Nature Network - add papers to profile by PMID

Nature Network v2 was launched on Valentines Day. Nature Network, in case you haven't heard of it before, is sort of like MySpace for scientists (except not crap). Previously it was restricted to scientists in the Boston area, but this new version allows anybody to sign up, network with others, post to blogs and forums, set up a profile... you get the idea.

There's space on your profile to enter the papers that you've authored, which is cool. Unfortunately for lazy people like me you have to enter the details of those papers manually (or at least you do for now).

Luckily the form HTML is of great semantic beauty. Thus: nnaddbypmid.user.js, a quick Greasemonkey script that fetches paper metadata from PubMed using the the EUtils. Follow the 'add publication' link on your Nature Network profile as normal, then fill in the PMID textbox and click on the new 'look up details' button. Voila! The other fields should get filled in automagically.

Connotea: basic integration with Word

Word 2007 has some built-in support for bibliographies and citations. It's pretty basic and has some, um, issues, but by using it you can get your Connotea bookmarks into Word fairly quickly.

Here's how:

1. Enter your Connotea username in the form at the bottom of this post, press 'get bookmarks' and wait for a couple of minutes while a script fetches your bookmarks via the API (if you have lots of bookmarks then this could take some time)


2. Save the resulting file (as .XML - "sources.xml" would be a good name).


3. Open up Word 2007


4. Click on the References tab. In the "Citations and Bibliography" panel click on "Manage Sources"


5. Click the Browse button and select the XML file you saved in step 2.


6. Any bookmarks in your Connotea library that had citation information attached to them should appear in the 'Sources Available' listbox. Select those appropriate to the document that you're writing and copy them across to 'Current List'.


7. You can now use the 'insert citation' and 'bibliography' buttons to insert citations and generate formatted bibliographies, respectively.
   

Con2Word XMLatron

Connotea username:

PLoS One / Postgenomic mashup

Chris Surridge has an interesting post over at the PLoS blog about the comments (or the lack thereof) on PLoS One papers. He mentions one paper in particular that has a long discussion thread associated with it on Gene Expression but no real comments on the actual PLoS One site.

As a temporary solution (?) to the problem of blog comments not being immediately accessible from the paper, summaries of notable manuscripts are going to be posted to the PLoS publishing blog with open comment threads. Based on the three posts already up I think this is a terrible idea.

Partly this is personal preference - I hate blogs that just replicate tables of contents - but more importantly I think that it misses the point.

People like the GNXP folks have taken the time and trouble to build up a loyal community that fosters debate and to create an environment in which visitors enjoy interacting with the site and with each other. Sticking up an abstract or two on your own blog just isn't going to compete with that, doesn't matter how much traffic you get.

Blog properly - engage your audience - or don't blog at all. It's a personal communication medium, that's one of the reasons why people feel more comfortable commenting in a blogging environment. A link and an abstract on a publisher's blog isn't personal, it's an advert. The PLoS One blogs are generally a good read at the moment, don't ruin them.

I'm not just PLoS bashing here: I like the ideas behind PLoS One and we do the same 'if we blog the abstract then people will comment!' thing at Nature on some blogs (the ones I don't read any more). The intention is good, it's just misguided, IMHO.

Anyway, I think that a better solution would be to embrace the existing science blogosphere and to explore ways of working with it more closely. As a proof of concept, here's a Greasemonkey script that adds science blog trackbacks to PLoS One.

It's doesn't look particularly nice, mainly because I didn't have time to style things very well. Feel free to do with it as you will, though (you could get it working with PLoS Two, for a start).

Talk by Tony Hey

Tony Hey from Microsoft came to NPG today and gave a talk about e-science. Four points about his visit:

1) He wasn't evil - in fact he was quite nice and had eminently sensible attitudes towards open source and interoperability, amongst other things.

2) myTea, the electronic lab notebook system mentioned before elsewhere on the bioinformatics blogs (can't find a link, suggest you don't use Google Blogsearch if you want to find one), looks nifty, although he was talking about it in the context of a chemistry lab.

3) He showed a table from webometrics.info, which is a site that measures how well different universities are using the web. The table in question was a ranking of universities worldwide based on the number of citations of papers produced there (I believe). His point was that universities that pushed free digital repositories of their papers did better in such rankings, as evidenced by the University of Southampton - home of EPrints - sitting in the top twenty. The University of Edinburgh came 28th - ahead of Cambridge and Oxford (either ERA has gotten much better since I was there or Cambridge and Oxford have sucky repositories, is all I can say).

4) Tony's talk used a couple of slides borrowed from an earlier Bill Gates presentation. Either Bill Gates is a slideshow wizard or he has a special employee (a PowerPeon?) to prettify things up for him. No jazz or zen, but lots of gradients and snappy graphics. I was impressed.

