87 Works

Data from: Mesozoic cupules and the origin of the angiosperm second integument

Gongle Shi, Fabiany Herrera, Patrick Herendeen, Elizabeth Clark & Peter Crane
This dataset is embargoed. Please contact Gongle Shi with any questions.

The distribution of Chrysaora melanaster and hydrographical conditions in the southeastern Bering Sea in 2018

Hongsheng Bi & Mary Beth Decker
Scyphozoan jellyfish are conspicuous components of marine ecosystems, which during a bloom, can impact food web structure and economically important fisheries. Jellyfish biomass in the southeastern Bering Sea (SEBS) is primarily comprised of Chrysaora melanaster and has varied widely over the past four decades, yet the underlying causes of these biomass fluctuations remain unclear. The present study investigated the spatial and seasonal dynamics of C. melanaster along the Alaska Peninsula in the SEBS using an...

Ericoid mycorrhizal shrubs alter the relationship between tree mycorrhizal dominance and soil carbon and nitrogen

Elisabeth Ward, Marlyse Duguid, Sara Kuebbing, James Lendemer, & Mark Bradford
1. Plant-fungal associations strongly influence forest carbon and nitrogen cycling. The prevailing framework for understanding these relationships is through the relative abundance of arbuscular (AM) versus ectomycorrhizal (EcM) trees. Ericoid mycorrhizal (ErM) shrubs are also common in forests and interactions between co-occurring ErM shrubs and AM and EcM trees could shift soil biogeochemical responses. Here we test hypotheses that the effects of ErM shrubs on soil carbon and nitrogen either extend or are redundant with...

Growing Computational Thinking and Literacy for Formerly Incarcerated Students: A Pathway to STEM careers

Larry Gladney
This is an REU pilot project proposal. This REU site will provide 6 formerly incarcerated (FI) undergraduates training in computational thinking (ct to distinguish from CT, the state abbreviation) and the opportunity to apply their understandings to Yale faculty research problems in STEM. A ct course will be offered in the mornings of the 10-week program. In the afternoons, each student will work on a computational research project they selected from faculty offerings. Students will...

Attention recruits frontal cortex in human infants

Cameron T Ellis, Lena J Skalaban, Tristan S Yates & Nicholas B Turk-Browne
Young infants learn about the world by overtly shifting their attention to perceptually salient events. In adults, attention recruits several brain regions spanning the frontal and parietal lobes. However, it is unclear whether these regions are sufficiently mature in infancy to support attention and, more generally, how infant attention is supported by the brain. We used event-related fMRI in 24 sessions from 20 awake behaving infants 3–12 months old while they performed a child-friendly attentional...

Weak interactions between strong interactors in an old-field ecosystem: Control of nitrogen cycling by coupled herbivores and detritivores

Robert Buchkowski & Oswald Schmitz
Interactions between herbivores and detritivores are common in greenhouse and laboratory experiments. Such interactions are thought to cause feedbacks in real ecosystems where the combined actions of these animals create either high or low nutrient cycling rates. There is limited evidence from factorial field experiments to support these expectations. We present the results of a three-year experiment wherein we factorially manipulated grasshopper herbivores and earthworm detritivores in an old-field ecosystem and tested for significant interaction...

Cloud-resolving modelling data from Fedorov et al. (2019)

Josh Studholme
Here we investigate tropical cyclogenesis in warm climates, focusing on the effect of reduced equator-to-pole temperature gradient relevant to past equable climates and, potentially, to future climate change. Using a cloud-system resolving model that explicitly represents moist convection, we conduct idealized experiments on a zonally periodic equatorial β-plane stretching from nearly pole-to-pole and covering roughly one-fifth of Earth’s circumference. To improve the representation of tropical cyclogenesis and mean climate at a horizontal resolution that would...

Data from: Functional attractors in microbial community assembly

Sylvie Estrela, Jean Vila, Nanxi Lu, Djordje Bajic, Maria Rebolleda-Gomez, Chang-Yu Chang, Josh Goldford, Alicia Sanchez-Gorostiaga & Alvaro Sanchez
For microbiome biology to become a more predictive science, we must identify which descriptive features of microbial communities are reproducible and predictable, which are not, and why. We address this question by experimentally studying parallelism and convergence in microbial community assembly in replicate glucose-limited habitats. Here, we show that the previously observed family-level convergence in these habitats reflects a reproducible metabolic organization, where the ratio of the dominant metabolic groups can be explained from a...

