Wednesday, June 07, 2017

Plant systematics & evolution of Potentilleae and Sibbalidia: new publication from Mike Moore

A new publication by Michael Moore, Associate Professor of Botany, and collaborators in China.

Feng T, Moore, Michael J, Yan M, Sun Y, Zhang H, Meng A, Li X, Jian S, Li J, Wang H. 2017. Phylogenetic study of the tribe Potentilleae (Rosaceae), with further insight into the disintegration of Sibbaldia. Journal of Systematics and Evolution 55(3):177-91.

Sibbaldia procumbens (5066467208)
Potentilleae, one of 10 tribes of the Rosaceae, are mainly distributed in alpine regions of the Northern Hemisphere. The taxonomy of Potentilleae has been challenging due to extensive hybridization, polyploidization, and/or apomixis characterizing several genera of Potentilleae, such as Alchemilla, Argentina, and Potentilla. To help clarify relationships within Potentilleae, a phylogenetic analysis of the tribe with an emphasis on the polyphyletic genus Sibbaldia was carried out using nuclear ribosomal internal and external transcribed spacer regions and the plastid trnL-F and trnS-G spacer regions. In agreement with previous phylogenetic analyses, three major clades were identified in the present study: the subtribe Fragariinae, the genera Argentina, and Potentilla. The 15 species of Sibbaldia were recovered in five distinct clades: three in subtribe Fragariinae, one in Argentina, and the last in Potentilla. The recently established genus Chamaecallis, comprising a single species formerly treated in Sibbaldia that has intermediate floral character states with respect to Fragariinae and Potentilla, was recovered as sister to Drymocallis. Morphological character state reconstruction indicated that a reduction in the number of stamens (10) is a derived character state that has arisen multiple times in Potentilleae. Molecular dating analyses agreed with previously published estimates and suggested that crown group Potentilleae arose in the Middle to Late Eocene, with most generic-level divergences occurring in the Oligocene and Miocene.  (from the publisher's website)

Thursday, May 25, 2017

Environmental Dashboard and Ground-state rotational constants examined: two very different areas of study by Oberlin researchers

Recent publications from faculty and staff (Oberlin affiliated authors are in bold font):

Clark, Shane; Petersen, John E; Frantz, Cindy M; Roose, Deborah; Ginn, Joel; Daneri DR. 2017. Teaching systems thinking to 4th and 5th graders using environmental dashboard display technology. Plos One 12(4):e0176322
Tackling complex environmental challenges requires the capacity to understand how relationships and interactions between parts result in dynamic behavior of whole systems. There has been convincing research that these "systems thinking" skills can be learned. However, there is little research on methods for teaching these skills to children or assessing their impact. The Environmental Dashboard is a technology that uses "sociotechnical" feedback-information feedback designed to affect thought and behavior. Environmental Dashboard (ED) combines real-time information on community resource use with images and words that reflect pro-environmental actions of community members. Prior research indicates that ED supports the development of systems thinking in adults. To assess its impact on children, the technology was installed in a primary school and children were passively exposed to ED displays. This resulted in no measurable impact on systems thinking skills. The next stage of this research examined the impact of actively integrating ED into lessons on electricity in 4th and 5th grade. This active integration enhanced both content-related systems thinking skills and content retention.

Demaison J, Craig Norman C, Gurusinghe R, Tubergen MJ, Rudolph HD, Coudert LH, Szalay PG, Csaszar AG. 2017. Fourier transform microwave spectrum of propene-3-d(1) (CH2=CHCH2D), quadrupole coupling constants of deuterium, and a semiexperimental equilibrium structure of propene. Journal of Physical Chemistry A 121(16):3155-66
The ground-state rotational spectrum of propene-3-d(1), CH2=CHCH2D, was measured by Fourier transform microwave spectroscopy. Transitions were assigned for the two conformers, one with the D atom in the symmetry plane (S) and the other with the D atom out of the plane (A). The energy difference between the two conformers was calculated to be 6.5 cm(-1), the S conformer having lower energy. The quadrupole hyperfine structure due to deuterium was resolved and analyzed for both conformers. The experimental quadrupole coupling and the centrifugal distortion constants compared favorably to their ab initio counterparts. Ground-state rotational constants, for the S conformer are 40582.157(9), 9067.024(1), and 7766.0165(12) MHz. Ground-state rotational constants for the A Conformer are 43403.75(3), 8658.961(2), and 7718.247(2) MHz. For the A conformer, a small tunneling splitting (19 MHz) due to internal rotation was observed and analyzed. Using the new rotational constants of this work as well as those previously determined for the C-13 species and for some deuterium-substituted species from the literature, a new semiexperimental equilibrium structure was determined and its high accuracy was confirmed. The difficulty in obtaining accurate coordinates for the out-of-plane hydrogen atom is discussed.

