views

Improving your Relationship with Mindfulness

by eHarmony Labs in eHarmony Labs Blog

Mindfulness: Learn how being open to new experiences and alternative perspectives can improve your relationship. ... Read more »

Burpee, L., & Langer, E. (2005) Mindfulness and Marital Satisfaction. Journal of Adult Development, 12(1), 43-51. DOI: 10.1007/s10804-005-1281-6  

  • June 4, 2012
  • 06:01 PM
  • 603 views

Journal of Neuroscience Methods paper: "Automated Cognome Construction and Semi-automated Hypothesis Generation"

by Bradley Voytek in Oscillatory Thoughts

The scientific method begins with a hypothesis about our reality that can be tested via experimental observation. Hypothesis formation is iterative, building off prior scientific knowledge. Before one can form a hypothesis, one must have a thorough understanding of previous research to ensure that the path of inquiry is founded upon a stable base of established facts. But how can a researcher perform a thorough, unbiased literature review when over one million scientific articles are published annually? The rate of scientific discovery has outpaced our ability to integrate knowledge in an unbiased, principled fashion. One solution may be via automated information aggregation. In this manuscript we show that, by calculating associations between concepts in the peer-reviewed literature, we can algorithmically synthesize scientific information and use that knowledge to help formulate plausible low-level hypotheses.Oh man I've been waiting to write this post for over a year now. I'm so. Flippin'. Excited.I'm really proud to announce that our paper, "Automated Cognome Construction and Semi-automated Hypothesis Generation" has been accepted for publication in the Journal of Neuroscience Methods.Here's the pre-print PDF.I've been writing about this project on this blog for quite a while now, mostly in talking about brainSCANr and the many, many rejections we received while trying to publish it along the way.Seventeen journals to be exact. Which is fun to note in the Rejections & Failures section of my CV. It makes a game out of failing!I'll start by telling the story of how this project got started, then get into some of the more sciencey details.Back in May 2010 I was invited to speak at the (now) annual Cognitive Science Student Association (CSSA) Conference run by the undergraduate CogSci student association at Berkeley. They're an incredibly talented group and I've had a lot of fun working with them over the years.At that conference I sat on a Q&A panel with a hell of a group of scientists, including George Lakoff and the Chair of Stanford's Psychology department, James McClelland (who helped pioneer Parallel Distributed Processing).Berkeley CSSA ConferenceOn that panel I A'd many Qs, one of which was a fairly high-level question about the challenge of integrating the wealth of neuroscientific literature. It was a variant on the classic line that neuroscience is "data rich but theory poor". This is a problem I'd been struggling with for a long time and I'd had a few ideas.In my response I said that one of our problems as a field was that we had so many different people with different backgrounds speaking different jargons who aren't effectively communicating. I followed with an off-hand comment that "The Literature" was actually pretty smart when taken as a system, but that we individual puny brains just weren't bright enough to integrate all that information. I went on to claim that, if there was some way to automatically integrate information from the peer-review literature, we could probably glean a lot of new insights.Well James McClelland really seemed to disagree with me, but the idea kept kicking around my brain for a while.One night, several months later (while watching Battlestar Galactica with my wife), I turned to her and explained my idea. She asked me how I was planning on coding it up and, after I explained it, she challenged me by saying that she could definitely code that faster than I could.Fast-forward a couple of hours to around 2am and she had her results. Bah.The idea boils down to a very simple (and probably simplistic) assumption that the more frequently two neuroscientific terms appear in the title or abstracts of papers together, the more likely those terms are to be associated. For example, if "learning" and all of its synonyms appears in 100 papers with "memory" and all of its synonyms while both of those terms appear in a total of 1000 papers without one another, then the probability of those two terms being associated is 100/1000, or 0.1.We calculated such probabilities for every pair of terms using a dictionary that we manually curated. It contained 124 brain regions, 291 cognitive functions, and 47 diseases. Brain region names and associated synonyms were selected from the NeuroNames database, cognitive functions were obtained from Russ Poldrack's Cognitive Atlas, and disease names are from the NIH. The initial population of the dictionary was meant to represent the broadest, most plausibly common search terms that were also relatively unique (and thus likely not to lead to spurious connections).We counted the number of published papers containing pairs of terms using the National Library of Medicine's ESearch utility and the count return type. Here's the example for "prefrontal cortex" and "striatum":Conjunction:http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&field=word&term=("prefrontal+cortex"+OR+"prefrontal+cortices")+AND+("striatum"+OR+"neostriatum"+OR+"corpus+striatum")&rettype=countDisjunctions:http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&field=word&term=("prefrontal+cortex"+OR+"prefrontal+cortices")+NOT+("striatum"+OR+"neostriatum"+OR+"corpus+striatum")&rettype=counthttp://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&field=word&term=("striatum"+OR+"neostriatum"+OR+"corpus+striatum")+NOT+("prefrontal+cortex"+OR+"prefrontal+cortices")&rettype=countHere's what the method looks like:Voytek & Voytek - Figure 1We note in our manuscript that this method is rife with caveats, but this wasn't meant to be an end-point, but rather a proof-of-concept beginning.In the end we get a full matrix of 175528 term pairs. Once we got this database we hacking together the brainSCANr website to allow people to play around with terms and their relationships. We wanted to create a tool for researchers and the public alike to use to help simplify the complexities of neuroscience. You enter a search term, it shows the relationships and gives you links to the relevant peer-reviewed papers.As an example, here's Alzheimer's:brainSCANr Alzheimer's diseaseMy wife and co-author(!) Jessica Voytek and I threw the first version together (with help from my Uber ... Read more »

