Friday, October 28, 2011

Royal Society opens its archives and launches Open Biology

Royal Society of London Open Access
Open access news from the Royal Society of London is very welcome.  Read more about the recently launched Open Biology, "a journal run for scientists by scientists." The Royal Society says that the editors and editorial board intend to "ensure a fair and speedy review process without recourse to unnecessary rounds of revision,"  It is very new, so check back often for more publications.

The Royal Society open archive announcement coincides with Open Access Week, and celebrates free access to any article  published more than 70 years ago. This is remarkable, considering the historically significant research findings published by the Royal Society.  Try the advanced search at the Royal Society site, and you'll find that the publication date range extends back to 1665. There are not many (any?) other sites on the Internet where you can find such an authentic and rich archive of scientific discovery. Explore!

Thursday, October 27, 2011

PLoS Blogs: Making Science Understandable and Accessible

Today on one of the Public Library of Science (PLoS) Blogs is an interesting account of gathering sediment cores from tropical mud, to document changes in precipitation over thousands of years by measuring amounts of hydrogen ions in the sediment.  What's so great about mucking around in the tropics to measure hydrogen ions?  As author Conor Myhrvold of MIT SciWrite explains, it gathers "physical evidence of recent manifestations of tropical climate change several thousand years ago to make sure the parameters in the [climate change] models are grounded in reality."  Reading this will give insight into what it takes, physically, to amass reliable data for understanding climate change, and a deeper appreciation for climate scientists' assessment of those data.  At the very least, it's a good way to balance what you may have heard from certain politicians. 

While at the PLoS Blogs site, take a moment to see all of the other perspectives offered there and link to the many wonderful open access PLoS journals.  Open Access Week ends soon - take this open access challenge and find an article that interests you (try DOAJ for a start) to forward to a friend or colleague, confident that he or she will also be able to read it in its entirety.  No subscription required.

Thursday, October 20, 2011

Going away for Fall Break? Need access to journal articles?

Information on remote access to the library's resources is here.  In a nutshell, do this:

  1. Download the VPN Client (Cisco) from the CIT website.
  2. Launch the client and login before trying to search library databases or download articles.
  3. Be sure the barcode on the back of your OCID has been input into the library's circulation system, if you will be requesting any items on the OhioLINK library catalog.  We can do that over the phone, if needed.  440-775-8310.

Problems?  Questions?  Contact science.library@oberlin.edu or chat with us on Meebo IM.

Have a great break!  The library will be open all week, Mon-Fri, 9-noon and 1-4:30, if you're staying on campus.

PubMed Central 10th Anniversary Video

PubMedCentral (PMC) celebrated its 10th Anniversary in 2010, and this commemorative video was posted by NCBI NLM in July 2011.  Just 12 minutes long, and definitely worth viewing despite the time elapsed since the video was distributed.  Establishing the open access archive was one of the most important developments in scientific communication in the past decade, and the video chronicles its rapid rise to prominence and influence on other repositories of scientific articles.  In addition to its role as an archive, PMC leads directly to NCBI and PubMed databases, with links to protein or nucleotide data or citing articles beyond those in the PMC, among other options.  See this 2009 article co-authored by biology professor Michael Moore and explore some of those linking options:
Rosid radiation and the rapid rise of angiosperm-dominated forests.
Proc Natl Acad Sci U S A. 2009 March 10; 106(10): 3853–3858.

Friday, October 14, 2011

Committed to Biodiversity? Go Swim with Sharks!

Shark Tourism is a growing business with a helpful purpose that may not be entirely clear to thrill seekers in wet suits - preserving the diversity of predators essential for maintaining ecosystem balance.  Listen to this great segment on Living on Earth, October 14, 2011, featuring Samuel “Doc” Gruber, a marine scientist at the University of Miami, who has been studying lemon sharks for 20 years from the beachfront lab he started on Bahamas’ Bimini island.

If you're considering a dip with sharks (or would prefer to appreciate them from afar), check out this magnificent reference book on our new book shelf:  The Sharks of North America / José I. Castro ; color illustrations by Diane Rome Peebles.  New York : Oxford University Press, c2011

Wednesday, October 12, 2011

PubMed: access to free medical articles online is unmatched

www.ncbi.nlm.nih.gov/m/pubmed/
Open Access Gem of the Week:
For rapid, effective and entirely free (to the user) indexing to open access medical literature, PubMed can't be duplicated or surpassed.  If you need to limit your search to medical articles that are freely available, PubMed is simply the best.  Do any search and notice on the far right of the results screen a link to "Free Full Text" -- there are many other limits and very powerful search options, but this is one of the most obvious and helpful for the public.

