84 Works

Flexible analysis of animal behavior via time-resolved embedding

Ryan York
Uncovering relationships between neural activity and behavior represents a critical challenge, one that would benefit from facile tools that can capture complex structures within large datasets. Here we demonstrate a generalizable strategy for capturing such structures across diverse behaviors: Time-REsolved BehavioraL Embedding (TREBLE). Using data from synthetic trajectories, adult and larval Drosophila, and mice we show how TREBLE captures both continuous and discrete behavioral dynamics, can uncover variation across individuals, detect the effects of optogenetic...

Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface

Daniel J O'Shea, Eric Trautmann, Xulu Sun, Karl Deisseroth & Krishna Shenoy
Calcium imaging has rapidly developed into a powerful tool for recording from large populations of neurons in vivo. Imaging in rhesus macaque motor cortex can enable the discovery of new principles of motor cortical function and can inform the design of next generation brain-computer interfaces (BCIs). Surface two-photon (2P) imaging, however, cannot presently access somatic calcium signals of neurons from all layers of macaque motor cortex due to photon scattering. Here, we demonstrate an implant...

Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure

Keith Bouma-Gregson, Alex Crits-Christoph, Matthew Olm, Mary Power & Jillian Banfield
The relative importance of separation by distance and by environment to population genetic diversity can be conveniently tested in river networks, where these two drivers are often independently distributed over space. To evaluate the importance of dispersal and environmental conditions in shaping microbial population structures, we performed genome-resolved metagenomic analyses of benthic Microcoleus-dominated cyanobacterial mats collected in the Eel and Russian River networks (California, USA). The 64 Microcoleus genomes were clustered into three species that...

Liquid chromatography tandem mass spectrometry of AMPA receptor containing vesicles

John Peters, Jeremy Leitz, Juan Oses-Prieto, Alma Burlingame & Axel Brunger
Regulated delivery of AMPA receptors (AMPARs) to the postsynaptic membrane is an essential step in synaptic strength modification, and in particular, long-term potentiation (LTP). While LTP has been extensively studied using electrophysiology and light microscopy, several questions regarding the molecular mechanisms of AMPAR delivery via trafficking vesicles remain outstanding, including the gross molecular make up of AMPAR trafficking organelles and identification and location of calcium sensors required for SNARE complex-dependent membrane fusion of such trafficking...

WaveMAP analysis of extracellular waveforms from monkey premotor cortex during decision-making

Eric Lee, Hymavathy Balasubramanian, Alexandra Tsolias, Stephanie Anakwe, Maria Medalla, Krishna Shenoy & Chandramouli Chandrasekaran
Cortical circuits are thought to contain a large number of cell types that coordinate to produce behavior. Current in vivo methods rely on clustering of specified features of extracellular waveforms to identify putative cell types, but these capture only a small amount of variation. Here, we develop a new method (WaveMAP) that combines non-linear dimensionality reduction with graph clustering to identify putative cell types. We apply WaveMAP to extracellular waveforms recorded from dorsal premotor cortex...

Two new hybrid populations expand the swordtail hybridization model system

Daniel Powell, Ben Moran, Bernard Kim, Shreya Banerjee, Stepfanie Aguillon, Paola Fascinetto-Zago, Quinn Langdon & Molly Schumer
Natural hybridization events provide unique windows into the barriers that keep species apart as well as the consequences of their breakdown. Here we characterize hybrid populations formed between the northern swordtail fish Xiphophorus cortezi and X. birchmanni from collection sites on two rivers. We use simulations and new genetic reference panels to develop sensitive and accurate local ancestry calling in this novel system. Strikingly, we find that hybrid populations on both rivers consist of two...

A global ecological signal of extinction risk in terrestrial vertebrates

Maya Munstermann, Noel Heim, Douglas McCauley, Jonathan Payne, Nathan Upham, Steve Wang & Matthew Knope
To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled a dataset on ecological traits for 18,016 species and tested, using phylogenetic comparative methods, which categories of habitat association, mode of locomotion, and feeding mode best predict extinction risk. We found that cave-dwelling amphibians, brachiating mammals (all of which are primates), aerial and scavenging birds, and pedal squamates are all disproportionately threatened with extinction. Across four vertebrate classes,...

Supporting data and code for \"Optical control of fast and processive engineered myosins in vitro and in living cells\"

Paul V. Ruijgrok, Sasha Zemsky & Zev Bryant
This repository makes data and code available to readers of Ruijgrok, Paul V. and Ghosh, Rajarshi P. et al. (Nature Chemical Biology 2021), and relies on that published paper for context. Five archives are included in this collection. “Source Data for Figures 1-5”, "Source Data for Extended Data Figures 3-4", and “Source Data for Supplementary Figures 3-11” contain all the data presented in figure panels in the main text, Extended Data, and Supplementary Information, respectively....

