14 Works

Data from \"Transferability of data-driven, many-body models for CO2 simulations in the vapor and liquid phases\"

Shuwen Yue & Marc Riera Riambau
This dataset comprises of data associated with the publication "Transferability of data-driven, many-body models for CO2 simulations in the vapor and liquid phases", which can be found at https://doi.org/10.1063/5.0080061. The data includes calculations for a Many-Body decomposition, virial coefficient calculations, orientational molecular scan energies, potential energy fields, correlation plots of training and testing data, vapor-liquid equilibrium simulations, liquid density simulations, and solid cell simulations.

Decoupled dust deposition and ocean productivity in the Antarctic Zone of the Southern Ocean over the past 1.5 million years

Michael E. Weber , Ian Bailey , Sidney R. Hemming , Yasmina M. Martos , Brendan T. Reilly , Thomas A. Ronge , Stefanie Brachfeld , Trevor Williams , Maureen Raymo , Simon T. Belt , Hendrik Vogel , Victoria Peck , Linda Armbrecht , Alix Cage , Fabricio G. Cardillo , Zhiheng Du , Gerson Fauth , Christopher J. Fogwill , Marga Garcia , Marlo Garnsworthy , Anna Glüder , Michelle Guitard , Marcus Gutjahr , Iván Hernández-Almeida , Frida S. Hoem … & Xufeng Zheng
Southern Ocean paleoceanography provides key insights into how iron fertilization and oceanic productivity developed through Pleistocene ice-ages and their role in influencing the carbon cycle. We report the first high-resolution record of dust deposition and ocean productivity for the Antarctic Zone, close to the main dust source, Patagonia. Our deep-ocean records cover the last 1.5 Ma, thus doubling that from Antarctic ice-cores. We find a ≥10-fold increase in dust deposition during glacials and a ≤5-fold...

DEPP: Deep learning enables extending species trees using single genes

Yueyu Jiang, Metin Balaban, Qiyun Zhu & Siavash Mirarab
Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. However, existing placement methods have a fundamental limitation: they assume that query sequences have evolved using specific models directly on the reference phylogeny. Thus, they can place single-gene data (e.g., 16S rRNA amplicons) onto their own gene tree. This practice is a proxy for a more ambitious goal: extending a (genome-wide) species tree given data from individual genes. No algorithm...

Viral protein instability enhances host-range evolvability

Hannah Strobel, Elijah Horwitz & Justin Meyer
Viruses are highly evolvable, but what traits endow this property? The high mutation rates of viruses certainly play a role, but factors that act above the genetic code, like protein thermostability, are also expected to contribute. We studied how the thermostability of a model virus, bacteriophage l, affects its ability to evolve to use a new receptor, a key evolutionary transition that can cause host-range evolution. Using directed evolution and synthetic biology techniques we generated...

COVID-19 survey in Baja California, Mexico, in February of 2021

Oscar E Zazueta, Richard S Garfein, J. Oggun Cano-Torres, César A Méndez-Lizárraga, Timothy C Rodwell, Raquel Muñiz-Salazar, Diego F Ovalle-Marroquín, Neiba G Yee, Idanya Rubí Serafín-Higuera, Susana González-Reyes, Jesus Rene Machado-Contreras, Lucy E Horton, Steffanie A Strathdee, Ruth Rodríguez, Linda Hill & Ietza Bojórquez-Chapela
Baja California is a State located in the north-western region of Mexico, which borders with the United States. This area is of particular importance in terms of epidemiological surveillance, given that the busiest port of entry to the U.S. is located in the Tijuana-San Diego region, which is also one of the busiest ports of entry in the world. During the first year of the COVID-19 pandemic, Baja California had the second mortality rate in...

Data from: Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish

Nidal Karagic, Andreas Härer, Axel Meyer & Julian Torres-Dowdall
Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth, turbidity and composition of the water body. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan...

Daily totals of odontocete acoustic presence at western North Atlantic acoustic monitoring sites

Rebecca E. Cohen, Kaitlin E. Frasier, Simone Baumann-Pickering, Sean Wiggins, Macey A. Rafter, Lauren M. Baggett & John A. Hildebrand
A combination of machine learning and expert analyst review was used to detect odontocete echolocation clicks, identify dominant click types, and classify clicks in 32 years of acoustic data collected at 11 autonomous monitoring sites in the western North Atlantic between 2016 and 2019. Previously-described click types for eight known odontocete species or genera were identified in this data set: Blainville’s beaked whales (Mesoplodon densirostris), Cuvier’s beaked whales (Ziphius cavirostris), Gervais’ beaked whales (Mesoplodon europaeus),...