Medline, the database underlying PubMed, can be simultaneously searched with Chemical Abstracts in SciFinder; with BIOSIS and the ISI citation indexes in Web of Knowledge; and with a whole host of databases in EbscoHost.  There are excellent reasons to search Medline in those different platforms, but none of them are freely accessible by the public, world-wide, and offer the same ease of quickly linking to free articles online.  PubMed:  our tax dollars at work, and worth every penny.  Try the advanced search interface with its "search builder" and be amazed at the options for creating a well-focused search.   PubMed Mobile provides access from just about anywhere, anytime.  Thank you, NCBI.

Thursday, October 06, 2011

Cool Citation Tracking Tools @ the Geek Fest - Oct. 11

Come to the library's Geek Fest on Tuesday October 11 and have fun following citations.  Truly, it will be fun!

  • Easily find Oberlin faculty members whose research has been referenced (cited) by hundreds of other authors in the past twenty years.  
  • See who has cited any published paper that interests you, from any discipline or time period, using the Web of Science - and, in one more step, find all of the papers related to those citing papers with the shared reference feature.  
  • Leaping (linking) from one citation to the next in mere milliseconds, all within the context of millions of scholarly articles indexed in the Web of Science - including Arts & Humanities Citation Index, Social Sciences Citation Index and the Science Citation Index.  Plus Conference Proceedings!

Once you've mastered the Web of Science, visit other stations around Azariah's Cafe, set up to delight you with new ways to find, store, organize and use information.  Food, beverages, friendly librarians, fellow students, writing tutors, prizes!  Mark your calendar...  be there!

Monday, September 26, 2011

Rain Barrel Workshop at the Oberlin Depot

Want to conserve water with your own rain barrel? Make your own? Head to the Oberlin Depot on Saturday, October 8, 2011.

OSWAMP-Oberlin Stormwater Management Project
Sign up for a RAIN BARREL WORKSHOP

Sat. Oct. 8, 2-5 pm
Oberlin Depot (beside the bike path, between S. Professor and S. Main St., just south of South Street)
Image from Chesapeake Bay Trust

Send $20 cash or check (made out to City of Avon Lake) before Oct. 1 to:
Annika Sullivan
OCMR 2515
Oberlin College
Oberlin OH 44074

Bring power tools!!!

Friday, September 23, 2011

Jennifer Crozier '09 published in Infectious Disease Reports

It is great to see a paper by former science library student assistant Jennifer Crozier '09 in Infectious Disease Reports, an Open Access, peer-reviewed journal published by PAGEPress, Pavia, Italy. Crozier is one of five authors of Nanoparticles containing siRNA to silence CD4 and CCR5 reduce expression of these receptors and inhibit HIV-1 infection in human female reproductive tract tissue explants. The article reports research under the direction of Susan K. Eszterhas and Alexandra L. Howell of the V.A. Medical Center, White River Junction, VT and Dartmouth Medical School Department of Microbiology and Immunology. PAGEPress is devoted to "open access knowledge" and credits Public Knowledge Project for Open Journal Systems (PKP | OJP)

Wednesday, September 21, 2011


Visit Open Access Week
Open Access Week will be celebrated world wide during Oberlin's Fall Break, so we will highlight Open Access resources in the sciences during the coming weeks. Some important Open Access journals are listed here. Have a favorite Open Access journal that isn't noted on the list? Let me know!

Tuesday, September 06, 2011

Summer slipped into September... need a study carrel?

After weeks of anticipation, the new academic year has begun!  It feels like late October already, but hot September weather is sure to hit us when we least need the distraction of summer breezes on top of September's academic expectations.  Regardless, the science library is a great place to study.  If you want a study carrel here, stop by and fill out an carrel application form.  Leave it at the circulation desk anytime before 4pm on Friday, September 9, and you will have complete consideration along with everyone else in your class and major (senior science majors are given priority).  More about Study Carrels in the science library.

Thursday, August 11, 2011

Julia Bair, 5th year double-degree student, publishes in Eur. J. Neurosci.

