99 Works

Homologous chromosomes undergo sequential quasi-stable interactions during meiotic prophase

Trent Newman
The pairing of homologous chromosomes in meiosis I is essential for sexual reproduction and is mediated, in part, by the formation and repair of Spo11-induced DNA double strand breaks (DSBs). In budding yeast, each cell receives 150-200 DSBs, yet only a fraction go on to form crossover products. How and why the cell initially coordinates so many interactions along each chromosome is not well understood. Using a fluorescent reporter-operator system (FROS), we measure the kinetics...

Should Central Banks Worry About Nonlinearities of their Large-Scale Macroeconomic Models?

Vadym Lepetyuk, Lilia Maliar & Serguei Maliar
How wrong could policymakers be when using linearized solutions to their macroeconomic models instead of nonlinear global solutions? This question became of much practical interest during the Great Recession and the recent zero lower bound crisis. We assess the importance of nonlinearities in a scaled-down version of the Terms of Trade Economic Model (ToTEM), the main projection and policy analysis model of the Bank of Canada. In a meticulously calibrated “baby” ToTEM model with 21...

ddRAD of Hawaiian Ariamnes spiders

Ellie Armstrong, Benoît Perez-Lamarque, Ke Bi, Leontine Becking, Jun Lim, Tyler Linderoth, Rosemary Gillespie & Henrik Krehenwinkel
The diversification of a host organism can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, coupled with a chronologically arranged series of volcanic mountains, to determine the evolutionary history of a host and its associated microbial communities, altogether forming the “holobiont”. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawaiʻi, and outgroup taxa on older islands, we tested whether...

Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment-dependent

Ken Thompson, Catherine Peichel, Diana Rennison, Matthew McGee, Arianne Albert, Timothy Vines, Anna Greenwood, Abigail Wark, Yaniv Brandvain, Molly Schumer & Dolph Schluter
Hybrid incompatibilities occur when interactions between opposite-ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are 'intrinsic', meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus...

Data from: How oscillating aerodynamic forces explain the timbre of the hummingbird's hum and other animals in flapping flight

Ben Hightower, Patrick Wijnings, Rick Scholte, Rivers Ingersoll, Diana Chin, Jade Nguyen, Daniel Shorr & David Lentink
The source of the hummingbird's distinctive hum is not fully understood, but there are clues to its origin in the acoustic nearfield. Hence we studied six freely hovering Anna’s hummingbirds, performing acoustic nearfield holography using a 2176 microphone array in vivo, while also directly measuring the 3D aerodynamic forces using a new aerodynamic force platform. We corroborate the acoustic measurements by developing a first-principles acoustic model that integrates the aerodynamic forces with wing kinematics, which...

Testing small scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

Peter Shum & Stephen Palumbi
DNA metabarcoding has been increasingly used to detail distributions of hundreds of species. Most analyses focus on creating molecular operation taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much less common is use of the sequence diversity within these MOTUs. Here we use the diversity of COI haplotypes within MOTUs from a California kelp forest to infer patterns of population abundance, dispersal and population history from 527 species of animals and algae from...

A satellite-based mobile warning system to reduce interactions with an endangered species

Matthew Breece, Matthew Oliver, Dewayne Fox, Edward Hale, Danielle Haulsee, Matthew Shatley, Steven Bograd, Elliott Hazen & Heather Welch
Earth observing satellites are a major research tool for spatially explicit ecosystem nowcasting and forecasting. However, there are practical challenges when integrating satellite data into usable real-time products for stakeholders. The need of forecast immediacy and accuracy means that forecast systems must account for missing data and data latency while delivering a timely, accurate and actionable product to stakeholders. This is especially true for species that have legal protection. Acipenser oxyrinchus oxyrinchus (Atlantic Sturgeon) were...

Data from: Association of venous outflow profiles and successful vessel reperfusion after thrombectomy

Tobias Djamsched Faizy
Background and Purpose: Robust arterial collaterals are associated with successful reperfusion after thrombectomy treatment of acute ischemic stroke due to large vessel occlusion (AIS-LVO). Excellent venous outflow (VO) reflects excellent tissue perfusion and collateral status in AIS-LVO patients. Objective: To determine whether favorable VO profiles assessed on pre-treatment CT angiography (CTA) images correlate with successful vessel reperfusion after thrombectomy in AIS-LVO patients. Materials and Methods: Multicenter retrospective cohort study of consecutive AIS-LVO patients treated by...

