99 Works

Cinematic virtual reality with head-motion parallax

Jayant Purushottam Thatte

Web-CDI: A system for online administration of the MacArthur-Bates Communicative Development Inventories

Benjamin Edward deMayo, Danielle Kellier, Mika Braginsky, Christina Bergmann, Cielke Hendriks, Caroline Rowland, Michael Frank & Virginia Marchman

Do tradeoffs govern plant species responses to different global change treatments?

J. Adam Langley, Emily Grman, Kevin Wilcox, Meghan Avolio, Kimberly Komatsu, Scott Collins, Sally Koerner, Melinda Smith, Andrew Baldwin, William Bowman, Nona Chiariello, Anu Eskelinen, Harry Harmens, Mark Hovenden, Kari Klanderud, Rebecca McCulley, Vladimir Onipchenko, Clare Robinson & Katharine Suding
Plants are subject to tradeoffs among growth strategies such that adaptations for optimal growth in one condition can preclude optimal growth in another. Thus, we hypothesized that the response of plant species abundance to one global change treatment would relate inversely to the response to a second treatment, particularly for treatment combinations that accentuate distinct traits. To address this hypothesis, we examined plant species abundances in 39 global change experiments manipulating CO2, nitrogen, phosphorus, water,...

Clinical Trial Transparency and Data-Sharing Among Bio-Pharmaceutical Companies and the Role of Company Size, Location, and Product Type: A Cross-Sectional Descriptive Analysis

Sydney Axson, Michelle Mello, Deborah Lincow, Catherine Yang, Cary Gross, Joseph Ross & Jennifer Miller
Objective: To examine company characteristics associated with better transparency and to apply a tool used to measure and improve clinical trial transparency among large companies and drugs, to smaller companies and biologics. Design: Cross-sectional descriptive analysis. Setting and participants. Novel drugs and biologics FDA approved in 2016 and 2017, and their company sponsors. Using established Good Pharma Scorecard (GPS) measures, companies and products were evaluated on their clinical trial registration, results dissemination, and FDA Amendments...

A peripheral immune signature of labor induction

Kazuo Ando, Julien Hédou, Brendan Carvalho, Ina Stelzer & Brice Gaudilliere
Approximately 1 in 4 pregnant women in the United States undergo labor induction. The onset and establishment of labor, particularly induced labor, is a complex and dynamic process influenced by multiple endocrine, inflammatory, and mechanical factors as well as obstetric and pharmacological interventions. The duration from labor induction to the onset of active labor remains unpredictable. Moreover, prolonged labor is associated with severe complications for the mother and her offspring, most importantly chorioamnionitis, uterine atony,...

Current status and future strategies for mentoring women in neurology

Christa San Luis Nobleza, Amtul Farheen, Ilena George, Divya Singhal, Regina Troxell, Jyoti Pillai, Logan Schneider, Catherine Lomen-Hoerth, Jennifer Graves & Stefano Sandrone
The American Academy of Neurology's (AAN) 2017 Gender Disparity Report identified improving mentorship as a key intervention to fill the leadership and pay gaps for women in neurology. Here we summarize the literature on mentoring women, provide an outline of ideal components of programs geared toward closing gender gaps, and present a mentoring program for AAN members. The strategies discussed share similarities with those for closing gaps related to race, ethnicity and religion. Developing effective...

Three-dimensional biofilm growth supports a mutualism involving matrix and nutrient sharing - related scripts and data

Heidi Arjes
This dataset contains the supporting scripts and data used to analyze co-culture fluorescent colony images in high-throughput. It contains some example images that can be used in the scripts. It also contains the script used to plot and determine the maximum growth rates of growth curves of some of the mutants and the script used to stitch overlapping microscope images.