Data from: Landscape Context Mediates Avian Habitat Choice in Tropical Forest Restoration

J. Leighton Reid, Chase D. Mendenhall, J. Abel Rosales, Rakan A. Zahawi & Karen D. Holl
Birds both promote and prosper from forest restoration. The ecosystem functions birds perform can increase the pace of forest regeneration and, correspondingly, increase the available habitat for birds and other forest-dependent species. The aim of this study was to learn how tropical forest restoration treatments interact with landscape tree cover to affect the structure and composition of a diverse bird assemblage. We sampled bird communities over two years in 13 restoration sites and two old-growth...

Data from: Association of venous outflow profiles and successful vessel reperfusion after thrombectomy

Tobias Djamsched Faizy
Background and Purpose: Robust arterial collaterals are associated with successful reperfusion after thrombectomy treatment of acute ischemic stroke due to large vessel occlusion (AIS-LVO). Excellent venous outflow (VO) reflects excellent tissue perfusion and collateral status in AIS-LVO patients. Objective: To determine whether favorable VO profiles assessed on pre-treatment CT angiography (CTA) images correlate with successful vessel reperfusion after thrombectomy in AIS-LVO patients. Materials and Methods: Multicenter retrospective cohort study of consecutive AIS-LVO patients treated by...

Data from: Mass extinctions alter extinction and origination dynamics with respect to body size

Pedro Monarrez, Noel Heim & Jonathan Payne
Whether mass extinctions and their associated recoveries represent an intensification of background extinction and origination dynamics versus a separate macroevolutionary regime remains a central debate in evolutionary biology. Previous focus has been on extinction, but origination dynamics may be equally or more important for long-term evolutionary outcomes. The evolution of animal body size is an ideal process to test for differences in macroevolutionary regimes, as body size is easily determined, comparable across distantly related taxa,...

Testing small scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

Peter Shum & Stephen Palumbi
DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operation taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from...

Data from: How oscillating aerodynamic forces explain the timbre of the hummingbird's hum and other animals in flapping flight

Ben Hightower, Patrick Wijnings, Rick Scholte, Rivers Ingersoll, Diana Chin, Jade Nguyen, Daniel Shorr & David Lentink
The source of the hummingbird's distinctive hum is not fully understood, but there are clues to its origin in the acoustic nearfield. Hence we studied six freely hovering Anna’s hummingbirds, performing acoustic nearfield holography using a 2176 microphone array in vivo, while also directly measuring the 3D aerodynamic forces using a new aerodynamic force platform. We corroborate the acoustic measurements by developing a first-principles acoustic model that integrates the aerodynamic forces with wing kinematics, which...

ddRAD of Hawaiian Ariamnes spiders

Ellie Armstrong, Benoît Perez-Lamarque, Ke Bi, Leontine Becking, Jun Lim, Tyler Linderoth, Rosemary Gillespie & Henrik Krehenwinkel
The diversification of a host organism can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, coupled with a chronologically arranged series of volcanic mountains, to determine the evolutionary history of a host and its associated microbial communities, altogether forming the “holobiont”. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawaiʻi, and outgroup taxa on older islands, we tested whether...

CATS tag example deployment

William Gough & David Cade
Biologging tags are capable of capturing high-resolution data from cryptic species that spend a significant portion of their lives in remote or inaccessible environments, such as below the sea surface. The advancement of biologging technologies over the last ~30 years has lead to an explosion of research into the hidden lives of these elusive animals. Information about locomotion, feeding, migratory patterns, reproduction, and metabolism have all been determined using data obtained with biologging tags. CATS...

Conservation of Birds in Fragmented Landscapes Requires Protected Areas

Robert Timmers, Marijke Van Kuijk, Pita Verweij, Jaboury Ghazoul, Yann Hautier, William Laurance, Stefan Arriaga-Weiss, Robert Askins, Corrado Battisti, Åke Berg, Gretchen Daily, Cristián Estades, Beatrice Frank, Reiko Kurosawa, Rosamund Pojar, John Woinarski & Merel Soons
For successful conservation of biodiversity, it is vital to know whether protected areas in increasingly fragmented landscapes effectively conserve species. However, how large habitat fragments must be and what level of protection is required to sustain species, remains poorly known. We compiled a global dataset on almost 2000 bird species in 741 forest fragments varying in size and protection status, and show that protection is associated with higher bird occurrence, especially for threatened species. Protection...

Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE

Thanaphong Phongpreecha, Chandresh Gajera, Candace Liu, Kausalia Vijayaragavan, Alan Chang, Martin Becker, Ramin Fallahzadeh, Rosemary Fernandez, Nadia Postupna, Emily Sherfield, Dmitry Tebaykin, Caitlin Latimer, Carol Shively, Thomas Register, Suzanne Craft, Kathleen Montine, Edward Fox, Kathleen Poston, C. Dirk Keene, Michael Angelo, Sean Bendall, Nima Aghaeepour & Thomas Montine
Synaptic molecular characterization is limited for Alzheimer’s disease (AD). Our newly invented mass cytometry-based method, Synaptometry by Time of Flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), non-human primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice...

The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models

Mallory Harris, Morgan Kain & Marissa Childs
Mathematical models of epidemics are important tools for predicting epidemic dynamics and evaluating interventions. Yet, because early models are built on limited information, it is unclear how long they will accurately capture epidemic dynamics. Using a stochastic SEIR model of COVID-19 fitted to reported deaths, we estimated transmission parameters at different time points during the first wave of the epidemic (March–June, 2020) in Santa Clara County, California. Although our estimated basic reproduction number (R0) remained...

Interactions with soil fungi alter density-dependence and neighborhood effects in a locally abundant dipterocarp species

Kabir Peay, Richard Segnitz & Sabrina Russo
Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition...

Predator-prey interactions of terrestrial invertebrates are determined by predator body size and species identity

Ana Miller-Ter Kuile, Austen Apigo, An Bui, Bartholomew DiFiore, Elizabeth Forbes, Michelle Lee, Devyn Orr, Daniel Preston, Rachel Behm, Taylor Bogar, Jasmine Childress, Rodolfo Dirzo, Maggie Klope, Kevin Lafferty, John McLaughlin, Marisa Morse, Carina Motta, Kevin Park, Katherine Plummer, David Weber, Ronald Young & Hillary Young
Predator-prey interactions shape ecosystem and can help maintain biodiversity. However, for many of the earth’s most biodiverse and abundant organisms, including terrestrial arthropods, these interactions are difficult or impossible to observe directly with traditional approaches. Based on previous theory, it is likely that predator-prey interactions for these organisms are shaped by a combination of predator traits, including body size and species-specific hunting strategies. In this study, we combined diet DNA metabarcoding data of 173 individual...

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment-dependent

Ken Thompson, Catherine Peichel, Diana Rennison, Matthew McGee, Arianne Albert, Timothy Vines, Anna Greenwood, Abigail Wark, Yaniv Brandvain, Molly Schumer & Dolph Schluter
Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are 'intrinsic', meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus...

Trophic rewilding benefits a tropical community through direct and indirect network effects

Pedro Uchoa Mittelman, Anna Rebello Landim, Luísa Genes, Ana Paula A. Assis, Carolina Starling-Manne, Paula V. Leonardo, Fernando A.S. Fernandez, & Alexandra Pires
Species reintroductions can be used as a conservation strategy to restore ecological interactions and the functionality of impoverished ecosystems. The ecological effects of reintroductions go beyond restoring pairwise interactions, because reintroductions can change how extant species are indirectly linked to each other in an ecological community. These indirect pathways, in turn, may shape a myriad of ecological and evolutionary processes operating in ecological systems. Here, we investigated how reintroductions may affect the direct and indirect...

A satellite-based mobile warning system to reduce interactions with an endangered species

Matthew Breece, Matthew Oliver, Dewayne Fox, Edward Hale, Danielle Haulsee, Matthew Shatley, Steven Bograd, Elliott Hazen & Heather Welch
Earth observing satellites are a major research tool for spatially explicit ecosystem nowcasting and forecasting. However, there are practical challenges when integrating satellite data into usable real-time products for stakeholders. The need of forecast immediacy and accuracy means that forecast systems must account for missing data and data latency while delivering a timely, accurate and actionable product to stakeholders. This is especially true for species that have legal protection. Acipenser oxyrinchus oxyrinchus (Atlantic Sturgeon) were...

Data Supplement for Digital Atlas of Dioceses and Ecclesiastical Provinces in Late Medieval Europe (1200-1500)

Rowan Dorin, Clara Romani, Lauren Schlansky & Claire Womack
This data supplement includes shapefiles and GeoJSON documents for the Digital Atlas of Dioceses and Ecclesiastical Provinces in Late Medieval Europe (1200-1500) Collection. Also included with this supplement is a list of contributors, map sources, a README file, and tabular metadata describing dioceses and provinces.

Stanford Geophysics Donor Data Collection

Donated by a company that prefers to remain anonymous.

Registration Year

  • 2021

Resource Types

  • Dataset


  • Stanford University
  • University of California, Santa Barbara
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  • The University of Texas at Austin
  • Princeton University
  • University of Georgia
  • Johns Hopkins University