146 Works

A Minimalist Approach to Facilitatory Effects in Stacked Relative Clauses

Aniello De Santo

CCG Supertagging as Top-down Tree Generation

Jakob Prange, Nathan Schneider & Vivek Srikumar

Machine learning meets library archives: Image Analysis to generate descriptive metadata

Harish Maringanti, Dhanushka Samarakoon & Bohan Zhu
$34,700 to develop and test a model for applying machine learning techniques to extract useful information from historical images to assist in and increase the efficiency of metadata creation for archives, libraries and museums of all types.

Flipping the Feedback: Formative Assessment in a Flipped Freshman Circuits Class

Donna H. Ziegenfuss & Cynthia M. Furse
This paper describes the application of formative assessment methods in a flipped freshman engineering circuits course. This student-centered approach provided value for the instructor seeking to improve the learning environment and content in real-time, and for the students who actively participated in the process of course improvement. Three types of assessment were used in this course: online formative course feedback every three weeks; weekly ‘muddiest point’ content feedback; and midterm exam scores. Data were assessed...

Data from: The ontogeny of fairness in seven societies

Peter R. Blake, Katherine McAuliffe, John Corbit, Tara C. Callaghan, Oumar Barry, Aleah Bowie, Lauren Kleutsch, Karen L. Kramer, Elizabeth Ross, Hurnan Vongsachang, Richard Wrangham & Felix Warneken
A sense of fairness plays a critical role in supporting human cooperation. Adult norms of fair resource sharing vary widely across societies, suggesting that culture shapes the acquisition of fairness behaviour during childhood. Here we examine how fairness behaviour develops in children from seven diverse societies, testing children from 4 to 15 years of age (n = 866 pairs) in a standardized resource decision task. We measured two key aspects of fairness decisions: disadvantageous inequity...

Data from: High-throughput sequencing of transposable element insertions suggests adaptive evolution of the invasive Asian Tiger Mosquito towards temperate environments

Clément Goubert, Hélène Henri, Guillaume Minard, Claire Valiente Moro, Patrick Mavingui, Cristina Vieira & Matthieu Boulesteix
Invasive species represent unique opportunities to evaluate the role of local adaptation during colonization of new environments. Among these species, the Asian tiger mosquito, Aedes albopictus, is a threatening vector of several human viral diseases, including dengue and chikungunya, and raises concerns about the Zika fever. Its broad presence in both temperate and tropical environments has been considered the reflection of great “ecological plasticity.” However, no study has been conducted to assess the role of...

Data from: A resorbable antibiotic-eluting polymer composite bone void filler for perioperative infection prevention in a rabbit radial defect model

Benjamin D. Brooks, Kristofer D.. Sinclair, David W. Grainger & Amanda E. Brooks
Nearly 1.3 million total joint replacement procedures are performed in the United States annually, with numbers projected to rise exponentially in the coming decades. Although finite infection rates for these procedures remain consistently low, device-related infections represent a significant cause of implant failure, requiring secondary or revision procedures. Revision procedures manifest several-fold higher infection recurrence rates. Importantly, many revision surgeries, infected or not, require bone void fillers to support the host bone and provide a...

Data from: Mate-guarding by male mandrills (Mandrillus sphinx) is associated with female MHC genotype

Joanna M. Setchell, Shane A. Richards, Kristin M. Abbott & Leslie A. Knapp
Female choice for male major histocompatibility complex (MHC) genotype has been widely tested, but the relationship between male mating strategies and female MHC genotype has received far less attention. Moreover, few studies of MHC-associated mate choice test for the fitness effects underlying such choice. We examined mate-guarding by male mandrills, a species with intense male–male competition and female offspring care. We developed a statistical model based on 10 years of observations to describe how the...

Data from: Bayesian estimation of the global biogeographical history of the Solanaceae

Julia Dupin, Nicholas J. Matzke, Tiina Särkinen, Sandra Knapp, Richard G. Olmstead, Lynn Bohs & Stacey D. Smith
Aim: The tomato family Solanaceae is distributed on all major continents except Antarctica and has its centre of diversity in South America. Its worldwide distribution suggests multiple long-distance dispersals within and between the New and Old Worlds. Here, we apply maximum likelihood (ML) methods and newly developed biogeographical stochastic mapping (BSM) to infer the ancestral range of the family and to estimate the frequency of dispersal and vicariance events resulting in its present-day distribution. Location:...

Data from: Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae)

Abigail J. Moore, William L. Moore & Bruce G. Baldwin
Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings....

Data from: Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

Jael Malenke, Brett Milash, Aaron Miller, Denise Dearing, J. R. Malenke, A. W. Miller & M. D. Dearing
Massively parallel sequencing has enabled the creation of novel, in-depth genetic tools for nonmodel, ecologically important organisms. We present the de novo transcriptome sequencing, analysis and microarray development for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of ecological and evolutionary interest, especially with respect to ingestion and hepatic metabolism of potentially toxic plant secondary compounds. We generated a liver transcriptome of the desert woodrat (Neotoma lepida) using the Roche 454 platform. The...

