CircleCount helps you better understand Google+

2013-05-15 21:23:27 (0 comments, 0 reshares, 0 +1s)

A great example of a blogger not understanding the difference between the prevalent live poliovirus vaccine (containing human-infecting virus which replicates and sheds) and the smallpox vaccine, made from a safe cow-infecting virus which cross-reacts with smallpox.

TL/DR: The Eradication of Smalpox is a TERRIBLE blueprint for Polio's Demise.

http://blogs.discovermagazine.com/bodyhorrors/?p=1289

2013-05-14 17:36:58 (0 comments, 0 reshares, 1 +1s)

What do the letters and numbers that we use to identify flu viruses mean?

Well, take H5N1. The H is for Hemagglutinin, HA for short. The N is for Neuraminidase, NA for short. These are two proteins on the surface of the virus. The human immune system can produce antibodies against these proteins to neutralize their function. The numbers tell us what type of HA or NA a given virus has on its surface. So, for example, H1N1 and H5N1 have different HA but very similar NA on their surface.

What do HA and NA do? Well, to simplify, HA allows to virus to bind and enter a cell. NA allows the newly formed virus to "cut its tether" and escape from a cell. So we name flu viruses after their cell entry and exit proteins. 

The new H7N9 virus is scary for multiple reasons, but one is that having HA type 7 and NA type 9 represents a novel challenge to the immune systems of... more »

2013-05-08 16:31:22 (0 comments, 0 reshares, 0 +1s)

The topic is mind-boggling. How does a community balance "forces imperiling sea turtles on the Pacific coast of Mexico’s Baja peninsula... with the need to sustain the economies and culture in the region’s fishing villages"?

What's more amazing is that this professional-looking documentary is a student project! 

¡Viva la Tortuga!!

2013-05-07 14:35:43 (0 comments, 0 reshares, 1 +1s)

I had a fascinating time at #CSE2013 , the Council for Science Editors meeting in Montreal. I tweeted about it some (@wtjackson) but G+ is a more relaxed way to sum it up.

I was mostly there for the social media panels, one of which I took part in. The upshot is that publishers believe this stuff matters, scientifically. This blows me away, because the most tweeted and blogged papers in my field are rarely the most scientifically interesting. I was the last speaker on social media and I think they were surprised to hear that as a researcher, neither conventional nor science-specific social media matter  much at the moment. I think there's an opportunity there but nobody's getting it quite right. It will happen, though.

The keynotes were amazing. Jeffrey Drazen MD, longtime editor-in-chief of The New England Journal of Medicine, gave a fantastic historical perspectiveon... more »

2013-05-07 13:06:00 (0 comments, 0 reshares, 0 +1s)

2013-04-26 17:59:03 (0 comments, 0 reshares, 0 +1s)

If you think virology should be more like a Jason Bourne movie...

"I met a representative of the Wistar Institute in the parking lot of a restaurant just off the New Jersey Turnpike, halfway between New York and Philadelphia. He handed me a white styrofoam box packed with ice, that contained  vials of the Koprowski vaccine. To the uninformed observer, it might have looked like a drug exchange."

From http://www.virology.ws/2013/04/26/hilary-koprowski-96/?utm_source=feedly&utm_medium=feed&utm_campaign=Feed%3A+VirologyBlog+(virology+blog)

2013-04-26 13:32:30 (0 comments, 0 reshares, 1 +1s)

2013-04-21 17:49:42 (0 comments, 0 reshares, 0 +1s)

2013-04-18 21:24:56 (0 comments, 0 reshares, 0 +1s)

Mike Taylor has built a new journal recommender tool ("Journal Finder - Beta"). It works really well - give it a try! http://www.miketaylor.org.uk/tmp/journal-finder.html

2013-04-16 15:08:35 (2 comments, 3 reshares, 5 +1s)

It's unfortunate that this needs to be said, but...
homeopathic preparations are WATER.

Assuming the unregulated person or persons doing the diluting use relatively sterile technique, the water will be at best harmless.