Tuesday, April 25, 2017

Deep learning discussed on the TED Radio Hour

Deep Learning / Ian Goodfellow, Joshua Bengio and
Aaron Courville.  MIT Press, 2016.
The TED Radio Hour on Friday, April 21, 2017 was titled The Digital Industrial Revolution, followed by the question, "As machine learning surpasses human intelligence, where does that leave us?"

During the session, TED speakers explored "ideas about the exciting — and terrifying — future of human-robot collaboration."

One of the speakers referenced deep learning, which immediately brought to mind this book on our new book shelf.  It defines deep learning as a "form of machine learning that enables computers to learn from experience and understand the work in terms of a hierarchy of concepts."  Seemingly benign, and the book's cover is soothing at first glance, with its profusion of blossoms.  On close examination, the cover art work has multiple layers of meaning, and it is this multiplicity of issues surrounding deep learning and neural networks that the TED Radio Hour speakers address.  It makes for fascinating listening!  The four talks are linked here:

Monday, April 17, 2017

Hormones at the hippocampus, caffeine cocrystals, lateral roots, and transcirptome: new publications

Four recent publications from Oberlin College science faculty (names indicated in bold). Student or alumni co-authors in the list below include Veronica Burnham, Christopher Sunday, Abigail Laman-Magarg, and Nicolas Vigilante.

As indexed in Web of Science
Burnham, Veronica, Christopher Sundby, Abigail Laman-Maharg, and Janice Thornton. 2017. Luteinizing hormone acts at the hippocampus to dampen spatial memory. Hormones and Behavior 89, : 55-63. Download: OhioLINK Electronic Journal Center

Laskowski, Marta and Kirsten H. ten Tusscher. 2017. Periodic lateral root priming: What makes it tick? Plant Cell 29, no. 3: 432-444. Download, open access, at Plant Cell

Vigilante, Nicolas J. and Manish A. Mehta. 2017. A C-13 solid-state NMR investigation of four cocrystals of caffeine and theophylline. Acta Crystallographica Section C-Structural Chemistry 73, : 234-243. Read the abstract online at publisher's site

Yang, Ya, Michael J. Moore, Samuel F. Brockington, Alfonso Timoneda, Tao Feng, Hannah E. Marx, Joseph F. Walker, and Stephen A. Smith. 2017. An efficient field and laboratory workflow for plant phylotranscriptomic projects. Applications in Plant Sciences 5, no. 3: 1600128. Download: BioOne

Monday, April 10, 2017

Happy National Library Week! Come get a book...

What better way to celebrate National Library Week than with a new good read?  Check out a book - enjoy your library.  We have a (very small) sweet treat for everyone who checks out a science library book (and reads it, we trust!).  Reserve materials don't count, despite how essential they are for your coursework, so find something great from a display or in the stacks of bookshelves in the middle of the library.

We've received hundreds of new books in the past three months - something is surely of interest to you!  We would be so happy to help you find your perfect read.

There are thousands and thousands of books online, too, beautifully cataloged in OBIS.  Click on the E-BOOKS tab for an easy way to limit your search to online books.

Friday, April 07, 2017

Unintended side effects of conservation: case study in China.

New publication from Assistant Professor of Geology Amanda Schmidt

Schmidt, Amanda H., Yongxian Li, and Ya Tang. 2017. Unintended side effects of conservation: A case study of changing land use in Jiuzhaigou, Sichuan, China. Mountain Research and Development 37, no. 1: 56-65.

Mountain Research and Development is an open access journal.

