130 Works

An electrophysiological marker of arousal level in humans

Janna Lendner, Randolph Helfrich, Bryce Mander, Luis Romundstad, Jack Lin, Matthew Walker, Pal Larsson & Robert Knight
Deep non-rapid eye movement sleep (NREM) and general anesthesia with propofol are prominent states of reduced arousal linked to the occurrence of synchronized oscillations in the electroencephalogram (EEG). Although rapid eye movement (REM) sleep is also associated with diminished arousal levels, it is characterized by a desynchronized, 'wake-like' EEG. This observation implies that reduced arousal states are not necessarily only defined by synchronous oscillatory activity. Using intracranial and surface EEG recordings in four independent data...

Divergence, gene flow and the origin of leapfrog geographic distributions: the history of color pattern variation in Phyllobates poison-dart frogs

Roberto Márquez, Tyler Linderoth, Daniel Mejía-Vargas, Rasmus Nielsen, Adolfo Amézquita & Marcus Kronforst
The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. Phyllobates poison frogs. We found evidence for high levels of gene flow between neighboring populations but not...

Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua

Henrik Krehenwinkel, Sophia Tsau, Susan Kennedy & Rosemary Gillespie
Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyze diversity and abundance of the spider’s gut microbes, and simultaneously characterize...

Data from: Using parsimony-guided tree proposals to accelerate convergence in Bayesian phylogenetic inference

Chi Zhang, John Huelsenbeck & Fredrik Ronquist
Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as `convergence')...

Context-dependent effects of relative temperature extremes on bill morphology in a songbird

Katie LaBarbera, Kyle J. Marsh, Kia R. R. Hayes & Talisin T. Hammond
Species increasingly face environmental extremes. While responses of morphological traits to changes in average environmental conditions are well-documented, responses to environmental extremes remain poorly understood. Bird bills contribute to thermoregulation, with considerable heat loss possible through the bill surface, and with bill morphology shaped by long-term thermal conditions. We used museum specimens to investigate the relationship of bill surface area (SA) in dark-eyed juncos Junco hyemalis to traditional measures of climate (temperature and precipitation) and...

Data from: Slow oscillation-spindle coupling predicts enhanced memory formation from childhood to adolescence

Michael A. Hahn, Dominik P.J. Heib, Manuel Schabus, Kerstin Hoedlmoser & Randolph F. Helfrich
Precise temporal coordination of slow oscillations (SO) and sleep spindles is a fundamental mechanism of sleep-dependent memory consolidation. SO and spindle morphology changes considerably throughout development. Critically, it remains unknown how the precise temporal coordination of these two sleep oscillations develops during brain maturation and whether their synchronization indexes the development of memory networks. Here, we use a longitudinal study design spanning from childhood to adolescence, where participants underwent polysomnography and performed a declarative word-pair...

Single-chain heteropolymers transport protons selectively and rapidly

Tao Jiang, Aaron Hall, Marco Eres, Zahra Hemmatian, Baofu Qiao, Yun Zhou, Zhiyuan Ruan, Andrew D. Couse, William T. Heller, Haiyan Huang, Monica Olvera De La Cruz, Marco Rolandi & Ting Xu
Precise protein sequencing and folding are believed to generate the natural channel structure and chemical diversity of proteins, both of which are essential to synthetically achieve proton transport performance comparable to that seen in natural systems. Geometrically defined channels have been fabricated using peptides, DNAs, carbon nanotubes, sequence-defined polymers and organic frameworks; however, none of these channels rivals the performance observed in their natural counterparts. Here we show that without forming an atomically structured channel,...

The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots

Claire Willing, Grady Pierroz, Devin Coleman-Derr & Todd Dawson
Experimental drought has been shown to delay the development of the root microbiome and increase the relative abundance of bacteria with thick cell walls, or monoderms, especially within the phylum Actinobacteria. However, the generalizability of these findings to natural systems or other diverse plant hosts remains unknown. Leveraging a natural gradient of water-availability across the coast redwood (Sequoia sempervirens) range, we tested three hypotheses: (1) that site-specific water-availability is an important predictor of bacterial community...

Notochord vacuoles absorb compressive bone growth during zebrafish spine formation

Jennifer Bagwell, James Norman, Kathryn Ellis, Brianna Peskin, James Hwang, Xiaoyan Ge, Stacy Nguyen, Sarah McMenamin, Didier Stanier & Michel Bagnat
The vertebral column or spine assembles around the notochord rod which contains a core made of large vacuolated cells. Each vacuolated cell possesses a single fluid-filled vacuole, and loss or fragmentation of these vacuoles in zebrafish leads to spine kinking. Here, we identified a mutation in the kinase gene dstyk that causes fragmentation of notochord vacuoles and a severe congenital scoliosis-like phenotype in zebrafish. Live imaging revealed that Dstyk regulates fusion of membranes with the...

