84 Works

OpenSense: Validation of IMU-based estimates of kinematics over long durations

Johanna O'Day, Scott Delp, Mazen Al Borno, Vanessa Ibarra, James Dunne, Ajay Seth, Ayman Habib, Carmichael Ong, Jennifer Hicks & Scott Uhlrich
Here we provide the dataset for validation of OpenSense, an open-source toolbox for Inertial-Measurement-Unit-based measurement of lower extremity kinematics over long durations (10 minutes). We computed IMU-based estimates of kinematics using sensor fusion and an inverse kinematics approach with a constrained biomechanical model. We measured kinematics for 11 subjects as they performed two 10-minute trials: (1) walking and turning, and (2) a repeated sequence of varied lower-extremity movements (sitting, standing, stair-climbing, side-stepping, walking, running). Subjects...

Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis

Nalin Ratnayeke, Mingyu Chung & Tobias Meyer
A fundamental concept in eukaryotic DNA replication is the temporal separation of G1 origin licensing from S phase origin firing. Re-replication and genome instability ensue if licensing occurs after DNA synthesis has started. In humans and other vertebrates, the E3 ubiquitin ligase CRL4Cdt2 starts to degrade the licensing factor Cdt1 after origins fire, raising the question of how cells prevent re-replication in early S phase. Here, using quantitative microscopy, we show that Cdt1 inhibits DNA...

Data for: Successful management of invasive rats across a fragmented landscape

Erin Rankin, Sarah Barney, Devin Leopold, Kainana Francisco, David Flaspohler, Tad Fukami, Christian Giardina, Daniel Gruner, Jessie Knowlton & William Pitt
This dataset is from the manuscript "Successful management of invasive rats across a fragmented landscape" and provides the details on snap trap and tracking card data in a broadscale rat removal effort 2011-2015 in the Upper Waiakea Forest Reserve on the Island of Hawai‘i. It describes the successful trapping efforts as well as long term tracking data, which allow us to describe patterns of habitat use of non-native vertebrate species in these naturally fragmented forests...

Data for: Imaging the short-lived hydroxyl-hydronium pair in ionized liquid water

Ming-Fu Lin, Narendra Singh, Shujia Liang, Mianzhen Mo, Joao Pedro Figueira Nunes, Kathryn Ledbetter, Jie Yang, Michael Kozina, Stephen Weathersby, Xiaozhe Shen, Amy Cordones, Thomas Wolf, Sri Chaitanya Das Pemmaraju, Matthias Ihme & Xijie Wang
The radiolysis of water is ubiquitous in nature and plays a critical role in numerous biochemical and technological applications. Although the elementary reaction pathways for the ionized water have been studied, the short-lived intermediate complex and structural dynamic response after the proton transfer reaction remain poorly understood. Using liquid-phase ultrafast electron diffraction technique to measure the intermolecular O··O and O··H bonds, we captured the short-lived radical-cation complex OH(H3O+) that was formed within 140 femtoseconds through...

Macrophage-derived IL-6 trans-signaling as a novel target in the pathogenesis of bronchopulmonary dysplasia (RNA-seq-P14-HYXvsNOX)

Dharmesh Hirani & Cristina Alvira
Rationale: Premature infants exposed to oxygen are at risk for bronchopulmonary dysplasia (BPD), which is characterized by lung growth arrest. Inflammation is important, but the mechanisms remain elusive. Here, we investigated inflammatory pathways and therapeutic targets in severe clinical and experimental BPD. Methods and Results: First, transcriptomic analysis with in-silico cellular deconvolution identified a lung-intrinsic M1-like-driven cytokine pattern in newborn mice after hyperoxia. These findings were confirmed by gene expression of macrophage-regulating chemokines (Ccl2, Ccl7,...

Cell type labels for all clustering and normalization combinations compared for CODEX multiplexed imaging

John Hickey
We performed CODEX (co-detection by indexing) multiplexed imaging on four sections of the human colon (ascending, transverse, descending, and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies. Subsequently images underwent standard CODEX image processing (tile stitching, drift compensation, cycle concatenation, background subtraction, deconvolution, and determination of best focal plane), and single cell segmentation. Output of this process was a dataframe of nearly 130,000 cells with fluorescence values quantified from each marker. We used this dataframe...