To give water to a child and expect it to protect the child from anything except dehydration is madness.

http://www.guardian.co.uk/society/2013/apr/15/homeopathy-measles-mp

2013-04-15 14:01:24 (2 comments, 0 reshares, 1 +1s)

More on the Elsevier takeover of Mendeley. Has it occurred to anyone that Elsevier just might understand that their anti-Open Access battle is over and they're buying access to Mendeley's userbase so they can move forward with a realistic yet still-revenue generating alternative model?

http://www.newyorker.com/online/blogs/elements/2013/04/elsevier-mendeley-journals-science-software.html

2013-04-12 18:43:07 (0 comments, 0 reshares, 0 +1s)

For the anniversary of the announcement of the successful polio vaccine trial, which was itself a contentious and debated announcement, here is the latest on polio eradication from The Lancet.

http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)60825-9/fulltext?rss=yes

2013-04-11 19:46:05 (0 comments, 1 reshares, 3 +1s)

A Microsoft researcher and Mendeley's head of academic outreach are having a debate about the Elsevier acquisition of Mendeley. It started on Twitter but has spilled over to the researcher's website comments section. Pull up a chair (and contribute, if you care about this stuff.)

http://www.zephoria.org/thoughts/archives/2013/04/11/mendeley-elsevier.html

2013-04-10 19:09:58 (0 comments, 0 reshares, 2 +1s)

Well, it's done. Mendeley is bought and paid for. Is this the beginning of a new era in social-reference-management-paper-discovery-whatever-else-Mendeley-does, or another startup swallowed up and never to be heard from again?

http://blogs.wsj.com/tech-europe/2013/04/10/reed-elsevier-buys-education-startup-mendeley/

2013-04-08 16:45:04 (1 comments, 2 reshares, 0 +1s)

At the risk of being pilloried, I will say that in my view sometimes the difference between these so-called predatory journals and legitimate journals is very small, but it is very real.

One thing the NYT didn't quite get across is the sheer volume of emails academics get every day from sketchy conferences and journals. It can be a dozen a day, easily, saying they want you on their editorial board or want you to be a speaker. It can be a challenge to ferret out the "real" ones from the predatory... 

http://www.nytimes.com/2013/04/08/health/for-scientists-an-exploding-world-of-pseudo-academia.html?_r=1&

2013-03-20 17:58:56 (0 comments, 0 reshares, 1 +1s)

I usually stick to viruses, but this is an important story and has directly affected friends, so here goes.

The "old" Whooping Cough vaccine was like what you learned about in school: a killed preparation of the bacterium, B. pertussis, which causes the disease. This trains your immune system to recognize live B. pertussis. It's a great vaccine but it causes some reactions, including fever and localized swelling. Parents do not like fever and localized swelling. (As a parent, I sympathize... but...)

The "new" Whooping Cough vaccine is acellular, meaning it contains parts of the bacteria but not the whole bacteria. It causes many fewer complications! Science wins! Except... wait for it... it's just not as good a vaccine. In fact, persons only vaccinated with the "new" vaccine have a significantly higher risk of contracting the bacterium than those... more »

2013-03-19 15:42:27 (0 comments, 0 reshares, 0 +1s)

Always cool when a new virus is found... “Theiler's disease-associated virus.” This makes another hepatitis virus in the Flaviviridae family, too. (After Hepatitis C Virus, of course.)

http://www.pnas.org/content/early/2013/03/15/1219217110.abstract

2013-03-15 14:14:14 (0 comments, 1 reshares, 2 +1s)

Recent research in our lab indicates the exciting possibility that safe, cheap, long-used antibacterial drugs might be potent antivirals against a common class of viruses. The basic research was published in an open access journal, and I’ve linked to it below, but in this post itself I’d like to give a simple explanation of how this came about and what it all means.

Malaria has long been treated by drugs that disrupt acidic compartments inside cells. These drugs, including chloroquine and quinine, block the low pH of these cell compartments. Low pH is required for many cellular processes. These drugs also inhibit some viruses which are known to have parts of their virus cycle that take place inside acidic cellular compartments. The best example is HIV, where blocking acidic compartments disrupts the modification of the well-studies viral surface protein gp120, a process which takespla... more »

2013-03-14 14:30:00 (3 comments, 0 reshares, 7 +1s)

Google has the right to do whatever they want - I paid nothing to use Google Reader and enjoyed it for years. I won't fight for them to save it or sign petitions.

I'll say this, though, as I migrate my RSS feeds to Feedly (for now). I suddenly find myself wondering what other options there are for the other Google sites I use. Outlook mail is pretty awesome. What about the best Docs replacement? 

G+ for now is the most flexible social media platform, if not the most widely used, but I think we know the other options in that arena.

#Reader  

2013-03-01 17:36:06 (0 comments, 0 reshares, 0 +1s)

It's a sad day to be a U.S. scientist.

