48 Works

Data from: A trait-based approach to predict population genetic structure in bees

Margarita M. Lopez-Uribe, Shalene Jha & Antonella Soro
Understanding population genetic structure is key to developing predictions about species susceptibility to environmental change, such as habitat fragmentation and climate change. It has been theorized that life-history traits may constrain some species in their dispersal and lead to greater signatures of population genetic structure. In this study, we use a quantitative comparative approach to assess if patterns of population genetic structure in bees are driven by three key species-level life-history traits: body size, sociality,...

Data from: A homeotic shift late in development drives mimetic color variation in a bumble bee

Li Tian, Sarthok Rasique Rahman, Briana D. Ezray, Luca Franzini, James P. Strange, Patrick Lhomme & Heather M. Hines
Natural phenotypic radiations, with their high diversity and convergence, are well-suited for informing how genomic changes translate to natural phenotypic variation. New genomic tools enable discovery in such traditionally non-model systems. Here, we characterize the genomic basis of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a group that has undergone extensive convergence of setal color patterns as a result of Müllerian mimicry. In western North America, multiple species converge on local mimicry patterns...

Analyses of vertical wind profile data from the VORTEX-Southeast 2017 field campaign

P. Markowski
This dataset contains observations from the Collaborative Lower Atmospheric Mobile Profiling System (CLAMPS) and NOAA Air Resources Laboratory, Atmospheric Turbulence and Diffusion Division) micrometeorological towers that were analyzed in the Markowski et al. (2019) study. That study used CLAMPS Doppler lidar observations of near-surface vertical wind profiles, and NOAA tower observations of near-surface shear and vertical momentum fluxes, both of which were obtained during the spring 2017 Verification of the Origins of Rotation in Tornadoes...

Observational and modeled dataset for determination of urban emissions of CO2 using an atmospheric inversion technique, Davos, Switzerland, 2011-2012.

N.L. Miles, T. Lauvaux, S.J. Richardson, A. Deng & D. Stauffer
Anthropogenic emissions from urban areas represent 70% of the fossil fuel carbon emitted globally according to carbon emission inventories. The observational and model data archived here were used in the first operational system able to monitor, in near–real time, daily emission estimates, using a mesoscale atmospheric inversion framework over the city of Davos, Switzerland, before, during, and after the World Economic Forum 2012 Meeting (WEF-2012). Two instruments that continuously measured atmospheric mixing ratios of greenhouse...

Ensemble model output of North American atmospheric CO2 simulation (full WRF-chem output)

S. Feng, T. Lauvaux, K.J. Davis, K. Keller, R. Rayner, T. Oda, K. Gurney, Y. Zhou, C. Williams, A.E. Schuh, J. Liu & I. Baker
The uncertainty in biospheric carbon dioxide (CO2) flux estimates drives divergent projections of future climate and uncertainty in prescriptions for climate mitigation. The terrestrial carbon sink can be inferred from atmospheric CO2 observations with transport models via inversion methods. Regional CO2 flux estimates remain uncertain due to the mixture of uncertainties caused by transport models, prior estimates of biospheric fluxes, large-scale CO2 boundary inflow, the assumptions in the inversion process, and the limited density of...

Electrodynamic Levitation Diffusion Chamber Measurements of the Mass Growth of Heterogeneously-Nucleated Ice Crystals Grown from the Vapor

A. Harrison, A. Moyle, M. Hanson & J.Y. Harrington
This data set comprises individual time-series for ice crystals grown in an electrodynamic levitation diffusion chamber. Descriptions of the chamber and experiments can be found in Harrison et al. (2016). Experiments were conducted by freezing small (approximately 10 micrometer radius) droplets heterogeneously using the bionucleant Snomax. Frozen droplets were levitated in the diffusion chamber and grown in a constant temperature, pressure, and supersaturation environment. The voltage ratio needed to levitate the particle was recorded as...

Delivery of mesenchymal stem cells-derived extracellular vesicles with enriched miR-185 inhibits progression of OPMD

Lin Wang, Panpan Yin, Jiaqi Wang, Yuanyuan Wang, Zheng Sun, Yu Zhou & Xiaobing Guan
Oral leukoplakia is one of the most common oral potentially malignant disorders (OPMDs) and its malignant transformation to oral cancer is highly associated with chronic inflammation. Extracellular vesicles (EVs) or exosome-delivered microRNAs modulate inflammatory responses and alleviate irritations that predisposes to cancer. We previously reported that microRNA-185 (miR-185) was significantly decreased in the buccal tissue of patients with oral cancer. In this study, we utilized genetically modified mesenchymal stem cells (MSCs) derived EVs with high...

Archival data and code in support of uncertainty quantification of climate system properties using the MIT Earth System Model (MESM)

Chris Forest, Alex Libardoni, Andrei P. Sokolov & Erwan Monier
This archive provides the climate model outputs, observational data, and analysis codes that were used to quantify uncertainty in the climate system response properties of the MIT Earth System Model (MESM). Three papers (Libardoni et al. 2018a, 2018b, 2019) include results using these data and codes to provide conditional probability distributions of equilibrium climate sensitivity (ECS), the transient climate response (TCR), and the net radiative forcing by aerosols. The analysis codes are either written in...