Underlying data for: Influence of temporally varying weatherability on CO2-climate coupling and ecosystem change in the late Paleozoic

Jon Richey, Isabel Montañez, Yves Goddéris, Cindy Looy, Neil Griffis & William DiMichele
This dataset contains the primary data used as input parameters in a mechanistic stomatal CO2 model (Franks et al., 2014 (Geophysical Research Letters)) and the Paleosol Barometer Uncertainty Quantifier (i.e., PBUQ; Breecker, 2013 (Geochemistry, Geophysics, Geosystems)), as well as age-adjusted CO2 data from Montañez et al., 2016 (Nature Geoscience). The stomatal parameters were measured by Richey et al., 2020 (Climate Of The Past) and the paleosol parameters are revised from Montañez et al., 2007 (Science)....

Data from: Association of genetic and climatic variability in giant sequoia, Sequoiadendron giganteum, reveals signatures of local adaptation along moisture-related gradients

Rainbow DeSilva & Richard Dodd
Uncovering the genetic basis of local adaptation is a major goal of evolutionary biology and conservation science alike. In an era of climate change, an understanding of how environmental factors shape adaptive diversity is crucial to predicting species response and directing management. Here, we investigate patterns of genomic variation in giant sequoia, an iconic and ecologically important tree species, using 1364 bi-allelic single nucleotide polymorphisms (SNPs). We use an FST outlier test and two genotype-environment...

Data from: A phylogeny for the Drosophila montium species group: a model clade for comparative analyses

William Conner, Emily Delaney, Michael Bronski, Paul Ginsberg, Timothy Wheeler, Kelly Richardson, Brooke Peckenpaugh, Kevin Kim, Masayoshi Watada, Ary Hoffmann, Michael Eisen, Artyom Kopp, Brandon Cooper & Michael Turelli
The Drosophila montium species group is a clade of 94 named species closely related to the model D. melanogaster species group. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times...

A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera

Ingrid Jordon-Thaden, James Beck, Catherine Rushworth, Michael Windham, Nicolas Diaz, Jason Cantley, Chris Martine & Carl Rothfels
Premise of the study: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of broad datasets with taxonomic and geographic sampling not otherwise possible. Here we evaluate the utility of a basic restriction site-associated DNA (ddRADseq) protocol with DNAs from four genera extracted from both silica-dried and herbarium tissue. Methods: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (ddRADseq) protocol. The...

High-throughput Synthesis and Transformations of CsPbBr nanocrystals characterized by UV-Vis Absorption and Fluorescence

Jakob C Dahl, Xingzhi Wang, Emory M. Chan & A. Paul Alivisatos
These experiments are a dataset of absorption and photoluminescence emission spectra of cesium lead bromide nanocrystals synthesized under different conditions, published as a companion dataset for “Elucidating the Weakly Reversible Cs-Pb-Br Perovskite Nanocrystal Reaction Network with High-Throughput Maps and Transformations” (https://doi.org/10.1021/jacs.0c04997). It also includes deconvolution of the absorption and emission spectra and other calculations, and a notebook including the deconvolution algorithm and some helpful visualization code.

Plumage patterns: ecological functions, evolutionary origins, and advances in quantification

Nicholas Mason
Birds exhibit remarkable variation in plumage patterns, both within individual feathers and among plumage patches. Differences in the size, shape, and location of pigments and structural colors comprise important visual signals involved in mate choice, social signaling, camouflage, and many other functions. While ornithologists have studied plumage patterns for centuries, recent technological advances in digital image acquisition and processing have transformed pattern quantification methods, enabling comprehensive, detailed data sets of pattern phenotypes that were heretofore...

Matlab applications for: A mechanical model to interpret distributed fiber optic strain measurement at displacement discontinuities

Shenghan Zhang, Han Liu, Jeffrey Cheng & Matthew DeJong
This repository publishes the data and Matlab app for the paper titled, "A Mechanical Model to Interpret Distributed Fiber Optic Strain Measurement at Displacement Discontinuities" published in Structural Health Monitoring. Distributed fiber optic (strain) sensing (DFOS), which provides the unique advantage of sensing damage (e.g. cracking) at locations that are not known a priori, has been increasingly used in civil engineering. Quantitative crack measurement requires the translation of a discontinuous displacement field at the crack...

Data from: Barrier Behavior Analysis (BaBA) reveals extensive effects of fencing on wide-ranging ungulates

Wenjing Xu, Nandintsetseg Dejid, Valentine Herrmann, Hall Sawyer & Arthur Middleton
1. As human activities expand globally, there is a growing need to identify and mitigate barriers to animal movements. Fencing is a pervasive human modification of the landscape that can impede the movements of wide-ranging animals. Previous research has largely focused on whether fences block movements altogether, but a more nuanced understanding of animals’ behavioral responses to fences may be critical for examining the ecological consequences and prioritizing conservation interventions. 2. We developed a spatial-...

