Thursday, October 29, 2009

Ohio Voters! Be Informed on Issue 2

in brief: This Chicken Urges Ohio to Vote NO on Issue 2 [George Jones Farm video]

Issue 2 on the Ohio state ballot would amend our state constitution to create a Livestock Care Standards Board, with very specific language regarding the appointment, membership and oversight responsibilities of the board. The proposal came about, in part, to forestall a ballot initiative from the Humane Society of the United States, which would have given voters the ability to consider issues such as the size of cages for egg-laying chickens and standards for "gestation confinement crates" for pregnant sows on large pig farms. The League of Women Voters of Ohio and Ohio Supreme Court Justice Maureen O’Connor agree that Issue 2 is inappropriate for the constitution, inserting language that is too specific for such a pivotal document, which should be a broad, clear statement of principles. The amendment attempts to control agriculture in a manner more appropriate for legislative action.

Other groups opposing this constitutional amendment include:
View the Ohio State Constitution here.

YouTube offers another testimonial: This Chicken Urges Ohio to Vote No on Issue 2

Issue 2 proponent's viewpoint: Ohioans for Livestock Care.

Tuesday, October 27, 2009

Brains and Bodies on the New Book Shelf

We received a big shipment of new books yesterday (hurray!) and there are now many glossy covered books on display illustrated with organisms of various kinds: elephants, snakes, very large rodents, chimps, turtles, fish, lizards, mollusks, flies, liverworts (very cool), the cuckoo, and the human animal (The Naked Man / Desmond Morris). The human form is considered from a different perspective in
Human cognition is explored in a number of different titles, including
There are plenty of other titles, just as appealing, for those interested in physics, geology, history of science, chemical biology, and more. Browse the title list online or stroll by our window display - it's right on the way from Craig Auditorium to West Lecture Hall, facing the Science Center Commons.

Monday, October 26, 2009

First US Book on Psychiatry Published 197 Years Ago

On this date in 1812, Medical inquiries and observations upon the diseases of the mind, by Benjamin Rush, M.D., was copyrighted. Published by Kimber and Richardson of Philadelphia, it was the first U.S. book on psychiatry. Oberlin College Library owns three editions in print, all shelved in Special Collections. We also link to digital versions of the book from records in OBIS [1812 digital version].

Works of Benjamin Rush are covered in a guide from Greenwood Press: Benjamin Rush, M.D. : a bibliographic guide / compiled by Claire G. Fox, Gordon L. Miller, and Jacquelyn C. Miller.

This tidbit of publishing history was taken from The Illustrated almanac of science, technology, and invention: day by day; facts, figures, and the fanciful / Raymond L. Francis. Shelved behind our reference desk [OBIS record], it is great fun to browse through. Also on this date in history the Erie Canal opened in upstate New York, connecting the Hudson River with Lake Erie; the washing machine was patented; and the mule first arrived in the United States (shipped from King Charles III of Spain to George Washington).

Thursday, October 22, 2009

PubMed Central Combines Free Access and Open Access

From a user's perspective, it's difficult to focus on the difference between open access and free access to a journal article -- especially if all one intends to do is read the paper for an assignment in an undergraduate course. The distinction is important. PubMed Central is primarily an archive providing free access to traditionally copyrighted works, with the accompanying restrictions on reuse. It is a fantastic resource, providing access to the complete digital archive for nearly 800 journals, excluding some portion of the current issues for many titles. In addition, PMC has the author manuscripts of articles published by NIH-funded researchers in various non-PMC journals.

A smaller number of journals are part of the Open Access subset, and are protected under Creative Commons license. The open access journals are easy to spot in the PMC list of titles, just look for the OA icon.

A relatively new OA journal in the PMC list is Beilstein Journal of Organic Chemistry, indicative of the broader range of subjects in the PMC archive than might be expected. The Beilstein Journal publishes reviews, preliminary communications and full research articles in all areas of organic chemistry.