Partial abstract and conclusions of the study:

Photos by Amanda Schmidt showing
treeless areas of the JNNR
"Toward the goals of returning the landscape of Jiuzhaigou National Nature Reserve (JNNR) to a perceived “natural” state and protecting the environment, the Reserve in 1998–2002 implemented forest preservation policies that included restrictions on forestry, agriculture, and animal herding practiced by resident Tibetans. ...As argued in prior studies in JNNR (Trac et al 2013; Urgenson et al 2014; Harrell et al 2016), we suggest that land managers carefully consider the baseline conditions to which they are trying to restore landscapes. If, as is the case in JNNR, landscapes have been altered by human activity for millennia (eg d'Alpoim Guedes et al 2015), it may not make sense to aim for restoration to a “natural” landscape that does not include people. Likewise, if management policies and changing economic conditions result in people relocating from traditional villages, complete assessments of natural hazards would enable those making relocation decisions to make informed choices about where to situate new developments."

Thursday, April 06, 2017

How to Spot Fake News - with thanks to IFLA and

Read the story behind the infographic.  IFLA is the International Federation of Library Associations and Institutions.  
How to Spot Fake News
IFLA infographic based on’s 2016 article "How to Spot Fake News"

Monday, March 27, 2017

Leslie Kwakye publishes in Frontiers in Integrative Neuroscience, with six student researchers

Members of the Kwakye lab recently published an article in this highly-regarded open access journal.  View the abstract and link to similar articles and reviews (such a helpful feature!) in PubMed.
Kyla D. Gibney, Enimielen Aligbe, Brady A. Eggleston, Sarah R. Nunes, Willa G. Kerkhoff, Cassandra L. Dean and Leslie D. Kwakye.
Visual Distractors Disrupt Audiovisual Integration Regardless of Stimulus Complexity.

Frontiers in Integrative Neuroscience, vol. 11, article number 1.  Jan. 20, 2017.
DOI: 10.3389/fnint.2017.00001
As of today, the article has been viewed 1,135 times, including 72 downloads.

Partial abstract:
"The intricate relationship between multisensory integration and attention has been extensively researched in the multisensory field; however, the necessity of attention for the binding of multisensory stimuli remains contested. In the current study, we investigated whether diverting attention from well-known multisensory tasks would disrupt integration and whether the complexity of the stimulus and task modulated this interaction. A secondary objective of this study was to investigate individual differences in the interaction of attention and multisensory integration... The results of this study indicate that attention plays a crucial role in multisensory integration for both highly complex and simple multisensory tasks and that attention may interact differently with multisensory processing in individuals who do not strongly integrate multisensory information."

Monday, March 20, 2017

Award honors the legacy of Dr. Eugene Garfield

We were pleased to learn of this new award from Clarivate Analytics:

"To honor the legacy of Dr. Eugene Garfield, the visionary founder of the Web of Science and a pioneer of Information Science, Clarivate Analytics created the “Eugene Garfield Information Sciences Pioneer Award.” The award will be given annually to at least one promising information scientist, selected by a board of prominent scientometricians.

"Clarivate Analytics, the home of the Web of Science and Journal Impact Factor, supports innovative research by individuals in the scientometric community through a thought leadership program, which gives researchers access to Web of Science data, as well as to scholarships such as the American Society of Information Science & Technology’s Outstanding Teacher Award and Dissertation Proposal Award. Both awards were created in the early 1980s by Dr. Garfield. This new award will enable additional researchers to advance the field and build on Dr. Garfield’s legacy.

"At least one prize will be given annually for the most innovative research in scientometrics, which can be applied to the field globally. It will be awarded to an early-career researcher (i.e., no more than PhD + 10 years) and based on the application criteria and on the researcher’s needs. In addition to the award, Clarivate Analytics will provide the successful applicant with in-kind support and access to Web of Science data."

Thursday, March 16, 2017

Communicating Science: more than just the facts, please

The library is celebrating great science writers with a display of engaging, delightful to read, fact-based books that draw in the reader with compelling stories.  
It will become a rotating display (figuratively and literally, once the new display rack arrives) of new books on science topics, written for a general audience.

The Internet abounds with wonderful science writing as well, of course.  Sean Carroll speaks to this very persuasively in his 2014 blog post, "Twenty-First Century Science Writers."

In 2015, Columbia Journalism Review highlighted "Six great pieces of science writing you may have missed this year."