Data from: Mass extinctions alter extinction and origination dynamics with respect to body size

Pedro Monarrez, Noel Heim & Jonathan Payne
Whether mass extinctions and their associated recoveries represent an intensification of background extinction and origination dynamics versus a separate macroevolutionary regime remains a central debate in evolutionary biology. Previous focus has been on extinction, but origination dynamics may be equally or more important for long-term evolutionary outcomes. The evolution of animal body size is an ideal process to test for differences in macroevolutionary regimes, as body size is easily determined, comparable across distantly related taxa,...

Trophic rewilding benefits a tropical community through direct and indirect network effects

Pedro Uchoa Mittelman, Anna Rebello Landim, Luísa Genes, Ana Paula A. Assis, Carolina Starling-Manne, Paula V. Leonardo, Fernando A.S. Fernandez, & Alexandra Pires
Species reintroductions can be used as a conservation strategy to restore ecological interactions and the functionality of impoverished ecosystems. The ecological effects of reintroductions go beyond restoring pairwise interactions, because reintroductions can change how extant species are indirectly linked to each other in an ecological community. These indirect pathways, in turn, may shape a myriad of ecological and evolutionary processes operating in ecological systems. Here, we investigated how reintroductions may affect the direct and indirect...

Single-synapse analyses of Alzheimer’s disease implicate pathologic tau, DJ1, CD47, and ApoE

Thanaphong Phongpreecha, Chandresh Gajera, Candace Liu, Kausalia Vijayaragavan, Alan Chang, Martin Becker, Ramin Fallahzadeh, Rosemary Fernandez, Nadia Postupna, Emily Sherfield, Dmitry Tebaykin, Caitlin Latimer, Carol Shively, Thomas Register, Suzanne Craft, Kathleen Montine, Edward Fox, Kathleen Poston, C. Dirk Keene, Michael Angelo, Sean Bendall, Nima Aghaeepour & Thomas Montine
Synaptic molecular characterization is limited for Alzheimer’s disease (AD). Our newly invented mass cytometry-based method, Synaptometry by Time of Flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), non-human primates (NHP), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice...

Predator-prey interactions of terrestrial invertebrates are determined by predator body size and species identity

Ana Miller-Ter Kuile, Austen Apigo, An Bui, Bartholomew DiFiore, Elizabeth Forbes, Michelle Lee, Devyn Orr, Daniel Preston, Rachel Behm, Taylor Bogar, Jasmine Childress, Rodolfo Dirzo, Maggie Klope, Kevin Lafferty, John McLaughlin, Marisa Morse, Carina Motta, Kevin Park, Katherine Plummer, David Weber, Ronald Young & Hillary Young
Predator-prey interactions shape ecosystem and can help maintain biodiversity. However, for many of the earth’s most biodiverse and abundant organisms, including terrestrial arthropods, these interactions are difficult or impossible to observe directly with traditional approaches. Based on previous theory, it is likely that predator-prey interactions for these organisms are shaped by a combination of predator traits, including body size and species-specific hunting strategies. In this study, we combined diet DNA metabarcoding data of 173 individual...

CATS tag example deployment

William Gough & David Cade
Biologging tags are capable of capturing high-resolution data from cryptic species that spend a significant portion of their lives in remote or inaccessible environments, such as below the sea surface. The advancement of biologging technologies over the last ~30 years has lead to an explosion of research into the hidden lives of these elusive animals. Information about locomotion, feeding, migratory patterns, reproduction, and metabolism have all been determined using data obtained with biologging tags. CATS...