Data from: Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

Sabine Hellwig, David A. Nix, Keith M. Gligorich, John M. O'Shea, Alun Thomas, Carrie L. Fuertes, Preetida J. Bhetariya, Gabor T. Marth, Mary P. Bronner, Hunter R. Underhill & John M. O’Shea
Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However, accurate detection of variant alleles, particularly during untargeted searches, remains a principal obstacle to widespread application of cell-free DNA in clinical oncology. In this study, isolation of short cell-free DNA fragments is shown to enrich for tumor variants and improve correction of PCR- and sequencing-associated errors. Subfractions of the mononucleosome of circulating cell-free DNA (ccfDNA) were isolated from...

Data from: Annual environmental variation influences host tolerance to parasites

Sabrina M. McNew, Sarah A. Knutie, Graham B. Goodman, Angela Theodosopoulos, Ashley Saulsberry, Janai Yepez R., Sarah E. Bush & Dale H. Clayton
When confronted with a parasite or pathogen, hosts can defend themselves by resisting or tolerating the attack. While resistance can be diminished when resources are limited, it is unclear how robust tolerance is to changes in environmental conditions. Here we investigate the sensitivity of tolerance in a single host population living in a highly variable environment. We manipulated the abundance of an invasive parasitic fly, Philornis downsi, in nests of Galápagos mockingbirds (Mimus parvulus) over...

Data from: Host defense triggers rapid adaptive radiation in experimentally evolving parasites

Sarah E. Bush, Scott M. Villa, Juan C. Altuna, Kevin P. Johnson, Michael D. Shapiro & Dale H. Clayton
Adaptive radiation occurs when the members of a single lineage evolve different adaptive forms in response to selection imposed by competitors or predators. Iconic examples include Darwin’s finches, Caribbean anoles, and Hawaiian silverswords, all of which live on islands. Although adaptive radiation is thought to be an important generator of biodiversity, most studies concern groups that have already diversified. Here we take the opposite approach. We experimentally triggered diversification in the descendants of a single...

Data from: Abortion legislation, maternal healthcare, fertility, female literacy, sanitation, violence against women, and maternal deaths: a natural experiment in 32 Mexican states

Elard Koch, Monique Chireau, Fernando Pliego, Joseph Stanford, Sebastián Haddad, Byron Calhoun, Paula Aracena, Miguel Bravo, Sebastián Gatica & John Thorp
Objective: To test whether there is an association between abortion legislation and maternal mortality outcomes after controlling for other factors thought to influence maternal health. Design: Population-based natural experiment. Setting and data sources: Official maternal mortality data from 32 federal states of Mexico between 2002 and 2011. Main outcomes: Maternal mortality ratio (MMR), MMR with any abortive outcome (MMRAO) and induced abortion mortality ratio (iAMR). Independent variables: Abortion legislation grouped as less (n=18) or more...

Data from: Rapid experimental evolution of reproductive isolation from a single natural population

Scott M. Villa, Juan C. Altuna, James S. Ruff, Andrew B. Beach, Lane I. Mulvey, Erik J. Poole, Heidi E. Campbell, Kevin P. Johnson, Michael D. Shapiro, Sarah E. Bush & Dale H. Clayton
Ecological speciation occurs when local adaptation generates reproductive isolation as a by-product of natural selection. Although ecological speciation is a fundamental source of diversification, the mechanistic link between natural selection and reproductive isolation remains poorly understood, especially in natural populations. Here, we show that experimental evolution of parasite body size over 4 y (approximately 60 generations) leads to reproductive isolation in natural populations of feather lice on birds. When lice are transferred to pigeons of...

Data from: Large birds travel farther in homogeneous environments

Marlee A. Tucker, Olga Alexandrou, , Keith L. Bildstein, Katrin Böhning-Gaese, Chloe Bracis, John N. Brzorad, Evan R. Buechley, David Cabot, Justin M. Calabrese, Carlos Carrapato, André Chiaradia, Lisa C. Davenport, Sarah C. Davidson, Mark Desholm, Christopher R. DeSorbo, Robert Domenech, Peter Enggist, William F. Fagan, Nina Farwig, Wolfgang Fiedler, Christen H. Fleming, Alastair Franke, John M. Fryxell, Clara García-Ripollés … & João Paulo Silva
Aim: Animal movement is an important determinant of individual survival, population dynamics, and ecosystem structure and function. Yet it is still unclear how local movements are related to resource availability and the spatial arrangement of resources. Using resident bird species and migratory bird species outside of the migratory period, we examined how the distribution of resources affect the movement patterns of both large terrestrial birds (e.g., raptors, bustards, hornbills) and waterbirds (e.g., cranes, storks, ducks,...