This afternoon I'm supposed to take part in a program encouraging 12-17 year-olds to go into science and that is not going to be easy. How can you encourage students to go into something their country will not value going forward?

Tom Levenson does a great job with perspective:
http://blogs.scientificamerican.com/guest-blog/2013/02/27/there-should-be-grandeur-basic-science-in-the-shadow-of-the-sequester/

2013-02-25 00:29:59 (1 comments, 0 reshares, 4 +1s)

If you don't subscribe to Spot The Station emails, do so immediately. The timing doesn't always work, the cloud cover doesn't always cooperate, but it's so worth it for the nights when you get to take the kids outside before dinner on a clear winter's night and watch the International Space Station zoom over your house. Thanks, NASA!

http://spotthestation.nasa.gov/

2013-02-23 06:20:13 (1 comments, 0 reshares, 2 +1s)

Extracellular vesicles (EVs) represent an important mode of intercellular communication by serving as vehicles for the transfer between cells of membrane and cytosolic proteins, lipids, and RNA. Incomplete understanding of the molecular mechanisms for EV formation and a lack of methods to interfere with the packaging of cargo or with vesicle release, however, limits what we know about their physiological relevance in vivo. Raposo and Stoorvogel review proposed mechanisms for EV formation, targeting, and function.

2013-02-22 16:24:55 (0 comments, 2 reshares, 1 +1s)

A good, balanced story from NPR about H5N1 research resuming in the U.S. They get it right; the strains concerned transmitted in ferrets, not people.
http://www.npr.org/blogs/health/2013/02/22/172582712/to-keep-deadly-bird-flu-in-the-lab-feds-set-rules-for-scientists

And to keep it light, here's the latest from The Onion.
http://www.theonion.com/articles/this-seasons-hottest-flu-fashions,31399/

2013-02-21 05:12:25 (0 comments, 0 reshares, 0 +1s)

OK, PeerJ and River Valley, nice work. Pdf is still not the best option, but single columns are a great start. Their internal hyperlinking to references and back is a little weak, and of course pdfs will never allow for dynamic figures linked to text, but hey, somebody's thinking about bringing the pdf into this decade!

http://blog.peerj.com/post/43558508113/the-thinking-behind-the-design-of-peerjs-pdfs

2013-02-20 18:15:36 (0 comments, 1 reshares, 1 +1s)

Interesting paper on rhinovirus and the immune response. The length of the telomeres (kind of like protective DNA endcaps) in some of your immune cells is related to the likelihood you can be infected by a cold virus and ultimately come down with a cold.

In fact, the clinical illness data are stronger than the infection data. This is actually slightly surprising, since the symptoms of a cold are usually attributed to immune responses, and short telomeres may make for weaker immune responses. (Leukocytes with short telomeres would not be expected to proliferate as well.) However, perhaps the increased ability of the virus to thrive contributes to increased colds, despite the weaker immune response. Alternatively, the types of T-cells implicated in the article may not be involved in cold symptoms.

http://jama.jamanetwork.com/article.aspx?articleid=1653523

2013-02-19 19:06:00 (0 comments, 3 reshares, 2 +1s)

This image has been going around today. From the other side, I'm constantly being told as a med school teacher that students want interactivity and multimedia etc. and we should include material for their iPads (they're required by the school to buy them.) Then I see students on facebook, imgur, reddit, etc. and I wonder...

http://imgur.com/gallery/N2PYK8S

2013-02-19 16:44:36 (2 comments, 0 reshares, 1 +1s)

There's a lot of "getting it" in this letter that went out today from the new EIC of Virology. SImpler submission, no page charges, and a reasonable open access embargo period. Many of the very issues I complained about when I gave my rant talk about publishing in DC last year. 

I don't know about the Streamline Reviews thing. Does this really help? When I get bad reviews, I don't really want those issues on the forefront of the mind of new reviewers from the next journal. I suppose there are situations where it could help, though. 

I'm putting the whole long thing here. It's a huge message that Virology has a huge clue about how to survive as a journal these days!