Data from: Landscape Context Mediates Avian Habitat Choice in Tropical Forest Restoration

J. Leighton Reid, Chase D. Mendenhall, J. Abel Rosales, Rakan A. Zahawi & Karen D. Holl
Birds both promote and prosper from forest restoration. The ecosystem functions birds perform can increase the pace of forest regeneration and, correspondingly, increase the available habitat for birds and other forest-dependent species. The aim of this study was to learn how tropical forest restoration treatments interact with landscape tree cover to affect the structure and composition of a diverse bird assemblage. We sampled bird communities over two years in 13 restoration sites and two old-growth...

Conservation of Birds in Fragmented Landscapes Requires Protected Areas

Robert Timmers, Marijke Van Kuijk, Pita Verweij, Jaboury Ghazoul, Yann Hautier, William Laurance, Stefan Arriaga-Weiss, Robert Askins, Corrado Battisti, Åke Berg, Gretchen Daily, Cristián Estades, Beatrice Frank, Reiko Kurosawa, Rosamund Pojar, John Woinarski & Merel Soons
For successful conservation of biodiversity, it is vital to know whether protected areas in increasingly fragmented landscapes effectively conserve species. However, how large habitat fragments must be and what level of protection is required to sustain species, remains poorly known. We compiled a global dataset on almost 2000 bird species in 741 forest fragments varying in size and protection status, and show that protection is associated with higher bird occurrence, especially for threatened species. Protection...

The impact of long-term non-pharmaceutical interventions on COVID-19 epidemic dynamics and control: the value and limitations of early models

Mallory Harris, Morgan Kain & Marissa Childs
Mathematical models of epidemics are important tools for predicting epidemic dynamics and evaluating interventions. Yet, because early models are built on limited information, it is unclear how long they will accurately capture epidemic dynamics. Using a stochastic SEIR model of COVID-19 fitted to reported deaths, we estimated transmission parameters at different time points during the first wave of the epidemic (March–June, 2020) in Santa Clara County, California. Although our estimated basic reproduction number (R0) remained...

Analyzing Default Risk and Liquidity Demand during a Financial Crisis: The Case of Canada

Jason Allen, Ali Hortaçsu & Jakub Kastl
This paper explores the reliability of using prices of credit default swap contracts (CDS) as indicators of default probabilities during the 2007/2008 financial crisis. We use data from the Canadian financial system to show that these publicly available risk measures, while indicative of initial problems of the financial system as a whole, do not seem to correspond to risks implied by the cross-sectional heterogeneity in bank behavior in short-term lending markets. Strategies in, and reliance...

Supporting data and code for \"Optical control of fast and processive engineered myosins in vitro and in living cells\"

Paul V. Ruijgrok, Sasha Zemsky & Zev Bryant
This repository makes data and code available to readers of Ruijgrok, Paul V. and Ghosh, Rajarshi P. et al. (Nature Chemical Biology 2021), and relies on that published paper for context. Five archives are included in this collection. “Source Data for Figures 1-5”, "Source Data for Extended Data Figures 3-4", and “Source Data for Supplementary Figures 3-11” contain all the data presented in figure panels in the main text, Extended Data, and Supplementary Information, respectively....

Interactions with soil fungi alter density-dependence and neighborhood effects in a locally abundant dipterocarp species

Kabir Peay, Richard Segnitz & Sabrina Russo
Seedling recruitment can be strongly affected by the composition of nearby plant species. At the neighborhood scale (on the order of tens of meters), adult conspecifics can modify soil chemistry and presence of host microbes (pathogens and mutualists) across their combined canopy area or rooting zones. At local or small spatial scales (on the order of one to few meters), conspecific seed or seedling density can influence the strength of intraspecific light and resource competition...

Scale Model Equations and Optimization for Annular Flow of Non-Newtonian Fluids Between Eccentric and Rotating Cylinders

Wei Zhang, Pooya Khodaparast, Amin Mehrabian & Amir Shojaei
A broad range of engineering applications involves helical flow of non-Newtonian fluids between two eccentric cylinders. These applications often require estimation of the frictional pressure losses along the axes of the cylinders. Laboratory flow loops are commonly used to study the flow characteristics at smaller scales of investigation. This study uses the laws of similarity and dimensional analysis to obtain a set of scaling equations between the laboratory and prototype scales of the described annular...

Cinematic virtual reality with head-motion parallax

Jayant Purushottam Thatte

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...

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...

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...

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