145 Works

A trait-based framework for predicting foodborne pathogen risk from wild birds

Olivia Smith, Elissa Olimpi, Nora Navarro-González, Kevin Cornell, Luke Frishkoff, Tobin Northfield, Timothy Bowles, Max Edworthy, Johnna Eilers, Zhen Fu, Karina Garcia, David Gonthier, Matthew Jones, Christina Kennedy, Christopher Latimer, Jeb Owen, Chika Sato, Joseph Taylor, Erin Wilson Rankin, William Snyder & Daniel Karp
Recent foodborne illness outbreaks have heightened pressures on growers to deter wildlife from farms, jeopardizing conservation efforts. However, it remains unclear which species, particularly birds, pose the greatest risk to food safety. Using >11,000 pathogen tests and 1,565 bird surveys covering 139 bird species from across the western U.S.A., we examined the importance of 11 traits in mediating wild bird risk to food safety. We tested whether traits associated with pathogen exposure (e.g., habitat associations,...

Strains and constructs for: A chimeric nuclease substitutes a phage CRISPR-Cas system to provide sequence specific immunity against subviral parasites

Zachary Barth & Kimberley Seed
Mobile genetic elements, elements that can move horizontally between genomes, have profound effects on their hosts fitness. The PLE is a mobile element that integrates into the chromosome of Vibrio cholerae and parasitizes the bacteriophage ICP1 to move between cells. This parasitism by PLE is such that it abolishes the production of ICP1 progeny and provides a defensive boon to the host cell population. In response to the severe parasitism imposed by PLE, ICP1 has...

Genomic data reveal the biogeographic and demographic history of Ammospiza sparrows in northeast tidal marshes

Jennifer Walsh, Adrienne Kovach, Phred Benham, Gemma Clucas, Virginia Winder & Irby Lovette
Aim: Shaped by both climate change and sea-level rise, tidal salt marshes represent ephemeral systems that are home to only a few, highly specialized species. The dynamic ecological histories and spatial complexities of these habitats, however, render it challenging to reconstruct the complete biogeographic histories of their endemic taxa. Here, we leverage three species of North American Ammospiza sparrows that inhabit tidal marshes ( Ammospiza caudacuta, A. maritima, and A. n. subvirgatus) and closely related...

Community composition influences ecosystem resistance and productivity more than species richness or intraspecific diversity

Matthew Bowker, M. Cristina Rengifo-Faiffer, Anita Antoninka, Henry Grover, Kirsten Coe, Kirsten Fisher, Brent Mishler, Mel Oliver & Lloyd Stark
Biodiversity describes the variety of life and may influence properties and processes of ecosystems, such as biomass production and resistance to disturbance. We investigated the effects of multiple facets of biodiversity – species richness and composition of the community, and intraspecific diversity in two key species – on both production and resistance of experimentally-assembled biological soil crusts (biocrusts). We found that productivity was most strongly influenced by community composition (variation in the presence and relative...

Assessing impacts of social-ecological diversity on resilience in a wetland coupled human and natural system: Data release

Nathan Van Schmidt, José Oviedo, Tracy Hruska, Lynn Huntsinger, Tony Kovach, A. Marm Kilpatrick, Norman Miller & Steven Beissinger
Theory posits that resilience of ecosystems increases when there is a diversity of agents (e.g., species) and linkages between them. If ecosystems are conceptualized as components of “coupled human and natural systems”, then a corollary would be that novel types of human-induced diversity may also foster resilience. We explored this hypothesis by studying how socially created diversity mediated the impact of a historically severe drought on a network of wetlands in the foothills of the...

Directionally biased habitat shifts and biogeographically informative cytonuclear discordance in the Hawaiian silversword alliance (Compositae)

Bruce Baldwin, Kenneth Wood & William Freyman
PREMISE OF THE STUDY: Expanded phylogenetic analyses of the endemic Hawaiian silversword alliance (Argyroxiphium, Dubautia, Wilkesia; Compositae) were undertaken to obtain enhanced resolution of habitat shifts, interisland dispersal, evolutionarily relevant hybridization, and clade diversity in this prominent example of adaptive radiation. METHODS: Samples spanning the geographic and ecological distributions of all recognized taxa were included in phylogenetic and biogeographic analyses of nuclear ribosomal DNA (nrDNA) and cpDNA sequences. Bayesian model testing approaches were used to...

