69 Works

Phonotactic learning with neural language models

Connor Mayer & Max Nelson
Computational models of phonotactics share much in common with language models, which assign probabilities to sequences of words. While state of the art language models are implemented using neural networks, phonotactic models have not followed suit. We present several neural models of phonotactics, and show that they perform favorably when compared to existing models. In addition, they provide useful insights into the role of representations on phonotactic learning and generalization. This work provides a promising...

Inside Out

Bridget Callaghan, Emily Towner, Kristen Chu, Danielle Ladensack, Tiffany Nassirian, Francesca Querdasi, Michael To, Maria Calderon Leon, Charis , Chloe Schwartz, Jessica Uy & SIYAN NUSSBAUM

Data from: Little giants: a rapidly invading seagrass alters ecosystem functioning relative to native foundation species

Ranjan Muthukrishnan, Kelcie L. Chiquillo, Candice Cross, Peggy Fong, Thomas Kelley, C. Anna Toline, Regina Zweng & Demian A. Willette
The spread of invasive species is a major component of global ecological change and how and when to manage particular species is a diicult empirical question. Ideally, these decisions should be based on the speciic impacts of invading species including both their efects on native competitors and how they may or may not play similar roles in broader ecosystem functioning. Halophila stipulacea is an invasive seagrass currently spreading through the Caribbean, and as seagrasses are...

Data from: eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.) - Part A

Zachary Gold, Adam Wall, Paul Barber, Emily Curd, N. Dean Pentcheff, Lee Ripma & Regina Wetzer
Fairy shrimp are integral components of vernal pool ecosystems, providing key food resources for migratory birds and amphibians. However, habitat degradation and land use change severely threaten the health of both vernal pools and the survival of fairy shrimp species. Branchinecta sandiegonensis has been particularly affected by urban and agricultural development in its small native range within San Diego County, California, USA. It is listed as an endangered species under both state and federal laws...

Data from: Environmental context shapes the long‐term role of nutrients in driving producer community trajectories in a top‐down dominated marine ecosystem

Rachel Clausing, Nicole E. Phillips & Peggy Fong
1. Two predominant anthropogenic impacts on ecosystems, nutrient enrichment and the removal of consumers, are predicted to interact in their effects on producer diversity. Yet, measures of diversity alone may not capture changes occurring in the underlying mechanisms structuring communities. Furthermore, evidence for these interactions in rocky intertidal systems is mixed and may be confounded by variable baseline productivity or short experimental durations that do not capture seasonality, environmental heterogeneity or successional processes. 2. We...

Iterative evolution of large-bodied hypercarnivory in canids benefits species but not clades

Mairin Balisi & Blaire Van Valkenburgh
Ecological specialization has costs and benefits at various scales: traits benefitting an individual may disadvantage its population, species or clade. In particular, large body size and hypercarnivory (diet over 70% meat) have evolved repeatedly in mammals; yet large hypercarnivores are thought to be trapped in a macroevolutionary “ratchet”, marching unilaterally toward decline. Here, we weigh the impact of this specialization on extinction risk using the rich fossil record of North American canids (dogs). In two...

Pelagiella exigua, an early Cambrian stem gastropod with chaetae: lophotrochozoan heritage and conchiferan novelty

Roger D. K. Thomas, Bruce Runnegar & Kerry Matt
Exceptionally well-preserved impressions of two bundles of bristles protrude from the apertures of small, spiral shells of Pelagiella exigua, recovered from the Kinzers Formation (Cambrian, Stage 4, “Olenellus Zone”, ~ 512 Ma) of Pennsylvania. These impressions are inferred to represent clusters of chitinous chaetae, comparable to those borne by annelid parapodia and some larval brachiopods. They provide an affirmative test in the early metazoan fossil record of the inference, from phylogenetic analyses of living taxa,...

On the cross-population generalizability of gene expression prediction models

Kevin L. Keys, Angel C.Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew W. Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. Lenoir, Jimmie Chun Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard & Christopher R. Gignoux
The genetic control of gene expression is a core component of human physiology. For the past several years, transcriptome-wide association studies have leveraged large datasets of linked genotype and RNA sequencing information to create a powerful gene-based test of association that has been used in dozens of studies. While numerous discoveries have been made, the populations in the training data are overwhelmingly of European descent, and little is known about the generalizability of these models...

Intracrater Terminal Dune Fields in Arabia Terra, Mars

Taylor Dorn & Mackenzie Day
Craters are the most prevalent basins and potential depo-centers of sediment on Mars. Within these craters and extending from them, terminal dune fields and wind streaks are abundant, indicating active sediment transport and providing a way to study how wind and sediment interact with crater topography. Here, we explore the role of craters as both sources and sinks in the modern martian sedimentary cycle. Our results show that craters with low albedo wind streaks (indicative...