Oberlin Group Authors in Open Access Journals at BioMedCentral

BioMedCentral (BMC) publishes 204 peer-reviewed open access journals; all of the research articles in those journals are "immediately and permanently available online without charge. A number of journals require an institutional or a personal subscription to view other content, such as reviews or paper reports." The Oberlin Group libraries have a consortial agreement with BMC, granting research staff and students from those institutions a 15% reduction in the article processing charges for manuscripts accepted for publication.

Learn more about publishing with BMC.

View articles authored by Oberlin Group researchers already published with BMC, including commentary from Steven Bachrach of Trinity University, proposing "a plan that both reduces the total cost of publishing chemistry and enriches the literature through incorporation of Open Data."
Chemistry publication making the revolution
Bachrach SM
Journal of Cheminformatics 2009, 1:2 (17 March 2009)
[Abstract] [Full Text] [PDF]

Wednesday, October 21, 2009

Open Access Journals in Geosciences

Since October is a celebration of the geological sciences (Year of Science) it seems appropriate to check the Directory of Open Access Journals for titles in the earth sciences. Here's the subject breakdown of journal titles in the DOAJ:
Geography (52 journals)
Geology (66 journals)
Geophysics and Geomagnetism (9 journals)
Meteorology and Climatology (20 journals)
Oceanography (21 journals)

Advances in Geosciences
from the European Geosciences Union and Copernicus Publications is one of those general geology titles. From the publisher: "Advances in Geosciences (ADGEO) is an international, interdisciplinary journal for fast publication of collections of short, but self-contained communications in the Earth, planetary and solar system sciences..."

ADGEO has the Spark Europe seal, an indication that it uses Creative Commons license and provides metadata to the DOAJ, to ensure the widest possible harvesting of article content. In addition, ADGEO content may be archived in ADS: The Smithsonian/NASA Astrophysics Data System [example].

Tuesday, October 20, 2009

Open Access Week: Highlighting PLoS Biology

PLoS Biology, according to citation analysis on ISI Web of Science, has published 1,539 articles from its inception in 2003. All of them - every single one - readily accessible to anyone with an Internet connection and the ability to download either pdf or xml formatted materials. The actual number is undoubtedly higher, since there is a small lag time between publication in PLoS Biology and indexing in Web of Science. Those 1,539 articles have been cited a total of 39,089 times, including all of the "self-citations" -- or 32,522 times without counting the self-citations.

The most frequently cited paper, with 462 citations to date (again, using ISI data):
John B, Enright AJ, Aravin A, et al., 2004. Human MicroRNA targets. PLoS Biology 2(11): 1862-1879 e363. doi:10.1371/journal.pbio.0020363

Scopus reports 485 citations to this article, noted directly on the PLoS Biology site.

Far more exciting than simple citation analysis, though, is the potential for scholars and readers to interact, with options for commenting on and rating an article, jumping to related work, sharing the article through social networking tools, and finding similar research through guided searches in other databases. The PLoS article metrics includes the total number of page views for articles published after June 2005, giving another indication of the impact of open access.

The following article, for example, has been viewed 26,932 times:

Prior H, Schwarz A, Güntürkün O, 2008 Mirror-Induced Behavior in the Magpie (Pica pica): Evidence of Self-Recognition . PLoS Biol 6(8): e202. doi:10.1371/journal.pbio.0060202

The search and browse options on PLoS are easy to understand and highly effective; and the content is quickly found through Google Scholar, ensuring good reader access. I especially appreciate the Weekly Editors' Picks, which led to this article today:

Hoff M, 2009 Male or Female? For Honeybees, a Single Gene Makes All the Difference. PLoS Biol 7(10): e1000186. doi:10.1371/journal.pbio.1000186

Follow PLoS on Twitter to keep up with new developments. See also the PLoS Blog.

Monday, October 19, 2009

Open Access Week Starts Today!

