69 Works

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...

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...

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.

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...

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...

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...

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

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...

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...

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...

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...

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,...

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...

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: 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...

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 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.

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 =...

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...

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...

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...

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...

Registration Year

  • 2021
    69

Resource Types

  • Dataset
    57
  • Text
    9
  • Image
    1
  • Interactive Resource
    1
  • Software
    1

Affiliations

  • Stanford University
    69
  • University of Pennsylvania
    3
  • The University of Texas at Arlington
    3
  • University of California, Santa Barbara
    3
  • University of California, Santa Cruz
    3
  • Princeton University
    2
  • University of Chicago
    2
  • Lawrence Berkeley National Laboratory
    2
  • Harvard University
    2
  • Swiss Federal Institute of Technology in Zurich
    2