A Simplified Model for the Intermediate Structure of Strong Fire Whirls

Forman A. Williams
A model is described for the overall structure of intense fire whirls, based on a spatially evolving vortex, with circulation enhancement driven by the axial acceleration of low-density gas in the core through the axial pressure gradient. The axial acceleration increases the entrainment rate into the core which, through mass conservation, increases the circulation if the angle between the tangential and radial velocity components remains fixed. The two-zone model employs general balance equations for regions...

Prey naiveté alters the balance of consumptive and non-consumptive predator effects and shapes trophic cascades in freshwater plankton

Henry Baker, Stephanie Li, Stefan Samu, Natalie Jones, Celia Symons & Jonathan Shurin
Predators drive trophic cascades by reducing prey biomass and altering prey traits, selecting for prey that exhibit constitutive and induced anti-predator defenses that decrease susceptibility to consumption. These defense traits are often costly, generating a tradeoff between consumptive (CEs) and non-consumptive predator effects (NCEs). The ecological and evolutionary experience that prey share with a given predator may determine their position along this tradeoff curve, affecting the nature and strength of top-down control of ecosystems. Conceptual...

Hair phenotype diversity across Indriidae lemurs

Elizabeth Tapanes, Rachel Jacobs, Ian Harryman, , Mitchell Irwin, Jason Kamilar & Brenda Bradley
Objectives: Hair (i.e., pelage/fur) is a salient feature of primate (including human) diversity and evolution—serving functions tied to thermoregulation, protection, camouflage, and signaling—but wild primate pelage evolution remains relatively understudied. Specifically, assessing multiple hypotheses across distinct phylogenetic scales is essential but is rarely conducted. We examine whole body hair color and density variation across Indriidae (Avahi, Indri, Propithecus)—a lineage that, like humans, exhibits vertical posture (i.e., their whole bodies are vertical to the sun). Materials...

Behavioral context affects social signal representations within single primate prefrontal cortex neurons

Adam Fishbein, Vladimir Jovanovic, Lisa De La Mothe, Kuo-Fen Lee & Cory Miller
We tested whether social signal processing in more traditional, head-restrained contexts is representative of the putative natural analog – social communication – by comparing responses to vocalizations within individual neurons in marmoset prefrontal cortex (PFC) across a series of behavioral contexts ranging from traditional to naturalistic. Although vocalization responsive neurons were evident in all contexts, cross-context consistency was notably limited. A response to these social signals when subjects were head-restrained was not predictive of a...

Leapfrog dynamics in phage-bacteria coevolution revealed by joint analysis of cross-infection phenotypes and whole genome sequencing

Animesh Gupta
Viruses and their hosts can undergo coevolutionary arms races where hosts evolve increased resistance and viruses evolve counter-resistance. Given these arms race dynamics (ARD), both players are predicted to evolve along a single trajectory as more recently evolved genotypes replace their predecessors. By coupling phenotypic and genomic analyses of coevolving populations of bacteriophage lambda and Escherichia coli, we find conflicting evidence for ARD. Virus-host infection phenotypes fit the ARD model, yet genomic analyses revealed fluctuating...

Data from: Phytoplankton functional composition determines limitation by nutrients and grazers across a lake productivity gradient

Marika Schulhof, Dedmer Van De Waal, Steven Declerck & Jonathan Shurin
Functional tradeoffs among ecologically important traits govern the diversity of communities and changes in species composition along environmental gradients. A tradeoff between predator defense and resource competitive ability has been invoked as a mechanism that may maintain diversity in lake phytoplankton. Tradeoffs may promote diversity in communities where grazing- and resource-limited taxa coexist, which determines the extent to which communities are resource- or consumer-controlled. In addition, changes in temperature may alter nutrient demands and grazing...

How 2 and 4 year old children coordinate joint actions with peers

Federico Rossano, Jack Terwilliger, Adrian Bangerter, Emilie Genty, Raphaela Heesen & Klaus Zuberbühler
The interaction engine hypothesis postulates a uniquely human ability and motivation for social interaction. A crucial juncture in the ontogeny of the interaction engine could be around 2-4 years of age, but observational studies of children in natural contexts are lacking. Moreover, data on the ontogenetic development of joint action coordination can provide critical human data for comparative research investigating the phylogenetic roots of the interaction engine. In this study we report on focal observations...

Registration Year

  • 2022
    14

Resource Types

  • Dataset
    12
  • Text
    2

Affiliations

  • University of California, San Diego
    14
  • Keele University
    1
  • University of Massachusetts Amherst
    1
  • University of Adelaide
    1
  • University of Plymouth
    1
  • Spanish Institute of Oceanography
    1
  • Stanford University
    1
  • Columbia University
    1
  • Princeton University
    1
  • Andalusian Earth Sciences Institute
    1