The Public Library of Science offers not just amazing peer-reviewed journal articles on a wide and growing range of scientific topics, it also provides a succinct definition of Open Access, which is nicely expanded at the Open Access Week web site. Once you've seen what PLoS offers, branch out completely by exploring the Directory of Open Access Journals (DOAJ).

Notice the statistics at DOAJ: As of today 319,631 articles are included in the DOAJ service, from 4370 journals. Do a search on Google Scholar - chances are, recent articles with high citation counts (i.e., many other authors cite those papers) are articles that were either published in an open access journal or have since been posted in an open access archive. Any search with a biomedical theme is bound to lead to BioMedCentral, with an abundance of open access research articles. More open access highlights will be forthcoming all week. For a detailed, yet highly readable explanation of open access, you can't go wrong with Peter Suber's account. Enjoy!

ObieSciLib is on Twitter! Keep in touch while you're on fall break.

The first day of Fall break is always very, very quiet in the library. If I was a student on campus I would certainly find something to do other than hide away in the library on this resplendent autumn day. The sun shimmering through green and yellow leaves outside the south-facing windows is very enticing. To the north, the wide spaces of north quad are filled with falling leaves, drifting across the empty green lawn. If you want to find out what excitement is happening inside, follow ObieSciLib on Twitter! (Okay, I lied, not much excitement at the moment.) If you do come indoors, you've got your pick of seats in the library and no competition at all for a computer. [photo from the Oberlin Science Center online tour]

Friday, October 16, 2009

Amygdala Regulates Perception of Personal Space

This month's issue of Nature Neuroscience features a report from researchers at California Institute of Technology, showing that an individual with "complete amygdala lesions lacked any sense of personal space." Someone with this type of damage to the amygdala region of the brain had an "abnormally small interpersonal distance preference." In other words, you might feel more than a tad uncomfortable while the other person leans in, seemingly unaware of the invisible personal boundary we erect between ourselves and others. [See earlier reports on this study at NPR Topics]

We manage to overcome the desire for personal space pretty quickly, at least for unavoidable and relatively brief periods of time (that sardine feeling in a crowded bus, say). Earlier studies documented the negative outcomes of persistent crowding stress (try a subject search on "crowding stress" in OBIS).

We do not subscribe to Nature Neuroscience online, so stop by the library and read the print issue. Learn more about the amygdala in The Human amygdala, edited by Paul J. Whalen and Elizabeth A. Phelps (on order for Oberlin's science library; request it through OhioLINK).

Two relevant, older books are available in our library: The Amygdala : a functional analysis and The Amygdala : neurobiological aspects of emotion, memory, and mental dysfunction.

Thursday, October 15, 2009

Emperor Penguins Marching To Extinction?

The October issue of Oceanus arrived today - in print - and is now on the current browsing rack by our front door. Oceanus can be read online, of course, and it is a lovely web site. But the print magazine draws attention to new research and concerns that you might otherwise miss. The October cover shows brilliant shades of red and pink, a harmless dye dumped into a stream atop the Greenland ice sheet to track water flow through cracks in the ice, slicking the bottom of the glacier and hastening its demise into the North Atlantic. Inside, there are many other captivating photos and stories, including the worrisome conclusion that melting sea ice could reduce the Terre Adelie penguin colony from its present size of 3,000 to only 400 breeding pairs by the end of the century [from a study published online PNAS Jan. 26, 2009]. An enduring image from the documentary March of the Penguins is of the thousands of male penguins huddled in a mass, sheltering eggs from blasting, frigid winds -- survival dependent on having enough individuals creating that collective incubation zone. Declining numbers can't be good for this collaborative strategy of reproductive success.

Friday, October 09, 2009

Jonathan D. Smith speaking on "making 'good' cholesterol better"

Jonathan D. Smith,Professor of Molecular Medicine,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, will speak here today on: “Reverse cholesterol transport: Making ‘good’ cholesterol better.” Craig Auditorium, 12:15 p.m.