Growth rates of populations evolved and assayed at two temperatures for 6500 generations

Jason Tarkington & Rebecca Zufall
Evolutionary biologists have long sought to understand what factors affect the repeatability of adaptive outcomes. To better understand the role of temperature in determining the repeatability of adaptive trajectories, we evolved populations of different genotypes of the ciliate Tetrahymena thermophila at low and high temperatures and followed changes in growth rate over 6,500 generations. As expected, growth rate increased with a decelerating rate for all populations; however, there were differences in the patterns of evolution...

Projected climate risk of aquatic food system benefits

Michelle Tigchelaar, William Cheung, Essam Mohammed, Michael Phillips, Hanna Payne, Elizabeth Selig, Colette Wabnitz, Muhammed Oyinlola, Thomas Frölicher, Jessica Gephart, Christopher Golden, Edward Allison, Abigail Bennett, Ling Cao, Jessica Fanzo, Benjamin Halpern, Fiorenza Micheli, Rosamond Naylor, Rashid Sumaila, Alessandro Tagliabue & Max Troell
Aquatic foods from marine and freshwater systems are critical to the nutrition, health, livelihoods, economies and culture of billions of people worldwide – but climate-related hazards may compromise their ability to provide these benefits. This analysis estimates national-level aquatic food system climate risk using a fuzzy logic modeling approach that connects climate hazards impacting marine and freshwater capture fisheries and aquaculture to their contributions to sustainable food system outcomes, and vulnerability to losing those contributions....

Quantum mechanical double slit for molecular scattering

Haowen Zhou, William E. Perreault, Nandini Mukherjee & Richard N. Zare
Interference observed in a double-slit experiment most conclusively demonstrates the wave properties of particles. We construct a quantum mechanical double-slit interferometer by rovibrationally exciting D2 (v=2, j=2) molecules in a biaxial state using Stark-induced adiabatic Raman passage. In D2(v=2, j=2)→D2(v=2, j'=0) rotational relaxation via a cold collision with ground state He, the entangled bond axis orientations in the biaxial state act as two slits generating two indistinguishable quantum mechanical pathways connecting initial and final states...

Land use impacts on parasitic infection: A cross-sectional epidemiological study on the role of irrigated agriculture in schistosome infection in a dammed landscape

Andrea Lund, David Rehkopf, Susanne Sokolow, M. Moustapha Sam, Nicolas Jouanard, Anne-Marie Schacht, Simon Senghor, Assane Fall, Gilles Riveau, Giulio De Leo & David Lopez-Carr
Background: Water resources development promotes agricultural expansion and food security. But are these benefits offset by increased infectious disease risk? Dam construction on the Senegal River in 1986 was followed by agricultural expansion and increased transmission of human schistosomes. Yet the mechanisms linking these processes at the individual and household levels remain unclear. We investigated the association between household land use and schistosome infection in children. Methods: We analyzed cross-sectional household survey data (n =...

The influence of climate and paleoclimate on distributions of global conifer clades depends on geographic range size

Mekala Sundaram & Andrew Leslie
Aim: We investigate how plant distributions are shaped by current and paleoclimate regimes. We specifically use global conifer biodiversity to test if paleoclimatic signatures are stronger in range-restricted taxa compared to widespread taxa. Location: Global Taxon: Coniferales Methods: We combine global geographic occurrences for 606 conifer species and 69 conifer genera with climate information (modern day and paleoclimate) to examine predictors of current conifer distribution. We test how climate predicts richness of range-restricted taxa and...

Contrasting fungal responses to wildfire across different ecosystem types

Gabriel Smith, Lucy Edy & Kabir Peay
We took topsoil samples in burned and unburned areas across two California ecosystem types (Sonoma, California, United States) with differing fire ecologies in the immediate aftermath of a damaging wildfire in 2017. From our soil samples, we extracted DNA, amplified and sequenced fungal communities, and also measured chemistry (C%, N% and pH). Soil fungal communities of fire‐dependent oak woodlands differ from those of neighbouring mixed evergreen forests. The latter are more strongly altered compositionally by...