Supplementary Materials - Adaptive Tree Proposals for Bayesian Phylogenetic Inference

Xavier Meyer
Bayesian inference of phylogeny with MCMC plays a key role in the study of evolution. Yet, this method still suffers from a practical challenge identified more than two decades ago: designing tree topology proposals that efficiently sample tree spaces. In this study, I introduce the concept of adaptive tree proposals for unrooted topologies, that is tree proposals adapting to the posterior distribution as it is estimated. I use this concept to elaborate two adaptive variants...

Data from: A reusable pipeline for large-scale fiber segmentation on unidirectional fiber beds using fully convolutional neural networks

Alexandre Fioravante De Siqueira, Stéfan Van Der Walt & Daniela Mayumi Ushizima
Fiber-reinforced ceramic-matrix composites are advanced materials resistant to high temperatures, with application to aerospace engineering. Their analysis depends on the detection of embedded fibers, with semi-supervised techniques usually employed to separate fibers within the fiber beds. Here we present an open computational pipeline to detect fibers in ex-situ X-ray computed tomography fiber beds. To separate the fibers in these samples, we tested four different architectures of fully convolutional neural networks. When comparing our neural network...

Resource quality determines the evolution of resistance and its genetic basis

Katherine Roberts, Sean Meaden, Stephen Sharpe, Toby Doyle, Suzanne Kay, Lewis Bartlett, Steve Paterson & Mike Boots
Parasites impose strong selection on their hosts, but the level of any evolved resistance may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource-mediated selection are rare, particularly in non-model organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and any associated trade-offs in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole genome re-sequencing we identify...

Transmission electron microscope images dataset for AutoDetect-mNP (triangular prisms)

Xingzhi Wang, Jie Li, Hyun Dong Ha, Jakob Dahl, Teresa Head-Gordon & Paul Alivisatos
AutoDetect-mNP is an unsupervised algorithm capable of detecting and segmenting particles from bright-field TEM images and classifying the particles based on their shapes, requiring minimum human intervention in the process. The algorithm was validated on TEM images of 4 different Au nanoparticle systems (nanorods with ~5 aspect ratio, nanorods with ~2 aspect ratio, mixture of the two nanorods, triangular nanoprisms). This dataset contains the unprocessed TEM images of the triangular prisms. For details regarding the...

Phylogeny and classification of the genus-group taxa of Loxandrina (Coleoptera, Carabidae, Abacetini)

Kipling Will
Bayesian and parsimony phylogenetic analyses of combined and partitioned datasets of molecular (partial sequences of 28S, wg, COI, and CAD) and morphological (51 characters of adults) data for exemplar taxa of five outgroup and 76 ingroup abacetine carabids resulted in a monophyletic Loxandrina Erwin & Sims, 1984 that is split into Australian and American clades. The genus Loxandrus LeConte, 1853 as previously delimited is not monophyletic relative to numerous genus-level taxa in Abacetini Chaudoir, 1873...

PSP FIELDS Digital Fields Board (DFB) AC-coupled Differential Voltage, V3-V4 Antennae, Dipole Mode, Bandpass filtered, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, David M. Malaspina, Alexandros Chasapis, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, dV34 data. The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. DFB AC bandpass data consist of peak and average values of the absolute value of bandpassed time series waveform data over a time interval equal to the reporting cadence. The AC bandpass data have the peak response frequency of each bin reported in the metadata. The...

PSP FIELDS Digital Fields Board (DFB) Searchcoil Magnetometer, SCM, Burst Waveform, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M Malaspina, Trevor A. Bowen, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment . DFB burst waveform data consist of short bursts of time-series data from various FIELDS sensors. These data have been filtered by both analog and digital filters. These data are pre-sorted by onboard competitive selection algorithms before storage by FIELDS. A subset of this stored burst...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Searchcoil Magnetometer, SCM, Spectra, Low Frequency, High Gain, u-component, Sensor coordinates, Level 2 (L2), 6.99054 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMulfhg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Searchcoil Magnetometer, SCM, Spectra, Low Frequency, High Gain, w-component, Sensor coordinates, Level 2 (L2), 6.99054 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMwlfhg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Fluxgate Magnetometer (MAG) Magnetic Field Vectors, Radial-Tangential-Normal, RTN, Coordinates, 4 samples/cycle, Level 2 (L2), 3.413 ms Data

Stuart D. Bale, Robert J. MacDowall, Andriy Koval, Marc Pulupa, Timothy Quinn & Peter Schroeder
Parker Solar Probe FIELDS Instrument Suite Fluxgate Magnetometer, MAG, Data: The time resolution of the MAG time series data varies with instrument mode ranging from 2.289 samples/s to 292.9 samples/s. These two data sampling rates corresponding to 2 samples or 256 samples per 0.874 s where 0.874 s is equal to 2^25 divided 38.4 MHz. The Magnetometer has four ranges: ±1024 nT, ±4096 nT, ±16,384 nT, and ±65,536 nT. The Magnetometer Range is selected by...