The description of our book display (Oberlin College Libraries tumblr, March 15) includes a long list of recommended articles - to that list, we add two by Dyani Sabin '14 (former Science Library Student Assistant):

Hawaii Could Become an All-Renewable All-Electric Car Paradise by 2045
Dyani Sabin Clean Energy February 21, 2017

The Blue Collar Job of the Future Is Solar Panel Installer
Dyani Sabin Solar Energy February 22, 2017.

It's remarkable how much one can learn (even those who are reluctant to approach science in any manner) when a good writer weaves the facts with an interesting story that brings home a strong message.

Thursday, March 09, 2017

Senior Ryanna Fossum co-authors a paper in Lithos

Oberlin College geology major Ryanna Fossum worked with researchers from the American Museum of Natural History and Rutgers State University Wright Rieman Labs on this project:

Zirakparvar, N. Alex; Setera, Jacob; Mathez, Edmond; Vantongeren, Jill; Fossum, Ryanna.  2017. The pre-Atlantic Hf isotope evolution of the east Laurentian continental margin: Insights from zircon in basement rocks and glacial tillites from northern New Jersey and southeastern New York. Lithos 272, : 69-83. 

From the Abstract:
This paper presents laser ablation U–Pb age and Hf isotope data for zircons from basement rocks and glacial deposits in northern New Jersey and southeastern New York. The purpose is to understand the eastern Laurentian continental margin's Hf isotope record in relation to its geologic evolution prior to the opening of the Atlantic Ocean.  
Access this at or the OhioLINK EJC.

Thursday, March 02, 2017

Brad Carter publishes in the journal Zebrafish

New publication from Brad Carter, Visiting Assistant Professor in Neuroscience, from research completed at the Whitehead Institute for Biomedical Research, Cambridge, Massachusetts.

Validation of Protein Knockout in Mutant Zebrafish Lines Using In Vitro Translation Assays.
Bradley S. Carter, Christian Cortés-Campos, Xiao Chen, Jasmine M. McCammon, and Hazel L. Sive.
Zebrafish. February 2017, 14(1): 73-76. doi:10.1089/zeb.2016.1326.  (full-text access for subscribers)

Advances in genome-editing technology have made creation of zebrafish mutant lines accessible to the community. Experimental validation of protein knockout is a critical step in verifying null mutants, but this can be a difficult task. Absence of protein can be confirmed by Western blotting; however, this approach requires target-specific antibodies that are generally not available for zebrafish proteins. We address this issue using in vitro translation assays, a fast and standard procedure that can be easily implemented.

Publication by Matthew Elrod and current students, alumnus

New publication from the Elrod lab, as indexed in the Web of Science
Authors:  William C. Thomas, Class of 2015; William D. Dresser, junior; Diego A. Cortés, senior; Matthew J. Elrod, Associate Professor of Chemistry and Biochemistry.
Gas Phase Oxidation of Campholenic Aldehyde and Solution Phase Reactivity of its Epoxide Derivative.
The Journal of Physical Chemistry A 2017 121 (1), 168-180
DOI: 10.1021/acs.jpca.6b08642  (access for American Chemical Society subscribers)

From the abstract: "On the basis of the rate constants determined for CA and CAE, it is likely that these species are reactive on atmospherically relevant time scales in the gas and aerosol phases, respectively. The results of the present study largely support a previous supposition that a-pinene-derived secondary organic aerosol may be influenced by the multiphase processing of various intermediate species, including those with epoxide functionality."

Tuesday, February 28, 2017

Eugene Garfield Obituary: Scientometrics Pioneer | The Scientist Magazine®

Eugene Garfield Obituary: Scientometrics Pioneer | The Scientist Magazine®: Eugene Garfield, founder of the Institute for Scientific Information and The Scientist, has passed away at age 91.