Just indexed in ISI Web of Knowledge and co-authored by Julia Bair, double-degree Bassoon performance/Neuroscience major from Glencoe, Illinois:

What subcortical-cortical relationships tell us about processing speech in noise.
Parbery-Clark, Alexandra; Marmel, Frederic; Bair, Julia; Kraus, Nina

EUROPEAN JOURNAL OF NEUROSCIENCE 33 (3): 549-557  FEB 2011 [access @ OhioLINK EJC]

Bair's co-authors are based in various departments at Northwestern University, Evanston, Illinois, including the Auditory Neuroscience Laboratory.  The team investigated the "effects of background noise on both subcortical- and cortical-evoked responses, and the relationships between them, in normal hearing young adults."

See a sample issue of the journal at Wiley Online Library.

Tuesday, August 09, 2011

Amanda Schmidt's latest post from China: digging for snails

Assistant Professor of Geology Amanda Schmidt is studying the properties of loess in China, as part of an effort to understand the natural hazards of a region characterized with this sediment. She writes from China: "These [samples] will be used to determine how strong [loess] is, what makes it break in blocks, and what makes it flow. We suspect that the original loess is rather weak and flows easily, but that once it has flowed and set up again, it is quite a bit stronger." Schmidt's posts appear in the New York Times Scientist at Work blog. The bit about snails refers to finding snails buried in undisturbed loess sediments, to use for dating the deposition age. Schmidt includes a great photo of the 3-year old daughter of the park science translator, enjoying her first time "playing in dirt," and helping to sort snails from sediment.

Monday, August 08, 2011

Basic Protocols Freely Accessible in JoVE

JoVE: Journal of Visualized Experiments is a peer-reviewed online journal of videos and other forms of visualization that demonstrate complex procedures, most of which are rather more specialized than needed for our curriculum -- but the "Basic Protocols" section includes 56 videos that are freely accessible and of potential use in the undergraduate laboratory.  See, for example, Generation of Single-Cell Suspensions from Mouse Neural Tissue, by Sandra Pennartz, Sandy Reiss, Rebecca Biloune, Doris Hasselmann, and Andreas Bosio. Free access to the protocol, which is accompanied by a written abstract and pdf describing the technique, is sponsored by Miltenyi Biotec.

Thursday, August 04, 2011

Biology major Dylan Holmes co-author in Animal Behavior

About the Journal
Congratulations to junior Dylan Holmes, who co-authored a paper appearing in the current issue of Animal Behavior:

Sing softly and carry a big stick: signals of aggressive intent in the song sparrow.
Akcay, Caglar; Tom, Mari E.; Holmes, Dylan; Campbell, S. Elizabeth; Beecher, Michael D.
Animal Behaviour 82 (2): 377-382 August 2011 [access at OhioLINK EJC]

Also recently published is an article by chemistry professor Matt Elrod:
Kinetics Study of the Aromatic Bicyclic Peroxy Radical plus NO Reaction: Overall Rate Constant and Nitrate Product Yield Measurements.  Elrod, Matthew J.
Journal of Physical Chemistry A 115 (28): 8125-8130 July 21, 2011 [access at ACS Publications]

Wednesday, August 03, 2011

Diving bell spider, sea urchin, Arctic ground squirrel: on journal covers this week

View this cover online (subscribers only)
We maintain print subscriptions to many journals still, even for those we also access online.  Serendipitous discovery motivated by intriguing journal covers is one benefit of maintaining a print collection.  Three issues received yesterday have gorgeous photographs that are best appreciated in hand - stop by and pick one up!

Seymour, R. S. and Hetz, S. K. (2011).  The diving bell and the spider: the physical gill of Argyroneta aquatica.  J. Exp. Biol. 214, 2175-2181.  Photo, Stefan K. Hetz.

The cover of Development (July 1)  shows the "mouth of an adult sea urchin (Lytechinus variegatus) as the animal attempts to consume a fragment of seaweed.  This still frame from a rapid time-lapse sequence taken by Sarah A. Elliott and Nobuo Ueda at the 2010 Woods Hold MBL Embryology Course was chosen by readers of the Node."  (Cover explanation taken from the table of contents)

Arctic ground squirrel (Urocitellus parryii)

A hibernating Arctic ground squirrel graces the cover of The Journal of Neuroscience, July 27, illustrating an article beginning on page 10752.