Schmidt M, & Lipson H. (2009) Distilling free-form natural laws from experimental data. Science (New York, N.Y.), 324(5923), 81-5. PMID: 19342586  

Bowden, D., & Dubach, M. (2003) NeuroNames 2002. Neuroinformatics, 1(1), 43-60. DOI: 10.1385/NI:1:1:043  

Yarkoni T, Poldrack RA, Nichols TE, Van Essen DC, & Wager TD. (2011) Large-scale automated synthesis of human functional neuroimaging data. Nature methods, 8(8), 665-70. PMID: 21706013  

Lein, E., Hawrylycz, M., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A., Boguski, M., Brockway, K., Byrnes, E.... (2006) Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445(7124), 168-176. DOI: 10.1038/nature05453  

  • June 4, 2012
  • 10:00 AM
  • 563 views

Should Bloggers Publicize Their Own Work?

by Mr Epidemiology in Mr Epidemiology

Science blog royalty SciCurious recently had a post up about whether it was okay for science bloggers to blog about their own work. Travis brought it up on his Science of Blogging site as well, and I started thinking about it. One of the big issues we struggle with as researchers is getting our research out [...]... Read more »

  • June 1, 2012
  • 12:13 PM
  • 719 views

Science/Scientists Under Attack…

by gunnardw in The Beast, the Bard and the Bot

Earlier this month, a group of so-called eco-anarchists (keep in mind though that eco-anarchism is a fairly wide designation, comprising diverse lines of thought) has sent a letter to an Italian newspaper in which they claim responsibility for shooting Roberto … Continue reading →... Read more »

  • June 1, 2012
  • 09:07 AM
  • 660 views

We need substitutes, not extras

by David Robertson in David Robertson

I check my phone. “Already inside, some good ales on.” I quickly flick my wallet open to see a £20 note, then open the door to my local pub. A wave of warm air, infused with familiar and somewhat questionable odours, washes over me. An evening of chatter and drinking with friends awaits. Unexpectedly, the [...]... Read more »

  • June 1, 2012
  • 08:00 AM
  • 826 views

An Open Letter to the Royal Society: Please employ a wikipedian in residence

by Duncan Hull in O'Really?