Introgression and species delimitation in the longear sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)

Daemin Kim, Bruce Bauer & Thomas Near
Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world’s most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, L. megalotis and L. peltastes, in the L. megalotis complex. Instead, evidence from...

Ecological opportunity from innnovation, not islands, drove the Anole lizard adaptive radiation

Edward Burress
Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists (‘ecomorphs’) evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in...

Supplementary data and code for ‘Oscillatory Spatiotemporal Signal Detection in Climate Studies: A Multiple-Taper Spectral Domain Approach’ (Mann and Park 1999)

M.E. Mann & J. Park
This chapter introduces a methodology for signal detection and reconstruction of irregular spatiotemporal oscillatory signals—the multiple-taper spectrum estimation method (MTM)–singular-value decomposition (SVD) methodology. This methodology is offered as an alternative technique which avoids most of the problems encountered in traditional techniques and provides an efficient exploratory method for climate signal detection. The associated signal-detection parameter—the local fractional variance spectrum (LFV) spectrum—yields the correct null distribution for a very general class of spatiotemporal climate noise processes...

Ocean and ice spin-up data for role of surface gravity waves in aquaplanet ocean climates

Joshua Studholme, Margarita Markina & Sergey Gulev
This data corresponds to the runs analysed in the manscript: Role of Surface Gravity Waves in Aquaplanet Ocean Climates (JAMES, 2021). In this work, we present a set of idealised numerical experiments that demonstrate the thermodynamic and dynamic implications of surface gravity waves for the oceanic climate of an aquaplanet. We study the impact of accounting for modulations by such waves upon air-sea momentum fluxes, Langmuir circulation and the Stokes-Coriolis force. This dataset is made...

Varying impacts of logging frequency on tree communities and carbon storage across evergreen and deciduous tropical forests in the Andaman Islands, India

Akshay Surendra, Anand Osuri & Jayashree Ratnam
The majority of Earth’s tropical forests have been selectively logged; some on repeated occasions. Selective logging is known to affect forest structure, composition and function in various ways, but how such effects vary with logging frequency and across forest types remains unclear. In the Andaman Archipelago in India, we examined adult and pole-sized trees in baseline (unlogged since 1990s), once-logged (logged between 2007 and 2014) and twice-logged (logged in early 1990s and between 2007 and...

Ultraconserved elements data for Amarsipus and Pelagiaria

Richard Harrington, Matt Friedman, Masaki Miya, Thomas Near & Matthew Campbell
Amarsipus carlsbergi is a rare mesopelagic fish distributed in the Indian and Pacific Oceans, and is the only species classified in the family Amarsipidae. Since its description in 1969, phylogenetic hypotheses have varied regarding its relationship with other percomorph lineages, but most have indicated a close relationship with the traditional suborder Stromateoidei. Molecular phylogenies place families previously classified in Stromateoidei within a diverse clade– Pelagiaria– that includes fishes such as tunas, cutlassfishes, and pomfrets. A...

Structure Here, Bias There: Hierarchical Generalization by Jointly Learning Syntactic Transformations

Karl Mulligan, Robert Frank & Tal Linzen

Comparing methods of tree-construction across mildly context-sensitive formalisms

Tim Hunter & Robert Frank

An unanticipated role for sphingosine kinase-2 in bone and in the anabolic effect of parathyroid hormone: Supplementary figures

Joanne Walker, Gang-Qing Yao, Edwin Siu, Meiling Zhu, Christine Simpson & Karl Insogna
Sphingosine-1-phosphate (S1P) is an anabolic clastokine. SPHK is the rate-limiting enzyme in S1P production and has two isoforms. To evaluate the roles of SPHK1 and SPHK2 in bone, we examined the skeletal phenotype of mice with selective deletion of SPHK1 in osteoclasts (SPHK1-Oc-/-) and mice in which the SPHK2 gene was deleted in all tissues (SPHK2-/-). SPHK1-Oc-/- had normal bone mass. By contrast, SPHK2-/- female mice had a 14% lower spinal BMD (p<0.01) and males...