The only evidence of the once imposing wall of volumes -
our neglected shelf list card for Science Citation Index.
I was sorry to read the news today of Dr. Garfield's passing.  It was an honor to meet Eugene Garfield when I was invited to participate in a users group forum at the Institute for Scientific Information in the mid-1980s.  He was very kind and welcoming, and surprised us with his self-deprecating humor in the face of our deference to his superior knowledge of citation metrics.  It seems like a life-time ago (and for the current generation of undergraduates, it is more than a life-time) that the science faculty here routed the library's copies of Current Contents, issued weekly, around each department as a way of keeping abreast of new research.  Likewise, the print volumes of Science Citation Index hit the recycling bin ages ago - perhaps directly to a landfill, in the pre-recycling era - and Web of Science competes mightily with Google Scholar and other databases for the same reliance from today's students as once shown by faculty to Current Contents.  Dr. Garfield's legacy is still very evident, even as formats and use patterns evolve.

Wednesday, January 25, 2017

Scientific Integrity Relies on Transparency and Open Communication

Sign seen at #WomensMarchOnWashington
The National Park Service Won't be Silenced and Rogue Scientists Race to Save Climate Data... are just two of recent headlines that indicate a growing unease and distrust between the new administration and the scientific community.  Another indication of strained relations is this list of recommendations for protecting yourself as a whistleblower, from Inside Climate News (no. 6 is especially chilling: "Consider buying a burner phone. Use cash.").

The second story was, in part, about researchers, computer scientists, librarians (yeah!), archivists and students at Van Pelt Library, University of Pennsylvania.  Listen to this story, which aired today, beautifully crafted by Susan Phillips of Here and Now.  It is reassuring to hear professional colleagues explaining the need for metadata and archiving.  Find the "bagged data" at  This sort of vigilance will be needed to keep scientific data and reports accessible - especially those funded by the government, at taxpayer expense.

The following comes from the "Rogue Scientists" story in Wired:
"But data, no matter how expertly it is harvested, isn’t useful divorced from its meaning. “It no longer has the beautiful context of being a website, it’s just a data set,” Allen says. [Laurie Allen, the assistant director for digital scholarship in the Penn libraries and the technical lead on the data rescuing event]
"That’s where the librarians came in. In order to be used by future researchers—or possibly used to repopulate the data libraries of a future, more science-friendly administration—the data would have to be untainted by suspicions of meddling. So the data must be meticulously kept under a “secure chain of provenance.” In one corner of the room, volunteers were busy matching data to descriptors like which agency the data came from, when it was retrieved, and who was handling it. Later, they hope, scientists can properly input a finer explanation of what the data actually describes."

Thank you, librarians and archivists.

Friday, January 13, 2017

Physics major Stella Ocker publishes in Astrophysical Journal

Congratulations to Stella Ocker, junior, for her publication in Astrophysical Journal, co-authored with Gordon Petrie of the National Solar Observatory (NSO).  Ocker's research took place in Boulder, Colorado as part of the NSO Research Experiences for Undergraduates Program sponsored by the National Science Foundation.

Spatial maps of solar active region NOAA 11158
Ocker, Stella Koch and Gordon Petrie. 2016. The effects of spatial smoothing on solar magnetic helicity parameters and the hemispheric helicity sign rule. Astrophysical Journal 832, no. 2: 162.

Partial abstract:
"The hemispheric preference for negative/positive helicity to occur in the northern/southern solar hemisphere provides clues to the causes of twisted, flaring magnetic fields. Previous studies on the hemisphere rule may have been affected by seeing from atmospheric turbulence. Using Hinode/SOT-SP data spanning 2006–2013, we studied the effects of two spatial smoothing tests that imitate atmospheric seeing: noise reduction by ignoring pixel values weaker than the estimated noise threshold, and Gaussian spatial smoothing."

Tuesday, January 03, 2017

Sociability and GABA receptor: implications for schizophrenia and autism

A new publication from Tracie Paine, Associate Professor of Neuroscience, and former students Nathan Swedlow '15 and Lucien Swetschinski '15, concludes that "changes in GABA signaling observed in conditions such as autism or schizophrenia may mediate the social withdrawal characteristic of these conditions. Moreover, they suggest that social withdrawal may be treated by drugs that potentiate GABA transmission." (C) 2016 Elsevier B.V. All rights reserved.

Paine, TA, Swedlow, N and Swetschinski, L. "Decreasing GABA Function within the Medial Prefrontal Cortex Or Basolateral Amygdala Decreases Sociability." Behavioural Brain Research 317, (JAN 15, 2017): 542-552.

View the full article on ScienceDirect (subscriber access only).