Dear Dr Jackson,
I am writing to introduce myself as the new Editor-in-Chief of Virology and to let you know about ways we are making Virology a more attractive place to sendp... more »

2013-02-19 15:48:45 (2 comments, 0 reshares, 0 +1s)

A great story, albeit one that will not work in any class I take part in teaching!

http://boingboing.net/2013/02/19/students-get-class-wide-as-by.html

2013-02-13 18:44:28 (2 comments, 1 reshares, 0 +1s)

Part of me wants a CNN interview with Wakefield to have spectacularly low ratings and be ignored. Part of me will not be able to look away (although I suppose I'm not counted in the ratings, right?)

Here's hoping the questions are appropriately tough.

http://edition.cnn.com/2011/HEALTH/01/05/autism.vaccines/index.html

2013-02-12 19:35:15 (0 comments, 2 reshares, 2 +1s)

Ever wonder where new viruses come from?

In this paper Runckel et. al. use poliovirus as a model of how RNA viruses, a group that includes the common cold, flu, and hepatitis A and C viruses, recombine their genomes.  When genomes recombine, novel viruses can result. The authors show that they can predict where polioviruses will recombine and prove their prediction by building a virus that recombines at higher frequency.  The GC-rich regions of the genome increase recombination frequency significantly.

A great model for studying virus recombination and perhaps a harbinger of how close we are to understanding viruses well enough to perform some truly complex forward engineering.

http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1003164

2013-02-12 14:51:48 (0 comments, 0 reshares, 0 +1s)

PeerJ is live today with, to say the least, an eclectic initial set of papers. Exciting times!

https://PeerJ.com 

2013-02-08 21:11:59 (0 comments, 0 reshares, 0 +1s)

I'll see your plush microbes and raise you....
http://www.lukejerram.com/glass/gallery

2013-02-07 16:14:44 (1 comments, 0 reshares, 0 +1s)

2013-02-05 20:48:40 (0 comments, 0 reshares, 0 +1s)

I'm curious, my experiences are purely anecdotal, but does it seem like a lot of academic paper reviewers not completing their task these days? Meaning they agree to review a paper, then don't review it in time or at all? 

This is troubling - better to say no, which I do when I have no time - but it also means that those of us who pay attention to deadlines (call it my good New England upbringing) are asked to review more and more...

http://rlv.zcache.com/douglas_adams_deadlines_quote_poster-rdf338b7c6de9448f8d741574721c0d0e_wfb_400.jpg

2013-02-05 16:46:12 (0 comments, 0 reshares, 0 +1s)

I always love getting personalized emails that begin like this... Thank you,  (salesperson name) for your message.

2013-01-31 14:26:00 (0 comments, 0 reshares, 4 +1s)

Should alumni withhold donations from the +Massachusetts Institute of Technology (MIT) until the four steps +Farhad Manjoo describes in this article happen? I gave last year, but the more I hear about their actions in the Aaron Swartz case the less inclined I am to keep giving...
 
http://www.slate.com/articles/technology/technology/2013/01/aaron_swartz_jstor_mit_can_honor_the_internet_activist_by_fighting_to_make.html

2013-01-28 17:58:23 (0 comments, 1 reshares, 2 +1s)

In my inbox from Elsevier this morning was an ad touting some new policies at Virology, a major journal in my field. Notably, all articles are now free to access after 12 months, and there are no page charges.

Elsevier has my attention. As I've said before, I don't believe all research must be open to everyone the instant it's published. After all, we embargo our own research until the moment of submission. A 6-12 month window of additional embargo is a reasonable compromise.

If the 12-month window is enough to attract library subscriptions, funding the elimination of page charges, then Elsevier may have hit a winning formula here. We'll see how hard the no-compromise instant-open-access crowd  hits back. 
more »

2013-01-23 23:27:36 (0 comments, 0 reshares, 0 +1s)

Walter Lewin produced problem set walk-throughs that were run on a continuous loop on the then-crude MIT cable system, and got me through MIT freshman physics. He then gave dazzling lectures during parents' weekend that convinced my family my education was actually worth $35K/year. It is with this background that I heartily endorse his edX class.

https://www.edx.org/courses/MITx/8.02x/2013_Spring/about

2013-01-18 21:16:42 (0 comments, 0 reshares, 2 +1s)

Nature Publishing is sending around a survey about Open Access; it's quite interesting. One of the statements I was asked to agree or disagree with was "I believe most funding agencies will require Open Access publishing within five years." Sounds like Nature's a little afraid...

2013-01-17 16:56:35 (1 comments, 0 reshares, 0 +1s)

WOW. That is all.