Data from: Trace fossils of possible parasites inside the gut contents of a hadrosaurid dinosaur, Upper Cretaceous Judith River Formation, Montana

Justin S. Tweet, Karen Chin & Allan A. Ekdale
Tiny sinuous trace fossils have been found within probable gut contents of an exceptionally preserved specimen of a hadrosaurid dinosaur, Brachylophosaurus canadensis, from the Judith River Formation of Montana. Approximately 280 examples of the trace fossils were observed in 19 samples of gut region material. The tubular structures typically are about 0.3 mm across. Many have thin calcareous linings or layers, and some exhibit fine surficial striae. At least two dozen of these trace fossils...

Data from: Sexual selection constrains the body mass of male but not female mice

James S. Ruff, Douglas H. Cornwall, Linda C. Morrison, Joseph W. Cauceglia, Adam C. Nelson, Shannon M. Gaukler, Shawn Meagher, Lara S. Carroll & Wayne K. Potts
Sexual size dimorphism results when female and male body size is influenced differently by natural and sexual selection. Typically, in polygynous species larger male body size is thought to be favored in competition for mates and constraints on maximal body size are due to countervailing natural selection on either sex; however, it has been postulated that sexual selection itself may result in stabilizing selection at an optimal mass. Here we test this hypothesis by retrospectively...

Data from: Revision of the first therocephalian, Theriognathus Owen (Therapsida: Whaitsiidae), and implications for cranial ontogeny and allometry in nonmammaliaform eutheriodonts

Adam Huttenlocker & Fernando Abdala
Historically, the whaitsiid therocephalian Theriognathus Owen was one of the earliest described nonmammalian therapsids, its morphology helping to link phylogenetically the Paleozoic synapsids of North America and southern Africa to their mammalian successors. However, decades of taxonomic over-splitting and superficial descriptions obscured the morphologic diversity of the genus, hindering its utility as a study system for the evolution of synapsid cranial function as well as its biostratigraphic significance in the Late Permian of southern Africa....

Data from: New material and systematic re-evaluation of Medusaceratops lokii (Dinosauria: Ceratopsidae) from the Judith River Formation (Campanian, Montana)

Kentaro Chiba, Michael J. Ryan, Federico Fanti, Mark A. Loewen & David C. Evans
Medusaceratops lokii is an enigmatic taxon of ceratopsid represented by partial parietals from the Mansfield bonebed in the Campanian Judith River Formation, Montana. Originally, all ceratopsid material collected from this bonebed was referred to the centrosaurine ceratopsid Albertaceratops, but subsequently two parietals were designated the types of the chasmosaurine, M. lokii, in part, because they were interpreted to have three epiparietals bilaterally. Here we describe new material from the bonebed that allows a systematic revision...

Data from: Phoretic dispersal influences parasite population genetic structure

Emily DiBlasi, Kevin P. Johnson, Sydney A. Stringham, Angela N. Hansen, Andrew B. Beach, Dale H. Clayton & Sarah E. Bush
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift, and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be done in the proper comparative context. Here we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of...

Data from: Reproduction does not adversely affect liver mitochondrial respiratory function but results in lipid peroxidation and increased antioxidants in house mice

Annelise V. Mowry, Andreas N. Kavazis, Aubrey E. Sirman, Wayne K. Potts & Wendy R. Hood
Reproduction is thought to come at a cost to longevity. Based on the assumption that increased energy expenditure during reproduction is associated with increased free-radical production by mitochondria, oxidative damage has been suggested to drive this trade-off. We examined the impact of reproduction on liver mitochondrial function by utilizing post-reproductive and non-reproductive house mice (Mus musculus) living under semi-natural conditions. The age-matched post-reproductive and non-reproductive groups were compared after the reproductive females returned to a...

Data from: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulate field fitness

Rachel Kerwin, Julie Feusier, Jason Corwin, Matthew Rubin, Catherine Lin, Alise Muok, Brandon Larson, Baohua Li, Bindu Joseph, Marta Francisco, Daniel Copeland, Cynthia Weinig & Daniel J. Kliebenstein
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific...

Data from: Fossil evidence of the avian vocal organ from the Mesozoic

Julia A. Clarke, Sankar Chatterjee, Zhiheng Li, Tobias Riede, Federico Angolin, Franz Goller, Marcelo P. Isasi, Daniel R. Martinioni, Francisco J. Mussel & Fernando E. Novas
From complex songs to simple honks, birds produce sounds using a unique vocal organ called the syrinx1, 2. Located close to the heart at the tracheobronchial junction, vocal folds or membranes attached to modified mineralized rings vibrate to produce sound1, 2, 3, 4, 5, 6, 7. Syringeal components were not thought to commonly enter the fossil record6, and the few reported fossilized parts of the syrinx are geologically young8, 9, 10, 11 (from the Pleistocene...

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