Jinka, T. R., O. Toien, and K. L. Drew. (2011).  Season primes the brain in an arctic hibernator to facilitate entrance into torpor mediated by Adenosine A1 receptors.  J. Neurosci. 31, 10752-10758.

Photo by Lesa Hollen and Leone Thieman.

Friday, July 22, 2011

Structure for cis,trans-1,4-Difluorobutadiene

View cover at acs.org
New publication by Professor Emeritus of Chemistry Norm Craig:

Semiexperimental Equilibrium Structure for cis,trans-1,4-Difluorobutadiene by the Mixed Estimation Method.  Demaison, Jean F.; Craig, Norman C.
Journal of Physical Chemistry A 115 (27): 8049-8054 published online June 8, 2011
[access at American Chemical Society Publications, for subscribers]

Friday, July 15, 2011

Belitsky Lab Research Presented at ACS Spring Meeting

The abstracts of two presentations by Associate Professor of Chemistry Jason Belitsky have been published as part of the proceedings from the 241st National Meeting and Exposition of the American Chemical Society, held in Anaheim, CA, March 27-31, 2011.

The first presentation was a collaboration with Oberlin students (Lye and Moore both graduated in 2011, Ellowitz expects to graduate in 2012).

Melanin-based coatings for environmental applications.
Lye, Diane; Moore, Christine; Ellowitz, Micah; Belitsky, Jason M.
Abstracts of Papers of the American Chemical Society 241:  CHED-547 March 27 2011
Structure image
from Wikipedia
This work involved immobilizing melanin from human hair and testing the binding of melanin and its synthetic analogs with heavy metals and dyes, and efforts toward heavy metal sequestration.

Melanin molecular recognition. Belitsky, Jason M.
Abstracts of Papers of the American Chemical Society 241: ORGN-676 March 27 2011
Belitsky's talk focused on analogs of eumelanin and their interactions with metal ions and boronic acids.  His research furthers understanding of colorimetric sensors for lead and inhibitors of synthetic melanin, including applications for molecular imprinting and inhibition.

The abstracts do not appear on the ACS website for viewing by the public, but may be found in SciFinder.

Friday, July 08, 2011

"It was a lark." -- Freeman Dyson, on the early Los Alamos community

On the new book shelf today is a very slim pamphlet, containing the transcript of the PBS production The Day After Trinity: J. Robert Oppenheimer and the Atomic Bomb (1981).  Transcribed and printed by PTV Publications, Kent, Ohio, this written record of the public broadcasting production by Jon Else gives a fascinating picture of gathering the best physicists and their students in the "boom town" of Los Alamos.  Under Oppenheimer's leadership, this group of brilliant thinkers, with "kind hearts and humanist feelings," went to work on a weapon of mass destruction.  The Day After Trinity explores how and why the atomic bomb was developed, in the context of relationships of the scientists working together under great stress.  "Their average age was 29, and their job was to construct a mechanism which would trigger, in a millionth of a second, a violet chain reaction.  They had two dance bands, a soda fountain, Boy Scouts, Girl Scouts, a radio station with no call letters, aa cyclotron, and 7,000 fire extinguishers," says the narrator.  Freeman Dyson, then a physicist with the Institute for Advanced Study, Princeton University, remarked "The most striking contraction is the fact that this man [Oppenheimer], who was so unworldly, so unpolitical in his youth, such a great scholar, so fond of metaphysical poetry, should suddenly emerge as the great administrator who put Los Alamos together and produced the atomic bomb."

It is still very thought-provoking reading, 30 years after the making of the documentary.  As we approach the 66th anniversary of the destruction of Hiroshima and Nakasaki, Oppenheimer's words remain relevant:  "I think the only hope for our future safety must lie in a collaboration, based on confidence and good faith, with the other peoples of the world."  [OBIS catalog record]

Friday, July 01, 2011

Faculty publication: Tracie Paine, in Neuropsychopharmacology

More into @ Nature.com
A new publication by Assistant Professor of Neuroscience Tracie Paine:

Schizophrenia- Like Attentional Deficits Following Blockade of Prefrontal Cortex GABA(A) Receptors.
Paine, Tracie A.; Slipp, Lauren E.; Carlezon, William A., Jr.
Neuropsychopharmacology 36 (8): 1703-1713 July 2011 [read the abstract]

Oberlin College Library does not have access to this journal (a print subscription costs $2,846 and an online site license would be considerably more).  We can obtain a copy through Interlibrary Loan.