Following is a list of Dr. Smith's cholesterol-related publications, taken from Medline (via EbscoHost), exported to and formatted according to the Council of Science Editors style
. It is a fast, easy way to create a list of references and keep track of all of the papers used for a research project. You can also share your Refworks folders with others, and link from Refworks to the full-text, if the reference was exported to Refworks from a database with OLinks. Refworks is available to everyone in the Oberlin College community. Click on Login, once you are at the Refworks site, to sign up for an individual account.

Brown ML, Yui K, Smith JD, LeBoeuf RC, Weng W, Umeda PK, Li R, Song R, Gianturco SH, Bradley WA. 2002. The murine macrophage apoB-48 receptor gene (apob-48r): Homology to the human receptor. J Lipid Res 43(8):1181-91.

Brubaker G, Peng D, Somerlot B, Abdollahian DJ, Smith JD. 2006. Apolipoprotein A-I lysine modification: Effects on helical content, lipid binding and cholesterol acceptor activity. Biochim Biophys Acta 1761(1):64-72.

Dansky HM, Shu P, Donavan M, Montagno J, Nagle DL, Smutko JS, Roy N, Whiteing S, Barrios J, McBride TJ, et al. 2002. A phenotype-sensitizing apoe-deficient genetic background reveals novel atherosclerosis predisposition loci in the mouse. Genetics 160(4):1599-608.

Le Goff W, Settle M, Greene DJ, Morton RE, Smith JD. 2006. Reevaluation of the role of the multidrug-resistant P-glycoprotein in cellular cholesterol homeostasis. J Lipid Res 47(1):51-8.

Le Goff W, Peng D, Settle M, Brubaker G, Morton RE, Smith JD. 2004. Cyclosporin A traps ABCA1 at the plasma membrane and inhibits ABCA1-mediated lipid efflux to apolipoprotein A-I. Arterioscler Thromb Vasc Biol 24(11):2155-61.

Peng D, Brubaker G, Wu Z, Zheng L, Willard B, Kinter M, Hazen SL, Smith JD. 2008. Apolipoprotein A-I tryptophan substitution leads to resistance to myeloperoxidase-mediated loss of function. Arterioscler Thromb Vasc Biol 28(11):2063-70.

Peng D, Wu Z, Brubaker G, Zheng L, Settle M, Gross E, Kinter M, Hazen SL, Smith JD. 2005. Tyrosine modification is not required for myeloperoxidase-induced loss of apolipoprotein A-I functional activities. J Biol Chem 280(40):33775-84.

Robertson JO, Li W, Silverstein RL, Topol EJ, Smith JD. 2009. Deficiency of LRP8 in mice is associated with altered platelet function and prolonged time for in vivo thrombosis. Thromb Res 123(4):644-52.

Smith JD and Topol EJ. 2006. Identification of atherosclerosis-modifying genes: Pathogenic insights and therapeutic potential. Expert Rev Cardiovasc Ther 4(5):703-9.

Smith JD, Waelde C, Horwitz A, Zheng P. 2002. Evaluation of the role of phosphatidylserine translocase activity in ABCA1-mediated lipid efflux. J Biol Chem 277(20):17797-803.

Smith JD, Bhasin JM, Baglione J, Settle M, Xu Y, Barnard J. 2006. Atherosclerosis susceptibility loci identified from a strain intercross of apolipoprotein E-deficient mice via a high-density genome scan. Arterioscler Thromb Vasc Biol 26(3):597-603.

Smith JD, Le Goff W, Settle M, Brubaker G, Waelde C, Horwitz A, Oda MN. 2004. ABCA1 mediates concurrent cholesterol and phospholipid efflux to apolipoprotein A-I. J Lipid Res 45(4):635-44.

Velez-Carrasco W, Merkel M, Twiss CO, Smith JD. 2008. Dietary methionine effects on plasma homocysteine and HDL metabolism in mice. J Nutr Biochem 19(6):362-70.