Compartmentalization of cerebrospinal fluid inflammation across the spectrum of HIV infection

Richard Price, Magnus Gisslen, Sheila Keating, Serena Spudich, Victor Arechiga, Sophie Stephenson, Henrik Zetterberg, Clara Di Germanio, Kaj Blennow, Lars Hagberg, Philip Norris, Julia Peterson, Barbara Shacklett & Constantin Yiannoutsos
Objective: To characterize the evolution of central nervous system (CNS) inflammation in HIV-1 infection applying a panel of cerebrospinal fluid (CSF) inflammatory biomarkers to grouped subjects representing a broad spectrum of systemic HIV-1 immune suppression, CNS injury and viral control. Methods: This is a cross-sectional analysis of archived CSF and blood samples, assessing concentrations of 10 functionally diverse soluble inflammatory biomarkers by immunoassays in 143 HIV-1-infected subjects divided into 8 groups: untreated primary HIV-1 infection...

Data from: Nutrient dominance governs the assembly of microbial communities in mixed nutrient environments

Sylvie Estrela, Alicia Sanchez-Gorostiaga, Jean Vila & Alvaro Sanchez
A major open question in microbial community ecology is whether we can predict how the components of a diet collectively determine the taxonomic composition of microbial communities. Motivated by this challenge, we investigate whether communities assembled in pairs of nutrients can be predicted from those assembled in every single nutrient alone. We first find that although the null, naturally additive model generally predicts well the family-level community composition, there exist systematic deviations from the additive...

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...

An objective-based prioritization approach to support trophic complexity through ecological restoration

Emma Ladouceur, Jennifer McGowan, Patrick Huber, Hugh Possingham, Davide Scridel, Roel Van Klink, Peter Poschlod, Hans Cornelissen, Costantino Bonomi & Borja Jiménez-Alfaro
1. Reassembling ecological communities and rebuilding habitats through active restoration treatments requires curating the selection of plant species to use in seeding and planting mixes. Ideally, these mixes should be assembled based on attributes that support ecosystem function and services, promote plant and animal species interactions and ecological networks in restoration while balancing project constraints. Despite these critical considerations, it is common for species mixes to be selected opportunistically. Reframing the selection of seed mixes...

Retinotopic organization of visual cortex in human infants

Cameron Ellis, Tristan Yates, Lena Skalaban, Vikranth Bejjanki, Michael Arcaro & Nicholas Turk-Browne
Vision develops rapidly during infancy, yet how visual cortex is organized during this period is unclear. In particular, it is unknown whether functional maps that organize the mature adult visual cortex are present in the infant striate and extrastriate cortex. Here we test the functional maturity of infant visual cortex by performing retinotopic mapping with fMRI. Infants aged 5–23 months had retinotopic maps, with alternating preferences for vertical and horizontal meridians indicative of area boundaries...

Monthly pCO2, gas transfer velocity and CO2 efflux rate in global streams and rivers (the GRADES river networks)

Shaoda Liu
The datasets contain monthly partial pressure of dissolved CO2 (pCO2, µatm), gas transfer velocity (k, m d-1), and CO2 efflux rate (g C m-2 d-1) estimates for global streams and rivers in both comma separated values (csv) and GeoTIFF formats. These datasets served as the base for monthly CO2 emission estimates for global streams and rivers and can be used to support regional terrestrial carbon balances. Original vector-version of products is based on the Global...

Forest phenoclusters for Argentina based on vegetation phenology and climate

Eduarda Silveira, Volker Radeloff, Guillermo Martínez Pastur, Sebastián Martinuzzi, Natalia Politi, Leonidas Lizarraga, Luis Rivera, Gregorio Gavier-Pizarro, He Yin, Yamina Rosas, Noelia Calamari, María Navarro, Yanina Sica, Ashley Olah, Julieta Bono & Anna Pidgeon
Forest biodiversity conservation and species distribution modeling greatly benefit from broad-scale forest maps depicting tree species or forest types rather than just presence and absence of forest, or coarse classifications. Ideally, such maps would stem from satellite image classification based on abundant field data for both model training and accuracy assessments, but such field-data does not exist in many parts of the globe. However, different forest types and tree species differ in their vegetation phenology,...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Text
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  • Output Management Plan


  • Yale University
  • University of Oxford
  • Institute of Oceanology. PP Shirshov Russian Academy of Sciences
  • Stanford University
  • University of California Los Angeles
  • University of Pennsylvania
  • University of Washington
  • Princeton University
  • University of Michigan-Ann Arbor
  • Texas A&M University