Delicious to Connotea, mk2

Ben Lund has written a script to transfer your bookmarks from Connotea to Delicious. Sure, it's in trendy Ruby, only twenty lines long and works great, but really, how rude.

To restore balance to the universe Konstantin Baierer has come up with diu2con.pl which is written in reliable Perl, is only slightly longer and also works great. It transfers your del.icio.us bookmarks to Connotea. It uses your del.icio.us login credentials, which means that it has none of the limitations of del2con.

(update: also check out Alf's Greasemonkey script that transfers del.icio.us bookmarks to Connotea, again using the two APIs. I'm undecided as to how many lines it counts as but... it's short).

Postgenomic Proceedings vol1 iss1

Faculty of 1000 may have all the recent worthy, boring papers but it doesn't have a 'science shiznit' section. For that you need the awesome collaborative filtering power of the science blogosphere.

I'm talking about those papers outside of your field that you actually want to read. Research that makes interesting anecdotes and tabloid headlines. Don't look so haughty. You love it. You regret spending the past five years writing about techniques for automatic gene annotation when you could have been watching Dutch people having sex in MRI machines. Admit it.

Anyway, here are some interesting papers and posts from the past couple of weeks on Postgenomic. It's deliberate that the papers aren't linked to directly: go read the relevant blog post, instead.

We're all crap at making decisions about our future
(via PsyBlog)

The idea of making mistakes about what we might want in the future has been termed 'miswanting' by Gilbert and Wilson (2000). They point to a range of studies finding we are poor at predicting what will make us happy in the future. My favourite is a simple experiment in which two groups of participants get free sandwiches if they participate in the experiment - a doozie for any undergraduate.

One group has to choose which sandwiches they want for an entire week in advance. The other group gets to choose which they want each day. A fascinating thing happens. People who choose their favourite sandwich each day at lunchtime also often choose the same sandwich. This group turns out to be reasonably happy with its choice.

Amazingly, though, people choosing in advance assume that what they'll want for lunch next week is a variety. And so they choose a turkey sandwich Monday, tuna on Tuesday, egg on Wednesday and so on. It turn out that when next week rolls around they generally don't like the variety they thought they would. In fact they are significantly less happy with their choices than the group who chose their sandwiches on the day.

Get any chocolates this Valentine's Day?
(via El Gentraso)

... it may just be to lower your resistance to accepting an extra large ejaculate.

Nuptial gifts are food items or inedible tokens that are transferred to females during courtship or copulation . Tokens are of no direct value to females, and it is unknown why females require such worthless gifts as a precondition of mating. One hypothesis is that token giving arose in species that gave nutritious gifts and males exploited female preferences for nutritional gifts by substituting more easily obtainable but worthless items.

[..]

In this review, I explore the proposition that nuptial gifts act as sensory traps: by exploiting the female's gustatory responses, the male may be able to entice females to accept superfluous matings and/or transfer greater volumes of ejaculate than are in the female's reproductive interests.

Gift composition is more likely to be tailored to increasing the attractiveness of the gift to the female and/or maximizing gift handling time than to suit the female's nutritional needs … evidence suggests that the gift enables the male to overcome the resistance of the female to accepting an extra large ejaculate.

The science of romatic love
(via neurodudes, in a roundabout way)

Maybe the controlling anger activity in the 'rejected in love' group was because you just made them sit in the waiting room with 17 intense lovebirds?

Mammals and birds regularly express mate preferences and make mate choices. Data on mate choice among mammals suggest that this behavioural 'attraction system' is associated with dopaminergic reward pathways in the brain. It has been proposed that intense romantic love, a human cross-cultural universal, is a developed form of this attraction system. To begin to determine the neural mechanisms associated with romantic attraction in humans, we used functional magnetic resonance imaging (fMRI) to study 17 people who were intensely 'in love'. Activation specific to the beloved occurred in the brainstem right ventral tegmental area and right postero-dorsal body of the caudate nucleus. These and other results suggest that dopaminergic reward and motivation pathways contribute to aspects of romantic love. We also used fMRI to study 15 men and women who had just been rejected in love. Preliminary analysis showed activity specific to the beloved in related regions of the reward system associated with monetary gambling for uncertain large gains and losses, and in regions of the lateral orbitofrontal cortex associated with theory of mind, obsessive/compulsive behaviours and controlling anger. These data contribute to our view that romantic love is one of the three primary brain systems that evolved in avian and mammalian species to direct reproduction. The sex drive evolved to motivate individuals to seek a range of mating partners; attraction evolved to motivate individuals to prefer and pursue specific partners; and attachment evolved to motivate individuals to remain together long enough to complete species-specific parenting duties. These three behavioural repertoires appear to be based on brain systems that are largely distinct yet interrelated, and they interact in specific ways to orchestrate reproduction, using both hormones and monoamines. Romantic attraction in humans and its antecedent in other mammalian species play a primary role: this neural mechanism motivates individuals to focus their courtship energy on specific others, thereby conserving valuable time and metabolic energy, and facilitating mate choice.