Wu Z, Wagner MA, Zheng L, Parks JS, Shy,Jacinto M.,,3rd, Smith JD, Gogonea V, Hazen SL. 2007. The refined structure of nascent HDL reveals a key functional domain for particle maturation and dysfunction. Nat Struct Mol Biol 14(9):861-8.

Zheng L, Settle M, Brubaker G, Schmitt D, Hazen SL, Smith JD, Kinter M. 2005. Localization of nitration and chlorination sites on apolipoprotein A-I catalyzed by myeloperoxidase in human atheroma and associated oxidative impairment in ABCA1-dependent cholesterol efflux from macrophages. J Biol Chem 280(1):38-47.

Zheng L, Nukuna B, Brennan M, Sun M, Goormastic M, Settle M, Schmitt D, Fu X, Thomson L, Fox PL, et al. 2004. Apolipoprotein A-I is a selective target for myeloperoxidase-catalyzed oxidation and functional impairment in subjects with cardiovascular disease. J Clin Invest 114(4):529-41.

Thursday, October 08, 2009

Can you imagine eating 16 sugar cubes at one time?

One lump or two? How about 16 lumps of sugar? That is just a little less than the sugar contained in a 20-ounce bottle of cola. Ouch. Just one of the "20 things you didn't know about sugar" (and might have been happier not to know) presented by Rebecca Coffey in the Discover October issue. Amaze your friends with more "20 things you didn't know" on Discover's Web site.

The October issue is fun reading, addressing Great Questions of Science, including:
  • What lies beyond the edge of the universe?
  • Where have all the bees gone?
  • How does physics really work?
  • What controls the chemistry of life?
  • Did evolution shape us to be generous?
And, a special report on the neurology of sex. Did you know "the parts of the brain that light up during sexual experiences are associated with some of our most sophisticated forms of thought?" You can watch a video of brain activity at

Read the whole issue in the science library! Now on the new journals display rack.

H1N1 Vaccine Plans

Heard on the Diane Rehm Show, Wednesday October 7: "Up to seven million doses are expected to be available in the U.S. this week. Who's going to get the vaccine, where, and why."
This was a very good discussion, and will answer most of your questions about the H1N1 flu vaccine. The college is working to get both the H1N1 and more seasonal flu vaccine on campus. Student Health Services (in Blackboard Oncampus for OC community) gives details. Get information on flu clinics in Lorain County.

Wednesday, October 07, 2009

Ribosomes, Proteins and X-Ray Crystallography: Nobel Prize in Chemistry

The Nobel Prize in Chemistry has been announced, and the intricacies of ribosomes as "protein-makers" in the cell are nicely explained in this Scientific American news article. Quoting from Scientific American news:"The prize will be equally split between biophysicist Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology in Cambridge in England, biochemist Thomas Steitz of Yale University and molecular biologist Ada Yonath of the Weizmann Institute of Science in Rehovot, Israel, for their work in using x-ray crystallography to get a precise, atomic-scale map of the ribosome—the protein-making machine in all cells with nuclei that makes life possible."

You are who you are because of ribosomes (yeah, ribosomes!) - and, of course, all of those other countless biochemical processes occurring in your body right this second. Learn more about the ribosome's role in this electronic book: Structural aspects of protein synthesis / Anders Liljas. It includes some lovely colored images, made possible by the work of this year's Nobel Prize winners.

A citation analysis of Thomas A. Steitz in the ISI Web of Science revealed that his papers have been cited an average of 680 times per year, with a total of 30,620 citations to his published work. The following paper from Science has been cited most often - 1,544 citations to date: Ban, N., P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science 289, (5481) (AUG 11): 905-20 [access in JSTOR, for JSTOR subscribers].