Data from: The American Kestrel (Falco sparverius) genoscape: implications for monitoring, management, and subspecies boundaries

Kristen Ruegg, Michaela Brinkmeyer, Christen M Bossu, Rachael Bay, Eric C Anderson & Julie Heath
Identifying population genetic structure is useful for inferring evolutionary process as well as defining subspecies boundaries and/or conservation units that can aid in species management. The American kestrel (Falco sparverius) is a widespread species with two described North American subspecies, (F. s. sparverius and F. s. paulus), the latter in the southeastern United States and the former across the remainder of its distribution. In many parts of their range, American kestrels have been declining, but...

Data from: Beyond the limits: identifying the high-frequency detectors in the anuran ear

Ariadna Cobo-Cuan, T. Ulmar Grafe & Peter M. Narins
Despite the predominance of low-frequency hearing in anuran amphibians, a few frog species have evolved high-frequency communication within certain environmental contexts. Huia cavitympanum is the most remarkable anuran with regard to upper frequency limits; it is the first frog species known to emit exclusively ultrasonic signals. Characteristics of the Distortion Product Otoacoustic Emissions from the amphibian papilla and the basilar papilla were analysed to gain insight into the structures responsible for high-frequency/ultrasound sensitivity. Our results...

Внутри горы бездействует... подтекст? К разгадке мандельштамовского кумира

Лада Панова
В настоящей статье предлагается расшифровка одного из самых темных стихотворений Осипа Мандельштама. Отправной точкой послужила следующая гипотеза: во «Внутри горы бездействует кумир» Мандельштам имеет дело с сакральностью власти автократа — феноменом, свойственным как Древнему Египту и Вавилону, так и русской истории, включая советский период. Образный строй стихотворения, его стилистика, словоупотребление, лирический сюжет и, наконец, причудливая, «матрешечная» интертекстуальная структура направлены на подрыв кумиропоклонничества по отношению к властителю. Недаром этот обобщенный персонаж показан отвратительным, старым, пережившим свой...

Разбор трех разборов. Автоэвристические заметки

Александр Жолковский
В статье разбираются три недавние работы автора: разборы трех очень разных текстов – «Темных аллей» Бунина, «Двух капитанов» Каверина и «Личной жизни» Зощенко, – между которыми обнаруживаются интересные сходства. Одно состоит в том, как долго автору открывалась некая, теперь представляющаяся окончательной, разгадка структуры каждого из текстов. Другое, более неожиданное, – в том, что эти произведения объединяет общая черта: «авторский» мотив, встроенный в три совершенно несходных нарратива. Заключительный раздел статьи посвящен теоретическим выводам из выявленных аналогий....

Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

Jonas Kuppler, Cécile H. Albert, Gregory M. Ames, W. Scott Armbruster, Gerhard Boenisch, Florian C. Boucher, Diane R. Campbell, Liedson T. Carneiro, Eduardo Chacón-Madrigal, Brian J. Enquist, Carlos R. Fonseca, José M. Gómez, Antoine Guisan, Pedro Higuchi, Dirk N. Karger, Jens Kattge, Michael Kleyer, Nathan J. B. Kraft, Anne-Amélie C. Larue-Kontić, Amparo Lázaro, Martin Lechleitner, Deirdre Loughnan, Vanessa Minden, Ülo Niinemets, Gerhard E. Overbeck … & Robert R. Junker
Aim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation...

An incoherent feedforward loop interprets NFkappaB/RelA dynamics to determine TNF-induced necroptosis decisions

Marie Oliver Metzig
Balancing cell death is essential to maintain healthy tissue homeostasis and prevent disease. Tumor necrosis factor (TNF) not only activates nuclear factor kB (NFkappaB), which coordinates the cellular response to inflammation, but may also trigger necroptosis, a pro-inflammatory form of cell death. Whether TNF-induced NFkappaB affects the fate decision to undergo TNF-induced necroptosis is unclear. Live-cell microscopy and model-aided analysis of death kinetics identified a molecular circuit that interprets TNF-induced NFkappaB/RelA dynamics to control necroptosis...

Data from: Olfaction at depth: cribriform plate size declines with dive depth and duration in aquatic arctoid carnivorans

Deborah Bird, Iman Hamid, Lester Fox-Rosales & Blaire Van Valkenburgh
It is widely accepted that obligate aquatic mammals, specifically toothed whales, rely relatively little on olfaction. There is less agreement about the importance of smell among aquatic mammals with residual ties to land, such as pinnipeds and sea otters. Field observations of marine carnivorans stress their keen use of smell while on land or pack ice. Yet, one dimension of olfactory ecology is often overlooked: while underwater, aquatic carnivorans forage “noseblind,” diving with nares closed,...