2013-01-15 13:45:06 (0 comments, 1 reshares, 3 +1s)

This is a fun posting by Carl Zimmer. Although he emphasizes that at many as ninety percent of influenza viruses are not replication competent, in fact, that's nothing in the world of viral incompetence! 

To put it in context, for every poliovirus that is capable of productively infecting a cell in culture, there are as many as a thousand that are incompetent. At least influenza has an excuse - there are eight RNA genome segments to assemble into the virion. Poliovirus has no such excuse -it only has one genome segment.

http://phenomena.nationalgeographic.com/2013/01/14/influenza-our-incompetent-enemy/

2013-01-14 19:28:23 (0 comments, 1 reshares, 0 +1s)

2013-01-13 20:18:53 (0 comments, 2 reshares, 2 +1s)

From The New Yorker, via N5N1 blog:

Unfortunately, high flu season is also the time when some of the smartest people I know act in the most irrational ways. On Friday, a highly educated, very smart colleague at The New Yorker explained her decision to remain unvaccinated with these words: “I never get a flu shot, and I never get the flu.”

O.K. Let’s play her game. Turn to whomever you are with and say these sentences out loud: “I never wear seat belts, and I never get killed in car crashes;” “I never use condoms, and I never become infected with sexually transmitted diseases;” “I eat red meat seven times a week, only exercise once a year, and I’ve never had a heart attack or a stroke.”
...
The flu vaccine is not perfect, but it’s what we have. It’s available at drug-store chains and malls, big-box superstores and, naturally, at your doctor’s office.Get one today.

more »

2013-01-13 17:09:38 (1 comments, 0 reshares, 0 +1s)

Much has been made in certain circles of Poliovirus making the cover of Time magazine this week. Vincent Racaniello had some interesting things to say on Virology Blog about it. I have a few things to add, both scientific and about the magazine press in general.

Poliovirus is not on the U.S. cover of Time, only the international versions.
This is apparently something of a trend: one cover for Americans and another for the rest of the world. While Poliovirus is on the world's Time covers, the U.S. got a scary looking operating chair with a headline about abortion rights. (See the below link for the covers.) I suppose this has to do with sales. Does anyone read print Time anymore, outside of maybe airports and doctor's waiting rooms? Does an abortionist's chair sell more than a structural image of poliovirus and its receptor? Guess so, in America.

I wasn't sure if... more »

2013-01-10 20:39:32 (0 comments, 1 reshares, 1 +1s)

As they say on boingboing.net, time for a "unicorn chaser" after the sad previous post. This made me laugh, and if you were to google "the opposite of important" this would deserve to be the first hit.

http://www.uproxx.com/tv/2013/01/an-important-discussion-about-stars-in-danger-the-high-dive/#respond

2013-01-10 18:38:01 (0 comments, 0 reshares, 1 +1s)

Not happy news, but an important read. I need to go find something fun to read (and maybe post - "unicorn chaser?")

http://www.wired.com/wiredscience/2013/01/polio-more-bad/

2013-01-08 19:57:38 (0 comments, 0 reshares, 2 +1s)

If you're a bench scientist these are fantastic.  "Overly Honest Methods."

https://twitter.com/search?q=%23OverlyHonestMethods

2012-12-21 18:18:40 (0 comments, 2 reshares, 1 +1s)

I sure hope he used what was in the freezer and didn't have to order the primers special. :)

http://www.itsokaytobesmart.com/post/38445200144/molecular-biology-proposal

2012-12-20 19:02:59 (0 comments, 0 reshares, 1 +1s)

I sent an email to my senators and representatives about the planned NIH budget sequestration that is part of the so-called fiscal cliff negotiations. I received a canned response from Wisconsin Senator Ron Johnson's office about "health care reform". The specifics of the message annoyed me enough that I responded. I reproduce the Senator's message, and my response, here.

-----
Dear Bill,
 
Thank you for taking the time to contact me regarding funding for the National Institute of Health and health research programs. 
 
America's free market system, not government, has produced the most successful economy in human history and our health care system should be no exception.  The free market guarantees the lowest possible price and the highest possible levels of quality and customer service.  
 
Unfortunately, the ObamaAdmin... more »

2012-12-18 22:12:13 (5 comments, 0 reshares, 1 +1s)

Another tragedy. How about we agree, as a society, never again to use vaccination campaigns as a cover for something else?

http://blogs.voanews.com/breaking-news/2012/12/18/attacks-on-polio-workers-kill-five-in-pakistan/