Data from: Reverse diel vertical movements of oceanic manta rays off the northern coast of Peru and implications for conservation

Samantha Andrzejaczek, Robert Schallert, Kerstin Forsberg, Natalie Arnoldi, Mariano Cabanillas, Wilmer Purizaca & Barbara Block
An understanding of the vertical movements of elasmobranchs across their range is crucial to defining critical habitat use, its overlap with anthropogenic activities, and subsequently managing such interactions. In this study, satellite telemetry was used to investigate the vertical habitat use of three oceanic manta rays (Mobula birostris) tagged on the northern coast of Peru. All three oceanic mantas exhibited patterns of reverse diel vertical migration, where vertical movements were significantly deeper at night than...

Data from: Gene expression plasticity and desert adaptation in house mice

Noelle Bittner, Katya Mack & Michael Nachman
Understanding how organisms adapt to new environments is a key problem in evolution, yet it remains unclear whether phenotypic plasticity generally facilitates or hinders this process. Here we studied evolved and plastic responses to water-stress in lab-born descendants of wild house mice (Mus musculus domesticus) collected from desert and non-desert environments and measured gene expression and organismal phenotypes under control and water-stressed conditions. After many generations in the lab, desert mice consumed significantly less water...

Decrypting cryptic crosswords: Semantically complex wordplay puzzles as a target for NLP

Joshua Rozner, Christopher Potts & Kyle Mahowald
Cryptic crosswords, the dominant crossword variety in the UK, are a promising target for advancing NLP systems that seek to process semantically complex, highly compositional language. Cryptic clues read like fluent natural language but are adversarially composed of two parts: a definition and a wordplay cipher requiring character-level manipulations. Expert humans use creative intelligence to solve cryptics, flexibly combining linguistic, world, and domain knowledge. In this paper, we make two main contributions. First, we present...

Drainage Canals in Southeast Asian Peatland

Nathan Dadap, Alison M Hoyt, Alexander R Cobb, Doruk Oner, Mateusz Kozinski, Pascal V Fua, Krishna Rao, Charles F Harvey & Alexandra G Konings
These images depict drainage canals and roads in peatlands in Borneo, Sumatra, and Peninsular Malaysia at 5 meter resolution. These canals were detected from July-September 2017 Planet Basemaps satellite imagery using a convolutional neural network. Please contact Nathan Dadap (ndadap@stanford.edu) with any questions.

Data from: Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila

Heather E. Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas JS Merritt, John E. Pool, Katherine O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov & Bernard Kim
To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20 widely dispersed populations. We identified parallel seasonal allele frequency shifts across North America and Europe, demonstrating that seasonal adaptation is a general phenomenon of temperate fly populations. Seasonally fluctuating polymorphisms are enriched at...

Data: Avian cultural services peak in tropical wet forests

Alejandra Echeverri, Daniel Karp, Luke Frishkoff, Jaya Krishnan, Robin Naidoo, Jiaying Zhao, Jim Zook & Kai Chan
The current biodiversity crisis involves major shifts in biological communities at local and regional scales. The consequences for Earth’s life-support systems are increasingly well-studied, but knowledge of how community shifts affect cultural services associated with wildlife lags behind. We integrated bird census data (three years across 150 point-count locations) with questionnaire surveys (>400 people) to evaluate changes in culturally important species across climate and land-use gradients in Costa Rica. For farmers, urbanites, and birdwatchers alike,...

High-resolution mapping of the period landscape reveals polymorphism in cell cycle frequency tuning

Zhengda Li, Shiyuan Wang, Meng Sun, Minjun Jin, Daniel Khain & Qiong Yang
Biological oscillators adapt to environmental changes with widely tunable frequencies, a property theoretical studies attributed to positive feedbacks. However, no experiments have tested this theory. Here, we created synthetic cells to independently tune the frequency and feedback strength of a cell-cycle oscillator, enabling continuous mapping of period landscape in response to network perturbations. We found that although inhibiting positive feedback of cyclin-dependent kinase (Cdk1) reduces the tunability, the reduction is not as significant as theoretically...