Exposure, hazard and vulnerability all contribute to Schistosoma haematobium re-infection in northern Senegal

Andrea Lund, Susanne Sokolow, Isabel Jones, Chelsea Wood, Sofia Ali, Andrew Chamberlin, Alioune Sy, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Raphael Ndione, Gilles Riveau, Giulio De Leo & David Lopez-Carr
The risk of infectious diseases, including snail-borne schistosomiasis, is determined by three interrelated components: exposure, hazard and vulnerability. For schistosomiasis, exposure occurs through behaviors involving water contact, but not without the environmental hazard of snails and parasites in the water. Socio-economic vulnerability makes it difficult to reduce exposure in the presence of hazard, because it increases reliance on hazardous activities and environments. We aimed to quantify the contributions of exposure, hazard and vulnerability to schistosome...

Nitrogen budget data

Tan Zou, Xin Zhang, Luis Lassaletta, Nathaniel Mueller, Francesco Tubiello, Matthew Lisk, Chaoqun Lu, Richard Conant, Christopher Dorich, James Gerber, Hanqin Tian, Tom Bruulsema, Tai Maaz, Kazuya Nishina, Benjamin Bodirsky, Alexander Popp, Lex Bouwman, Arthur Beusen, Jinfeng Chang, Petr Havlík, David Leclère, Josep Canadell, Robert Jackson, Patrick Heffer, Nathan Wanner … & Eric Davidson
Input-output estimates of nitrogen (N) on cropland are essential for improving N management and better understanding the global N cycle. Here, we compare 13 N budget datasets covering 115 countries and regions over 1961-2015. Though most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in Tg N yr-1) and associated min-max ranges were 73 (64-84) for global harvested crop N; 161...

Data from: Regional movements of satellite-tagged whale sharks Rhincodon typus in the Gulf of Aden

Samantha Andrzejaczek
To gain insight into whale shark (Rhincodon typus) movement patterns in the Western Indian Ocean, we deployed eight pop-up satellite tags at an aggregation site in the Arta Bay region of the Gulf of Tadjoura, Djibouti in the winter months of 2012, 2016 and 2017. Tags revealed movements ranging from local-scale around the Djibouti aggregation site, regional movements along the coastline of Somaliland, movements north into the Red Sea, and a large-scale (>1000 km) movement...

Temperature effect on polymerase fidelity

Yuan Xue, Ido Braslavsky & Stephen Quake
The discovery of extremophiles helped enable the development of groundbreaking technology such as polymerase chain reaction. Temperature variation is often an essential step of these technology platforms, but the effect of temperature on the error rate of polymerases from different origins is under-explored. We applied high-throughput sequencing to profile the error rates of DNA polymerases from psychrophilic, mesophilic, and thermophilic origins with single-molecule resolution. We found that reaction temperature substantially increases substitution and deletion error...

Ecological genomics of distinct bleaching tolerances among cryptic coral species

Noah Rose
Reef-building coral species are experiencing an unprecedented decline due to increasing frequency and intensity of marine heatwaves and associated bleaching-induced mortality. Closely related species of reef building corals from the Acropora hyacinthus species complex differ in heat tolerance and in their association with heat-tolerant symbionts, as well as growth rate, colony morphology and skeletal density. We used low-coverage full genome sequencing of 114 colonies monitored across the 2015 bleaching event in American Samoa to determine...

Complexity character scores for fossil and extant vascular plant reproductive structures

Andrew Leslie
Morphological diversity and complexity are notable features of multicellular life, although whether they evolve gradually or in early bursts is unclear. Vascular plant reproductive structures, such as flowers, are familiar examples of complicated morphology, and here we analyze changes in complexity over time using a simple approach based on the number of part types. We find that reproductive complexity increased in two pulses separated by nearly 250 million years of stasis, including an initial Devonian...

Economic evaluation of sea-level rise adaptation strongly influenced by hydrodynamic feedbacks: Dataset 2

Robert Griffin, Michelle Hummell, Katie Arkema & Anne Guerry
Coastal communities rely on levees and seawalls as critical protection against sea-level rise; in the U.S. alone, $300 billion in shoreline armoring costs are forecast by 2100. But despite the local flood risk reduction benefits, these structures can exacerbate flooding and associated damages along other parts of the shoreline—particularly in coastal bays and estuaries, where nearly 500 million people globally are at risk from sea-level rise. The magnitude and spatial distribution of the economic impact...