Data from: Clonal diversity impacts coral cover in Acropora cervicornis thickets: potential relationships between density, growth and polymorphisms

Crawford Drury, Justin B. Greer, Iliana Baums, Brooke Gintert & Diego Lirman
As coral reefs decline, cryptic sources of resistance and resilience to stress may be increasingly important for the persistence of these communities. Among these sources, inter‐ and intraspecific diversity remain understudied on coral reefs but extensively impact a variety of traits in other ecosystems. We use a combination of field and sequencing data at two sites in Florida and two in the Dominican Republic to examine clonal diversity and genetic differentiation of high‐ and low‐density...

Data from: Physician champions’ perspectives and practices on electronic health records implementation: challenges and strategies

Xinning Gui, Yunan Chen, Xiaomu Zhou, Tera L. Reynolds, Kai Zheng & David A. Hanauer
Objective: Physician champions are “boots on the ground” physician leaders who facilitate the implementation of, and transition to, new health information technology (HIT) systems within an organization. They are commonly cited as key personnel in HIT implementations, yet little research has focused on their practices and perspectives. Methods: We addressed this research gap through a qualitative study of physician champions that aimed to capture their challenges and strategies during a large-scale HIT implementation. Email interviews...

Radiolysis of macromolecular organic material in Mars-relevant mineral matrices

A.C. Fox, J.L. Eigenbrode & C. Herrera
The fate of organic material on Mars after deposition is crucial to interpreting the source of these molecules. Previous work has addressed how various organic compounds at millimeter depths in sediments respond to ultraviolet (UV) radiation. In contrast, this study addressed how high-energy particle radiation (200-MeV protons, simulating the effect of galactic cosmic rays at depths of < 4-5 cm) influences organic macromolecules in sediments. Specifically, we report the generation of organic-acid radiolysis products after...

Tower-based atmospheric CO2 mole fractions (raw, uncalibrated) measured as part of the National Carbon Program’s Mid Continent Intensive, U.S. Upper Midwest, 2007-2009

N.L. Miles, S.J. Richardson, B.J. Haupt & K.J. Davis
A total of nine communication tower-based CO2 sensors were located within a 500 x 800 km2 area within the Mid Continental Intensive (MCI) study region in the U.S. Upper Midwest from May 2007 through November 2009. With the goal of oversampling the MCI region, The Pennsylvania State University deployed instruments at five towers: Centerville (Iowa), Galesville (Wisconsin), Kewanee (Illinois), Mead (Nebraska), and Round Lake (Minnesota). Here we publish the raw, uncalibrated data from these five...

Cavity ring-down spectroscopic measurements of CO2 mole fraction in State College, Pennsylvania, 2017-2018.

S.J. Richardson, N.L. Miles, T. Lauvaux, B.J. Haupt & K.J. Davis
Carbon dioxide (CO2) mole fractions were measured at three locations near State College, Pennsylvania, using cavity ring-down spectrometers (Picarro, Inc.). This dataset includes raw data and hourly averages. The instruments were calibrated via four NOAA tertiary tanks prior to deployment, but no field calibrations were applied. The air samples were not dried. The locations of the measurements were Rock Springs (40°43'15.3"N 77°55'54.1"W, 10 m AGL), Walker Building roof (40°47'36.1"N 77°52'02.0"W, 30 m AGL), and Houserville...

Single-cell NDIR-based measurements of atmospheric C02 mole fractions measured at Ameriflux towers, 2006 - 2016

N.L. Miles, S.J. Richardson, B.J. Haupt, K.J. Davis, B. Stephens & A. Watt
Data collected via relatively low-cost, high-precision CO2 mixing ratio measurement systems, developed in collaboration with NCAR-ATD, are reported here. These data were collected to support inverse analyses of the terrestrial carbon balance at regional to continental scales. The systems use LICOR-820 non-dispersive infrared analyzers rather than the more expensive, but lower noise LICOR-6262 or LICOR-7000, since fast time response is not required for this application and the noise of the LICOR-820 can be reduced sufficiently...

Overfishing and the ecological impacts of extirpating large parrotfish from Caribbean coral reefs

Andrew Shantz, Mark Ladd & Deron Burkepile
The unique traits of large animals often allow them to fulfill functional roles in ecosystems that small animals cannot. However, large animals are also at greater risk from human activities. Thus, it is critical to understand how losing large animals impacts ecosystem function. In the oceans, selective fishing for large animals alters the demographics and size-structure of numerous species. While the community-wide impacts of losing large animals is a major theme in terrestrial research, the...