Fellows of the Wiki Society? To improve public engagement with Science and Scientists, the Royal Society should employ a wikipedian in residence. Here’s why:... Read more »

Daub, J., Gardner, P., Tate, J., Ramskold, D., Manske, M., Scott, W., Weinberg, Z., Griffiths-Jones, S., & Bateman, A. (2008) The RNA WikiProject: Community annotation of RNA families. RNA, 14(12), 2462-2464. DOI: 10.1261/rna.1200508  

Wodak, S., Mietchen, D., Collings, A., Russell, R., & Bourne, P. (2012) Topic Pages: PLoS Computational Biology Meets Wikipedia. PLoS Computational Biology, 8(3). DOI: 10.1371/journal.pcbi.1002446  

  • May 31, 2012
  • 12:05 PM
  • 576 views

Alcoholic extracts of Aloe vera for diabetic rats

by SS in Scientific scrutiny

This 2008 paper describes the antidiabetic activity of an Aloe vera gel extract with histological data to show the changes in STZ-induced diabetic rats.  This critique of the paper highlights the use of important data like extract doses (2004 J.Med. Food paper by Rajasekaran et al.), expected results, key hypotheses from earlier papers and the omission of important details such as the preparation of the different extracts of which the test extract was chosen as the best one.  I couldn't get the 2004 J.Med.Food paper but the 2006 paper in Clin. and Exper. Pharmacol. Physiol. by the same authors mentions some of the data in the 2004 paper.  Four extracts made (DATA NOT SHOWN). Extract 2 taken for further study.  The gel is refluxed with absolute ethanol and dried in a rotary vacuum evaporator of 80 degrees C.  If alcohol can actually extract some of the polysaccharides in the gel, drying at 80 degrees C will cook this extract which is probably why the authors get greenish brown powder.   A 2008 review by C. T. Ramachandra and P. Srinivasa Rao in the American Journal of Agricultural and Biological Sciences (vol. 3, issue 2, pages 502-510) mentions that Aloe vera gel can be heated to 65 degrees Celsius for less than 15 min or to 85-95 degrees Celsius for 1-2 min.  Even if oxidation of certain compounds in the gel is important for antidiabetic activity, this heating at 80 degrees Celsius is a long one!  Contrast this with the procedure described by Rajasekaran et al. in a 2006 paper.  The pulp (or gel) was lyophilized, extracted with 95% ethanol and dried (no temperature mentioned) to remove the solvent.  These authors also published a paper in 2004 in J. Med. Food which has been cited by Noor et al. in the 2008 paper.The 2006 paper by Rajasekaran et al. summarizes the reduction in blood glucose in STZ-induced rats receiving a dose of 300 mg/kg Aloe vera relative to control diabetic rats (21 days after administration).  The 2008 Noor et al. paper uses the same dose of 300 mg/kg Aloe vera extract (also three weeks) and gets approximately the same effect.  In fact, Rajasekaran et al. used 55 mg/kg bw STZ to induce diabetes, Noor et al. used 30 mg/kg STZ.                   Ghannam et al. (1986) used dried sap of Aloe vera and Rajasekaran et al. (2004, 2006) used 95% ethanol to extract Aloe vera pulp.  Helal et al. (2003) already showed antidiabetic activity of Aloe vera in alloxan-treated diabetic rats.  Would alcohol not extract the same principles water can PLUS other more non-polar molecules?  Could these kidney-related changes be due to the higher dose of STZ than due to alcohol used for the extraction?This 2008 Noor et al. paper represents the increasing trend for peer reviewers to not have much time to read the manuscripts to do a thorough job and for the omission of important experimental details that will leave readers unable to reproduce much of the work described in the paper.  ... Read more »

  • May 29, 2012
  • 11:32 PM
  • 440 views

What is Science Literacy?

by Steve Easterbrook in Serendipity

A few people today have pointed me at the new paper by Dan Kahan & colleagues (1), which explores competing explanations for why lots of people don’t regard climate change as a serious problem. I’ve blogged about Dan’s work before – the studies they do are very well designed, and address important questions. If you’re [...]... Read more »

Kahan, D., Peters, E., Wittlin, M., Slovic, P., Ouellette, L., Braman, D., & Mandel, G. (2012) The polarizing impact of science literacy and numeracy on perceived climate change risks. Nature Climate Change. DOI: 10.1038/nclimate1547  

Maienschein, J. (1998) Scientific Literacy. Science, 281(5379), 917-917. DOI: 10.1126/science.281.5379.917  

William F. McComas. (1998) The Principle Elements of the Nature of Science: Dispelling the Myths. The Nature of Science in Science Education. info:/

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