Economic evaluation of sea-level rise adaptation strongly influenced by hydrodynamic feedbacks: Dataset 1

Robert Griffin, Michelle Hummel, Katie Arkema & Anne Guerry
Coastal communities rely on levees and seawalls as critical protection against sea-level rise; in the U.S. alone, $300 billion in shoreline armoring costs are forecast by 2100. But despite the local flood risk reduction benefits, these structures can exacerbate flooding and associated damages along other parts of the shoreline—particularly in coastal bays and estuaries, where nearly 500 million people globally are at risk from sea-level rise. The magnitude and spatial distribution of the economic impact...

Dynamic plant-soil microbe interactions: the neglected effect of soil conditioning time

Po-Ju Ke, Peter Zee & Tadashi Fukami
Plant-soil feedbacks (PSF) may change in strength over the life of plant individuals as plants continue to modify the soil microbial community. However, the temporal variation in PSF is rarely quantified and its impacts on plant communities remain unknown. Using a chronosequence reconstructed from annual aerial photos of a coastal dune ecosystem, we characterized >20-year changes in soil microbial communities associated with individuals of the four dominant perennial species, one legume and three non-legume. We...

Data from: Scale-dependent effects of forest restoration on Neotropical fruit bats

J. Leighton Reid, Chase D. Mendenhall, Rakan A. Zahawi & Karen D. Holl
Neotropical fruit bats (family Phyllostomidae) facilitate forest regeneration on degraded lands by dispersing shrub and tree seeds. Accordingly, if fruit bats can be attracted to restoration sites, seed dispersal could be enhanced. We surveyed bat communities at 10 sites in southern Costa Rica to evaluate whether restoration treatments attracted more fruit bats if trees were planted on degraded farmlands in plantations or island configurations versus natural regeneration. We also compared the relative influence of tree...

Five year pediatric use of a digital wearable fitness device: lessons from a pilot case study

Kimayani Butte, Amir Bahmani, Atul Butte, Xiao Li & Michael Snyder
Objectives: Wearable fitness devices are increasingly used by the general population, with new applications being proposed and designed for healthy adults as well as adults with chronic diseases. Fewer, if any, studies of these devices have been conducted in healthy adolescents and teenagers, especially over a long period of time. The goal of this work was to document the successes and challenges involved in 5 years of a wearable fitness device use in a pediatric...

Public parks and the pandemic: how park usage has been affected by COVID-19 policies

Joel Abraham, Zoe Volenec, Alexander Becker & Andrew Dobson
Public parks serve an important societal function as recreational spaces for diverse communities of people, with well documented physical and mental health benefits. As such, parks may be crucial for how people have handled effects of the COVID-19 pandemic, particularly the increasingly limited recreational opportunities, widespread financial uncertainty, and consequent heightened anxiety. Despite the documented benefits of parks, however, many states have instituted park shutdown orders due to fears that public parks could facilitate SARS-CoV-2...

EcoTyper: a machine learning framework for large-scale identification of cell type-specific transcriptional states and cellular ecosystems

Bogdan-Alexandru Luca, Chloé Steen, Armon Azizi, Andrew Gentles, Arash Ash Alizadeh & Aaron Newman
EcoTyper is a machine learning framework for large-scale identification of cell type-specific transcriptional states and their co-association patterns from bulk, single-cell, and spatially resolved gene expression data. EcoTyper performs the following major steps: 1) In silico purification: This step enables imputation of cell type-specific gene expression profiles from bulk tissue transcriptomes, using CIBERSORTx (Newman et al., Nature Biotechnology 2019). 2) Cell state discovery: This step enables identification and quantitation of cell type-specific transcriptional states. 3)...

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,...

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...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text
  • Interactive Resource
  • Image
  • Journal Article
  • Software


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