Data from: Physical and social cues shape nest-site preference and prey capture behavior in social spiders

Gabriella Najm, Angelika Pe, Jonathan Pruitt & Noa Pinter-Wollman
Animals often face conflicting demands when making movement decisions. To examine the decision process of social animals, we evaluated nest site preferences of the social spider Stegodyphus dumicola. Colonies engage in collective web building, constructing three-dimensional nests and two-dimensional capture webs on trees and fences. We examined how individuals and groups decide where to construct a nest based on habitat structure and conspecific presence. Individuals had a strong preference for three dimensional-substrates and conspecific presence....

Pulsed electromagnetic field (PEMF) transiently stimulates the rate of mineralization in a 3-dimensional ring culture model of osteogenesis

Paul Benya, Aaron Kavanaugh, Martin Zakarian, Philip Söderlind, Tea Jashashvili, Nianli Zhang, Eric Waldorff, James Ryaby & Fabrizio Billi
Pulsed Electromagnetic Frequencies (PEMF) have shown efficacy in bone repair and yet the optimum characteristics of this modality and its molecular mechanism remain unclear. To determine the effects of timing of PEMF treatment we present a three-dimensional ring culture model of osteogenesis that demonstrates strong de novo generation of collagen and mineral matrix and exhibits stimulation by PEMF in multiple stages over 62 days of culture. Mouse postnatal day 2 calvarial pre-osteoblasts were cast within...

Right-wing Authoritarianism, Left-wing Authoritarianism, and pandemic-mitigation authoritarianism

Joseph H. Manson
On April 22, 2020, 549 U.S. resident users of Prolific.co completed (1) the Authoritarianism-Conservatism-Traditionalism Scales (Duckitt, Bizumic, Kruauss, and Heled, 2010), (2) the 22-item short form of the Left-Wing Authoritarianism Index (Costello and Lilienfeld, 2019), (3) their level of endorsement of 19 policies that could possibly mitigate the impact of the COVID-19 pandemic, and (4) a set of demographic questions (age, gender, ethnicity, pre-pandemic household income, and highest educational attainment). They were also asked to...

Persistent panmixia despite extreme habitat loss and population decline in the threatened tricolored blackbird (Agelaius tricolor)

Kelly Barr
Habitat loss and alteration have driven many species into decline, often to the point of requiring protection and intervention to avert extinction. Genomic data provide the opportunity to inform conservation and recovery efforts with details about vital evolutionary processes with a resolution far beyond that of traditional genetic approaches. The tricolored blackbird (Agelaius tricolor) has suffered severe losses during the previous century largely due to anthropogenic impacts on their habitat. Using a dataset composed of...

Ancient balancing selection maintains incompatible versions of the galactose pathway in yeast (Figure creation)

James Boocock, Meru Sadhu, Joshua Bloom, Arun Durvasula & Leonid Kruglyak
Metabolic pathways differ between species, but are expected to be similar within a species. We discovered two functional, incompatible versions of the galactose pathway in S. cerevisiae. We identified a 3-locus genetic interaction for growth in galactose, and used precisely engineered alleles to show that is arises from variation in the metabolic genes GAL2, GAL1/10/7, and PGM1, and that the reference allele of PGM1 is incompatible with the alternative alleles of the other genes. Multi-locus...

Population structure, inbreeding and stripe pattern abnormalities in plains zebras

Brenda Larison
One of the most iconic wild equids, the plains zebra occupies a broad region of sub-Saharan Africa and exhibits a wide range of phenotypic diversity in stripe patterns that have been used to classify multiple sub-species. After decades of relative stability, albeit with a loss of at least one recognized subspecies, the total population of plains zebras has undergone an approximate 25% decline since 2002. Individuals with abnormal stripe patterns have been recognized in recent...

On collaborative reinforcement learning to optimize the redistribution of critical medical supplies throughout the COVID-19 pandemic

Bryan Bednarski
Objective: This work investigates how reinforcement learning and deep learning models can facilitate the near-optimal redistribution of medical equipment in order to bolster public health responses to future crises similar to the COVID-19 pandemic. Materials and Methods: The system presented is simulated with disease impact statistics from the Institute of Health Metrics (IHME), Center for Disease Control, and Census Bureau[1, 2, 3]. We present a robust pipeline for data preprocessing, future demand inference, and a...

Data from: Using a newly introduced framework to measure ecological stressor interactions

Elif Tekin, Eleanor Diamant, Mauricio Cruz-Loya, Vivien Enriquez, Nina Singh, Van Savage & Pamela Yeh
Understanding how stressors combine to affect population abundances and trajectories is a fundamental ecological problem with increasingly important implications worldwide. Generalizations about interactions among stressors are challenging due to different categorization methods and how stressors vary across species and systems. Here, we propose using a newly introduced framework to analyze data from the last 25 years on ecological stressor interactions, e.g. combined effects of temperature, salinity, and nutrients on population survival and growth. We contrast...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

Registration Year

  • 2020
    69

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  • Dataset
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Affiliations

  • University of California Los Angeles
    59
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  • Virginia Tech
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    3
  • University of California, San Francisco
    3
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    3
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    2
  • David Geffen School of Medicine at UCLA
    2