Tuesday, October 06, 2009

Your Cell Phone, the Internet Backbone, Digital Cameras, all dependent on Nobel Prize winners

NPR's Richard Harris did a fine job of explaining the ubiquitous, essential nature of glass fiber optics and semiconductors, the research developments of three scientists who will share the Nobel Prize for Physics this year. The Nobel Committee said that the work of Charles K. Kao, Willard S. Boyle and George E. Smith made possible the "foundation of our networked society." The invention of the Charge-Couple Device or CCD (Boyle and Smith, working at Bell Labs in New Jersey) is a great example of scientists pursuing basic research, seeking a solution to a known problem, and discovering something very exciting with unforeseen benefits for the future. The CCD allows images to be captured digitally rather than on film. Kao's glass fibers, carrying information as light rather electricity, have literally transformed the world of information - certainly the work of librarians - and made possible development of the Internet.

Read some history in this 2001 book, available electronically
Building the global fiberoptics superhighway / C. David Chaffee

The 1970 paper by Boyle and Smith, "Charge coupled semiconductor devices," published in the Bell System Technical Journal, 49(4): 587-93, has been cited nearly 480 times as of this morning, according to a cited reference search in ISI Web of Science.

Monday, October 05, 2009

Telomeres are the Focus of Nobel Prize Winners' Research

NPR's Morning Edition presented an excellent summary of the significance of the research of Elizabeth Blackburn, Carol W. Greider, and Jack Szostak, who share this year's Nobel Prize in Physiology or Medicine. "The scientists all study telomeres — structures that act like caps on the ends of chromosomes and protect them when cells divide. Chromosomes are the long strands of DNA that contain a living creature's genetic code." Elizabeth Blackburn of the University of California, San Francisco, is the subject of a recent book, Elizabeth Blackburn and the story of telomeres : deciphering the ends of DNA / Catherine Brady. MIT Press, c2007.

Learn more about the role of telomeres in aging and disease, in this electronic book accessible in the OhioLINK Electronic Book Center and at Telomeres and telomerase in aging, disease, and cancer : molecular mechanisms of adult stem cell ageing / K. Lenhard Rudolph, editor. Springer, c2008.

An older book, The telomere by David Kipling, provides a good overview. Find it in the Science library [QH600.3 .K57 1995].

Friday, October 02, 2009

OhioLINK systems off-line on Saturday

Due to a required repair to the Ohio State University electrical systems, all OhioLINK servers will be off-line on Saturday, from 4 a.m. until 8 p.m., or until the work is completed. This includes all databases with rave as part of the server address: Biological Abstracts, GeoRef, and Inspec; as well as the combined library catalog and Electronic Journal Center (EJC).

Updates during downtime will be available on Twitter and Facebook.

You can still use Academic Search Complete, plus other EBSCOHost databases (including Medline Full Text), and export references to your RefWorks account to access later. Or create your own account in Academic Search Complete (click on MyEBSCOHost in the upper right of the search screen to begin), and save all of your references to a folder you can access any time. The Find It! link will be saved with each reference, in RefWorks and MyEBSCOHost, so following the links later is a piece of cake.

Thursday, October 01, 2009

Celebrating Geosciences and Planet Earth: October in the Year of Science

We are celebrating the geosciences and planet earth all of October, as the Year of Science enters its last quarter. The planet, our very foundation and life-sustaining island home, so often under-appreciated as simply dirt beneath our feet, is an astoundingly complex system of transformative forces and myriad types of materials. Awesome power is displayed from the minute crystallization of igneous rock and the interplay of organic decomposition in sedimentary layers to vast movements of crustal plates. It is impossible to study earth science without an understanding of chemistry, physics, biology and evolution, at the least, and the geosciences inform all of those disciplines as well. Explore some of the big ideas in geology with the
We are also in the last part of the International Year of Planet Earth; and will observe Earth Science Week this month!

We have so many wonderful new books in the geology section, it is impossible to highlight more than a few. Start with The revolution in geology from the Renaissance to the enlightenment for a bit of historical context, and gain a better understanding of this continent with Ghost mountains and vanished oceans : North America from birth to middle age. Here are just a few more to entice you to read:
There is so much more - the Library's guide to geology research resources is a good place to start!