Dataset for: Fiber optic sensing of concrete cracking and rebar deformation using several types of cable

Shenghan Zhang, Han Liu, Aziz Sandotin Coulibaly Abdoul & Matthew DeJong
Distributed fiber optic sensing (DFOS) is increasingly being applied in civil engineering. One recently emerging type of DFOS, Optical Frequency Domain Reflectometry (OFDR), offers improved accuracy and resolution. This repository contains the data set and post processing for an experimental study conducted at University of California, Berkeley that investigates the ability of OFDR, implemented using several types of fiber optic cable, to detect concrete cracking and large strain steel deformation. More specifically, the experimental investigation...

Data from: Making job postings more equitable: evidence-based recommendations from an analysis of data professionals job postings between 2013-2018

Amy Neeser & Joanna Thielen
Over the last decade, many academic libraries have hired data professionals in order to offer research data services. As these positions often require different types of experience than traditional librarian positions, there is an increased interest in hiring professionals from outside the typical library and information science (LIS) pipeline. There has also been an increased interest in academic libraries and higher education more broadly to incorporate the principles and practices of diversity, equity, inclusion, and...

Controls on range shifts of coastal Californian bivalves during the peak of the last interglacial and baseline predictions for today

Emily Orzechowski & Seth Finnegan
As the most recent time in Earth history when global temperatures were warmer than at present, the peak of the last interglacial (Marine Isotope Substage [MIS] 5e; ~120,000 years ago) can serve as a pre-anthropogenic baseline for a warmer near-future world. Here we use a new compilation of 22 fossil localities in California that have been reliably dated to Marine Isotope Stage (MIS) 5e to establish baseline expectations for contemporary bivalve species movements by identifying...

Technical appendices from: Affordable housing without public subsidies: rent-setting practices in small rental properties

Nathaniel Decker
Rental housing affordability is a severe problem for low- and moderate-income families across the US. While some renters benefit from subsidies or rent-regulation, most low-income renters live in unsubsidized, unregulated units, particularly in low-cost 1- to 4-unit properties. Some of these small rental properties are low-cost because they are low quality or are in low-demand neighborhoods, but there has long been speculation that many of these units are low-cost because their owners set rents below...

Nocturnal dispersal flight of crickets: behavioural and physiological responses to cool environmental temperatures

Caroline Williams, Baojun Sun, Christopher Huebner, Lisa Treidel, Kevin Roberts, G.J. Kenagy & Rebecca Clark
1. Flight of nocturnal insects may be limited by cool nighttime environmental temperatures. We used laboratory and field experiments to explore the thermal basis of nocturnal flight in wing-polymorphic Gryllus lineaticeps crickets consisting of long-winged (LW), flight-capable morphs and short-winged (SW), flight-incapable morphs. These crickets are a model for life history evolution and loss of flight, but their thermal requirements for flight have been unknown. We hypothesized that LW crickets achieve warm body temperatures required...

Data from: Effect of pharmacological manipulation of the renin-angiotensin system upon pro-inflammatory responses to acute sleep fragmentation

David Ensminger, Nicholas Wheeler, Kristen Eads & Noah Ashley
With the world-wide rise in obesity, the prevalence of obstructive sleep apnea has increased, which leads to disordered sleep patterns and consequently inflammation in brain and peripheral tissues. As hypertension is associated with obesity, it is unclear whether increased vascular sheer forces from elevated blood pressure promote inflammation during fragmented sleep. To test this possibility, we pharmacologically manipulated the renin-angiotensin system (RAS) of male C57BL6/j mice using angiotensin and captopril to elevate and reduce blood...

Data from: Recognizing pulses of extinction from clusters of last occurrences

Joshua Zimmt, Steven Holland, Seth Finnegan & Charles Marshall
The distribution of last occurrences of fossil taxa in a stratigraphic column are used to infer the pattern, timing, and tempo of extinction from the fossil record. Clusters of last occurrences are commonly interpreted as an abrupt pulse of extinction. However, stratigraphic architecture alone can produce clusters of last occurrences that can be misinterpreted as an extinction pulse. These clusters will typically occur in strata that immediately underlie facies changes and sequence-stratigraphic surfaces. It has...

Data from: What makes a fang? phylogenetic and ecological controls on tooth evolution in rear-fanged snakes

Erin Westeen, Andrew Durso, Michael Grundler, Daniel Rabosky & Alison Davis Rabosky
Background: Fangs are a putative key innovation that revolutionized prey capture and feeding in snakes, and – along with their associated venom phenotypes – have made snakes perhaps the most medically-significant vertebrate animals. Several snake clades are known for their forward-positioned fangs, and these clades (Elapidae; Viperidae) contain the majority of snakes that are traditionally considered venomous. However, many other snakes are "rear-fanged": they possess potentially venom-delivering teeth situated at the rear end of the...

Registration Year

  • 2020

Resource Types

  • Dataset


  • University of California, Berkeley
  • University of California, Davis
  • Cornell University
  • University of Minnesota
  • University of Georgia
  • University of Washington
  • Stanford University
  • Duke University
  • Ehime University
  • University of Pennsylvania