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"