PSP FIELDS Digital Fields Board (DFB) AC-coupled Searchcoil Magnetometer, SCM, Spectra, Medium Frequency, High Gain, x-component, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMvlfhg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB AC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Differential Voltage, V3-V4 Antennae, Dipole Mode, Bandpass filtered, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, David M. Malaspina, Alexandro Chasapis, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, dV34 data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB AC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Searchcoil Magnetometer, SCM, Cross Spectra, d-component, e-component, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Alexandros Chasapis, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board (DFB), SCMXlfhg ⨯ SCMXlfhg cross spectra data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC cross spectra data for a pair of input channels consist of: Power spectral densities, Real and imaginary parts of the spectral cross term, Coherence, and Phase where all as a function of...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Searchcoil Magnetometer, SCM, Cross Spectra, v-component, w-component, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Alexandros Chasapis, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board (DFB), SCMvlfhg ⨯ SCMwlfhg cross spectra data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC cross spectra data for a pair of input channels consist of: Power spectral densities, Real and imaginary parts of the spectral cross term, Coherence, and Phase where all as a function of...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Differential Voltage, V1-V2 Antennae, Dipole Mode, Spectra, High Gain, Sensor coordinates, Level 2 (L2), 6.99054 s Data

Stuart D. Bale, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, dV12hg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

PSP FIELDS Digital Fields Board (DFB) DC-coupled Searchcoil Magnetometer, SCM, Spectra, Low Frequency, High Gain, d-component, Sensor coordinates, Level 2 (L2), 6.99054 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
PSP FIELDS Digital Fields Board, DFB, SCMdlfhg data: The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. For a full description of the FIELDS experiment. DFB DC spectra data consist of power spectral densities as a function of frequency and time. These spectra are averaged over both frequency and time. The Level 2 data products contained in this data file have been calibrated...

Nodal seismic experiment at the Berkeley section of the Hayward fault

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The nodal array consisting of 182 FairfieldNodal ZLand 3C sensors was deployed around the University of California Berkeley campus. A main objective is to image the Hayward fault with high resolution through ambient noise surface wave tomography. The sensors were deployed from late November 2020 through early January 2021.

PSP FIELDS Digital Fields Board (DFB) AC-coupled Searchcoil Magnetometer, SCM, Cross Spectra, e-component, f-component, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D. Bale, Thierry Dudok de Wit, David M. Malaspina, Alexandros Chasapis, Marc Pulupa, Timothy Quinn & Peter Schroeder
The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. DFB AC cross spectra data for a pair of input channels consist of: Power spectral densities, Real and imaginary parts of the spectral cross term, Coherence, Phase. The Level 2 data products have been calibrated for: The Hanning window used in the spectral calculation, DFB in-band gain, DFB analog filter gain response, DFB digital...

PSP FIELDS Digital Fields Board (DFB) AC-coupled Differential Voltage, V1-V2 Antennae, Dipole Mode, Spectra, High Gain, Sensor coordinates, Level 2 (L2), 0.873813 s Data

Stuart D Bale, David M. Malaspina, Katherine A. Goodrich, Marc Pulupa, Timothy Quinn & Peter Schroeder
The DFB is the low frequency, less than 75 kHz, component of the FIELDS experiment on the Parker Solar Probe spacecraft. DFB AC cross spectra data for a pair of input channels consist of: Power spectral densities, Real and imaginary parts of the spectral cross term, Coherence, Phase. The Level 2 data products have been calibrated for: The Hanning window used in the spectral calculation, DFB in-band gain, DFB analog filter gain response, DFB digital...

Registration Year

  • 2021
    145

Resource Types

  • Dataset
    145

Affiliations

  • University of California, Berkeley
    144
  • Laboratory for Atmospheric and Space Physics
    30
  • University of Orléans
    25
  • Goddard Space Flight Center
    5
  • University of Washington
    3
  • Stanford University
    3
  • Utah State University
    3
  • University of California, Davis
    3
  • National Research Institute for Agriculture, Food and Environment
    2
  • University of Pretoria
    2