Tower footprints for the Indianapolis Flux Experiment network (2012-2015)

T. Lauvaux, A. Deng, N.L. Miles, S.J. Richardson & K. Davis
Tower footprints represent the surface area that influenced an atmospheric mixing ratio observation measured at one of the 13 tower locations of the INFLUX network (https://sites.psu.edu/influx/site-information/). These footprints were generated to map in space and time the sensitivity of any given hourly atmospheric observation sampled between September 2012 to September 2015 by the network. The footprints were created by coupling the Lagrangian Particle Dispersion Model (LPDM) described by Uliasz [1994] to the WRF-FDDA modeling system...

Data from: Cross-boundary human impacts compromise the Serengeti-Mara ecosystem

Michiel P. Veldhuis, Mark E. Ritchie, Joseph O. Ogutu, Thomas A. Morrison, Colin M. Beale, Anna B. Estes, William Mwakilema, Gordon O. Ojwang, Catherine L. Parr, James Probert, Patrick W. Wargute, J. Grant C. Hopcraft & Han Olff
Protected areas provide major benefits for humans in the form of ecosystem services, but landscape degradation by human activity at their edges may compromise their ecological functioning. Using multiple lines of evidence from 40 years of research in the Serengeti-Mara ecosystem, we find that such edge degradation has effectively “squeezed” wildlife into the core protected area and has altered the ecosystem’s dynamics even within this 40,000-square-kilometer ecosystem. This spatial cascade reduced resilience in the core...

Substantial genetic divergence and lack of recent gene flow support cryptic speciation in a colour polymorphic bumble bee (Bombus bifarius) species complex

Guillaume Ghisbain, Jeffrey D. Lozier, Sarthok Rasique Rahman, Briana D. Ezray, Li Tian, Jonah M. Ulmer, Sam D. Heraghty, James P. Strange, Pierre Rasmont & Heather M. Hines
Phenotypic polymorphism can constitute an inherent challenge for species delimitation. This issue is exemplified in bumble bees (Bombus), where species can exhibit high colour variation across their range, but otherwise exhibit little morphological variation to distinguish them from close relatives. We examine the species status of one of the most abundant North American bumble bees, Bombus bifarius Cresson, which historically was comprised of two major taxa, bifarius s.s. (sensu stricto) and nearcticus. These sublineages are...

Gridded influence functions for NOAA tall towers for January 2010

D. Wesloh & T. Lauvaux
The data provides influence functions, also called tower concentration footprints, for nine towers in the NOAA Greenhouse Gas tall tower reference network. The influence functions are five dimensional arrays: the first two correspond to the mole fraction observations, the third to the time before the observation, and the last two to the spatial extent of the fluxes. Coordinates and transform parameters are provided to express the spatial locations of the fluxes in latitude and longitude...

Island Rainfall Enhancement in the Maritime Continent

J.H. Ruppert & X. Chen
The hypothesis that the islands of the Maritime Continent (MC) enhance total rainfall and time-mean upward motion is tested using a convection-permitting regional model. Sensitivity experiments with the islands removed greatly diminish both rainfall and upward motion, supporting the hypothesis. We examine the individual factors in this enhancement, isolating the impacts of the diurnal cycle from those of basic-state (i.e., constant) forcing of orography and the land surface. We find that the basic-state forcing by...

Enhanced and unified anatomical labeling for a common mouse brain atlas

Uree Chon, Daniel Vanselow, Keith Cheng & Yongsoo Kim
Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, here we adopt the FP labels into the CCF to merge two labels in...

Data from: The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections

Nina Wale, Matthew J. Jones, Derek G. Sim, Andrew F. Read & Aaron A. King
Hosts defend themselves against pathogens by mounting an immune response. Fully understanding the immune response as a driver of host disease and pathogen evolution requires a quantitative account of its impact on parasite population dynamics. Here, we use a data-driven modeling approach to quantify the birth and death processes underlying the dynamics of infections of the rodent malaria parasite, Plasmodium chabaudi, and the red blood cells (RBCs) it targets. We decompose the immune response into...

Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits

Gerrit Angst, Kevin E. Mueller, David M. Eissenstat, Susan Trumbore, Katherine H. Freeman, Sarah E. Hobbie, Jon Chorover, Jacek Oleksyn, Peter B. Reich & Carsten W. Mueller
Rising atmospheric CO2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40‐year‐old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and...

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Manure decreases herbivore performance but increases early-season damage on corn in the greenhouse and field

E. Rown & J.F. Tooker
Many farmers use manure as an alternative to inorganic fertilizer. Previous research has shown that manure can decrease plant susceptibility to herbivores, but the mechanisms remain unclear. To determine how manure affects herbivore performance in a greenhouse setting, we fertilized corn with stacked cow manure or an equivalent amount of NPK fertilizer and measured caterpillar development, plant nutritional content, and defenses. After four weeks of growth, we allowed fall armyworm (Spodoptera frugiperda) or black cutworm...

Registration Year

  • 2019

Resource Types

  • Dataset


  • Pennsylvania State University
  • University of Cambridge
  • Shanghai University of Sport
  • Sun Yat-sen University
  • Zhejiang University
  • The University of Texas at Austin
  • University of Michigan–Ann Arbor
  • Jilin University
  • Xuan Wu Hospital of the Capital Medical University
  • Xiamen University