Transmission electron micrographs of AMPAR containing vesicles

John Peters, Jeremy Leitz, Juan Oses-Prieto, Alma Burlingame & Axel Brunger
Here we present transmission electron micrographs of AMPAR containing vesicles. AMPAR containing vesicles were purified from whole mouse brain via immunoisolation, applied to a copper electron microscopy grid, and stained with uranyl acetate. Vesicles were imaged at a range of magnifications from 4,000 to 15,000. Included in these data are immunoelectron micrographs where we probed for synaptobrevin-2, synaptophysin-1, GluA2, and GluA3.

Spore size data for free-sporing extant and fossil plants

Andrew Leslie
The evolution of different spore size classes, or heterospory, is a fundamental reproductive innovation in land plants. The appearance of heterospory is particularly notable during the Devonian, when most known origins of the trait occur. Here we provide a perspective on the evolution of heterospory during this time interval, particularly from the late Early Devonian through the Middle Devonian (Emsian to Givetian stages; 408-383 Ma), which shows an unusually high concentration of heterospory origins. We...

Transcriptional acclimation and spatial differentiation characterize drought response by the ectomycorrhizal fungus Suillus pungens

Kabir Peay
Changing precipitation regimes are a challenge for forest health under future climate scenarios. If belowground symbionts can acclimate to changing moisture regimes it may buffer forest trees from these changes. In this study we exposed the ectomycorrhizal fungus Suillus pungens to acute and chronic drought stress and used RNASeq of both ectomycorrhizal roots and extraradical mycelium to gauge the magnitude of stress, identify key genes involved in drought response, and gauge potential ecosystem consequences of...

Predictability and parallelism in the contemporary evolution of hybrid genomes

Quinn K. Langdon, Daniel L. Powell, Bernard Kim, Shreya M. Banerjee, Cheyenne Payne, Tristram O. Dodge, Ben Moran, Paola Fascinetto-Zago & Molly Schumer
Hybridization between species is widespread across the tree of life. As a result, many species, including our own, harbor regions of their genome derived from hybridization. Despite the recognition that this process is widespread, we understand little about how the genome stabilizes following hybridization, and whether the mechanisms driving this stabilization tend to be shared across species. Here, we dissect the drivers of variation in local ancestry across the genome in replicated hybridization events between...

Seasonal particle responses to near-bed shear stress in a shallow, wave- and current-driven environment

Grace Chang, Galen Egan, Frank Spada, Craig Jones, Stephen Monismith & Oliver Fringer
Novel analysis of in-situ acoustic and optical data collected in a shallow, wave- and current-driven environment enabled determination of: (1) particle characteristics that were most affected by near-bed physical forcing over seasonal scales, and (2) characteristic shear stress, tchar, at which the rate of change to particle characteristics was most pronounced. Near-bed forcing and particle responses varied by season. Results indicated that moderate tchar values of 0.125 Pa drove changes in particle composition during summer....

Phenotypic plasticity in plant defense across life stages: inducibility, transgenerational induction, and transgenerational priming in wild radish

Mar Sobral & Rodolfo Dirzo
As they develop, many plants deploy shifts in anti-herbivore defense allocation due to changing costs and benefits of their defensive traits. Plant defenses are known to be primed or directly induced by herbivore damage within generations, and across generations by long-lasting epigenetic mechanisms. However, little is known about the ontogenetic trajectories of epigenetically inducible defensive traits across generations and their consequences. To help fill this knowledge gap, we conducted a multigenerational experiment to determine whether...

Registration Year

  • 2021
    84

Resource Types

  • Dataset
    84

Affiliations

  • Stanford University
    84
  • University of California, Santa Barbara
    4
  • University of Washington
    3
  • The University of Texas at Arlington
    3
  • University of California, Berkeley
    3
  • University of Pennsylvania
    2
  • The University of Texas at Austin
    2
  • Princeton University
    2
  • University of Georgia
    2
  • Johns Hopkins University
    2