Music preferences and personality
(via PsyBlog and MindHacks)

How is information about people conveyed through their preferences for certain kinds of music? Here we show that individuals use their music preferences to communicate information about their personalities to observers, and that observers can use such information to form impressions of others. Study 1 revealed that music was the most common topic in conversations among strangers given the task of getting acquainted. Why was talk about music so prevalent? Study 2 showed that (a) observers were able to form consensual and accurate impressions on the basis of targets' music preferences, (b) music preferences were related to targets' personalities, (c) the specific cues that observers used tended to be the ones that were valid, and (d) music preferences reveal information that is different from that obtained in other zero-acquaintance contexts. Discussion focuses on the mechanisms that may underlie the links between personality and music preferences.

From PsyBlog:

What some music preferences mean for personality:

• Likes vocals: extraverted
• Likes country: emotionally stable. On the face of it, this is bizarre really because country music is all about heartache. Either the emotionally stable are attracted to country music or it has a calming effect on the unstable!
• Likes jazz: intellectual

This raises the question of why people listen to particular types of music. One theory is that people simply find some music more pleasant for aesthetic or cognitive reasons. Another is that people use music to regulate their mood: I want to get hyper for a night out so I put on some dance music. Another is that music is related to identity; people listen to music that expresses they way they see themselves. It seems likely that a combination of all these theories is probably true.

Boys grow breasts after using lavender and tea tree oils
(via MedPundit)

The first, aged four, had been experiencing symptoms for two to three weeks. His mother said she had recently begun applying a 'healing balm' containing lavender oil to his skin.

The second boy, who was 10, had been developing enlarged breast tissue over the previous five months.When questioned, it emerged that he was using a shampoo and hair gel containing lavender oil and tea tree oil every morning.

The third boy, aged seven, had a one-month history of gynaecomastia. He had been using lavender-scented soaps and skin lotions. His twin used the soap, but not the lotions, and had not developed the condition.

Each of the boys stopped using the relevant products, and several months later the tissue growth was found to have subsided.

The researchers confirmed their suspicion that the oils acted like estrogens by exposing cultured estrogen-responsive breast cancer cells to them. The cells behaved as if they were in the presence of estrogen, and the response was greater the greater the dose of the oils.

Listening to music while you exercise: does it make a difference?
(via Sciencebase)

This study examined the effects of loudness and tempo of background music on exercise performance. A total of 30 volunteers performed five 10-min exercise sessions on a treadmill. The music listened to whilst exercising was either fast/loud, fast/quiet, slow/loud, slow/quiet or absent. Measures of running speed, heart rate, perceived exertion and affect were taken. Significant effects and interactions were found for running speed and heart rate across the different music tempo and loudness levels. More positive affect was observed during the music condition in comparison to the 'no music' condition. No significant differences for perceived exertion were found across conditions. These results confirm that fast, loud music might be played to enhance optimal exercising, and show how loudness and tempo interact.

Shocker: big pharma uses sneaky marketing techniques
(via a comment in a BMC journal)

BACKGROUND: Patient organisations may be exposed to conflicts of interest and undue influence through pharmaceutical industry (Pharma) donations. We examined advertising and disclosure of financial support by pharmaceutical companies on the websites of major patient organisations. METHOD: Sixty-nine national and international patient organisations covering 10 disease states were identified using a defined Google search strategy. These were assessed for indicators of transparency, advertising, and disclosure of Pharma funding using an abstraction tool and inspection of annual reports. Data were analysed by simple tally, with medians calculated for financial data. RESULTS: Patient organisations websites were clear about their identity, target audience and intention but only a third were clear on how they derived their funds. Only 4/69 websites stated advertising and conflict of interest policies. Advertising was generally absent. 54% of sites included an annual report, but financial reporting and disclosure of donors varied substantially. Corporate donations were itemised in only 7/37 reports and none gave enough information to show the proportion of funding from Pharma. 45% of organisations declared Pharma funding on their website but the annual reports named more Pharma donors than did the websites (median 6 vs. 1). One third of websites showed one or more company logos and/or had links to Pharma websites. Pharma companies' introductions were present on 10% of websites, some of them mentioning specific products. Two patient organisations had obvious close ties to Pharma. [..]