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Sequence matrix and tree files for Spatial phylogenetics of the native California flora (Thornhill et al. BMC Biology)

Andrew Thornhill, Bruce Baldwin, William Freyman, Sonia Nosratinia, Matthew Kling, Naia Morueta-Holme, Thomas Madsen, David Ackerly, Brent Mishler & Andrew Thornhill
This is the DNA sequence alignment for the 1083 OTUs used in Thornhill et al. 2017. We defined monophyletic OTUs at the finest scale possible given data availability and current understanding of the evolutionary relationships of Californian plant lineages. Using all 5258 species described in The Jepson eFlora (http://ucjeps.berkeley.edu/eflora/) as a starting point, a thorough literature search was undertaken to find molecular phylogenetic studies that had included California taxa. Genera were split into finer level...

Salmon Creek Watershed Stable Isotope Data

Cleo Woelfle-Erskine
Stable isotope (O and H) data collected from stream pools, piezometers, springs, and wells in the Salmon Creek watershed in 2014 and 2016.

Salmon Creek salmonid and habitat data 2012-14

Cleo Woelfle-Erskine
Data from snorkel surveys of intermittent streams during the summer rearing period (May-October) and associated habitat data. Part of a long-term study of Fay and Tannery Creeks.

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...

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...

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.

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,...

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...

Videos of Gold Nanorods Etching in Graphene Liquid Cell Transmission Electron Microscopy- 38 mM FeCl3

Matthew Hauwiller, Justin Ondry & A. Paul Alivisatos
Premade gold nanorods were etched in a graphene liquid cell and imaged using Transmission Electron Microscopy (TEM). An aqueous solution of gold nanorods, Tris Buffer-HCl, and FeCl3 was encapsulated between graphene sheets. The final concentration of FeCl3 was 38 mM. Through a combination of the electron beam-generated radiolysis products and the FeCl3, the nanorods underwent non-equilibrium etching. See associated papers for more details.

Berkeley High Resolution (BEHR) OMI NO2 v3.0C - Gridded pixels, daily profiles

Qindan Zhu, Joshua Laughner & Ron Cohen
The BEHR reprocesses tropospheric NO2 columns from the Ozone Monitoring Instrument (OMI) satellite using high resolution a priori NO2 profiles, surface reflectivity, and surface elevation data. This product uses NO2 profiles for the day retrieved, simulated by the WRF-Chem model at 12 km spatial resolution. The use of high spatial resolution NO2 profiles has been shown to better resolve urban/rural differences in NO2 column densities, and the use of day-to-day (rather than monthly average) profiles...

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: Fragmented and isolated: limited gene flow coupled with weak isolation by environment in the paleoendemic giant sequoia (Sequoiadendron giganteum)

Rainbow DeSilva & Richard Dodd
PREMISE: Patterns of genetic structure across a species’ range reflect the long-term interplay between genetic drift, gene flow, and selection. Given the importance of gene flow in preventing the loss of diversity through genetic drift among spatially isolated populations, understanding the dynamics of gene flow and the factors that influence connectivity across a species’ range is a major goal for conservation of genetic diversity. Here we present a detailed look at gene flow dynamics of...

Berkeley High Resolution (BEHR) OMI NO2 - Native pixels, daily profiles

Joshua Laughner, Qindan Zhu & Ron Cohen
The BEHR OMI NO2 product reprocesses tropospheric NO2 columns from the Ozone Monitoring Instrument (OMI) satellite using high resolution a priori NO2 profiles, surface reflectivity, and surface elevation data. This product uses NO2 profiles for the day retrieved, simulated by the WRF-Chem model at 12 km spatial resolution. The use of high spatial resolution NO2 profiles has been shown to better resolve urban/rural differences in NO2 column densities, and the use of day-to-day (rather than...

Data from: Knowledge, provision of information and barriers to high quality medication abortion provision by pharmacists in Uttar Pradesh, India

Nadia Diamond-Smith, Joanna Percher, Malvika Saxena, Pravesh Dwivedi & Aradhana Srivastava
Background: Almost three quarters of the 16 millions abortions in India were medication abortion (MA) purchased outside of facilities. Past research has shown low quality of care given to clients seeking MA from pharmacists in this setting. Most purchasers of MA from pharmacies in India are men, further complicating the pathway to high quality information for women taking MA. Developing interventions that can improve the information and quality of interactions for women obtaining MA through...

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...

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...

Nitrogen isotope fractionation during archaeal ammonia oxidation: coupled estimates from measurements of residual ammonium and accumulated nitrite

Wolfgang Wanek & Maria Mooshammer
The naturally occurring nitrogen (N) isotopes, 15N and 14N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO2-), performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase...

Data from: VolcanoFinder: genomic scans for adaptive introgression

Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio & Joachim Hermisson
Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method---VolcanoFinder---to detect recent events of adaptive introgression using polymorphism data...

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...

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...

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: Agricultural practices for food safety threaten pest control services for fresh produce

Daniel S. Karp, Rebekah Moses, Sasha Gennet, Matthew S. Jones, Shimat Joseph, Leithen K. M'Gonigle, Lauren C. Ponisio, William E. Snyder & Claire Kremen
Over the past decade, several foodborne disease outbreaks provoked widespread reforms to the fresh produce industry. Subsequent concerns about wildlife vectors and contaminated manures created pressure on growers to discontinue use of manure-based composts and remove nearby semi-natural vegetation. Despite widespread adoption, impacts of these practices on ecosystem services such as pest control have not been assessed. We used a landscape-scale field experiment to quantify associations between compost applications, semi-natural vegetation, pest control services and...

Data from: Mosquito saliva increases endothelial permeability in the skin, immune cell migration, and dengue pathogenesis during antibody-dependent enhancement

Michael A. Schmid, Dustin R. Glasner, Sanjana Shah, Daniela Michlmayr, Laura D. Kramer, & Eva Harris
Dengue remains the most prevalent arthropod-borne viral disease in humans. While probing for blood vessels, Aedes aegypti and Ae. albopictus mosquitoes transmit the four serotypes of dengue virus (DENV1-4) by injecting virus-containing saliva into the skin. Even though arthropod saliva is known to facilitate transmission and modulate host responses to other pathogens, the full impact of mosquito saliva on dengue pathogenesis is still not well understood. Inoculating mice lacking the interferon-α/β receptor intradermally with DENV...

Data from: Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements

Christopher E. Ellison, Doris Bachtrog & Christopher E Ellison
Transposable elements (TEs) allow rewiring of regulatory networks, and the recent amplification of the ISX element dispersed 77 functional but suboptimal binding sites for the dosage compensation complex to a newly formed X chromosome in Drosophila. Here we identify two linked refining mutations within ISX that interact epistatically to increase binding affinity to the dosage compensation complex. Selection has increased the frequency of this derived haplotype in the population, which is fixed at 30% of...

Data from: Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar

Jérôme Fuchs, Juan L. Parra, Steven M. Goodman, Marie Jeanne Raherilalao, Jeremy Vanderwal & Rauri C. K. Bowie
We conduct a phylogeographic study of the Crested Drongo (Dicrurus forficatus forficatus), a broadly distributed bird species on Madagascar. We first determined the demographic and spatial pattern inferred from mitochondrial and nuclear data, and then compared these results with predictions from a present to 0.120-Myr-old reconstruction of the spatial dynamics of the range of D. f. forficatus on Madagascar, enabling putative areas of stability (lineage persistence) to be detected. Weak genetic structure along an east–west...

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  • University of California, Berkeley
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